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Merge branch 'lammps:develop' into intpos

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This commit is contained in:
Oliver Henrich
2021-10-27 21:29:56 +01:00
committed by GitHub
parent 20fec49635 c9da75ef85
commit addb087aac
998 changed files with 31731 additions and 8500 deletions
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2
.github/CODEOWNERS vendored
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@ -83,7 +83,7 @@ src/library.* @sjplimp
src/main.cpp @sjplimp
src/min_*.* @sjplimp
src/memory.* @sjplimp
src/modify.* @sjplimp
src/modify.* @sjplimp @stanmoore1
src/molecule.* @sjplimp
src/my_page.h @sjplimp
src/my_pool_chunk.h @sjplimp

2
.github/workflows/codeql-analysis.yml vendored
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@ -3,7 +3,7 @@ name: "CodeQL Code Analysis"
on:
push:
branches: [master]
branches: [develop]
jobs:
analyze:

33
.github/workflows/compile-msvc.yml vendored Normal file
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@ -0,0 +1,33 @@
# GitHub action to build LAMMPS on Windows with Visual C++
name: "Native Windows Compilation"
on:
push:
branches: [develop]
jobs:
build:
name: Windows Compilation Test
if: ${{ github.repository == 'lammps/lammps' }}
runs-on: windows-latest
steps:
- name: Checkout repository
uses: actions/checkout@v2
with:
fetch-depth: 2
- name: Building LAMMPS via CMake
shell: bash
run: |
cmake -C cmake/presets/windows.cmake \
-S cmake -B build \
-D BUILD_SHARED_LIBS=on \
-D LAMMPS_EXCEPTIONS=on
cmake --build build --config Release
- name: Run LAMMPS executable
shell: bash
run: |
./build/Release/lmp.exe -h
./build/Release/lmp.exe -in bench/in.lj

2
.github/workflows/unittest-macos.yml vendored
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@ -3,7 +3,7 @@ name: "Unittest for MacOS"
on:
push:
branches: [master]
branches: [develop]
jobs:
build:

7
.gitignore vendored
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@ -37,8 +37,8 @@ vgcore.*
.Trashes
ehthumbs.db
Thumbs.db
.clang-format
.lammps_history
.vs
#cmake
/build*
@ -49,3 +49,8 @@ Thumbs.db
/Testing
/cmake_install.cmake
/lmp
out/Debug
out/RelWithDebInfo
out/Release
out/x86
out/x64

63
cmake/CMakeLists.txt
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@ -81,22 +81,40 @@ check_for_autogen_files(${LAMMPS_SOURCE_DIR})
include(CheckIncludeFileCXX)
# set required compiler flags and compiler/CPU arch specific optimizations
if((CMAKE_CXX_COMPILER_ID STREQUAL "Intel") OR (CMAKE_CXX_COMPILER_ID STREQUAL "IntelLLVM"))
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -restrict")
if(CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.3 OR CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.4)
set(CMAKE_TUNE_DEFAULT "-xCOMMON-AVX512")
if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
if(CMAKE_SYSTEM_NAME STREQUAL "Windows")
if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /Qrestrict")
endif()
if(CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.3 OR CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.4)
set(CMAKE_TUNE_DEFAULT "/QxCOMMON-AVX512")
else()
set(CMAKE_TUNE_DEFAULT "/QxHost")
endif()
else()
set(CMAKE_TUNE_DEFAULT "-xHost")
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -restrict")
if(CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.3 OR CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.4)
set(CMAKE_TUNE_DEFAULT "-xCOMMON-AVX512")
else()
set(CMAKE_TUNE_DEFAULT "-xHost")
endif()
endif()
endif()
# we require C++11 without extensions
# we require C++11 without extensions. Kokkos requires at least C++14 (currently)
set(CMAKE_CXX_STANDARD 11)
if(PKG_KOKKOS AND (CMAKE_CXX_STANDARD LESS 14))
set(CMAKE_CXX_STANDARD 14)
endif()
set(CMAKE_CXX_STANDARD_REQUIRED ON)
set(CMAKE_CXX_EXTENSIONS OFF CACHE BOOL "Use compiler extensions")
# ugly hack for MSVC which by default always reports an old C++ standard in the __cplusplus macro
# ugly hacks for MSVC which by default always reports an old C++ standard in the __cplusplus macro
# and prints lots of pointless warnings about "unsafe" functions
if(MSVC)
add_compile_options(/Zc:__cplusplus)
add_compile_options(/wd4244)
add_compile_options(/wd4267)
add_compile_definitions(_CRT_SECURE_NO_WARNINGS)
endif()
# export all symbols when building a .dll file on windows
@ -281,6 +299,11 @@ else()
target_include_directories(mpi_stubs PUBLIC $<BUILD_INTERFACE:${LAMMPS_SOURCE_DIR}/STUBS>)
if(BUILD_SHARED_LIBS)
target_link_libraries(lammps PRIVATE mpi_stubs)
if(MSVC)
target_link_libraries(lmp PRIVATE mpi_stubs)
target_include_directories(lmp INTERFACE $<BUILD_INTERFACE:${LAMMPS_SOURCE_DIR}/STUBS>)
target_compile_definitions(lmp INTERFACE $<INSTALL_INTERFACE:LAMMPS_LIB_NO_MPI>)
endif(MSVC)
target_include_directories(lammps INTERFACE $<BUILD_INTERFACE:${LAMMPS_SOURCE_DIR}/STUBS>)
target_compile_definitions(lammps INTERFACE $<INSTALL_INTERFACE:LAMMPS_LIB_NO_MPI>)
else()
@ -468,9 +491,12 @@ foreach(HEADER cmath)
endif(NOT FOUND_${HEADER})
endforeach(HEADER)
set(MATH_LIBRARIES "m" CACHE STRING "math library")
mark_as_advanced( MATH_LIBRARIES )
target_link_libraries(lammps PRIVATE ${MATH_LIBRARIES})
# 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")
mark_as_advanced(STANDARD_MATH_LIB)
if(STANDARD_MATH_LIB)
target_link_libraries(lammps PRIVATE ${STANDARD_MATH_LIB})
endif()
######################################
# Generate Basic Style files
@ -591,15 +617,12 @@ foreach(PKG_WITH_INCL CORESHELL QEQ OPENMP DPD-SMOOTH KOKKOS OPT INTEL GPU)
endforeach()
if(PKG_PLUGIN)
if(BUILD_SHARED_LIBS)
target_compile_definitions(lammps PRIVATE -DLMP_PLUGIN)
else()
message(WARNING "Plugin loading will not work unless BUILD_SHARED_LIBS is enabled")
endif()
# link with -ldl or equivalent for plugin loading; except on Windows
if(NOT ${CMAKE_SYSTEM_NAME} STREQUAL "Windows")
target_link_libraries(lammps PRIVATE ${CMAKE_DL_LIBS})
endif()
target_compile_definitions(lammps PRIVATE -DLMP_PLUGIN)
endif()
# link with -ldl or equivalent for plugin loading; except on Windows
if(NOT ${CMAKE_SYSTEM_NAME} STREQUAL "Windows")
target_link_libraries(lammps PRIVATE ${CMAKE_DL_LIBS})
endif()
######################################################################
@ -608,7 +631,7 @@ endif()
# and after everything else that is compiled locally
######################################################################
if(CMAKE_SYSTEM_NAME STREQUAL "Windows")
target_link_libraries(lammps PRIVATE -lwsock32 -lpsapi)
target_link_libraries(lammps PRIVATE "wsock32;psapi")
endif()
######################################################

55
cmake/CMakeSettings.json Normal file
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@ -0,0 +1,55 @@
{
"configurations": [
{
"name": "x64-Debug-MSVC",
"generator": "Ninja",
"configurationType": "Debug",
"buildRoot": "${workspaceRoot}\\build\\${name}",
"installRoot": "${workspaceRoot}\\install\\${name}",
"cmakeCommandArgs": "-S ${workspaceRoot}\\cmake -C ${workspaceRoot}\\cmake\\presets\\windows.cmake",
"buildCommandArgs": "",
"ctestCommandArgs": "",
"inheritEnvironments": [ "msvc_x64_x64" ],
"variables": [
{
"name": "BUILD_SHARED_LIBS",
"value": "True",
"type": "BOOL"
},
{
"name": "BUILD_TOOLS",
"value": "True",
"type": "BOOL"
},
{
"name": "LAMMPS_EXCEPTIONS",
"value": "True",
"type": "BOOL"
}
]
},
{
"name": "x64-Debug-Clang",
"generator": "Ninja",
"configurationType": "Debug",
"buildRoot": "${workspaceRoot}\\build\\${name}",
"installRoot": "${workspaceRoot}\\install\\${name}",
"cmakeCommandArgs": "-S ${workspaceRoot}\\cmake -C ${workspaceRoot}\\cmake\\presets\\windows.cmake",
"buildCommandArgs": "",
"ctestCommandArgs": "",
"inheritEnvironments": [ "clang_cl_x64" ],
"variables": [
{
"name": "BUILD_TOOLS",
"value": "True",
"type": "BOOL"
},
{
"name": "LAMMPS_EXCEPTIONS",
"value": "True",
"type": "BOOL"
}
]
}
]
}

4
cmake/Modules/GTest.cmake
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@ -7,8 +7,8 @@ else()
endif()
include(ExternalProject)
set(GTEST_URL "https://github.com/google/googletest/archive/release-1.10.0.tar.gz" CACHE STRING "URL for GTest tarball")
set(GTEST_MD5 "ecd1fa65e7de707cd5c00bdac56022cd" CACHE STRING "MD5 checksum of GTest tarball")
set(GTEST_URL "https://github.com/google/googletest/archive/release-1.11.0.tar.gz" CACHE STRING "URL of googletest source")
set(GTEST_MD5 "e8a8df240b6938bb6384155d4c37d937" CACHE STRING "MD5 sum for googletest source")
mark_as_advanced(GTEST_URL)
mark_as_advanced(GTEST_MD5)
ExternalProject_Add(googletest

2
cmake/Modules/LAMMPSUtils.cmake
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@ -85,7 +85,7 @@ endfunction(GenerateBinaryHeader)
# fetch missing potential files
function(FetchPotentials pkgfolder potfolder)
if (EXISTS "${pkgfolder}/potentials.txt")
if(EXISTS "${pkgfolder}/potentials.txt")
file(STRINGS "${pkgfolder}/potentials.txt" linelist REGEX "^[^#].")
foreach(line ${linelist})
string(FIND ${line} " " blank)

4
cmake/Modules/OpenCLLoader.cmake
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@ -1,6 +1,6 @@
message(STATUS "Downloading and building OpenCL loader library")
set(OPENCL_LOADER_URL "${LAMMPS_THIRDPARTY_URL}/opencl-loader-2021.06.30.tar.gz" CACHE STRING "URL for OpenCL loader tarball")
set(OPENCL_LOADER_MD5 "f9e55dd550cfbf77f46507adf7cb8fd2" CACHE STRING "MD5 checksum of OpenCL loader tarball")
set(OPENCL_LOADER_URL "${LAMMPS_THIRDPARTY_URL}/opencl-loader-2021.09.18.tar.gz" CACHE STRING "URL for OpenCL loader tarball")
set(OPENCL_LOADER_MD5 "3b3882627964bd02e5c3b02065daac3c" CACHE STRING "MD5 checksum of OpenCL loader tarball")
mark_as_advanced(OPENCL_LOADER_URL)
mark_as_advanced(OPENCL_LOADER_MD5)

98
cmake/Modules/Packages/GPU.cmake
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@ -71,44 +71,47 @@ if(GPU_API STREQUAL "CUDA")
# build arch/gencode commands for nvcc based on CUDA toolkit version and use choice
# --arch translates directly instead of JIT, so this should be for the preferred or most common architecture
set(GPU_CUDA_GENCODE "-arch=${GPU_ARCH}")
# Fermi (GPU Arch 2.x) is supported by CUDA 3.2 to CUDA 8.0
if((CUDA_VERSION VERSION_GREATER_EQUAL "3.2") AND (CUDA_VERSION VERSION_LESS "9.0"))
string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_20,code=[sm_20,compute_20] ")
endif()
# Kepler (GPU Arch 3.0) is supported by CUDA 5 to CUDA 10.2
if((CUDA_VERSION VERSION_GREATER_EQUAL "5.0") AND (CUDA_VERSION VERSION_LESS "11.0"))
string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_30,code=[sm_30,compute_30] ")
endif()
# Kepler (GPU Arch 3.5) is supported by CUDA 5 to CUDA 11
if((CUDA_VERSION VERSION_GREATER_EQUAL "5.0") AND (CUDA_VERSION VERSION_LESS "12.0"))
string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_35,code=[sm_35,compute_35]")
endif()
# Maxwell (GPU Arch 5.x) is supported by CUDA 6 and later
if(CUDA_VERSION VERSION_GREATER_EQUAL "6.0")
string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_50,code=[sm_50,compute_50] -gencode arch=compute_52,code=[sm_52,compute_52]")
endif()
# Pascal (GPU Arch 6.x) is supported by CUDA 8 and later
if(CUDA_VERSION VERSION_GREATER_EQUAL "8.0")
string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_60,code=[sm_60,compute_60] -gencode arch=compute_61,code=[sm_61,compute_61]")
endif()
# Volta (GPU Arch 7.0) is supported by CUDA 9 and later
if(CUDA_VERSION VERSION_GREATER_EQUAL "9.0")
string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_70,code=[sm_70,compute_70]")
endif()
# Turing (GPU Arch 7.5) is supported by CUDA 10 and later
if(CUDA_VERSION VERSION_GREATER_EQUAL "10.0")
string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_75,code=[sm_75,compute_75]")
endif()
# Ampere (GPU Arch 8.0) is supported by CUDA 11 and later
if(CUDA_VERSION VERSION_GREATER_EQUAL "11.0")
string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_80,code=[sm_80,compute_80]")
endif()
# Ampere (GPU Arch 8.6) is supported by CUDA 11.1 and later
if(CUDA_VERSION VERSION_GREATER_EQUAL "11.1")
string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_86,code=[sm_86,compute_86]")
endif()
# apply the following to build "fat" CUDA binaries only for known CUDA toolkits
if(CUDA_VERSION VERSION_GREATER_EQUAL "12.0")
message(WARNING "Unsupported CUDA version. Use at your own risk.")
message(WARNING "Untested CUDA Toolkit version. Use at your own risk")
else()
# Fermi (GPU Arch 2.x) is supported by CUDA 3.2 to CUDA 8.0
if((CUDA_VERSION VERSION_GREATER_EQUAL "3.2") AND (CUDA_VERSION VERSION_LESS "9.0"))
string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_20,code=[sm_20,compute_20] ")
endif()
# Kepler (GPU Arch 3.0) is supported by CUDA 5 to CUDA 10.2
if((CUDA_VERSION VERSION_GREATER_EQUAL "5.0") AND (CUDA_VERSION VERSION_LESS "11.0"))
string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_30,code=[sm_30,compute_30] ")
endif()
# Kepler (GPU Arch 3.5) is supported by CUDA 5 to CUDA 11
if((CUDA_VERSION VERSION_GREATER_EQUAL "5.0") AND (CUDA_VERSION VERSION_LESS "12.0"))
string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_35,code=[sm_35,compute_35]")
endif()
# Maxwell (GPU Arch 5.x) is supported by CUDA 6 and later
if(CUDA_VERSION VERSION_GREATER_EQUAL "6.0")
string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_50,code=[sm_50,compute_50] -gencode arch=compute_52,code=[sm_52,compute_52]")
endif()
# Pascal (GPU Arch 6.x) is supported by CUDA 8 and later
if(CUDA_VERSION VERSION_GREATER_EQUAL "8.0")
string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_60,code=[sm_60,compute_60] -gencode arch=compute_61,code=[sm_61,compute_61]")
endif()
# Volta (GPU Arch 7.0) is supported by CUDA 9 and later
if(CUDA_VERSION VERSION_GREATER_EQUAL "9.0")
string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_70,code=[sm_70,compute_70]")
endif()
# Turing (GPU Arch 7.5) is supported by CUDA 10 and later
if(CUDA_VERSION VERSION_GREATER_EQUAL "10.0")
string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_75,code=[sm_75,compute_75]")
endif()
# Ampere (GPU Arch 8.0) is supported by CUDA 11 and later
if(CUDA_VERSION VERSION_GREATER_EQUAL "11.0")
string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_80,code=[sm_80,compute_80]")
endif()
# Ampere (GPU Arch 8.6) is supported by CUDA 11.1 and later
if(CUDA_VERSION VERSION_GREATER_EQUAL "11.1")
string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_86,code=[sm_86,compute_86]")
endif()
endif()
cuda_compile_fatbin(GPU_GEN_OBJS ${GPU_LIB_CU} OPTIONS ${CUDA_REQUEST_PIC}
@ -214,13 +217,20 @@ elseif(GPU_API STREQUAL "OPENCL")
elseif(GPU_API STREQUAL "HIP")
if(NOT DEFINED HIP_PATH)
if(NOT DEFINED ENV{HIP_PATH})
set(HIP_PATH "/opt/rocm/hip" CACHE PATH "Path to which HIP has been installed")
set(HIP_PATH "/opt/rocm/hip" CACHE PATH "Path to HIP installation")
else()
set(HIP_PATH $ENV{HIP_PATH} CACHE PATH "Path to which HIP has been installed")
set(HIP_PATH $ENV{HIP_PATH} CACHE PATH "Path to HIP installation")
endif()
endif()
set(CMAKE_MODULE_PATH "${HIP_PATH}/cmake" ${CMAKE_MODULE_PATH})
find_package(HIP REQUIRED)
if(NOT DEFINED ROCM_PATH)
if(NOT DEFINED ENV{ROCM_PATH})
set(ROCM_PATH "/opt/rocm" CACHE PATH "Path to ROCm installation")
else()
set(ROCM_PATH $ENV{ROCM_PATH} CACHE PATH "Path to ROCm installation")
endif()
endif()
list(APPEND CMAKE_PREFIX_PATH ${HIP_PATH} ${ROCM_PATH})
find_package(hip REQUIRED)
option(HIP_USE_DEVICE_SORT "Use GPU sorting" ON)
if(NOT DEFINED HIP_PLATFORM)
@ -322,10 +332,11 @@ elseif(GPU_API STREQUAL "HIP")
set_directory_properties(PROPERTIES ADDITIONAL_MAKE_CLEAN_FILES "${LAMMPS_LIB_BINARY_DIR}/gpu/*_cubin.h ${LAMMPS_LIB_BINARY_DIR}/gpu/*.cu.cpp")
hip_add_library(gpu STATIC ${GPU_LIB_SOURCES})
add_library(gpu STATIC ${GPU_LIB_SOURCES})
target_include_directories(gpu PRIVATE ${LAMMPS_LIB_BINARY_DIR}/gpu)
target_compile_definitions(gpu PRIVATE -D_${GPU_PREC_SETTING} -DMPI_GERYON -DUCL_NO_EXIT)
target_compile_definitions(gpu PRIVATE -DUSE_HIP)
target_link_libraries(gpu PRIVATE hip::host)
if(HIP_USE_DEVICE_SORT)
# add hipCUB
@ -374,8 +385,9 @@ elseif(GPU_API STREQUAL "HIP")
endif()
endif()
hip_add_executable(hip_get_devices ${LAMMPS_LIB_SOURCE_DIR}/gpu/geryon/ucl_get_devices.cpp)
add_executable(hip_get_devices ${LAMMPS_LIB_SOURCE_DIR}/gpu/geryon/ucl_get_devices.cpp)
target_compile_definitions(hip_get_devices PRIVATE -DUCL_HIP)
target_link_libraries(hip_get_devices hip::host)
if(HIP_PLATFORM STREQUAL "nvcc")
target_compile_definitions(gpu PRIVATE -D__HIP_PLATFORM_NVCC__)

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

@ -1,6 +1,8 @@
########################################################################
# As of version 3.3.0 Kokkos requires C++14
set(CMAKE_CXX_STANDARD 14)
if(CMAKE_CXX_STANDARD LESS 14)
message(FATAL_ERROR "The KOKKOS package requires the C++ standard to be set to at least C++14")
endif()
########################################################################
# consistency checks and Kokkos options/settings required by LAMMPS
if(Kokkos_ENABLE_CUDA)

8
cmake/Modules/Packages/LATTE.cmake
View File

@ -19,6 +19,14 @@ if(DOWNLOAD_LATTE)
set(LATTE_MD5 "820e73a457ced178c08c71389a385de7" CACHE STRING "MD5 checksum of LATTE tarball")
mark_as_advanced(LATTE_URL)
mark_as_advanced(LATTE_MD5)
# CMake cannot pass BLAS or LAPACK library variable to external project if they are a list
list(LENGTH BLAS_LIBRARIES} NUM_BLAS)
list(LENGTH LAPACK_LIBRARIES NUM_LAPACK)
if((NUM_BLAS GREATER 1) OR (NUM_LAPACK GREATER 1))
message(FATAL_ERROR "Cannot compile downloaded LATTE library due to a technical limitation")
endif()
include(ExternalProject)
ExternalProject_Add(latte_build
URL ${LATTE_URL}

5
cmake/Modules/Packages/MACHDYN.cmake
View File

@ -7,8 +7,9 @@ endif()
option(DOWNLOAD_EIGEN3 "Download Eigen3 instead of using an already installed one)" ${DOWNLOAD_EIGEN3_DEFAULT})
if(DOWNLOAD_EIGEN3)
message(STATUS "Eigen3 download requested - we will build our own")
set(EIGEN3_URL "https://gitlab.com/libeigen/eigen/-/archive/3.3.9/eigen-3.3.9.tar.gz" CACHE STRING "URL for Eigen3 tarball")
set(EIGEN3_MD5 "609286804b0f79be622ccf7f9ff2b660" CACHE STRING "MD5 checksum of Eigen3 tarball")
set(EIGEN3_URL "https://download.lammps.org/thirdparty/eigen-3.4.0.tar.gz" CACHE STRING "URL for Eigen3 tarball")
set(EIGEN3_MD5 "4c527a9171d71a72a9d4186e65bea559" CACHE STRING "MD5 checksum of Eigen3 tarball")
mark_as_advanced(EIGEN3_URL)
mark_as_advanced(EIGEN3_MD5)
include(ExternalProject)

10
cmake/Modules/Packages/ML-HDNNP.cmake
View File

@ -45,12 +45,12 @@ if(DOWNLOAD_N2P2)
# get path to MPI include directory when cross-compiling to windows
if((CMAKE_SYSTEM_NAME STREQUAL Windows) AND CMAKE_CROSSCOMPILING)
get_target_property(N2P2_MPI_INCLUDE MPI::MPI_CXX INTERFACE_INCLUDE_DIRECTORIES)
set(N2P2_PROJECT_OPTIONS "-I ${N2P2_MPI_INCLUDE} -DMPICH_SKIP_MPICXX=1")
set(N2P2_PROJECT_OPTIONS "-I${N2P2_MPI_INCLUDE}")
set(MPI_CXX_COMPILER ${CMAKE_CXX_COMPILER})
endif()
if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
get_target_property(N2P2_MPI_INCLUDE MPI::MPI_CXX INTERFACE_INCLUDE_DIRECTORIES)
set(N2P2_PROJECT_OPTIONS "-I ${N2P2_MPI_INCLUDE} -DMPICH_SKIP_MPICXX=1")
set(N2P2_PROJECT_OPTIONS "-I${N2P2_MPI_INCLUDE}")
set(MPI_CXX_COMPILER ${CMAKE_CXX_COMPILER})
endif()
endif()
@ -69,6 +69,12 @@ if(DOWNLOAD_N2P2)
# echo final flag for debugging
message(STATUS "N2P2 BUILD OPTIONS: ${N2P2_BUILD_OPTIONS}")
# must have "sed" command to compile n2p2 library (for now)
find_program(HAVE_SED sed)
if(NOT HAVE_SED)
message(FATAL_ERROR "Must have 'sed' program installed to compile 'n2p2' library for ML-HDNNP package")
endif()
# download compile n2p2 library. much patch MPI calls in LAMMPS interface to accommodate MPI-2 (e.g. for cross-compiling)
include(ExternalProject)
ExternalProject_Add(n2p2_build

21
cmake/Modules/Packages/ML-PACE.cmake
View File

@ -1,11 +1,11 @@
set(PACELIB_URL "https://github.com/ICAMS/lammps-user-pace/archive/refs/tags/v.2021.10.25.tar.gz" CACHE STRING "URL for PACE evaluator library sources")
set(PACELIB_URL "https://github.com/ICAMS/lammps-user-pace/archive/refs/tags/v.2021.4.9.tar.gz" CACHE STRING "URL for PACE evaluator library sources")
set(PACELIB_MD5 "4db54962fbd6adcf8c18d46e1798ceb5" CACHE STRING "MD5 checksum of PACE evaluator library tarball")
set(PACELIB_MD5 "a2ac3315c41a1a4a5c912bcb1bc9c5cc" CACHE STRING "MD5 checksum of PACE evaluator library tarball")
mark_as_advanced(PACELIB_URL)
mark_as_advanced(PACELIB_MD5)
# download library sources to build folder
file(DOWNLOAD ${PACELIB_URL} ${CMAKE_BINARY_DIR}/libpace.tar.gz SHOW_PROGRESS EXPECTED_HASH MD5=${PACELIB_MD5})
file(DOWNLOAD ${PACELIB_URL} ${CMAKE_BINARY_DIR}/libpace.tar.gz EXPECTED_HASH MD5=${PACELIB_MD5}) #SHOW_PROGRESS
# uncompress downloaded sources
execute_process(
@ -14,12 +14,19 @@ execute_process(
WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
)
file(GLOB PACE_EVALUATOR_INCLUDE_DIR ${CMAKE_BINARY_DIR}/lammps-user-pace-*/USER-PACE)
file(GLOB PACE_EVALUATOR_SOURCES ${CMAKE_BINARY_DIR}/lammps-user-pace-*/USER-PACE/*.cpp)
file(GLOB lib-pace ${CMAKE_BINARY_DIR}/lammps-user-pace-*)
add_subdirectory(${lib-pace}/yaml-cpp build-yaml-cpp)
set(YAML_CPP_INCLUDE_DIR ${lib-pace}/yaml-cpp/include)
file(GLOB PACE_EVALUATOR_INCLUDE_DIR ${lib-pace}/ML-PACE)
file(GLOB PACE_EVALUATOR_SOURCES ${lib-pace}/ML-PACE/*.cpp)
list(FILTER PACE_EVALUATOR_SOURCES EXCLUDE REGEX pair_pace.cpp)
add_library(pace STATIC ${PACE_EVALUATOR_SOURCES})
set_target_properties(pace PROPERTIES CXX_EXTENSIONS ON OUTPUT_NAME lammps_pace${LAMMPS_MACHINE})
target_include_directories(pace PUBLIC ${PACE_EVALUATOR_INCLUDE_DIR})
target_link_libraries(lammps PRIVATE pace)
target_include_directories(pace PUBLIC ${PACE_EVALUATOR_INCLUDE_DIR} ${YAML_CPP_INCLUDE_DIR})
target_link_libraries(pace PRIVATE yaml-cpp-pace)
target_link_libraries(lammps PRIVATE pace)

4
cmake/Modules/Packages/ML-QUIP.cmake
View File

@ -38,7 +38,7 @@ if(DOWNLOAD_QUIP)
set(temp "${temp}HAVE_LOCAL_E_MIX=0\nHAVE_QC=0\nHAVE_GAP=1\nHAVE_DESCRIPTORS_NONCOMMERCIAL=1\n")
set(temp "${temp}HAVE_TURBOGAP=0\nHAVE_QR=1\nHAVE_THIRDPARTY=0\nHAVE_FX=0\nHAVE_SCME=0\nHAVE_MTP=0\n")
set(temp "${temp}HAVE_MBD=0\nHAVE_TTM_NF=0\nHAVE_CH4=0\nHAVE_NETCDF4=0\nHAVE_MDCORE=0\nHAVE_ASAP=0\n")
set(temp "${temp}HAVE_CGAL=0\nHAVE_METIS=0\nHAVE_LMTO_TBE=0\n")
set(temp "${temp}HAVE_CGAL=0\nHAVE_METIS=0\nHAVE_LMTO_TBE=0\nHAVE_SCALAPACK=0\n")
file(WRITE ${CMAKE_BINARY_DIR}/quip.config "${temp}")
message(STATUS "QUIP download via git requested - we will build our own")
@ -50,7 +50,7 @@ if(DOWNLOAD_QUIP)
GIT_TAG origin/public
GIT_SHALLOW YES
GIT_PROGRESS YES
PATCH_COMMAND cp ${CMAKE_BINARY_DIR}/quip.config <SOURCE_DIR>/arch/Makefile.lammps
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
INSTALL_COMMAND ""

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

@ -12,6 +12,13 @@ if(DOWNLOAD_MSCG)
mark_as_advanced(MSCG_URL)
mark_as_advanced(MSCG_MD5)
# CMake cannot pass BLAS or LAPACK library variable to external project if they are a list
list(LENGTH BLAS_LIBRARIES} NUM_BLAS)
list(LENGTH LAPACK_LIBRARIES NUM_LAPACK)
if((NUM_BLAS GREATER 1) OR (NUM_LAPACK GREATER 1))
message(FATAL_ERROR "Cannot compile downloaded MSCG library due to a technical limitation")
endif()
include(ExternalProject)
ExternalProject_Add(mscg_build
URL ${MSCG_URL}

5
cmake/Modules/Packages/SCAFACOS.cmake
View File

@ -23,6 +23,11 @@ if(DOWNLOAD_SCAFACOS)
file(DOWNLOAD ${LAMMPS_THIRDPARTY_URL}/scafacos-1.0.1-fix.diff ${CMAKE_CURRENT_BINARY_DIR}/scafacos-1.0.1.fix.diff
EXPECTED_HASH MD5=4baa1333bb28fcce102d505e1992d032)
find_program(HAVE_PATCH patch)
if(NOT HAVE_PATCH)
message(FATAL_ERROR "The 'patch' program is required to build the ScaFaCoS library")
endif()
include(ExternalProject)
ExternalProject_Add(scafacos_build
URL ${SCAFACOS_URL}

5
cmake/Modules/Packages/VORONOI.cmake
View File

@ -26,6 +26,11 @@ if(DOWNLOAD_VORO)
set(VORO_BUILD_OPTIONS CXX=${CMAKE_CXX_COMPILER} CFLAGS=${VORO_BUILD_CFLAGS})
endif()
find_program(HAVE_PATCH patch)
if(NOT HAVE_PATCH)
message(FATAL_ERROR "The 'patch' program is required to build the voro++ library")
endif()
ExternalProject_Add(voro_build
URL ${VORO_URL}
URL_MD5 ${VORO_MD5}

4
cmake/Modules/Tools.cmake
View File

@ -25,7 +25,9 @@ if(BUILD_TOOLS)
get_filename_component(MSI2LMP_SOURCE_DIR ${LAMMPS_TOOLS_DIR}/msi2lmp/src ABSOLUTE)
file(GLOB MSI2LMP_SOURCES ${MSI2LMP_SOURCE_DIR}/[^.]*.c)
add_executable(msi2lmp ${MSI2LMP_SOURCES})
target_link_libraries(msi2lmp PRIVATE ${MATH_LIBRARIES})
if(STANDARD_MATH_LIB)
target_link_libraries(msi2lmp PRIVATE ${STANDARD_MATH_LIB})
endif()
install(TARGETS msi2lmp DESTINATION ${CMAKE_INSTALL_BINDIR})
install(FILES ${LAMMPS_DOC_DIR}/msi2lmp.1 DESTINATION ${CMAKE_INSTALL_MANDIR}/man1)
endif()

25
cmake/iwyu/iwyu-extra-map.imp
View File

@ -1,7 +1,28 @@
[
{ include: [ "<bits/types/struct_rusage.h>", private, "<sys/resource.h>", public ] },
{ include: [ "<bits/exception.h>", public, "<exception>", public ] },
{ include: [ "@<Eigen/.*>", private, "<Eigen/Eigen>", public ] },
{ include: [ "@<gtest/.*>", private, "\"gtest/gtest.h\"", public ] },
{ include: [ "@<gmock/.*>", private, "\"gmock/gmock.h\"", public ] },
{ include: [ "@<gmock/.*>", private, "\"gmock/gmock.h\"", public ] },
{ include: [ "@<(cell|c_loops|container).hh>", private, "<voro++.hh>", public ] },
{ include: [ "@\"atom_vec_.*.h\"", public, "\"style_atom.h\"", public ] },
{ include: [ "@\"body_.*.h\"", public, "\"style_body.h\"", public ] },
{ include: [ "@\"compute_.*.h\"", public, "\"style_compute.h\"", public ] },
{ include: [ "@\"fix_.*.h\"", public, "\"style_fix.h\"", public ] },
{ include: [ "@\"dump_.*.h\"", public, "\"style_dump.h\"", public ] },
{ include: [ "@\"min_.*.h\"", public, "\"style_minimize.h\"", public ] },
{ include: [ "@\"reader_.*.h\"", public, "\"style_reader.h\"", public ] },
{ include: [ "@\"region_.*.h\"", public, "\"style_region.h\"", public ] },
{ include: [ "@\"pair_.*.h\"", public, "\"style_pair.h\"", public ] },
{ include: [ "@\"angle_.*.h\"", public, "\"style_angle.h\"", public ] },
{ include: [ "@\"bond_.*.h\"", public, "\"style_bond.h\"", public ] },
{ include: [ "@\"dihedral_.*.h\"", public, "\"style_dihedral.h\"", public ] },
{ include: [ "@\"improper_.*.h\"", public, "\"style_improper.h\"", public ] },
{ include: [ "@\"kspace_.*.h\"", public, "\"style_kspace.h\"", public ] },
{ include: [ "@\"nbin_.*.h\"", public, "\"style_nbin.h\"", public ] },
{ include: [ "@\"npair_.*.h\"", public, "\"style_npair.h\"", public ] },
{ include: [ "@\"nstenci_.*.h\"", public, "\"style_nstencil.h\"", public ] },
{ include: [ "@\"ntopo_.*.h\"", public, "\"style_ntopo.h\"", public ] },
{ include: [ "<float.h>", public, "<cfloat>", public ] },
{ include: [ "<limits.h>", public, "<climits>", public ] },
{ include: [ "<bits/types/struct_tm.h>", private, "<ctime>", public ] },
]

30
cmake/presets/hip_amd.cmake Normal file
View File

@ -0,0 +1,30 @@
# preset that will enable hip (clang/clang++) with support for MPI and OpenMP (on Linux boxes)
# prefer flang over gfortran, if available
find_program(CLANG_FORTRAN NAMES flang gfortran f95)
set(ENV{OMPI_FC} ${CLANG_FORTRAN})
set(CMAKE_CXX_COMPILER "hipcc" CACHE STRING "" FORCE)
set(CMAKE_C_COMPILER "hipcc" CACHE STRING "" FORCE)
set(CMAKE_Fortran_COMPILER ${CLANG_FORTRAN} CACHE STRING "" FORCE)
set(CMAKE_CXX_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE)
set(CMAKE_CXX_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
set(CMAKE_CXX_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
set(CMAKE_Fortran_FLAGS_DEBUG "-Wall -Wextra -g -std=f2003" CACHE STRING "" FORCE)
set(CMAKE_Fortran_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG -std=f2003" CACHE STRING "" FORCE)
set(CMAKE_Fortran_FLAGS_RELEASE "-O3 -DNDEBUG -std=f2003" CACHE STRING "" FORCE)
set(CMAKE_C_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE)
set(CMAKE_C_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
set(CMAKE_C_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
set(MPI_CXX "hipcc" CACHE STRING "" FORCE)
set(MPI_CXX_COMPILER "mpicxx" CACHE STRING "" FORCE)
unset(HAVE_OMP_H_INCLUDE CACHE)
set(OpenMP_C "hipcc" CACHE STRING "" FORCE)
set(OpenMP_C_FLAGS "-fopenmp" CACHE STRING "" FORCE)
set(OpenMP_C_LIB_NAMES "omp" CACHE STRING "" FORCE)
set(OpenMP_CXX "hipcc" CACHE STRING "" FORCE)
set(OpenMP_CXX_FLAGS "-fopenmp" CACHE STRING "" FORCE)
set(OpenMP_CXX_LIB_NAMES "omp" CACHE STRING "" FORCE)
set(OpenMP_omp_LIBRARY "libomp.so" CACHE PATH "" FORCE)

1
cmake/presets/most.cmake
View File

@ -24,6 +24,7 @@ set(ALL_PACKAGES
DRUDE
EFF
EXTRA-COMPUTE
EXTRA-DUMP
EXTRA-FIX
EXTRA-MOLECULE
EXTRA-PAIR

64
cmake/presets/windows.cmake Normal file
View File

@ -0,0 +1,64 @@
set(WIN_PACKAGES
ASPHERE
BOCS
BODY
BROWNIAN
CG-DNA
CG-SDK
CLASS2
COLLOID
COLVARS
CORESHELL
DIELECTRIC
DIFFRACTION
DIPOLE
DPD-BASIC
DPD-MESO
DPD-REACT
DPD-SMOOTH
DRUDE
EFF
EXTRA-COMPUTE
EXTRA-DUMP
EXTRA-FIX
EXTRA-MOLECULE
EXTRA-PAIR
FEP
GRANULAR
INTERLAYER
KSPACE
MANIFOLD
MANYBODY
MC
MEAM
MISC
ML-IAP
ML-SNAP
MOFFF
MOLECULE
MOLFILE
OPENMP
ORIENT
PERI
PHONON
POEMS
PTM
QEQ
QTB
REACTION
REAXFF
REPLICA
RIGID
SHOCK
SMTBQ
SPH
SPIN
SRD
TALLY
UEF
YAFF)
foreach(PKG ${WIN_PACKAGES})
set(PKG_${PKG} ON CACHE BOOL "" FORCE)
endforeach()

2
doc/doxygen/Doxyfile.in
View File

@ -435,6 +435,8 @@ INPUT = @LAMMPS_SOURCE_DIR@/utils.cpp \
@LAMMPS_SOURCE_DIR@/my_pool_chunk.cpp \
@LAMMPS_SOURCE_DIR@/my_pool_chunk.h \
@LAMMPS_SOURCE_DIR@/math_eigen.h \
@LAMMPS_SOURCE_DIR@/platform.h \
@LAMMPS_SOURCE_DIR@/platform.cpp \
# The EXCLUDE_SYMLINKS tag can be used to select whether or not files or
# directories that are symbolic links (a Unix file system feature) are excluded

12
doc/github-development-workflow.md
View File

@ -33,9 +33,9 @@ when necessary.
## Pull Requests
ALL changes to the LAMMPS code and documentation, however trivial, MUST
be submitted as a pull request to GitHub. All changes to the "master"
be submitted as a pull request to GitHub. All changes to the "develop"
branch must be made exclusively through merging pull requests. The
"unstable" and "stable" branches, respectively are only to be updated
"release" and "stable" branches, respectively are only to be updated
upon patch or stable releases with fast-forward merges based on the
associated tags. Pull requests may also be submitted to (long-running)
feature branches created by LAMMPS developers inside the LAMMPS project,
@ -123,16 +123,16 @@ and thus were this comment should be placed.
LAMMPS uses a continuous release development model with incremental
changes, i.e. significant effort is made - including automated pre-merge
testing - that the code in the branch "master" does not get easily
testing - that the code in the branch "develop" does not get easily
broken. These tests are run after every update to a pull request. More
extensive and time consuming tests (including regression testing) are
performed after code is merged to the "master" branch. There are patch
performed after code is merged to the "develop" branch. There are patch
releases of LAMMPS every 3-5 weeks at a point, when the LAMMPS
developers feel, that a sufficient amount of changes have happened, and
the post-merge testing has been successful. These patch releases are
marked with a `patch_<version date>` tag and the "unstable" branch
marked with a `patch_<version date>` tag and the "release" branch
follows only these versions (and thus is always supposed to be of
production quality, unlike "master", which may be temporary broken, in
production quality, unlike "develop", which may be temporary broken, in
the case of larger change sets or unexpected incompatibilities or side
effects.

2
doc/lammps.1
View File

@ -1,4 +1,4 @@
.TH LAMMPS "31 August 2021" "2021-08-31"
.TH LAMMPS "1" "29 September 2021" "2021-09-29"
.SH NAME
.B LAMMPS
\- Molecular Dynamics Simulator.

2
doc/msi2lmp.1
View File

@ -1,4 +1,4 @@
.TH MSI2LMP "v3.9.9" "2018-11-05"
.TH MSI2LMP "1" "v3.9.9" "2018-11-05"
.SH NAME
.B MSI2LMP
\- Converter for Materials Studio files to LAMMPS

13
doc/src/Build_development.rst
View File

@ -58,13 +58,16 @@ Report missing and unneeded '#include' statements (CMake only)
The conventions for how and when to use and order include statements in
LAMMPS are documented in :doc:`Modify_style`. To assist with following
these conventions one can use the `Include What You Use tool <https://include-what-you-use.org/>`_.
This is still under development and for large and complex projects like LAMMPS
This tool is still under development and for large and complex projects like LAMMPS
there are some false positives, so suggested changes need to be verified manually.
It is recommended to use at least version 0.14, which has much fewer incorrect
reports than earlier versions.
It is recommended to use at least version 0.16, which has much fewer incorrect
reports than earlier versions. To install the IWYU toolkit, you need to have
the clang compiler **and** its development package installed. Download the IWYU
version that matches the version of the clang compiler, configure, build, and
install it.
The necessary steps to generate the report can be enabled via a
CMake variable:
The necessary steps to generate the report can be enabled via a CMake variable
during CMake configuration.
.. code-block:: bash

2
doc/src/Build_diskspace.rst
View File

@ -14,7 +14,7 @@ environments with restricted disk space capacity it may be needed to
reduce the storage requirements. Here are some suggestions:
- Create a so-called shallow repository by cloning only the last commit
instead of the full project history by using ``git clone git@github.com:lammps/lammps --depth=1 --branch=master``.
instead of the full project history by using ``git clone git@github.com:lammps/lammps --depth=1 --branch=develop``.
This reduces the downloaded size to about half. With ``--depth=1`` it is not possible to check out different
versions/branches of LAMMPS, using ``--depth=1000`` will make multiple recent versions available at little
extra storage needs (the entire git history had nearly 30,000 commits in fall 2021).

15
doc/src/Build_manual.rst
View File

@ -33,12 +33,15 @@ various tools and files. Some of them have to be installed (see below). For
the rest the build process will attempt to download and install them into
a python virtual environment and local folders.
A current version of the manual (latest patch release, aka unstable
branch) is is available online at:
`https://docs.lammps.org/Manual.html <https://docs.lammps.org/Manual.html>`_.
A version of the manual corresponding to the ongoing development (aka master branch)
is available online at: `https://docs.lammps.org/latest/
<https://docs.lammps.org/latest/>`_
A current version of the manual (latest patch release, that is the state
of the *release* branch) is is available online at:
`https://docs.lammps.org/ <https://docs.lammps.org/>`_.
A version of the manual corresponding to the ongoing development (that is
the state of the *develop* branch) is available online at:
`https://docs.lammps.org/latest/ <https://docs.lammps.org/latest/>`_
A version of the manual corresponding to the latest stable LAMMPS release
(that is the state of the *stable* branch) is available online at:
`https://docs.lammps.org/stable/ <https://docs.lammps.org/stable/>`_
Build using GNU make
--------------------

35
doc/src/Build_settings.rst
View File

@ -71,7 +71,8 @@ LAMMPS can use them if they are available on your system.
-D FFTW3_INCLUDE_DIR=path # path to FFTW3 include files
-D FFTW3_LIBRARY=path # path to FFTW3 libraries
-D FFT_FFTW_THREADS=on # enable using threaded FFTW3 libraries
-D FFTW3_OMP_LIBRARY=path # path to FFTW3 OpenMP wrapper libraries
-D FFT_FFTW_THREADS=on # enable using OpenMP threaded FFTW3 libraries
-D MKL_INCLUDE_DIR=path # ditto for Intel MKL library
-D FFT_MKL_THREADS=on # enable using threaded FFTs with MKL libraries
-D MKL_LIBRARY=path # path to MKL libraries
@ -320,9 +321,7 @@ following settings:
.. code-block:: make
LMP_INC = -DLAMMPS_JPEG
LMP_INC = -DLAMMPS_PNG
LMP_INC = -DLAMMPS_FFMPEG
LMP_INC = -DLAMMPS_JPEG -DLAMMPS_PNG -DLAMMPS_FFMPEG <other LMP_INC settings>
JPG_INC = -I/usr/local/include # path to jpeglib.h, png.h, zlib.h header files if make cannot find them
JPG_PATH = -L/usr/lib # paths to libjpeg.a, libpng.a, libz.a (.so) files if make cannot find them
@ -353,8 +352,10 @@ Read or write compressed files
-----------------------------------------
If this option is enabled, large files can be read or written with
gzip compression by several LAMMPS commands, including
:doc:`read_data <read_data>`, :doc:`rerun <rerun>`, and :doc:`dump <dump>`.
compression by ``gzip`` or similar tools by several LAMMPS commands,
including :doc:`read_data <read_data>`, :doc:`rerun <rerun>`, and
:doc:`dump <dump>`. Currently supported compression tools are:
``gzip``, ``bzip2``, ``zstd``, and ``lzma``.
.. tabs::
@ -363,23 +364,23 @@ gzip compression by several LAMMPS commands, including
.. code-block:: bash
-D WITH_GZIP=value # yes or no
# default is yes if CMake can find gzip, else no
-D GZIP_EXECUTABLE=path # path to gzip executable if CMake cannot find it
# default is yes if CMake can find the gzip program, else no
.. tab:: Traditional make
.. code-block:: make
LMP_INC = -DLAMMPS_GZIP
LMP_INC = -DLAMMPS_GZIP <other LMP_INC settings>
This option requires that your operating system fully supports the "popen()"
function in the standard runtime library and that a ``gzip`` executable can be
found by LAMMPS during a run.
This option requires that your operating system fully supports the
"popen()" function in the standard runtime library and that a ``gzip``
or other executable can be found by LAMMPS in the standard search path
during a run.
.. note::
On some clusters with high-speed networks, using the "fork()" library
call (required by "popen()") can interfere with the fast communication
On clusters with high-speed networks, using the "fork()" library call
(required by "popen()") can interfere with the fast communication
library and lead to simulations using compressed output or input to
hang or crash. For selected operations, compressed file I/O is also
available using a compression library instead, which is what the
@ -451,7 +452,7 @@ those systems:
.. code-block:: make
LMP_INC = -DLAMMPS_LONGLONG_TO_LONG
LMP_INC = -DLAMMPS_LONGLONG_TO_LONG <other LMP_INC settings>
----------
@ -478,7 +479,7 @@ e.g. to Python. Of course, the calling code has to be set up to
.. code-block:: make
LMP_INC = -DLAMMPS_EXCEPTIONS
LMP_INC = -DLAMMPS_EXCEPTIONS <other LMP_INC settings>
.. note::
@ -519,7 +520,7 @@ executable, not the library.
.. code-block:: make
LMP_INC = -DLAMMPS_TRAP_FPE
LMP_INC = -DLAMMPS_TRAP_FPE <other LMP_INC settings>
After compilation with this flag set, the LAMMPS executable will stop
and produce a core dump when a division by zero, overflow, illegal math

44
doc/src/Build_windows.rst
View File

@ -4,6 +4,7 @@ Notes for building LAMMPS on Windows
* :ref:`General remarks <generic>`
* :ref:`Running Linux on Windows <linux>`
* :ref:`Using GNU GCC ported to Windows <gnu>`
* :ref:`Using Visual Studio <msvc>`
* :ref:`Using a cross-compiler <cross>`
----------
@ -31,13 +32,13 @@ pre-compiled Windows binary packages are sufficient for your needs. If
it is necessary for you to compile LAMMPS on a Windows machine
(e.g. because it is your main desktop), please also consider using a
virtual machine software and compile and run LAMMPS in a Linux virtual
machine, or - if you have a sufficiently up-to-date Windows 10
installation - consider using the Windows subsystem for Linux. This
optional Windows feature allows you to run the bash shell from Ubuntu
from within Windows and from there on, you can pretty much use that
shell like you are running on an Ubuntu Linux machine (e.g. installing
software via apt-get and more). For more details on that, please see
:doc:`this tutorial <Howto_wsl>`.
machine, or - if you have a sufficiently up-to-date Windows 10 or
Windows 11 installation - consider using the Windows subsystem for
Linux. This optional Windows feature allows you to run the bash shell
from Ubuntu from within Windows and from there on, you can pretty much
use that shell like you are running on an Ubuntu Linux machine
(e.g. installing software via apt-get and more). For more details on
that, please see :doc:`this tutorial <Howto_wsl>`.
.. _gnu:
@ -67,6 +68,35 @@ requiring changes to the LAMMPS source code, or figure out corrections
yourself, please report them on the lammps-users mailing list, or file
them as an issue or pull request on the LAMMPS GitHub project.
.. _msvc:
Using Microsoft Visual Studio
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Following the integration of the :doc:`platform namespace
<Developer_platform>` into the LAMMPS code base, portability of LAMMPS
to be compiled on Windows using Visual Studio has been significantly
improved. This has been tested with Visual Studio 2019 (aka version
16). Not all features and packages in LAMMPS are currently supported
out of the box, but a preset ``cmake/presets/windows.cmake`` is provided
that contains the packages that have been compiled successfully. You
must use the CMake based build procedure, and either use the integrated
CMake support of Visual Studio or use an external CMake installation to
create build files for the Visual Studio build system. Please note that
on launching Visual Studio it will scan the directory tree and likely
miss the correct master ``CMakeLists.txt``. Try to open the
``cmake/CMakeSettings.json`` and use those CMake configurations as a
starting point. It is also possible to configure and compile LAMMPS
from the command line with a CMake binary from `cmake.org <https://cmake.org>`_.
To support running in parallel you can compile with OpenMP enabled using
the OPENMP package or install Microsoft MPI (including the SDK) and compile
LAMMPS with MPI enabled.
This is work in progress and you should contact the LAMMPS developers
via GitHub, the forum, or the mailing list, if you have questions or
LAMMPS specific problems.
.. _cross:
Using a cross-compiler

2
doc/src/Commands_fix.rst
View File

@ -23,6 +23,7 @@ OPT.
:columns: 5
* :doc:`accelerate/cos <fix_accelerate_cos>`
* :doc:`acks2/reaxff (k) <fix_acks2_reaxff>`
* :doc:`adapt <fix_adapt>`
* :doc:`adapt/fep <fix_adapt_fep>`
* :doc:`addforce <fix_addforce>`
@ -103,6 +104,7 @@ OPT.
* :doc:`manifoldforce <fix_manifoldforce>`
* :doc:`mdi/engine <fix_mdi_engine>`
* :doc:`meso/move <fix_meso_move>`
* :doc:`mol/swap <fix_mol_swap>`
* :doc:`momentum (k) <fix_momentum>`
* :doc:`momentum/chunk <fix_momentum>`
* :doc:`move <fix_move>`

2
doc/src/Developer.rst
View File

@ -11,10 +11,12 @@ of time and requests from the LAMMPS user community.
:maxdepth: 1
Developer_org
Developer_parallel
Developer_flow
Developer_write
Developer_notes
Developer_plugins
Developer_unittest
Classes
Developer_platform
Developer_utils

120
doc/src/Developer_par_comm.rst Normal file
View File

@ -0,0 +1,120 @@
Communication
^^^^^^^^^^^^^
Following the partitioning scheme in use all per-atom data is
distributed across the MPI processes, which allows LAMMPS to handle very
large systems provided it uses a correspondingly large number of MPI
processes. Since The per-atom data (atom IDs, positions, velocities,
types, etc.) To be able to compute the short-range interactions MPI
processes need not only access to data of atoms they "own" but also
information about atoms from neighboring sub-domains, in LAMMPS referred
to as "ghost" atoms. These are copies of atoms storing required
per-atom data for up to the communication cutoff distance. The green
dashed-line boxes in the :ref:`domain-decomposition` figure illustrate
the extended ghost-atom sub-domain for one processor.
This approach is also used to implement periodic boundary
conditions: atoms that lie within the cutoff distance across a periodic
boundary are also stored as ghost atoms and taken from the periodic
replication of the sub-domain, which may be the same sub-domain, e.g. if
running in serial. As a consequence of this, force computation in
LAMMPS is not subject to minimum image conventions and thus cutoffs may
be larger than half the simulation domain.
.. _ghost-atom-comm:
.. figure:: img/ghost-comm.png
:align: center
ghost atom communication
This figure shows the ghost atom communication patterns between
sub-domains for "brick" (left) and "tiled" communication styles for
2d simulations. The numbers indicate MPI process ranks. Here the
sub-domains are drawn spatially separated for clarity. The
dashed-line box is the extended sub-domain of processor 0 which
includes its ghost atoms. The red- and blue-shaded boxes are the
regions of communicated ghost atoms.
Efficient communication patterns are needed to update the "ghost" atom
data, since that needs to be done at every MD time step or minimization
step. The diagrams of the `ghost-atom-comm` figure illustrate how ghost
atom communication is performed in two stages for a 2d simulation (three
in 3d) for both a regular and irregular partitioning of the simulation
box. For the regular case (left) atoms are exchanged first in the
*x*-direction, then in *y*, with four neighbors in the grid of processor
sub-domains.
In the *x* stage, processor ranks 1 and 2 send owned atoms in their
red-shaded regions to rank 0 (and vice versa). Then in the *y* stage,
ranks 3 and 4 send atoms in their blue-shaded regions to rank 0, which
includes ghost atoms they received in the *x* stage. Rank 0 thus
acquires all its ghost atoms; atoms in the solid blue corner regions
are communicated twice before rank 0 receives them.
For the irregular case (right) the two stages are similar, but a
processor can have more than one neighbor in each direction. In the
*x* stage, MPI ranks 1,2,3 send owned atoms in their red-shaded regions to
rank 0 (and vice versa). These include only atoms between the lower
and upper *y*-boundary of rank 0's sub-domain. In the *y* stage, ranks
4,5,6 send atoms in their blue-shaded regions to rank 0. This may
include ghost atoms they received in the *x* stage, but only if they
are needed by rank 0 to fill its extended ghost atom regions in the
+/-*y* directions (blue rectangles). Thus in this case, ranks 5 and
6 do not include ghost atoms they received from each other (in the *x*
stage) in the atoms they send to rank 0. The key point is that while
the pattern of communication is more complex in the irregular
partitioning case, it can still proceed in two stages (three in 3d)
via atom exchanges with only neighboring processors.
When attributes of owned atoms are sent to neighboring processors to
become attributes of their ghost atoms, LAMMPS calls this a "forward"
communication. On timesteps when atoms migrate to new owning processors
and neighbor lists are rebuilt, each processor creates a list of its
owned atoms which are ghost atoms in each of its neighbor processors.
These lists are used to pack per-atom coordinates (for example) into
message buffers in subsequent steps until the next reneighboring.
A "reverse" communication is when computed ghost atom attributes are
sent back to the processor who owns the atom. This is used (for
example) to sum partial forces on ghost atoms to the complete force on
owned atoms. The order of the two stages described in the
:ref:`ghost-atom-comm` figure is inverted and the same lists of atoms
are used to pack and unpack message buffers with per-atom forces. When
a received buffer is unpacked, the ghost forces are summed to owned atom
forces. As in forward communication, forces on atoms in the four blue
corners of the diagrams are sent, received, and summed twice (once at
each stage) before owning processors have the full force.
These two operations are used many places within LAMMPS aside from
exchange of coordinates and forces, for example by manybody potentials
to share intermediate per-atom values, or by rigid-body integrators to
enable each atom in a body to access body properties. Here are
additional details about how these communication operations are
performed in LAMMPS:
- When exchanging data with different processors, forward and reverse
communication is done using ``MPI_Send()`` and ``MPI_IRecv()`` calls.
If a processor is "exchanging" atoms with itself, only the pack and
unpack operations are performed, e.g. to create ghost atoms across
periodic boundaries when running on a single processor.
- For forward communication of owned atom coordinates, periodic box
lengths are added and subtracted when the receiving processor is
across a periodic boundary from the sender. There is then no need to
apply a minimum image convention when calculating distances between
atom pairs when building neighbor lists or computing forces.
- The cutoff distance for exchanging ghost atoms is typically equal to
the neighbor cutoff. But it can also chosen to be longer if needed,
e.g. half the diameter of a rigid body composed of multiple atoms or
over 3x the length of a stretched bond for dihedral interactions. It
can also exceed the periodic box size. For the regular communication
pattern (left), if the cutoff distance extends beyond a neighbor
processor's sub-domain, then multiple exchanges are performed in the
same direction. Each exchange is with the same neighbor processor,
but buffers are packed/unpacked using a different list of atoms. For
forward communication, in the first exchange a processor sends only
owned atoms. In subsequent exchanges, it sends ghost atoms received
in previous exchanges. For the irregular pattern (right) overlaps of
a processor's extended ghost-atom sub-domain with all other processors
in each dimension are detected.

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Long-range interactions
^^^^^^^^^^^^^^^^^^^^^^^
For charged systems, LAMMPS can compute long-range Coulombic
interactions via the FFT-based particle-particle/particle-mesh (PPPM)
method implemented in :doc:`kspace style pppm and its variants
<kspace_style>`. For that Coulombic interactions are partitioned into
short- and long-range components. The short-ranged portion is computed
in real space as a loop over pairs of charges within a cutoff distance,
using neighbor lists. The long-range portion is computed in reciprocal
space using a kspace style. For the PPPM implementation the simulation
cell is overlaid with a regular FFT grid in 3d. It proceeds in several stages:
a) each atom's point charge is interpolated to nearby FFT grid points,
b) a forward 3d FFT is performed,
c) a convolution operation is performed in reciprocal space,
d) one or more inverse 3d FFTs are performed, and
e) electric field values from grid points near each atom are interpolated to compute
its forces.
For any of the spatial-decomposition partitioning schemes each processor
owns the brick-shaped portion of FFT grid points contained within its
sub-domain. The two interpolation operations use a stencil of grid
points surrounding each atom. To accommodate the stencil size, each
processor also stores a few layers of ghost grid points surrounding its
brick. Forward and reverse communication of grid point values is
performed similar to the corresponding :doc:`atom data communication
<Developer_par_comm>`. In this case, electric field values on owned
grid points are sent to neighboring processors to become ghost point
values. Likewise charge values on ghost points are sent and summed to
values on owned points.
For triclinic simulation boxes, the FFT grid planes are parallel to
the box faces, but the mapping of charge and electric field values
to/from grid points is done in reduced coordinates where the tilted
box is conceptually a unit cube, so that the stencil and FFT
operations are unchanged. However the FFT grid size required for a
given accuracy is larger for triclinic domains than it is for
orthogonal boxes.
.. _fft-parallel:
.. figure:: img/fft-decomp-parallel.png
:align: center
parallel FFT in PPPM
Stages of a parallel FFT for a simulation domain overlaid
with an 8x8x8 3d FFT grid, partitioned across 64 processors.
Within each of the 4 diagrams, grid cells of the same color are
owned by a single processor; for simplicity only cells owned by 4
or 8 of the 64 processors are colored. The two images on the left
illustrate brick-to-pencil communication. The two images on the
right illustrate pencil-to-pencil communication, which in this
case transposes the *y* and *z* dimensions of the grid.
Parallel 3d FFTs require substantial communication relative to their
computational cost. A 3d FFT is implemented by a series of 1d FFTs
along the *x-*, *y-*, and *z-*\ direction of the FFT grid. Thus the FFT
grid cannot be decomposed like atoms into 3 dimensions for parallel
processing of the FFTs but only in 1 (as planes) or 2 (as pencils)
dimensions and in between the steps the grid needs to be transposed to
have the FFT grid portion "owned" by each MPI process complete in the
direction of the 1d FFTs it has to perform. LAMMPS uses the
pencil-decomposition algorithm as shown in the :ref:`fft-parallel` figure.
Initially (far left), each processor owns a brick of same-color grid
cells (actually grid points) contained within in its sub-domain. A
brick-to-pencil communication operation converts this layout to 1d
pencils in the *x*-dimension (center left). Again, cells of the same
color are owned by the same processor. Each processor can then compute
a 1d FFT on each pencil of data it wholly owns using a call to the
configured FFT library. A pencil-to-pencil communication then converts
this layout to pencils in the *y* dimension (center right) which
effectively transposes the *x* and *y* dimensions of the grid, followed
by 1d FFTs in *y*. A final transpose of pencils from *y* to *z* (far
right) followed by 1d FFTs in *z* completes the forward FFT. The data
is left in a *z*-pencil layout for the convolution operation. One or
more inverse FFTs then perform the sequence of 1d FFTs and communication
steps in reverse order; the final layout of resulting grid values is the
same as the initial brick layout.
Each communication operation within the FFT (brick-to-pencil or
pencil-to-pencil or pencil-to-brick) converts one tiling of the 3d grid
to another, where a tiling in this context means an assignment of a
small brick-shaped subset of grid points to each processor, the union of
which comprise the entire grid. The parallel `fftMPI library
<https://lammps.github.io/fftmpi/>`_ written for LAMMPS allows arbitrary
definitions of the tiling so that an irregular partitioning of the
simulation domain can use it directly. Transforming data from one
tiling to another is implemented in `fftMPI` using point-to-point
communication, where each processor sends data to a few other
processors, since each tile in the initial tiling overlaps with a
handful of tiles in the final tiling.
The transformations could also be done using collective communication
across all $P$ processors with a single call to ``MPI_Alltoall()``, but
this is typically much slower. However, for the specialized brick and
pencil tiling illustrated in :ref:`fft-parallel` figure, collective
communication across the entire MPI communicator is not required. In
the example an :math:`8^3` grid with 512 grid cells is partitioned
across 64 processors; each processor owns a 2x2x2 3d brick of grid
cells. The initial brick-to-pencil communication (upper left to upper
right) only requires collective communication within subgroups of 4
processors, as illustrated by the 4 colors. More generally, a
brick-to-pencil communication can be performed by partitioning *P*
processors into :math:`P^{\frac{2}{3}}` subgroups of
:math:`P^{\frac{1}{3}}` processors each. Each subgroup performs
collective communication only within its subgroup. Similarly,
pencil-to-pencil communication can be performed by partitioning *P*
processors into :math:`P^{\frac{1}{2}}` subgroups of
:math:`P^{\frac{1}{2}}` processors each. This is illustrated in the
figure for the :math:`y \Rightarrow z` communication (center). An
eight-processor subgroup owns the front *yz* plane of data and performs
collective communication within the subgroup to transpose from a
*y*-pencil to *z*-pencil layout.
LAMMPS invokes point-to-point communication by default, but also
provides the option of partitioned collective communication when using a
:doc:`kspace_modify collective yes <kspace_modify>` command to switch to
that mode. In the latter case, the code detects the size of the
disjoint subgroups and partitions the single *P*-size communicator into
multiple smaller communicators, each of which invokes collective
communication. Testing on a large IBM Blue Gene/Q machine at Argonne
National Labs showed a significant improvement in FFT performance for
large processor counts; partitioned collective communication was faster
than point-to-point communication or global collective communication
involving all *P* processors.
Here are some additional details about FFTs for long-range and related
grid/particle operations that LAMMPS supports:
- The fftMPI library allows each grid dimension to be a multiple of
small prime factors (2,3,5), and allows any number of processors to
perform the FFT. The resulting brick and pencil decompositions are
thus not always as well-aligned but the size of subgroups of
processors for the two modes of communication (brick/pencil and
pencil/pencil) still scale as :math:`O(P^{\frac{1}{3}})` and
:math:`O(P^{\frac{1}{2}})`.
- For efficiency in performing 1d FFTs, the grid transpose
operations illustrated in Figure \ref{fig:fft} also involve
reordering the 3d data so that a different dimension is contiguous
in memory. This reordering can be done during the packing or
unpacking of buffers for MPI communication.
- For large systems and particularly a large number of MPI processes,
the dominant cost for parallel FFTs is often the communication, not
the computation of 1d FFTs, even though the latter scales as :math:`N
\log(N)` in the number of grid points *N* per grid direction. This is
due to the fact that only a 2d decomposition into pencils is possible
while atom data (and their corresponding short-range force and energy
computations) can be decomposed efficiently in 3d.
This can be addressed by reducing the number of MPI processes involved
in the MPI communication by using :doc:`hybrid MPI + OpenMP
parallelization <Speed_omp>`. This will use OpenMP parallelization
inside the MPI domains and while that may have a lower parallel
efficiency, it reduces the communication overhead.
As an alternative it is also possible to start a :ref:`multi-partition
<partition>` calculation and then use the :doc:`verlet/split
integrator <run_style>` to perform the PPPM computation on a
dedicated, separate partition of MPI processes. This uses an integer
"1:*p*" mapping of *p* sub-domains of the atom decomposition to one
sub-domain of the FFT grid decomposition and where pairwise non-bonded
and bonded forces and energies are computed on the larger partition
and the PPPM kspace computation concurrently on the smaller partition.
- LAMMPS also implements PPPM-based solvers for other long-range
interactions, dipole and dispersion (Lennard-Jones), which can be used
in conjunction with long-range Coulombics for point charges.
- LAMMPS implements a ``GridComm`` class which overlays the simulation
domain with a regular grid, partitions it across processors in a
manner consistent with processor sub-domains, and provides methods for
forward and reverse communication of owned and ghost grid point
values. It is used for PPPM as an FFT grid (as outlined above) and
also for the MSM algorithm which uses a cascade of grid sizes from
fine to coarse to compute long-range Coulombic forces. The GridComm
class is also useful for models where continuum fields interact with
particles. For example, the two-temperature model (TTM) defines heat
transfer between atoms (particles) and electrons (continuum gas) where
spatial variations in the electron temperature are computed by finite
differences of a discretized heat equation on a regular grid. The
:doc:`fix ttm/grid <fix_ttm>` command uses the ``GridComm`` class
internally to perform its grid operations on a distributed grid
instead of the original :doc:`fix ttm <fix_ttm>` which uses a
replicated grid.

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Neighbor lists
^^^^^^^^^^^^^^
To compute forces efficiently, each processor creates a Verlet-style
neighbor list which enumerates all pairs of atoms *i,j* (*i* = owned,
*j* = owned or ghost) with separation less than the applicable
neighbor list cutoff distance. In LAMMPS the neighbor lists are stored
in a multiple-page data structure; each page is a contiguous chunk of
memory which stores vectors of neighbor atoms *j* for many *i* atoms.
This allows pages to be incrementally allocated or deallocated in blocks
as needed. Neighbor lists typically consume the most memory of any data
structure in LAMMPS. The neighbor list is rebuilt (from scratch) once
every few timesteps, then used repeatedly each step for force or other
computations. The neighbor cutoff distance is :math:`R_n = R_f +
\Delta_s`, where :math:`R_f` is the (largest) force cutoff defined by
the interatomic potential for computing short-range pairwise or manybody
forces and :math:`\Delta_s` is a "skin" distance that allows the list to
be used for multiple steps assuming that atoms do not move very far
between consecutive time steps. Typically the code triggers
reneighboring when any atom has moved half the skin distance since the
last reneighboring; this and other options of the neighbor list rebuild
can be adjusted with the :doc:`neigh_modify <neigh_modify>` command.
On steps when reneighboring is performed, atoms which have moved outside
their owning processor's sub-domain are first migrated to new processors
via communication. Periodic boundary conditions are also (only)
enforced on these steps to ensure each atom is re-assigned to the
correct processor. After migration, the atoms owned by each processor
are stored in a contiguous vector. Periodically each processor
spatially sorts owned atoms within its vector to reorder it for improved
cache efficiency in force computations and neighbor list building. For
that atoms are spatially binned and then reordered so that atoms in the
same bin are adjacent in the vector. Atom sorting can be disabled or
its settings modified with the :doc:`atom_modify <atom_modify>` command.
.. _neighbor-stencil:
.. figure:: img/neigh-stencil.png
:align: center
neighbor list stencils
A 2d simulation sub-domain (thick black line) and the corresponding
ghost atom cutoff region (dashed blue line) for both orthogonal
(left) and triclinic (right) domains. A regular grid of neighbor
bins (thin lines) overlays the entire simulation domain and need not
align with sub-domain boundaries; only the portion overlapping the
augmented sub-domain is shown. In the triclinic case it overlaps the
bounding box of the tilted rectangle. The blue- and red-shaded bins
represent a stencil of bins searched to find neighbors of a particular
atom (black dot).
To build a local neighbor list in linear time, the simulation domain is
overlaid (conceptually) with a regular 3d (or 2d) grid of neighbor bins,
as shown in the :ref:`neighbor-stencil` figure for 2d models and a
single MPI processor's sub-domain. Each processor stores a set of
neighbor bins which overlap its sub-domain extended by the neighbor
cutoff distance :math:`R_n`. As illustrated, the bins need not align
with processor boundaries; an integer number in each dimension is fit to
the size of the entire simulation box.
Most often LAMMPS builds what it calls a "half" neighbor list where
each *i,j* neighbor pair is stored only once, with either atom *i* or
*j* as the central atom. The build can be done efficiently by using a
pre-computed "stencil" of bins around a central origin bin which
contains the atom whose neighbors are being searched for. A stencil
is simply a list of integer offsets in *x,y,z* of nearby bins
surrounding the origin bin which are close enough to contain any
neighbor atom *j* within a distance :math:`R_n` from any atom *i* in the
origin bin. Note that for a half neighbor list, the stencil can be
asymmetric since each atom only need store half its nearby neighbors.
These stencils are illustrated in the figure for a half list and a bin
size of :math:`\frac{1}{2} R_n`. There are 13 red+blue stencil bins in
2d (for the orthogonal case, 15 for triclinic). In 3d there would be
63, 13 in the plane of bins that contain the origin bin and 25 in each
of the two planes above it in the *z* direction (75 for triclinic). The
reason the triclinic stencil has extra bins is because the bins tile the
bounding box of the entire triclinic domain and thus are not periodic
with respect to the simulation box itself. The stencil and logic for
determining which *i,j* pairs to include in the neighbor list are
altered slightly to account for this.
To build a neighbor list, a processor first loops over its "owned" plus
"ghost" atoms and assigns each to a neighbor bin. This uses an integer
vector to create a linked list of atom indices within each bin. It then
performs a triply-nested loop over its owned atoms *i*, the stencil of
bins surrounding atom *i*'s bin, and the *j* atoms in each stencil bin
(including ghost atoms). If the distance :math:`r_{ij} < R_n`, then
atom *j* is added to the vector of atom *i*'s neighbors.
Here are additional details about neighbor list build options LAMMPS
supports:
- The choice of bin size is an option; a size half of :math:`R_n` has
been found to be optimal for many typical cases. Smaller bins incur
additional overhead to loop over; larger bins require more distance
calculations. Note that for smaller bin sizes, the 2d stencil in the
figure would be more semi-circular in shape (hemispherical in 3d),
with bins near the corners of the square eliminated due to their
distance from the origin bin.
- Depending on the interatomic potential(s) and other commands used in
an input script, multiple neighbor lists and stencils with different
attributes may be needed. This includes lists with different cutoff
distances, e.g. for force computation versus occasional diagnostic
computations such as a radial distribution function, or for the
r-RESPA time integrator which can partition pairwise forces by
distance into subsets computed at different time intervals. It
includes "full" lists (as opposed to half lists) where each *i,j* pair
appears twice, stored once with *i* and *j*, and which use a larger
symmetric stencil. It also includes lists with partial enumeration of
ghost atom neighbors. The full and ghost-atom lists are used by
various manybody interatomic potentials. Lists may also use different
criteria for inclusion of a pair interaction. Typically this simply
depends only on the distance between two atoms and the cutoff
distance. But for finite-size coarse-grained particles with
individual diameters (e.g. polydisperse granular particles), it can
also depend on the diameters of the two particles.
- When using :doc:`pair style hybrid <pair_hybrid>` multiple sub-lists
of the master neighbor list for the full system need to be generated,
one for each sub-style, which contains only the *i,j* pairs needed to
compute interactions between subsets of atoms for the corresponding
potential. This means not all *i* or *j* atoms owned by a processor
are included in a particular sub-list.
- Some models use different cutoff lengths for pairwise interactions
between different kinds of particles which are stored in a single
neighbor list. One example is a solvated colloidal system with large
colloidal particles where colloid/colloid, colloid/solvent, and
solvent/solvent interaction cutoffs can be dramatically different.
Another is a model of polydisperse finite-size granular particles;
pairs of particles interact only when they are in contact with each
other. Mixtures with particle size ratios as high as 10-100x may be
used to model realistic systems. Efficient neighbor list building
algorithms for these kinds of systems are available in LAMMPS. They
include a method which uses different stencils for different cutoff
lengths and trims the stencil to only include bins that straddle the
cutoff sphere surface. More recently a method which uses both
multiple stencils and multiple bin sizes was developed; it builds
neighbor lists efficiently for systems with particles of any size
ratio, though other considerations (timestep size, force computations)
may limit the ability to model systems with huge polydispersity.
- For small and sparse systems and as a fallback method, LAMMPS also
supports neighbor list construction without binning by using a full
:math:`O(N^2)` loop over all *i,j* atom pairs in a sub-domain when
using the :doc:`neighbor nsq <neighbor>` command.
- Dependent on the "pair" setting of the :doc:`newton <newton>` command,
the "half" neighbor lists may contain **all** pairs of atoms where
atom *j* is a ghost atom (i.e. when the newton pair setting is *off*)
For the newton pair *on* setting the atom *j* is only added to the
list if its *z* coordinate is larger, or if equal the *y* coordinate
is larger, and that is equal, too, the *x* coordinate is larger. For
homogeneously dense systems that will result in picking neighbors from
a same size sector in always the same direction relative to the
"owned" atom and thus it should lead to similar length neighbor lists
and thus reduce the chance of a load imbalance.

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OpenMP Parallelism
^^^^^^^^^^^^^^^^^^
The styles in the INTEL, KOKKOS, and OPENMP package offer to use OpenMP
thread parallelism to predominantly distribute loops over local data
and thus follow an orthogonal parallelization strategy to the
decomposition into spatial domains used by the :doc:`MPI partitioning
<Developer_par_part>`. For clarity, this section discusses only the
implementation in the OPENMP package as it is the simplest. The INTEL
and KOKKOS package offer additional options and are more complex since
they support more features and different hardware like co-processors
or GPUs.
One of the key decisions when implementing the OPENMP package was to
keep the changes to the source code small, so that it would be easier to
maintain the code and keep it in sync with the non-threaded standard
implementation. this is achieved by a) making the OPENMP version a
derived class from the regular version (e.g. ``PairLJCutOMP`` from
``PairLJCut``) and overriding only methods that are multi-threaded or
need to be modified to support multi-threading (similar to what was done
in the OPT package), b) keeping the structure in the modified code very
similar so that side-by-side comparisons are still useful, and c)
offloading additional functionality and multi-thread support functions
into three separate classes ``ThrOMP``, ``ThrData``, and ``FixOMP``.
``ThrOMP`` provides additional, multi-thread aware functionality not
available in the corresponding base class (e.g. ``Pair`` for
``PairLJCutOMP``) like multi-thread aware variants of the "tally"
functions. Those functions are made available through multiple
inheritance so those new functions have to have unique names to avoid
ambiguities; typically ``_thr`` is appended to the name of the function.
``ThrData`` is a classes that manages per-thread data structures.
It is used instead of extending the corresponding storage to per-thread
arrays to avoid slowdowns due to "false sharing" when multiple threads
update adjacent elements in an array and thus force the CPU cache lines
to be reset and re-fetched. ``FixOMP`` finally manages the "multi-thread
state" like settings and access to per-thread storage, it is activated
by the :doc:`package omp <package>` command.
Avoiding data races
"""""""""""""""""""
A key problem when implementing thread parallelism in an MD code is
to avoid data races when updating accumulated properties like forces,
energies, and stresses. When interactions are computed, they always
involve multiple atoms and thus there are race conditions when multiple
threads want to update per-atom data of the same atoms. Five possible
strategies have been considered to avoid this:
1) restructure the code so that there is no overlapping access possible
when computing in parallel, e.g. by breaking lists into multiple
parts and synchronizing threads in between.
2) have each thread be "responsible" for a specific group of atoms and
compute these interactions multiple times, once on each thread that
is responsible for a given atom and then have each thread only update
the properties of this atom.
3) use mutexes around functions and regions of code where the data race
could happen
4) use atomic operations when updating per-atom properties
5) use replicated per-thread data structures to accumulate data without
conflicts and then use a reduction to combine those results into the
data structures used by the regular style.
Option 5 was chosen for the OPENMP package because it would retain the
performance for the case of 1 thread and the code would be more
maintainable. Option 1 would require extensive code changes,
particularly to the neighbor list code; options 2 would have incurred a
2x or more performance penalty for the serial case; option 3 causes
significant overhead and would enforce serialization of operations in
inner loops and thus defeat the purpose of multi-threading; option 4
slows down the serial case although not quite as bad as option 2. The
downside of option 5 is that the overhead of the reduction operations
grows with the number of threads used, so there would be a crossover
point where options 2 or 4 would result in faster executing. That is
why option 2 for example is used in the GPU package because a GPU is a
processor with a massive number of threads. However, since the MPI
parallelization is generally more effective for typical MD systems, the
expectation is that thread parallelism is only used for a smaller number
of threads (2-8). At the time of its implementation, that number was
equivalent to the number of CPU cores per CPU socket on high-end
supercomputers.
Thus arrays like the force array are dimensioned to the number of atoms
times the number of threads when enabling OpenMP support and inside the
compute functions a pointer to a different chunk is obtained by each thread.
Similarly, accumulators like potential energy or virial are kept in
per-thread instances of the ``ThrData`` class and then only reduced and
stored in their global counterparts at the end of the force computation.
Loop scheduling
"""""""""""""""
Multi-thread parallelization is applied by distributing (outer) loops
statically across threads. Typically this would be the loop over local
atoms *i* when processing *i,j* pairs of atoms from a neighbor list.
The design of the neighbor list code results in atoms having a similar
number of neighbors for homogeneous systems and thus load imbalances
across threads are not common and typically happen for systems where
also the MPI parallelization would be unbalanced, which would typically
have a more pronounced impact on the performance. This same loop
scheduling scheme can also be applied to the reduction operations on
per-atom data to try and reduce the overhead of the reduction operation.
Neighbor list parallelization
"""""""""""""""""""""""""""""
In addition to the parallelization of force computations, also the
generation of the neighbor lists is parallelized. As explained
previously, neighbor lists are built by looping over "owned" atoms and
storing the neighbors in "pages". In the OPENMP variants of the
neighbor list code, each thread operates on a different chunk of "owned"
atoms and allocates and fills its own set of pages with neighbor list
data. This is achieved by each thread keeping its own instance of the
:cpp:class:`MyPage <LAMMPS_NS::MyPage>` page allocator class.

89
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@ -0,0 +1,89 @@
Partitioning
^^^^^^^^^^^^
The underlying spatial decomposition strategy used by LAMMPS for
distributed-memory parallelism is set with the :doc:`comm_style command
<comm_style>` and can be either "brick" (a regular grid) or "tiled".
.. _domain-decomposition:
.. figure:: img/domain-decomp.png
:align: center
domain decomposition
This figure shows the different kinds of domain decomposition used
for MPI parallelization: "brick" on the left with an orthogonal
(left) and a triclinic (middle) simulation domain, and a "tiled"
decomposition (right). The black lines show the division into
sub-domains and the contained atoms are "owned" by the corresponding
MPI process. The green dashed lines indicate how sub-domains are
extended with "ghost" atoms up to the communication cutoff distance.
The LAMMPS simulation box is a 3d or 2d volume, which can be orthogonal
or triclinic in shape, as illustrated in the :ref:`domain-decomposition`
figure for the 2d case. Orthogonal means the box edges are aligned with
the *x*, *y*, *z* Cartesian axes, and the box faces are thus all
rectangular. Triclinic allows for a more general parallelepiped shape
in which edges are aligned with three arbitrary vectors and the box
faces are parallelograms. In each dimension box faces can be periodic,
or non-periodic with fixed or shrink-wrapped boundaries. In the fixed
case, atoms which move outside the face are deleted; shrink-wrapped
means the position of the box face adjusts continuously to enclose all
the atoms.
For distributed-memory MPI parallelism, the simulation box is spatially
decomposed (partitioned) into non-overlapping sub-domains which fill the
box. The default partitioning, "brick", is most suitable when atom
density is roughly uniform, as shown in the left-side images of the
:ref:`domain-decomposition` figure. The sub-domains comprise a regular
grid and all sub-domains are identical in size and shape. Both the
orthogonal and triclinic boxes can deform continuously during a
simulation, e.g. to compress a solid or shear a liquid, in which case
the processor sub-domains likewise deform.
For models with non-uniform density, the number of particles per
processor can be load-imbalanced with the default partitioning. This
reduces parallel efficiency, as the overall simulation rate is limited
by the slowest processor, i.e. the one with the largest computational
load. For such models, LAMMPS supports multiple strategies to reduce
the load imbalance:
- The processor grid decomposition is by default based on the simulation
cell volume and tries to optimize the volume to surface ratio for the sub-domains.
This can be changed with the :doc:`processors command <processors>`.
- The parallel planes defining the size of the sub-domains can be shifted
with the :doc:`balance command <balance>`. Which can be done in addition
to choosing a more optimal processor grid.
- The recursive bisectioning algorithm in combination with the "tiled"
communication style can produce a partitioning with equal numbers of
particles in each sub-domain.
.. |decomp1| image:: img/decomp-regular.png
:width: 24%
.. |decomp2| image:: img/decomp-processors.png
:width: 24%
.. |decomp3| image:: img/decomp-balance.png
:width: 24%
.. |decomp4| image:: img/decomp-rcb.png
:width: 24%
|decomp1| |decomp2| |decomp3| |decomp4|
The pictures above demonstrate different decompositions for a 2d system
with 12 MPI ranks. The atom colors indicate the load imbalance of each
sub-domain with green being optimal and red the least optimal.
Due to the vacuum in the system, the default decomposition is unbalanced
with several MPI ranks without atoms (left). By forcing a 1x12x1
processor grid, every MPI rank does computations now, but number of
atoms per sub-domain is still uneven and the thin slice shape increases
the amount of communication between sub-domains (center left). With a
2x6x1 processor grid and shifting the sub-domain divisions, the load
imbalance is further reduced and the amount of communication required
between sub-domains is less (center right). And using the recursive
bisectioning leads to further improved decomposition (right).

28
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@ -0,0 +1,28 @@
Parallel algorithms
-------------------
LAMMPS is designed to enable running simulations in parallel using the
MPI parallel communication standard with distributed data via domain
decomposition. The parallelization aims to be efficient result in good
strong scaling (= good speedup for the same system) and good weak
scaling (= the computational cost of enlarging the system is
proportional to the system size). Additional parallelization using GPUs
or OpenMP can also be applied within the sub-domain assigned to an MPI
process. For clarity, most of the following illustrations show the 2d
simulation case. The underlying algorithms in those cases, however,
apply to both 2d and 3d cases equally well.
.. note::
The text and most of the figures in this chapter were adapted
for the manual from the section on parallel algorithms in the
:ref:`new LAMMPS paper <lammps_paper>`.
.. toctree::
:maxdepth: 1
Developer_par_part
Developer_par_comm
Developer_par_neigh
Developer_par_long
Developer_par_openmp

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@ -0,0 +1,152 @@
Platform abstraction functions
------------------------------
The ``platform`` sub-namespace inside the ``LAMMPS_NS`` namespace
provides a collection of wrapper and convenience functions and utilities
that perform common tasks for which platform specific code would be
required or for which a more high-level abstraction would be convenient
and reduce duplicated code. This reduces redundant implementations and
encourages consistent behavior and thus has some overlap with the
:doc:`"utils" sub-namespace <Developer_utils>`.
Time functions
^^^^^^^^^^^^^^
.. doxygenfunction:: cputime
:project: progguide
.. doxygenfunction:: walltime
:project: progguide
.. doxygenfunction:: usleep
:project: progguide
Platform information functions
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
.. doxygenfunction:: os_info
:project: progguide
.. doxygenfunction:: compiler_info
:project: progguide
.. doxygenfunction:: cxx_standard
:project: progguide
.. doxygenfunction:: openmp_standard
:project: progguide
.. doxygenfunction:: mpi_vendor
:project: progguide
.. doxygenfunction:: mpi_info
:project: progguide
.. doxygenfunction:: compress_info
:project: progguide
File and path functions and global constants
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
.. doxygenvariable:: filepathsep
:project: progguide
.. doxygenvariable:: pathvarsep
:project: progguide
.. doxygenfunction:: guesspath
:project: progguide
.. doxygenfunction:: path_basename
:project: progguide
.. doxygenfunction:: path_join
:project: progguide
.. doxygenfunction:: file_is_readable
:project: progguide
.. doxygenfunction:: is_console
:project: progguide
.. doxygenfunction:: path_is_directory
:project: progguide
.. doxygenfunction:: current_directory
:project: progguide
.. doxygenfunction:: list_directory
:project: progguide
.. doxygenfunction:: chdir
:project: progguide
.. doxygenfunction:: mkdir
:project: progguide
.. doxygenfunction:: rmdir
:project: progguide
.. doxygenfunction:: unlink
:project: progguide
Standard I/O function wrappers
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
.. doxygenvariable:: END_OF_FILE
:project: progguide
.. doxygenfunction:: ftell
:project: progguide
.. doxygenfunction:: fseek
:project: progguide
.. doxygenfunction:: ftruncate
:project: progguide
.. doxygenfunction:: popen
:project: progguide
.. doxygenfunction:: pclose
:project: progguide
Environment variable functions
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
.. doxygenfunction:: putenv
:project: progguide
.. doxygenfunction:: list_pathenv
:project: progguide
.. doxygenfunction:: find_exe_path
:project: progguide
Dynamically loaded object or library functions
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
.. doxygenfunction:: dlopen
:project: progguide
.. doxygenfunction:: dlclose
:project: progguide
.. doxygenfunction:: dlsym
:project: progguide
.. doxygenfunction:: dlerror
:project: progguide
Compressed file I/O functions
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
.. doxygenfunction:: has_compress_extension
:project: progguide
.. doxygenfunction:: compressed_read
:project: progguide
.. doxygenfunction:: compressed_write
:project: progguide

34
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@ -7,7 +7,9 @@ a collection of convenience functions and utilities that perform common
tasks that are required repeatedly throughout the LAMMPS code like
reading or writing to files with error checking or translation of
strings into specific types of numbers with checking for validity. This
reduces redundant implementations and encourages consistent behavior.
reduces redundant implementations and encourages consistent behavior and
thus has some overlap with the :doc:`"platform" sub-namespace
<Developer_platform>`.
I/O with status check and similar functions
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
@ -60,6 +62,9 @@ silently returning the result of a partial conversion or zero in cases
where the string is not a valid number. This behavior allows to more
easily detect typos or issues when processing input files.
Similarly the :cpp:func:`logical() <LAMMPS_NS::utils::logical>` function
will convert a string into a boolean and will only accept certain words.
The *do_abort* flag should be set to ``true`` in case this function
is called only on a single MPI rank, as that will then trigger the
a call to ``Error::one()`` for errors instead of ``Error::all()``
@ -83,6 +88,9 @@ strings for compliance without conversion.
.. doxygenfunction:: tnumeric
:project: progguide
.. doxygenfunction:: logical
:project: progguide
String processing
^^^^^^^^^^^^^^^^^
@ -95,6 +103,12 @@ and parsing files or arguments.
.. doxygenfunction:: strdup
:project: progguide
.. doxygenfunction:: lowercase
:project: progguide
.. doxygenfunction:: uppercase
:project: progguide
.. doxygenfunction:: trim
:project: progguide
@ -137,21 +151,6 @@ and parsing files or arguments.
.. doxygenfunction:: is_double
:project: progguide
File and path functions
^^^^^^^^^^^^^^^^^^^^^^^^^
.. doxygenfunction:: guesspath
:project: progguide
.. doxygenfunction:: path_basename
:project: progguide
.. doxygenfunction:: path_join
:project: progguide
.. doxygenfunction:: file_is_readable
:project: progguide
Potential file functions
^^^^^^^^^^^^^^^^^^^^^^^^
@ -203,6 +202,9 @@ Convenience functions
.. doxygenfunction:: date2num
:project: progguide
.. doxygenfunction:: current_date
:project: progguide
Customized standard functions
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

4
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@ -29,7 +29,9 @@ of code in the header before include guards:
.. code-block:: c
#ifdef FIX_CLASS
FixStyle(print/vel,FixPrintVel)
// clang-format off
FixStyle(print/vel,FixPrintVel);
// clang-format on
#else
/* the definition of the FixPrintVel class comes here */
...

3
doc/src/Errors_debug.rst
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@ -40,11 +40,10 @@ We use it to show how to identify the origin of a segmentation fault.
After recompiling LAMMPS and running the input you should get something like this:
.. code-block:
.. code-block::
$ ./lmp -in in.melt
LAMMPS (19 Mar 2020)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
using 1 OpenMP thread(s) per MPI task
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
Created orthogonal box = (0 0 0) to (16.796 16.796 16.796)

10
doc/src/Errors_messages.rst
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@ -7879,19 +7879,19 @@ keyword to allow for additional bonds to be formed
*Unexpected end of -reorder file*
Self-explanatory.
*Unexpected empty line in AngleCoeffs section*
*Unexpected empty line in Angle Coeffs section*
Read a blank line where there should be coefficient data.
*Unexpected empty line in BondCoeffs section*
*Unexpected empty line in Bond Coeffs section*
Read a blank line where there should be coefficient data.
*Unexpected empty line in DihedralCoeffs section*
*Unexpected empty line in Dihedral Coeffs section*
Read a blank line where there should be coefficient data.
*Unexpected empty line in ImproperCoeffs section*
*Unexpected empty line in Improper Coeffs section*
Read a blank line where there should be coefficient data.
*Unexpected empty line in PairCoeffs section*
*Unexpected empty line in Pair Coeffs section*
Read a blank line where there should be coefficient data.
*Unexpected end of custom file*

4
doc/src/Examples.rst
View File

@ -80,7 +80,7 @@ Lowercase directories
+-------------+------------------------------------------------------------------+
| friction | frictional contact of spherical asperities between 2d surfaces |
+-------------+------------------------------------------------------------------+
| gcmc | Grand Canonical Monte Carlo (GCMC) via the fix gcmc command |
| mc | Monte Carlo features via fix gcmc, widom and other commands |
+-------------+------------------------------------------------------------------+
| granregion | use of fix wall/region/gran as boundary on granular particles |
+-------------+------------------------------------------------------------------+
@ -205,7 +205,7 @@ Uppercase directories
+------------+--------------------------------------------------------------------------------------------------+
| KAPPA | compute thermal conductivity via several methods |
+------------+--------------------------------------------------------------------------------------------------+
| MC | using LAMMPS in a Monte Carlo mode to relax the energy of a system |
| MC-LOOP | using LAMMPS in a Monte Carlo mode to relax the energy of a system in a input script loop |
+------------+--------------------------------------------------------------------------------------------------+
| PACKAGES | examples for specific packages and contributed commands |
+------------+--------------------------------------------------------------------------------------------------+

133
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@ -7,11 +7,11 @@ LAMMPS GitHub tutorial
This document describes the process of how to use GitHub to integrate
changes or additions you have made to LAMMPS into the official LAMMPS
distribution. It uses the process of updating this very tutorial as
an example to describe the individual steps and options. You need to
be familiar with git and you may want to have a look at the
`git book <http://git-scm.com/book/>`_ to reacquaint yourself with some
of the more advanced git features used below.
distribution. It uses the process of updating this very tutorial as an
example to describe the individual steps and options. You need to be
familiar with git and you may want to have a look at the `git book
<http://git-scm.com/book/>`_ to familiarize yourself with some of the
more advanced git features used below.
As of fall 2016, submitting contributions to LAMMPS via pull requests
on GitHub is the preferred option for integrating contributed features
@ -37,15 +37,15 @@ username or e-mail address and password.
**Forking the repository**
To get changes into LAMMPS, you need to first fork the `lammps/lammps`
repository on GitHub. At the time of writing, *master* is the preferred
repository on GitHub. At the time of writing, *develop* is the preferred
target branch. Thus go to `LAMMPS on GitHub <https://github.com/lammps/lammps>`_
and make sure branch is set to "master", as shown in the figure below.
and make sure branch is set to "develop", as shown in the figure below.
.. image:: JPG/tutorial_branch.png
:align: center
If it is not, use the button to change it to *master*\ . Once it is, use the
fork button to create a fork.
If it is not, use the button to change it to *develop*. Once it is, use
the fork button to create a fork.
.. image:: JPG/tutorial_fork.png
:align: center
@ -64,11 +64,12 @@ LAMMPS development.
**Adding changes to your own fork**
Additions to the upstream version of LAMMPS are handled using *feature
branches*\ . For every new feature, a so-called feature branch is
branches*. For every new feature, a so-called feature branch is
created, which contains only those modification relevant to one specific
feature. For example, adding a single fix would consist of creating a
branch with only the fix header and source file and nothing else. It is
explained in more detail here: `feature branch workflow <https://www.atlassian.com/git/tutorials/comparing-workflows/feature-branch-workflow>`_.
explained in more detail here: `feature branch workflow
<https://www.atlassian.com/git/tutorials/comparing-workflows/feature-branch-workflow>`_.
**Feature branches**
@ -94,8 +95,8 @@ The above command copies ("clones") the git repository to your local
machine to a directory with the name you chose. If none is given, it will
default to "lammps". Typical names are "mylammps" or something similar.
You can use this local clone to make changes and
test them without interfering with the repository on GitHub.
You can use this local clone to make changes and test them without
interfering with the repository on GitHub.
To pull changes from upstream into this copy, you can go to the directory
and use git pull:
@ -103,28 +104,45 @@ and use git pull:
.. code-block:: bash
$ cd mylammps
$ git checkout master
$ git pull https://github.com/lammps/lammps
$ git checkout develop
$ git pull https://github.com/lammps/lammps develop
You can also add this URL as a remote:
.. code-block:: bash
$ git remote add lammps_upstream https://www.github.com/lammps/lammps
$ git remote add upstream https://www.github.com/lammps/lammps
At this point, you typically make a feature branch from the updated master
From then on you can update your upstream branches with:
.. code-block:: bash
$ git fetch upstream
and then refer to the upstream repository branches with
`upstream/develop` or `upstream/release` and so on.
At this point, you typically make a feature branch from the updated
branch for the feature you want to work on. This tutorial contains the
workflow that updated this tutorial, and hence we will call the branch
"github-tutorial-update":
.. code-block:: bash
$ git checkout -b github-tutorial-update master
$ git fetch upstream
$ git checkout -b github-tutorial-update upstream/develop
Now that we have changed branches, we can make our changes to our local
repository. Just remember that if you want to start working on another,
unrelated feature, you should switch branches!
.. note::
Committing changes to the *develop*, *release*, or *stable* branches
is strongly discouraged. While it may be convenient initially, it
will create more work in the long run. Various texts and tutorials
on using git effectively discuss the motivation for this.
**After changes are made**
After everything is done, add the files to the branch and commit them:
@ -287,28 +305,32 @@ After each push, the automated checks are run again.
LAMMPS developers may add labels to your pull request to assign it to
categories (mostly for bookkeeping purposes), but a few of them are
important: needs_work, work_in_progress, test-for-regression, and
full-regression-test. The first two indicate, that your pull request
is not considered to be complete. With "needs_work" the burden is on
exclusively on you; while "work_in_progress" can also mean, that a
LAMMPS developer may want to add changes. Please watch the comments
to the pull requests. The two "test" labels are used to trigger
extended tests before the code is merged. This is sometimes done by
LAMMPS developers, if they suspect that there may be some subtle
side effects from your changes. It is not done by default, because
those tests are very time consuming.
important: *needs_work*, *work_in_progress*, *run_tests*,
*test_for_regression*, and *ready_for_merge*. The first two indicate,
that your pull request is not considered to be complete. With
"needs_work" the burden is on exclusively on you; while
"work_in_progress" can also mean, that a LAMMPS developer may want to
add changes. Please watch the comments to the pull requests. The two
"test" labels are used to trigger extended tests before the code is
merged. This is sometimes done by LAMMPS developers, if they suspect
that there may be some subtle side effects from your changes. It is not
done by default, because those tests are very time consuming. The
*ready_for_merge* label is usually attached when the LAMMPS developer
assigned to the pull request considers this request complete and to
trigger a final full test evaluation.
**Reviews**
As of Summer 2018, a pull request needs at least 1 approving review
from a LAMMPS developer with write access to the repository.
In case your changes touch code that certain developers are associated
with, they are auto-requested by the GitHub software. Those associations
are set in the file
`.github/CODEOWNERS <https://github.com/lammps/lammps/blob/master/.github/CODEOWNERS>`_
Thus if you want to be automatically notified to review when anybody
changes files or packages, that you have contributed to LAMMPS, you can
add suitable patterns to that file, or a LAMMPS developer may add you.
As of Fall 2021, a pull request needs to pass all automatic tests and at
least 1 approving review from a LAMMPS developer with write access to
the repository before it is eligible for merging. In case your changes
touch code that certain developers are associated with, they are
auto-requested by the GitHub software. Those associations are set in
the file `.github/CODEOWNERS
<https://github.com/lammps/lammps/blob/develop/.github/CODEOWNERS>`_ Thus
if you want to be automatically notified to review when anybody changes
files or packages, that **you** have contributed to LAMMPS, you can add
suitable patterns to that file, or a LAMMPS developer may add you.
Otherwise, you can also manually request reviews from specific developers,
or LAMMPS developers - in their assessment of your pull request - may
@ -329,7 +351,7 @@ LAMMPS developer (including him/herself) or c) Axel Kohlmeyer (akohlmey).
After the review, the developer can choose to implement changes directly
or suggest them to you.
* Case c) means that the pull request has been assigned to the developer
overseeing the merging of pull requests into the master branch.
overseeing the merging of pull requests into the *develop* branch.
In this case, Axel assigned the tutorial to Steve:
@ -351,11 +373,11 @@ Sometimes, however, you might not feel comfortable having other people
push changes into your own branch, or maybe the maintainers are not sure
their idea was the right one. In such a case, they can make changes,
reassign you as the assignee, and file a "reverse pull request", i.e.
file a pull request in your GitHub repository to include changes in the
branch, that you have submitted as a pull request yourself. In that
case, you can choose to merge their changes back into your branch,
possibly make additional changes or corrections and proceed from there.
It looks something like this:
file a pull request in **your** forked GitHub repository to include
changes in the branch, that you have submitted as a pull request
yourself. In that case, you can choose to merge their changes back into
your branch, possibly make additional changes or corrections and proceed
from there. It looks something like this:
.. image:: JPG/tutorial_reverse_pull_request.png
:align: center
@ -419,7 +441,7 @@ This merge also shows up on the lammps GitHub page:
**After a merge**
When everything is fine, the feature branch is merged into the master branch:
When everything is fine, the feature branch is merged into the *develop* branch:
.. image:: JPG/tutorial_merged.png
:align: center
@ -433,8 +455,8 @@ branch!
.. code-block:: bash
$ git checkout master
$ git pull master
$ git checkout develop
$ git pull https://github.com/lammps/lammps develop
$ git branch -d github-tutorial-update
If you do not pull first, it is not really a problem but git will warn
@ -442,6 +464,7 @@ you at the next statement that you are deleting a local branch that
was not yet fully merged into HEAD. This is because git does not yet
know your branch just got merged into LAMMPS upstream. If you
first delete and then pull, everything should still be fine.
You can display all branches that are fully merged by:
Finally, if you delete the branch locally, you might want to push this
to your remote(s) as well:
@ -453,14 +476,14 @@ to your remote(s) as well:
**Recent changes in the workflow**
Some changes to the workflow are not captured in this tutorial. For
example, in addition to the master branch, to which all new features
should be submitted, there is now also an "unstable" and a "stable"
branch; these have the same content as "master", but are only updated
after a patch release or stable release was made.
Furthermore, the naming of the patches now follow the pattern
"patch_<Day><Month><Year>" to simplify comparisons between releases.
Finally, all patches and submissions are subject to automatic testing
and code checks to make sure they at the very least compile.
example, in addition to the *develop* branch, to which all new features
should be submitted, there is also a *release* and a *stable* branch;
these have the same content as *develop*, but are only updated after a
patch release or stable release was made. Furthermore, the naming of
the patches now follow the pattern "patch_<Day><Month><Year>" to
simplify comparisons between releases. Finally, all patches and
submissions are subject to automatic testing and code checks to make
sure they at the very least compile.
A discussion of the LAMMPS developer GitHub workflow can be found in the file
`doc/github-development-workflow.md <https://github.com/lammps/lammps/blob/master/doc/github-development-workflow.md>`_
`doc/github-development-workflow.md <https://github.com/lammps/lammps/blob/develop/doc/github-development-workflow.md>`_

80
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@ -2,8 +2,8 @@ Thermostats
===========
Thermostatting means controlling the temperature of particles in an MD
simulation. :doc:`Barostatting <Howto_barostat>` means controlling the
pressure. Since the pressure includes a kinetic component due to
simulation. :doc:`Barostatting <Howto_barostat>` means controlling
the pressure. Since the pressure includes a kinetic component due to
particle velocities, both these operations require calculation of the
temperature. Typically a target temperature (T) and/or pressure (P)
is specified by the user, and the thermostat or barostat attempts to
@ -26,11 +26,13 @@ can be invoked via the *dpd/tstat* pair style:
* :doc:`pair_style dpd/tstat <pair_dpd>`
:doc:`Fix nvt <fix_nh>` only thermostats the translational velocity of
particles. :doc:`Fix nvt/sllod <fix_nvt_sllod>` also does this, except
that it subtracts out a velocity bias due to a deforming box and
integrates the SLLOD equations of motion. See the :doc:`Howto nemd <Howto_nemd>` page for further details. :doc:`Fix nvt/sphere <fix_nvt_sphere>` and :doc:`fix nvt/asphere <fix_nvt_asphere>` thermostat not only translation
velocities but also rotational velocities for spherical and aspherical
particles.
particles. :doc:`Fix nvt/sllod <fix_nvt_sllod>` also does this,
except that it subtracts out a velocity bias due to a deforming box
and integrates the SLLOD equations of motion. See the :doc:`Howto
nemd <Howto_nemd>` page for further details. :doc:`Fix nvt/sphere
<fix_nvt_sphere>` and :doc:`fix nvt/asphere <fix_nvt_asphere>`
thermostat not only translation velocities but also rotational
velocities for spherical and aspherical particles.
.. note::
@ -40,25 +42,31 @@ particles.
e.g. molecular systems. The latter can be tricky to do correctly.
DPD thermostatting alters pairwise interactions in a manner analogous
to the per-particle thermostatting of :doc:`fix langevin <fix_langevin>`.
to the per-particle thermostatting of :doc:`fix langevin
<fix_langevin>`.
Any of the thermostatting fixes can be instructed to use custom temperature
computes that remove bias which has two effects: first, the current
calculated temperature, which is compared to the requested target temperature,
is calculated with the velocity bias removed; second, the thermostat adjusts
only the thermal temperature component of the particle's velocities, which are
the velocities with the bias removed. The removed bias is then added back
to the adjusted velocities. See the doc pages for the individual
fixes and for the :doc:`fix_modify <fix_modify>` command for
instructions on how to assign a temperature compute to a
thermostatting fix. For example, you can apply a thermostat to only
the x and z components of velocity by using it in conjunction with
:doc:`compute temp/partial <compute_temp_partial>`. Of you could
thermostat only the thermal temperature of a streaming flow of
particles without affecting the streaming velocity, by using
:doc:`compute temp/profile <compute_temp_profile>`.
Any of the thermostatting fixes can be instructed to use custom
temperature computes that remove bias which has two effects: first,
the current calculated temperature, which is compared to the requested
target temperature, is calculated with the velocity bias removed;
second, the thermostat adjusts only the thermal temperature component
of the particle's velocities, which are the velocities with the bias
removed. The removed bias is then added back to the adjusted
velocities. See the doc pages for the individual fixes and for the
:doc:`fix_modify <fix_modify>` command for instructions on how to
assign a temperature compute to a thermostatting fix.
Below is a list of some custom temperature computes that can be used like that:
For example, you can apply a thermostat only to atoms in a spatial
region by using it in conjunction with :doc:`compute temp/region
<compute_temp_region>`. Or you can apply a thermostat to only the x
and z components of velocity by using it with :doc:`compute
temp/partial <compute_temp_partial>`. Of you could thermostat only
the thermal temperature of a streaming flow of particles without
affecting the streaming velocity, by using :doc:`compute temp/profile
<compute_temp_profile>`.
Below is a list of custom temperature computes that can be used like
that:
* :doc:`compute_temp_asphere`
* :doc:`compute_temp_body`
@ -72,8 +80,6 @@ Below is a list of some custom temperature computes that can be used like that:
* :doc:`compute_temp_rotate`
* :doc:`compute_temp_sphere`
.. note::
Only the nvt fixes perform time integration, meaning they update
@ -86,17 +92,17 @@ Below is a list of some custom temperature computes that can be used like that:
* :doc:`fix nve/sphere <fix_nve_sphere>`
* :doc:`fix nve/asphere <fix_nve_asphere>`
Thermodynamic output, which can be setup via the
:doc:`thermo_style <thermo_style>` command, often includes temperature
values. As explained on the page for the
:doc:`thermo_style <thermo_style>` command, the default temperature is
setup by the thermo command itself. It is NOT the temperature
associated with any thermostatting fix you have defined or with any
compute you have defined that calculates a temperature. The doc pages
for the thermostatting fixes explain the ID of the temperature compute
they create. Thus if you want to view these temperatures, you need to
specify them explicitly via the :doc:`thermo_style custom <thermo_style>` command. Or you can use the
:doc:`thermo_modify <thermo_modify>` command to re-define what
Thermodynamic output, which can be setup via the :doc:`thermo_style
<thermo_style>` command, often includes temperature values. As
explained on the page for the :doc:`thermo_style <thermo_style>`
command, the default temperature is setup by the thermo command
itself. It is NOT the temperature associated with any thermostatting
fix you have defined or with any compute you have defined that
calculates a temperature. The doc pages for the thermostatting fixes
explain the ID of the temperature compute they create. Thus if you
want to view these temperatures, you need to specify them explicitly
via the :doc:`thermo_style custom <thermo_style>` command. Or you can
use the :doc:`thermo_modify <thermo_modify>` command to re-define what
temperature compute is used for default thermodynamic output.
----------

47
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@ -9,7 +9,8 @@ has several advantages:
command.
* You can create your own development branches to add code to LAMMPS.
* You can submit your new features back to GitHub for inclusion in
LAMMPS.
LAMMPS. For that you should first create your own :doc:`fork on
GitHub <Howto_github>`.
You must have `git <git_>`_ installed on your system to use the
commands explained below to communicate with the git servers on
@ -20,35 +21,53 @@ provides `limited support for subversion clients <svn_>`_.
As of October 2016, the official home of public LAMMPS development is
on GitHub. The previously advertised LAMMPS git repositories on
git.lammps.org and bitbucket.org are now deprecated or offline.
git.lammps.org and bitbucket.org are now offline or deprecated.
.. _git: https://git-scm.com
.. _svn: https://help.github.com/en/github/importing-your-projects-to-github/working-with-subversion-on-github
You can follow LAMMPS development on 3 different git branches:
You can follow the LAMMPS development on 3 different git branches:
* **stable** : this branch is updated with every stable release
* **unstable** : this branch is updated with every patch release
* **master** : this branch continuously follows ongoing development
* **stable** : this branch is updated with every stable release;
updates are always "fast forward" merges from *develop*
* **release** : this branch is updated with every patch release;
updates are always "fast forward" merges from *develop*
* **develop** : this branch follows the ongoing development and
is updated with every merge commit of a pull request
To access the git repositories on your box, use the clone command to
create a local copy of the LAMMPS repository with a command like:
.. code-block:: bash
$ git clone -b unstable https://github.com/lammps/lammps.git mylammps
$ git clone -b release https://github.com/lammps/lammps.git mylammps
where "mylammps" is the name of the directory you wish to create on
your machine and "unstable" is one of the 3 branches listed above.
your machine and "release" is one of the 3 branches listed above.
(Note that you actually download all 3 branches; you can switch
between them at any time using "git checkout <branch name>".)
.. note::
The complete git history of the LAMMPS project is quite large because
it contains the entire commit history of the project since fall 2006,
which includes the time when LAMMPS was managed with subversion. This
also includes commits that have added and removed some large files
(mostly by accident). If you do not need access to the entire commit
history, you can speed up the "cloning" process and reduce local disk
space requirements by using the *--depth* git command line flag thus
create a "shallow clone" of the repository that contains only a
subset of the git history. Using a depth of 1000 is usually sufficient
to include the head commits of the *develop* and the *release* branches.
To include the head commit of the *stable* branch you may need a depth
of up to 10000.
Once the command completes, your directory will contain the same files
as if you unpacked a current LAMMPS tarball, with the exception, that
the HTML documentation files are not included. They can be fetched
from the LAMMPS website by typing ``make fetch`` in the doc directory.
Or they can be generated from the content provided in doc/src by
typing ``make html`` from the doc directory.
Or they can be generated from the content provided in ``doc/src`` by
typing ``make html`` from the ``doc`` directory.
After initial cloning, as bug fixes and new features are added to
LAMMPS you can stay up-to-date by typing the following git commands
@ -56,9 +75,9 @@ from within the "mylammps" directory:
.. code-block:: bash
$ git checkout unstable # not needed if you always stay in this branch
$ git checkout stable # use one of these 3 checkout commands
$ git checkout master # to choose the branch to follow
$ git checkout release # not needed if you always stay in this branch
$ git checkout stable # use one of these 3 checkout commands
$ git checkout develop # to choose the branch to follow
$ git pull
Doing a "pull" will not change any files you have added to the LAMMPS
@ -81,7 +100,7 @@ Stable versions and what tagID to use for a particular stable version
are discussed on `this page <https://www.lammps.org/bug.html#version>`_.
Note that this command will print some warnings, because in order to get
back to the latest revision and to be able to update with ``git pull``
again, you will need to do ``git checkout unstable`` (or
again, you will need to do ``git checkout release`` (or
check out any other desired branch) first.
Once you have updated your local files with a ``git pull`` (or ``git

59
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@ -4,28 +4,41 @@ Citing LAMMPS
Core Algorithms
^^^^^^^^^^^^^^^
Since LAMMPS is a community project, there is not a single one
publication or reference that describes **all** of LAMMPS.
The canonical publication that describes the foundation, that is
the basic spatial decomposition approach, the neighbor finding,
and basic communications algorithms used in LAMMPS is:
The paper mentioned below is the best overview of LAMMPS, but there are
also publications describing particular models or algorithms implemented
in LAMMPS or complementary software that is has interfaces to. Please
see below for how to cite contributions to LAMMPS.
`S. Plimpton, Fast Parallel Algorithms for Short-Range Molecular Dynamics, J Comp Phys, 117, 1-19 (1995). <http://www.sandia.gov/~sjplimp/papers/jcompphys95.pdf>`_
.. _lammps_paper:
So any project using LAMMPS (or a derivative application using LAMMPS as
a simulation engine) should cite this paper. A new publication
describing the developments and improvements of LAMMPS in the 25 years
since then is currently in preparation.
The latest canonical publication that describes the basic features, the
source code design, the program structure, the spatial decomposition
approach, the neighbor finding, basic communications algorithms, and how
users and developers have contributed to LAMMPS is:
`LAMMPS - A flexible simulation tool for particle-based materials modeling at the atomic, meso, and continuum scales, Comp. Phys. Comm. (accepted 09/2021), DOI:10.1016/j.cpc.2021.108171 <https://doi.org/10.1016/j.cpc.2021.108171>`_
So a project using LAMMPS or a derivative application that uses LAMMPS
as a simulation engine should cite this paper. The paper is expected to
be published in its final form under the same DOI in the first half
of 2022. Please also give the URL of the LAMMPS website in your paper,
namely https://www.lammps.org.
The original publication describing the parallel algorithms used in the
initial versions of LAMMPS is:
`S. Plimpton, Fast Parallel Algorithms for Short-Range Molecular Dynamics, J Comp Phys, 117, 1-19 (1995). <http://www.sandia.gov/~sjplimp/papers/jcompphys95.pdf>`_
DOI for the LAMMPS code
^^^^^^^^^^^^^^^^^^^^^^^
LAMMPS developers use the `Zenodo service at CERN
<https://zenodo.org/>`_ to create digital object identifies (DOI) for
stable releases of the LAMMPS code. There are two types of DOIs for the
LAMMPS source code: the canonical DOI for **all** versions of LAMMPS,
which will always point to the **latest** stable release version is:
LAMMPS developers use the `Zenodo service at CERN <https://zenodo.org/>`_
to create digital object identifies (DOI) for stable releases of the
LAMMPS source code. There are two types of DOIs for the LAMMPS source code.
The canonical DOI for **all** versions of LAMMPS, which will always
point to the **latest** stable release version is:
- DOI: `10.5281/zenodo.3726416 <https://dx.doi.org/10.5281/zenodo.3726416>`_
@ -45,11 +58,13 @@ about LAMMPS and its features.
Citing contributions
^^^^^^^^^^^^^^^^^^^^
LAMMPS has many features and that use either previously published
methods and algorithms or novel features. It also includes potential
parameter filed for specific models. Where available, a reminder about
references for optional features used in a specific run is printed to
the screen and log file. Style and output location can be selected with
the :ref:`-cite command-line switch <cite>`. Additional references are
LAMMPS has many features that use either previously published methods
and algorithms or novel features. It also includes potential parameter
files for specific models. Where available, a reminder about references
for optional features used in a specific run is printed to the screen
and log file. Style and output location can be selected with the
:ref:`-cite command-line switch <cite>`. Additional references are
given in the documentation of the :doc:`corresponding commands
<Commands_all>` or in the :doc:`Howto tutorials <Howto>`.
<Commands_all>` or in the :doc:`Howto tutorials <Howto>`. So please
make certain, that you provide the proper acknowledgments and citations
in any published works using LAMMPS.

2
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@ -19,7 +19,7 @@ software and open-source distribution, see `www.gnu.org <gnuorg_>`_
or `www.opensource.org <opensource_>`_. The legal text of the GPL as it
applies to LAMMPS is in the LICENSE file included in the LAMMPS distribution.
.. _gpl: https://github.com/lammps/lammps/blob/master/LICENSE
.. _gpl: https://github.com/lammps/lammps/blob/develop/LICENSE
.. _lgpl: https://www.gnu.org/licenses/old-licenses/lgpl-2.1.html

2
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@ -26,7 +26,7 @@ available online are listed below.
* `Tutorials <https://www.lammps.org/tutorials.html>`_
* `Pre- and post-processing tools for LAMMPS <https://www.lammps.org/prepost.html>`_
* `Other software usable with LAMMPS <https://www.lammps.org/offsite.html>`_
* `Other software usable with LAMMPS <https://www.lammps.org/external.html>`_
* `Viz tools usable with LAMMPS <https://www.lammps.org/viz.html>`_
* `Benchmark performance <https://www.lammps.org/bench.html>`_

2
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@ -34,7 +34,7 @@ simple example demonstrating its use:
int lmpargc = sizeof(lmpargv)/sizeof(const char *);
/* create LAMMPS instance */
handle = lammps_open_no_mpi(lmpargc, lmpargv, NULL);
handle = lammps_open_no_mpi(lmpargc, (char **)lmpargv, NULL);
if (handle == NULL) {
printf("LAMMPS initialization failed");
lammps_mpi_finalize();

2
doc/src/Manual_version.rst
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@ -7,7 +7,7 @@ correctly and reliably at all times. You can follow its development
in a public `git repository on GitHub <https://github.com/lammps/lammps>`_.
Whenever we fix a bug or update or add a feature, it will be merged into
the `master` branch of the git repository. When a sufficient number of
the *develop* branch of the git repository. When a sufficient number of
changes have accumulated *and* the software passes a set of automated
tests, we release it in the next *patch* release, which are made every
few weeks. Info on patch releases are on `this website page

4
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@ -115,8 +115,8 @@ External contributions
If you prefer to do so, you can also develop and support your add-on
feature **without** having it included in the LAMMPS distribution, for
example as a download from a website of your own. See the `Offsite
LAMMPS packages and tools <https://www.lammps.org/offsite.html>`_ page
example as a download from a website of your own. See the `External
LAMMPS packages and tools <https://www.lammps.org/external.html>`_ page
of the LAMMPS website for examples of groups that do this. We are happy
to advertise your package and website from that page. Simply email the
`developers <https://www.lammps.org/authors.html>`_ with info about your

29
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@ -305,19 +305,22 @@ you are uncertain, please ask.
FILE pointers and only be done on MPI rank 0. Use the :cpp:func:`utils::logmesg`
convenience function where possible.
- header files should only include the absolute minimum number of
include files and **must not** contain any ``using`` statements;
rather the include statements should be put into the corresponding
implementation files. For implementation files, the
"include-what-you-use" principle should be employed. However, when
including the ``pointers.h`` header (or one of the base classes
derived from it) certain headers will be included and thus need to be
specified. These are: `mpi.h`, `cstddef`, `cstdio`, `cstdlib`,
`string`, `utils.h`, `fmt/format.h`, `climits`, `cinttypes`. This also
means any header can assume that `FILE`, `NULL`, and `INT_MAX` are
defined.
- Header files, especially those defining a "style", should only use
the absolute minimum number of include files and **must not** contain
any ``using`` statements. Typically that would be only the header for
the base class. Instead any include statements should be put into the
corresponding implementation files and forward declarations be used.
For implementation files, the "include what you use" principle should
be employed. However, there is the notable exception that when the
``pointers.h`` header is included (or one of the base classes derived
from it) certain headers will always be included and thus do not need
to be explicitly specified.
These are: `mpi.h`, `cstddef`, `cstdio`, `cstdlib`, `string`, `utils.h`,
`vector`, `fmt/format.h`, `climits`, `cinttypes`.
This also means any such file can assume that `FILE`, `NULL`, and
`INT_MAX` are defined.
- header files that define a new LAMMPS style (i.e. that have a
- Header files that define a new LAMMPS style (i.e. that have a
``SomeStyle(some/name,SomeName);`` macro in them) should only use the
include file for the base class and otherwise use forward declarations
and pointers; when interfacing to a library use the PIMPL (pointer
@ -325,7 +328,7 @@ you are uncertain, please ask.
that contains all library specific data (and thus requires the library
header) but use a forward declaration and define the struct only in
the implementation file. This is a **strict** requirement since this
is where type clashes between packages and hard to fine bugs have
is where type clashes between packages and hard to find bugs have
regularly manifested in the past.
- Please use clang-format only to reformat files that you have

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16
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@ -2,17 +2,25 @@ Basics of running LAMMPS
========================
LAMMPS is run from the command line, reading commands from a file via
the -in command line flag, or from standard input.
Using the "-in in.file" variant is recommended:
the -in command line flag, or from standard input. Using the "-in
in.file" variant is recommended (see note below). The name of the
LAMMPS executable is either ``lmp`` or ``lmp_<machine>`` with
`<machine>` being the machine string used when compiling LAMMPS. This
is required when compiling LAMMPS with the traditional build system
(e.g. with ``make mpi``), but optional when using CMake to configure and
build LAMMPS:
.. code-block:: bash
$ lmp_serial -in in.file
$ lmp_serial < in.file
$ lmp -in in.file
$ lmp < in.file
$ /path/to/lammps/src/lmp_serial -i in.file
$ mpirun -np 4 lmp_mpi -in in.file
$ mpiexec -np 4 lmp -in in.file
$ mpirun -np 8 /path/to/lammps/src/lmp_mpi -in in.file
$ mpirun -np 6 /usr/local/bin/lmp -in in.file
$ mpiexec -n 6 /usr/local/bin/lmp -in in.file
You normally run the LAMMPS command in the directory where your input
script is located. That is also where output files are produced by
@ -23,7 +31,7 @@ executable itself can be placed elsewhere.
.. note::
The redirection operator "<" will not always work when running
in parallel with mpirun; for those systems the -in form is required.
in parallel with mpirun or mpiexec; for those systems the -in form is required.
As LAMMPS runs it prints info to the screen and a logfile named
*log.lammps*\ . More info about output is given on the

2
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@ -14,7 +14,7 @@ Intel Xeon Phi co-processors.
The `Benchmark page <https://www.lammps.org/bench.html>`_ of the LAMMPS
website gives performance results for the various accelerator
packages discussed on the :doc:`Speed packages <Speed_packages>` doc
packages discussed on the :doc:`Accelerator packages <Speed_packages>`
page, for several of the standard LAMMPS benchmark problems, as a
function of problem size and number of compute nodes, on different
hardware platforms.

2
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@ -7,7 +7,7 @@ steps are often necessary to setup and analyze a simulation. A list
of such tools can be found on the `LAMMPS webpage <lws_>`_ at these links:
* `Pre/Post processing <https://www.lammps.org/prepost.html>`_
* `Offsite LAMMPS packages & tools <https://www.lammps.org/offsite.html>`_
* `External LAMMPS packages & tools <https://www.lammps.org/external.html>`_
* `Pizza.py toolkit <pizza_>`_
The last link for `Pizza.py <pizza_>`_ is a Python-based tool developed at

4
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@ -1,7 +1,7 @@
Styles with a *gpu*, *intel*, *kk*, *omp*, or *opt* suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
hardware, as discussed on the :doc:`Accelerator packages <Speed_packages>`
page. The accelerated styles take the same arguments and should
produce the same results, except for round-off and precision issues.
@ -13,5 +13,5 @@ You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
:doc:`suffix <suffix>` command in your input script.
See the :doc:`Speed packages <Speed_packages>` page for more
See the :doc:`Accelerator packages <Speed_packages>` page for more
instructions on how to use the accelerated styles effectively.

18
doc/src/angle_charmm.rst
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@ -56,23 +56,7 @@ radian\^2.
----------
Styles with a *gpu*, *intel*, *kk*, *omp*, or *opt* suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
page. The accelerated styles take the same arguments and should
produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, INTEL, KOKKOS,
OPENMP and OPT packages, respectively. They are only enabled if
LAMMPS was built with those packages. See the :doc:`Build package <Build_package>` page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
:doc:`suffix <suffix>` command in your input script.
See :doc:`Speed packages <Speed_packages>` page for more
instructions on how to use the accelerated styles effectively.
.. include:: accel_styles.rst
----------

23
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@ -319,28 +319,9 @@ styles; see the :doc:`Modify <Modify>` doc page.
----------
Styles with a *kk* suffix are functionally the same as the
corresponding style without the suffix. They have been optimized to
run faster, depending on your available hardware, as discussed in on
the :doc:`Speed packages <Speed_packages>` doc page. The accelerated
styles take the same arguments and should produce the same results,
except for round-off and precision issues.
.. include:: accel_styles.rst
Note that other acceleration packages in LAMMPS, specifically the GPU,
INTEL, OPENMP, and OPT packages do not use accelerated atom
styles.
The accelerated styles are part of the KOKKOS package. They are only
enabled if LAMMPS was built with those packages. See the :doc:`Build
package <Build_package>` page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the :doc:`-suffix command-line
switch <Run_options>` when you invoke LAMMPS, or you can use the
:doc:`suffix <suffix>` command in your input script.
See the :doc:`Speed packages <Speed_packages>` page for more
instructions on how to use the accelerated styles effectively.
----------
Restrictions
""""""""""""

2
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@ -166,6 +166,7 @@ page are followed by one or more of (g,i,k,o,t) to indicate which
accelerated styles exist.
* :doc:`accelerate/cos <fix_accelerate_cos>` - apply cosine-shaped acceleration to atoms
* :doc:`acks2/reaxff <fix_acks2_reaxff>` - apply ACKS2 charge equilibration
* :doc:`adapt <fix_adapt>` - change a simulation parameter over time
* :doc:`adapt/fep <fix_adapt_fep>` - enhanced version of fix adapt
* :doc:`addforce <fix_addforce>` - add a force to each atom
@ -246,6 +247,7 @@ accelerated styles exist.
* :doc:`manifoldforce <fix_manifoldforce>` - restrain atoms to a manifold during minimization
* :doc:`mdi/engine <fix_mdi_engine>` - connect LAMMPS to external programs via the MolSSI Driver Interface (MDI)
* :doc:`meso/move <fix_meso_move>` - move mesoscopic SPH/SDPD particles in a prescribed fashion
* :doc:`mol/swap <fix_mol_swap>` - Monte Carlo atom type swapping with a molecule
* :doc:`momentum <fix_momentum>` - zero the linear and/or angular momentum of a group of atoms
* :doc:`momentum/chunk <fix_momentum>` - zero the linear and/or angular momentum of a chunk of atoms
* :doc:`move <fix_move>` - move atoms in a prescribed fashion

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@ -0,0 +1,118 @@
.. index:: fix acks2/reaxff
.. index:: fix acks2/reaxff/kk
fix acks2/reaxff command
========================
Accelerator Variants: *acks2/reaxff/kk*
Syntax
""""""
.. parsed-literal::
fix ID group-ID acks2/reaxff Nevery cutlo cuthi tolerance params args
* ID, group-ID are documented in :doc:`fix <fix>` command
* acks2/reaxff = style name of this fix command
* Nevery = perform ACKS2 every this many steps
* cutlo,cuthi = lo and hi cutoff for Taper radius
* tolerance = precision to which charges will be equilibrated
* params = reaxff or a filename
Examples
""""""""
.. code-block:: LAMMPS
fix 1 all acks2/reaxff 1 0.0 10.0 1.0e-6 reaxff
fix 1 all acks2/reaxff 1 0.0 10.0 1.0e-6 param.acks2
Description
"""""""""""
Perform the atom-condensed Kohn-Sham DFT to second order (ACKS2) charge
equilibration method as described in :ref:`(Verstraelen) <Verstraelen>`.
ACKS2 impedes unphysical long-range charge transfer sometimes seen with
QEq (e.g. for dissociation of molecules), at increased computational
cost. It is typically used in conjunction with the ReaxFF force field
model as implemented in the :doc:`pair_style reaxff <pair_reaxff>`
command, but it can be used with any potential in LAMMPS, so long as it
defines and uses charges on each atom. For more technical details about
the charge equilibration performed by fix acks2/reaxff, see the
:ref:`(O'Hearn) <O'Hearn>` paper.
The ACKS2 method minimizes the electrostatic energy of the system by
adjusting the partial charge on individual atoms based on interactions
with their neighbors. It requires some parameters for each atom type.
If the *params* setting above is the word "reaxff", then these are
extracted from the :doc:`pair_style reaxff <pair_reaxff>` command and
the ReaxFF force field file it reads in. If a file name is specified
for *params*\ , then the parameters are taken from the specified file
and the file must contain one line for each atom type. The latter form
must be used when performing QeQ with a non-ReaxFF potential. The lines
should be formatted as follows:
.. parsed-literal::
bond_softness
itype chi eta gamma bcut
where the first line is the global parameter *bond_softness*. The
remaining 1 to Ntypes lines include *itype*, the atom type from 1 to
Ntypes, *chi*, the electronegativity in eV, *eta*, the self-Coulomb
potential in eV, *gamma*, the valence orbital exponent, and *bcut*, the
bond cutoff distance. Note that these 4 quantities are also in the
ReaxFF potential file, except that eta is defined here as twice the eta
value in the ReaxFF file. Note that unlike the rest of LAMMPS, the units
of this fix are hard-coded to be A, eV, and electronic charge.
**Restart, fix_modify, output, run start/stop, minimize info:**
No information about this fix is written to :doc:`binary restart files
<restart>`. No global scalar or vector 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 invoked during :doc:`energy minimization <minimize>`.
----------
.. include:: accel_styles.rst
----------
Restrictions
""""""""""""
This fix is part of the REAXFF 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 does not correctly handle interactions involving multiple
periodic images of the same atom. Hence, it should not be used for
periodic cell dimensions less than 10 angstroms.
This fix may be used in combination with :doc:`fix efield <fix_efield>`
and will apply the external electric field during charge equilibration,
but there may be only one fix efield instance used, it may only use a
constant electric field, and the electric field vector may only have
components in non-periodic directions.
Related commands
""""""""""""""""
:doc:`pair_style reaxff <pair_reaxff>`, :doc:`fix qeq/reaxff <fix_qeq_reaxff>`
**Default:** none
----------
.. _O'Hearn:
**(O'Hearn)** O'Hearn, Alperen, Aktulga, SIAM J. Sci. Comput., 42(1), C1-C22 (2020).
.. _Verstraelen:
**(Verstraelen)** Verstraelen, Ayers, Speybroeck, Waroquier, J. Chem. Phys. 138, 074108 (2013).

103
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@ -73,51 +73,51 @@ is the same after the swap as it was before the swap, even though the
atom masses have changed.
The *semi-grand* keyword can be set to *yes* to switch to the
semi-grand canonical ensemble as discussed in :ref:`(Sadigh) <Sadigh>`. This
means that the total number of each particle type does not need to be
conserved. The default is *no*, which means that the only kind of swap
allowed exchanges an atom of one type with an atom of a different
given type. In other words, the relative mole fractions of the swapped
atoms remains constant. Whereas in the semi-grand canonical ensemble,
the composition of the system can change. Note that when using
*semi-grand*, atoms in the fix group whose type is not listed
in the *types* keyword are ineligible for attempted
conversion. An attempt is made to switch
the selected atom (if eligible) to one of the other listed types
with equal probability. Acceptance of each attempt depends upon the Metropolis criterion.
semi-grand canonical ensemble as discussed in :ref:`(Sadigh)
<Sadigh>`. This means that the total number of each particle type does
not need to be conserved. The default is *no*, which means that the
only kind of swap allowed exchanges an atom of one type with an atom
of a different given type. In other words, the relative mole fractions
of the swapped atoms remains constant. Whereas in the semi-grand
canonical ensemble, the composition of the system can change. Note
that when using *semi-grand*, atoms in the fix group whose type is not
listed in the *types* keyword are ineligible for attempted
conversion. An attempt is made to switch the selected atom (if
eligible) to one of the other listed types with equal
probability. Acceptance of each attempt depends upon the Metropolis
criterion.
The *mu* keyword allows users to specify chemical
potentials. This is required and allowed only when using *semi-grand*\ .
All chemical potentials are absolute, so there is one for
each swap type listed following the *types* keyword.
In semi-grand canonical ensemble simulations the chemical composition
of the system is controlled by the difference in these values. So
shifting all values by a constant amount will have no effect
on the simulation.
The *mu* keyword allows users to specify chemical potentials. This is
required and allowed only when using *semi-grand*\ . All chemical
potentials are absolute, so there is one for each swap type listed
following the *types* keyword. In semi-grand canonical ensemble
simulations the chemical composition of the system is controlled by
the difference in these values. So shifting all values by a constant
amount will have no effect on the simulation.
This command may optionally use the *region* keyword to define swap
volume. The specified region must have been previously defined with a
:doc:`region <region>` command. It must be defined with side = *in*\ .
Swap attempts occur only between atoms that are both within the
:doc:`region <region>` command. It must be defined with side = *in*\
. Swap attempts occur only between atoms that are both within the
specified region. Swaps are not otherwise attempted.
You should ensure you do not swap atoms belonging to a molecule, or
LAMMPS will soon generate an error when it tries to find those atoms.
LAMMPS will warn you if any of the atoms eligible for swapping have a
non-zero molecule ID, but does not check for this at the time of
LAMMPS will eventually generate an error when it tries to find those
atoms. LAMMPS will warn you if any of the atoms eligible for swapping
have a non-zero molecule ID, but does not check for this at the time of
swapping.
If not using *semi-grand* this fix checks to ensure all atoms of the
given types have the same atomic charge. LAMMPS does not enforce this
in general, but it is needed for this fix to simplify the
swapping procedure. Successful swaps will swap the atom type and charge
of the swapped atoms. Conversely, when using *semi-grand*, it is assumed that all the atom
types involved in switches have the same charge. Otherwise, charge
would not be conserved. As a consequence, no checks on atomic charges are
performed, and successful switches update the atom type but not the
atom charge. While it is possible to use *semi-grand* with groups of
atoms that have different charges, these charges will not be changed when the
atom types change.
in general, but it is needed for this fix to simplify the swapping
procedure. Successful swaps will swap the atom type and charge of the
swapped atoms. Conversely, when using *semi-grand*, it is assumed that
all the atom types involved in switches have the same
charge. Otherwise, charge would not be conserved. As a consequence, no
checks on atomic charges are performed, and successful switches update
the atom type but not the atom charge. While it is possible to use
*semi-grand* with groups of atoms that have different charges, these
charges will not be changed when the atom types change.
Since this fix computes total potential energies before and after
proposed swaps, so even complicated potential energy calculations are
@ -133,23 +133,24 @@ OK, including the following:
Some fixes have an associated potential energy. Examples of such fixes
include: :doc:`efield <fix_efield>`, :doc:`gravity <fix_gravity>`,
:doc:`addforce <fix_addforce>`, :doc:`langevin <fix_langevin>`,
:doc:`restrain <fix_restrain>`, :doc:`temp/berendsen <fix_temp_berendsen>`,
:doc:`temp/rescale <fix_temp_rescale>`, and :doc:`wall fixes <fix_wall>`.
For that energy to be included in the total potential energy of the
system (the quantity used when performing GCMC moves),
you MUST enable the :doc:`fix_modify <fix_modify>` *energy* option for
that fix. The doc pages for individual :doc:`fix <fix>` commands
specify if this should be done.
:doc:`restrain <fix_restrain>`, :doc:`temp/berendsen
<fix_temp_berendsen>`, :doc:`temp/rescale <fix_temp_rescale>`, and
:doc:`wall fixes <fix_wall>`. For that energy to be included in the
total potential energy of the system (the quantity used when
performing GCMC moves), you MUST enable the :doc:`fix_modify
<fix_modify>` *energy* option for that fix. The doc pages for
individual :doc:`fix <fix>` commands specify if this should be done.
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
This fix writes the state of the fix to :doc:`binary restart files <restart>`. This includes information about the random
number generator seed, the next timestep for MC exchanges, the number
of exchange attempts and successes etc. See
the :doc:`read_restart <read_restart>` command for info on how to
re-specify a fix in an input script that reads a restart file, so that
the operation of the fix continues in an uninterrupted fashion.
This fix writes the state of the fix to :doc:`binary restart files
<restart>`. This includes information about the random number
generator seed, the next timestep for MC exchanges, the number of
exchange attempts and successes etc. See the :doc:`read_restart
<read_restart>` command for info on how to re-specify a fix in an
input script that reads a restart file, so that the operation of the
fix continues in an uninterrupted fashion.
.. note::
@ -165,12 +166,13 @@ by various :doc:`output commands <Howto_output>`. The vector values are
the following global cumulative quantities:
* 1 = swap attempts
* 2 = swap successes
* 2 = swap accepts
The vector values calculated by this fix are "extensive".
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>`.
the :doc:`run <run>` command. This fix is not invoked during
:doc:`energy minimization <minimize>`.
Restrictions
""""""""""""
@ -184,7 +186,8 @@ Related commands
:doc:`fix nvt <fix_nh>`, :doc:`neighbor <neighbor>`,
:doc:`fix deposit <fix_deposit>`, :doc:`fix evaporate <fix_evaporate>`,
:doc:`delete_atoms <delete_atoms>`, :doc:`fix gcmc <fix_gcmc>`
:doc:`delete_atoms <delete_atoms>`, :doc:`fix gcmc <fix_gcmc>`,
:doc:`fix mol/swap <fix_mol_swap>`
Default
"""""""

5
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@ -8,9 +8,8 @@ fix brownian command
fix brownian/sphere command
===========================
fix brownian/sphere command
===========================
fix brownian/asphere command
============================
Syntax
""""""

25
doc/src/fix_langevin.rst
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@ -138,16 +138,18 @@ temperature with optional time-dependence as well.
Like other fixes that perform thermostatting, this fix can be used
with :doc:`compute commands <compute>` that remove a "bias" from the
atom velocities. E.g. removing the center-of-mass velocity from a
group of atoms or removing the x-component of velocity from the
calculation. This is not done by default, but only if the
:doc:`fix_modify <fix_modify>` command is used to assign a temperature
compute to this fix that includes such a bias term. See the doc pages
for individual :doc:`compute commands <compute>` to determine which ones
include a bias. In this case, the thermostat works in the following
manner: bias is removed from each atom, thermostatting is performed on
the remaining thermal degrees of freedom, and the bias is added back
in.
atom velocities. E.g. to apply the thermostat only to atoms within a
spatial :doc:`region <region>`, or to remove the center-of-mass
velocity from a group of atoms, or to remove the x-component of
velocity from the calculation.
This is not done by default, but only if the :doc:`fix_modify
<fix_modify>` command is used to assign a temperature compute to this
fix that includes such a bias term. See the doc pages for individual
:doc:`compute temp commands <compute>` to determine which ones include
a bias. In this case, the thermostat works in the following manner:
bias is removed from each atom, thermostatting is performed on the
remaining thermal degrees of freedom, and the bias is added back in.
The *damp* parameter is specified in time units and determines how
rapidly the temperature is relaxed. For example, a value of 100.0 means
@ -183,7 +185,8 @@ omega (which is derived from the angular momentum in the case of
aspherical particles).
The rotational temperature of the particles can be monitored by the
:doc:`compute temp/sphere <compute_temp_sphere>` and :doc:`compute temp/asphere <compute_temp_asphere>` commands with their rotate
:doc:`compute temp/sphere <compute_temp_sphere>` and :doc:`compute
temp/asphere <compute_temp_asphere>` commands with their rotate
options.
For the *omega* keyword there is also a scale factor of

25
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@ -167,17 +167,20 @@ functions, and include :doc:`thermo_style <thermo_style>` command
keywords for the simulation box parameters and timestep and elapsed
time. Thus it is easy to specify a time-dependent temperature.
Like other fixes that perform thermostatting, this fix can be used with
:doc:`compute commands <compute>` that remove a "bias" from the atom
velocities. E.g. removing the center-of-mass velocity from a group of
atoms. This is not done by default, but only if the
:doc:`fix_modify <fix_modify>` command is used to assign a temperature
compute to this fix that includes such a bias term. See the doc pages
for individual :doc:`compute commands <compute>` to determine which ones
include a bias. In this case, the thermostat works in the following
manner: bias is removed from each atom, thermostatting is performed on
the remaining thermal degrees of freedom, and the bias is added back
in. NOTE: this feature has not been tested.
Like other fixes that perform thermostatting, this fix can be used
with :doc:`compute commands <compute>` that remove a "bias" from the
atom velocities. E.g. to apply the thermostat only to atoms within a
spatial :doc:`region <region>`, or to remove the center-of-mass
velocity from a group of atoms, or to remove the x-component of
velocity from the calculation.
This is not done by default, but only if the :doc:`fix_modify
<fix_modify>` command is used to assign a temperature compute to this
fix that includes such a bias term. See the doc pages for individual
:doc:`compute temp commands <compute>` to determine which ones include
a bias. In this case, the thermostat works in the following manner:
bias is removed from each atom, thermostatting is performed on the
remaining thermal degrees of freedom, and the bias is added back in.
Note: The temperature thermostatting the core-Drude particle pairs
should be chosen low enough, so as to mimic as closely as possible the

170
doc/src/fix_mol_swap.rst Normal file
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@ -0,0 +1,170 @@
.. index:: fix mol/swap
fix mol/swap command
=====================
Syntax
""""""
.. parsed-literal::
fix ID group-ID mol/swap N X itype jtype seed T keyword value ...
* ID, group-ID are documented in :doc:`fix <fix>` command
* atom/swap = style name of this fix command
* N = invoke this fix every N steps
* X = number of swaps to attempt every N steps
* itype,jtype = two atom types to swap with each other
* seed = random # seed (positive integer)
* T = scaling temperature of the MC swaps (temperature units)
* zero or more keyword/value pairs may be appended to args
* keyword = *ke*
.. parsed-literal::
*ke* value = *no* or *yes*
*no* = no conservation of kinetic energy after atom swaps
*yes* = kinetic energy is conserved after atom swaps
Examples
""""""""
.. code-block:: LAMMPS
fix 2 all mol/swap 100 1 2 3 29494 300.0 ke no
fix mySwap fluid mol/swap 500 10 1 2 482798 1.0
Description
"""""""""""
This fix performs Monte Carlo swaps of two specified atom types within
a randomly selected molecule. Two possible use cases are as follows.
First, consider a mixture of some molecules with atoms of itype and
other molecules with atoms of jtype. The fix will select a random
molecule and attempt to swap all the itype atoms to jtype for the
first kind of molecule, or all the jtype atoms to itype for the second
kind. Because the swap will only take place if it is energetically
favorable, the fix can be used to determine the miscibility of 2
different kinds of molecules much more quickly than just dynamics
would do it.
Second, consider diblock co-polymers with two types of monomers itype
and jtype. The fix will select a random molecule and attempt to do a
itype <--> jtype swap of all those monomers within the molecule. Thus
the fix can be used to find the energetically favorable fractions of
two flavors of diblock co-polymers.
Intra-molecular swaps of atom types are attempted every N timesteps. On
that timestep, X swaps are attempted. For each attempt a single
molecule ID is randomly selected. The range of possible molecule IDs
from loID to hiID is pre-computed before each run begins. The
loID/hiID is set for the molecule with the smallest/largest ID which
has any itype or jtype atoms in it. Note that if you define a system
with many molecule IDs between loID and hiID which have no itype or
jtype atoms, then the fix will be inefficient at performing swaps.
Also note that if atoms with molecule ID = 0 exist, they are not
considered molecules by this fix; they are assumed to be solvent atoms
or molecules.
Candidate atoms for swapping must also be in the fix group. Atoms
within the selected molecule which are not itype or jtype are ignored.
When an atom is swapped from itype to jtype (or vice versa), if
charges are defined, the charge values for itype versus jtype atoms
are also swapped. This requires that all itype atoms in the system
have the same charge value. Likewise all jtype atoms in the system
must have the same charge value. If this is not the case, LAMMPS
issues a warning that it cannot swap charge values.
If the *ke* keyword is set to yes, which is the default, and the
masses of itype and jtype atoms are different, then when a swap
occurs, the velocity of the swapped atom is rescaled by the sqrt of
the mass ratio, so as to conserve the kinetic energy of the atom.
----------
The potential energy of the entire system is computed before and after
each swap is performed within a single molecule. The specified
temperature T is used in the Metropolis criterion to accept or reject
the attempted swap. If the swap is rejected all swapped values are
reversed.
The potential energy calculations can include systems and models with
the following features:
* manybody pair styles, including EAM
* hybrid pair styles
* long-range electrostatics (kspace)
* triclinic systems
* potential energy contributions from other fixes
For the last bullet point, fixes can have an associated potential
energy. Examples of such fixes include: :doc:`efield <fix_efield>`,
:doc:`gravity <fix_gravity>`, :doc:`addforce <fix_addforce>`,
:doc:`langevin <fix_langevin>`, :doc:`restrain <fix_restrain>`,
:doc:`temp/berendsen <fix_temp_berendsen>`, :doc:`temp/rescale
<fix_temp_rescale>`, and :doc:`wall fixes <fix_wall>`. For that
energy to be included in the total potential energy of the system (the
quantity used for the swap accept/reject decision), you MUST enable
the :doc:`fix_modify <fix_modify>` *energy* option for that fix. The
doc pages for individual :doc:`fix <fix>` commands specify if this
should be done.
.. note::
One comment on computational efficiency. If the cutoff lengths
defined for the pair style are different for itype versus jtype
atoms (for any of their interactions with any other atom type), then
a new neighbor list needs to be generated for every attempted swap.
This is potentially expensive if N is small or X is large.
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
This fix writes the state of the fix to :doc:`binary restart files
<restart>`. This includes information about the random number
generator seed, the next timestep for MC exchanges, the number of
exchange attempts and successes etc. See the :doc:`read_restart
<read_restart>` command for info on how to re-specify a fix in an
input script that reads a restart file, so that the operation of the
fix continues in an uninterrupted fashion.
.. note::
For this to work correctly, the timestep must **not** be changed
after reading the restart with :doc:`reset_timestep <reset_timestep>`.
The fix will try to detect it and stop with an error.
None of the :doc:`fix_modify <fix_modify>` options are relevant to this
fix.
This fix computes a global vector of length 2, which can be accessed
by various :doc:`output commands <Howto_output>`. The vector values are
the following global cumulative quantities:
* 1 = swap attempts
* 2 = swap accepts
The vector values calculated by this fix are "extensive".
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
""""""""""""
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.
Related commands
""""""""""""""""
:doc:`fix atom/swap <fix_atom_swap>`, :doc:`fix gcmc <fix_gcmc>`
Default
"""""""
The option default is ke = yes.

27
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@ -486,19 +486,20 @@ temperature or pressure during thermodynamic output via the
compute-ID. It also means that changing attributes of *thermo_temp*
or *thermo_press* will have no effect on this fix.
Like other fixes that perform thermostatting, fix nvt and fix npt can
be used with :doc:`compute commands <compute>` that calculate a
temperature after removing a "bias" from the atom velocities.
E.g. removing the center-of-mass velocity from a group of atoms or
only calculating temperature on the x-component of velocity or only
calculating temperature for atoms in a geometric region. This is not
done by default, but only if the :doc:`fix_modify <fix_modify>` command
is used to assign a temperature compute to this fix that includes such
a bias term. See the doc pages for individual :doc:`compute commands <compute>` to determine which ones include a bias. In
this case, the thermostat works in the following manner: the current
temperature is calculated taking the bias into account, bias is
removed from each atom, thermostatting is performed on the remaining
thermal degrees of freedom, and the bias is added back in.
Like other fixes that perform thermostatting, this fix can be used
with :doc:`compute commands <compute>` that remove a "bias" from the
atom velocities. E.g. to apply the thermostat only to atoms within a
spatial :doc:`region <region>`, or to remove the center-of-mass
velocity from a group of atoms, or to remove the x-component of
velocity from the calculation.
This is not done by default, but only if the :doc:`fix_modify
<fix_modify>` command is used to assign a temperature compute to this
fix that includes such a bias term. See the doc pages for individual
:doc:`compute temp commands <compute>` to determine which ones include
a bias. In this case, the thermostat works in the following manner:
bias is removed from each atom, thermostatting is performed on the
remaining thermal degrees of freedom, and the bias is added back in.
----------

30
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View File

@ -48,8 +48,9 @@ can also have a bias velocity removed from them before thermostatting
takes place; see the description below.
Additional parameters affecting the thermostat and barostat are
specified by keywords and values documented with the :doc:`fix npt <fix_nh>` command. See, for example, discussion of the *temp*,
*iso*, *aniso*, and *dilate* keywords.
specified by keywords and values documented with the :doc:`fix npt
<fix_nh>` command. See, for example, discussion of the *temp*, *iso*,
*aniso*, and *dilate* keywords.
The particles in the fix group are the only ones whose velocities and
positions are updated by the velocity/position update portion of the
@ -89,18 +90,19 @@ It also means that changing attributes of *thermo_temp* or
*thermo_press* will have no effect on this fix.
Like other fixes that perform thermostatting, this fix can be used
with :doc:`compute commands <compute>` that calculate a temperature
after removing a "bias" from the atom velocities. E.g. removing the
center-of-mass velocity from a group of atoms or only calculating
temperature on the x-component of velocity or only calculating
temperature for atoms in a geometric region. This is not done by
default, but only if the :doc:`fix_modify <fix_modify>` command is used
to assign a temperature compute to this fix that includes such a bias
term. See the doc pages for individual :doc:`compute commands <compute>` to determine which ones include a bias. In
this case, the thermostat works in the following manner: the current
temperature is calculated taking the bias into account, bias is
removed from each atom, thermostatting is performed on the remaining
thermal degrees of freedom, and the bias is added back in.
with :doc:`compute commands <compute>` that remove a "bias" from the
atom velocities. E.g. to apply the thermostat only to atoms within a
spatial :doc:`region <region>`, or to remove the center-of-mass
velocity from a group of atoms, or to remove the x-component of
velocity from the calculation.
This is not done by default, but only if the :doc:`fix_modify
<fix_modify>` command is used to assign a temperature compute to this
fix that includes such a bias term. See the doc pages for individual
:doc:`compute temp commands <compute>` to determine which ones include
a bias. In this case, the thermostat works in the following manner:
bias is removed from each atom, thermostatting is performed on the
remaining thermal degrees of freedom, and the bias is added back in.
----------

25
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@ -87,18 +87,19 @@ It also means that changing attributes of *thermo_temp* or
*thermo_press* will have no effect on this fix.
Like other fixes that perform thermostatting, this fix can be used
with :doc:`compute commands <compute>` that calculate a temperature
after removing a "bias" from the atom velocities. E.g. removing the
center-of-mass velocity from a group of atoms or only calculating
temperature on the x-component of velocity or only calculating
temperature for atoms in a geometric region. This is not done by
default, but only if the :doc:`fix_modify <fix_modify>` command is used
to assign a temperature compute to this fix that includes such a bias
term. See the doc pages for individual :doc:`compute commands <compute>` to determine which ones include a bias. In
this case, the thermostat works in the following manner: the current
temperature is calculated taking the bias into account, bias is
removed from each atom, thermostatting is performed on the remaining
thermal degrees of freedom, and the bias is added back in.
with :doc:`compute commands <compute>` that remove a "bias" from the
atom velocities. E.g. to apply the thermostat only to atoms within a
spatial :doc:`region <region>`, or to remove the center-of-mass
velocity from a group of atoms, or to remove the x-component of
velocity from the calculation.
This is not done by default, but only if the :doc:`fix_modify
<fix_modify>` command is used to assign a temperature compute to this
fix that includes such a bias term. See the doc pages for individual
:doc:`compute temp commands <compute>` to determine which ones include
a bias. In this case, the thermostat works in the following manner:
bias is removed from each atom, thermostatting is performed on the
remaining thermal degrees of freedom, and the bias is added back in.
----------

27
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@ -400,19 +400,20 @@ temperature or pressure during thermodynamic output via the
compute-ID. It also means that changing attributes of *thermo_temp*
or *thermo_press* will have no effect on this fix.
Like other fixes that perform thermostatting, fix npt/cauchy can
be used with :doc:`compute commands <compute>` that calculate a
temperature after removing a "bias" from the atom velocities.
E.g. removing the center-of-mass velocity from a group of atoms or
only calculating temperature on the x-component of velocity or only
calculating temperature for atoms in a geometric region. This is not
done by default, but only if the :doc:`fix_modify <fix_modify>` command
is used to assign a temperature compute to this fix that includes such
a bias term. See the doc pages for individual :doc:`compute commands <compute>` to determine which ones include a bias. In
this case, the thermostat works in the following manner: the current
temperature is calculated taking the bias into account, bias is
removed from each atom, thermostatting is performed on the remaining
thermal degrees of freedom, and the bias is added back in.
Like other fixes that perform thermostatting, this fix can be used
with :doc:`compute commands <compute>` that remove a "bias" from the
atom velocities. E.g. to apply the thermostat only to atoms within a
spatial :doc:`region <region>`, or to remove the center-of-mass
velocity from a group of atoms, or to remove the x-component of
velocity from the calculation.
This is not done by default, but only if the :doc:`fix_modify
<fix_modify>` command is used to assign a temperature compute to this
fix that includes such a bias term. See the doc pages for individual
:doc:`compute temp commands <compute>` to determine which ones include
a bias. In this case, the thermostat works in the following manner:
bias is removed from each atom, thermostatting is performed on the
remaining thermal degrees of freedom, and the bias is added back in.
----------

25
doc/src/fix_npt_sphere.rst
View File

@ -103,18 +103,19 @@ appropriate compute-ID. It also means that changing attributes of
*thermo_temp* or *thermo_press* will have no effect on this fix.
Like other fixes that perform thermostatting, this fix can be used
with :doc:`compute commands <compute>` that calculate a temperature
after removing a "bias" from the atom velocities. E.g. removing the
center-of-mass velocity from a group of atoms or only calculating
temperature on the x-component of velocity or only calculating
temperature for atoms in a geometric region. This is not done by
default, but only if the :doc:`fix_modify <fix_modify>` command is used
to assign a temperature compute to this fix that includes such a bias
term. See the doc pages for individual :doc:`compute commands <compute>` to determine which ones include a bias. In
this case, the thermostat works in the following manner: the current
temperature is calculated taking the bias into account, bias is
removed from each atom, thermostatting is performed on the remaining
thermal degrees of freedom, and the bias is added back in.
with :doc:`compute commands <compute>` that remove a "bias" from the
atom velocities. E.g. to apply the thermostat only to atoms within a
spatial :doc:`region <region>`, or to remove the center-of-mass
velocity from a group of atoms, or to remove the x-component of
velocity from the calculation.
This is not done by default, but only if the :doc:`fix_modify
<fix_modify>` command is used to assign a temperature compute to this
fix that includes such a bias term. See the doc pages for individual
:doc:`compute temp commands <compute>` to determine which ones include
a bias. In this case, the thermostat works in the following manner:
bias is removed from each atom, thermostatting is performed on the
remaining thermal degrees of freedom, and the bias is added back in.
----------

25
doc/src/fix_nvt_asphere.rst
View File

@ -72,18 +72,19 @@ It also means that changing attributes of *thermo_temp* will have no
effect on this fix.
Like other fixes that perform thermostatting, this fix can be used
with :doc:`compute commands <compute>` that calculate a temperature
after removing a "bias" from the atom velocities. E.g. removing the
center-of-mass velocity from a group of atoms or only calculating
temperature on the x-component of velocity or only calculating
temperature for atoms in a geometric region. This is not done by
default, but only if the :doc:`fix_modify <fix_modify>` command is used
to assign a temperature compute to this fix that includes such a bias
term. See the doc pages for individual :doc:`compute commands <compute>` to determine which ones include a bias. In
this case, the thermostat works in the following manner: the current
temperature is calculated taking the bias into account, bias is
removed from each atom, thermostatting is performed on the remaining
thermal degrees of freedom, and the bias is added back in.
with :doc:`compute commands <compute>` that remove a "bias" from the
atom velocities. E.g. to apply the thermostat only to atoms within a
spatial :doc:`region <region>`, or to remove the center-of-mass
velocity from a group of atoms, or to remove the x-component of
velocity from the calculation.
This is not done by default, but only if the :doc:`fix_modify
<fix_modify>` command is used to assign a temperature compute to this
fix that includes such a bias term. See the doc pages for individual
:doc:`compute temp commands <compute>` to determine which ones include
a bias. In this case, the thermostat works in the following manner:
bias is removed from each atom, thermostatting is performed on the
remaining thermal degrees of freedom, and the bias is added back in.
----------

25
doc/src/fix_nvt_body.rst
View File

@ -69,18 +69,19 @@ It also means that changing attributes of *thermo_temp* will have no
effect on this fix.
Like other fixes that perform thermostatting, this fix can be used
with :doc:`compute commands <compute>` that calculate a temperature
after removing a "bias" from the atom velocities. E.g. removing the
center-of-mass velocity from a group of atoms or only calculating
temperature on the x-component of velocity or only calculating
temperature for atoms in a geometric region. This is not done by
default, but only if the :doc:`fix_modify <fix_modify>` command is used
to assign a temperature compute to this fix that includes such a bias
term. See the doc pages for individual :doc:`compute commands <compute>` to determine which ones include a bias. In
this case, the thermostat works in the following manner: the current
temperature is calculated taking the bias into account, bias is
removed from each atom, thermostatting is performed on the remaining
thermal degrees of freedom, and the bias is added back in.
with :doc:`compute commands <compute>` that remove a "bias" from the
atom velocities. E.g. to apply the thermostat only to atoms within a
spatial :doc:`region <region>`, or to remove the center-of-mass
velocity from a group of atoms, or to remove the x-component of
velocity from the calculation.
This is not done by default, but only if the :doc:`fix_modify
<fix_modify>` command is used to assign a temperature compute to this
fix that includes such a bias term. See the doc pages for individual
:doc:`compute temp commands <compute>` to determine which ones include
a bias. In this case, the thermostat works in the following manner:
bias is removed from each atom, thermostatting is performed on the
remaining thermal degrees of freedom, and the bias is added back in.
----------

74
doc/src/fix_nvt_sllod.rst
View File

@ -37,15 +37,16 @@ trajectory consistent with the canonical ensemble.
This thermostat is used for a simulation box that is changing size
and/or shape, for example in a non-equilibrium MD (NEMD) simulation.
The size/shape change is induced by use of the :doc:`fix deform <fix_deform>` command, so each point in the simulation box
can be thought of as having a "streaming" velocity. This
position-dependent streaming velocity is subtracted from each atom's
actual velocity to yield a thermal velocity which is used for
temperature computation and thermostatting. For example, if the box
is being sheared in x, relative to y, then points at the bottom of the
box (low y) have a small x velocity, while points at the top of the
box (hi y) have a large x velocity. These velocities do not
contribute to the thermal "temperature" of the atom.
The size/shape change is induced by use of the :doc:`fix deform
<fix_deform>` command, so each point in the simulation box can be
thought of as having a "streaming" velocity. This position-dependent
streaming velocity is subtracted from each atom's actual velocity to
yield a thermal velocity which is used for temperature computation and
thermostatting. For example, if the box is being sheared in x,
relative to y, then points at the bottom of the box (low y) have a
small x velocity, while points at the top of the box (hi y) have a
large x velocity. These velocities do not contribute to the thermal
"temperature" of the atom.
.. note::
@ -60,13 +61,15 @@ contribute to the thermal "temperature" of the atom.
consistent.
The SLLOD equations of motion, originally proposed by Hoover and Ladd
(see :ref:`(Evans and Morriss) <Evans3>`), were proven to be equivalent to
Newton's equations of motion for shear flow by :ref:`(Evans and Morriss) <Evans3>`. They were later shown to generate the desired
velocity gradient and the correct production of work by stresses for
all forms of homogeneous flow by :ref:`(Daivis and Todd) <Daivis>`. As
implemented in LAMMPS, they are coupled to a Nose/Hoover chain
thermostat in a velocity Verlet formulation, closely following the
implementation used for the :doc:`fix nvt <fix_nh>` command.
(see :ref:`(Evans and Morriss) <Evans3>`), were proven to be
equivalent to Newton's equations of motion for shear flow by
:ref:`(Evans and Morriss) <Evans3>`. They were later shown to generate
the desired velocity gradient and the correct production of work by
stresses for all forms of homogeneous flow by :ref:`(Daivis and Todd)
<Daivis>`. As implemented in LAMMPS, they are coupled to a
Nose/Hoover chain thermostat in a velocity Verlet formulation, closely
following the implementation used for the :doc:`fix nvt <fix_nh>`
command.
.. note::
@ -94,27 +97,28 @@ underscore + "temp", and the group for the new compute is the same as
the fix group.
Note that this is NOT the compute used by thermodynamic output (see
the :doc:`thermo_style <thermo_style>` command) with ID = *thermo_temp*.
This means you can change the attributes of this fix's temperature
(e.g. its degrees-of-freedom) via the
:doc:`compute_modify <compute_modify>` command or print this temperature
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* will have no
effect on this fix.
the :doc:`thermo_style <thermo_style>` command) with ID =
*thermo_temp*. This means you can change the attributes of this fix's
temperature (e.g. its degrees-of-freedom) via the :doc:`compute_modify
<compute_modify>` command or print this temperature 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* will have no effect on this fix.
Like other fixes that perform thermostatting, this fix can be used
with :doc:`compute commands <compute>` that calculate a temperature
after removing a "bias" from the atom velocities. E.g. removing the
center-of-mass velocity from a group of atoms or only calculating
temperature on the x-component of velocity or only calculating
temperature for atoms in a geometric region. This is not done by
default, but only if the :doc:`fix_modify <fix_modify>` command is used
to assign a temperature compute to this fix that includes such a bias
term. See the doc pages for individual :doc:`compute commands <compute>` to determine which ones include a bias. In
this case, the thermostat works in the following manner: the current
temperature is calculated taking the bias into account, bias is
removed from each atom, thermostatting is performed on the remaining
thermal degrees of freedom, and the bias is added back in.
with :doc:`compute commands <compute>` that remove a "bias" from the
atom velocities. E.g. to apply the thermostat only to atoms within a
spatial :doc:`region <region>`, or to remove the center-of-mass
velocity from a group of atoms, or to remove the x-component of
velocity from the calculation.
This is not done by default, but only if the :doc:`fix_modify
<fix_modify>` command is used to assign a temperature compute to this
fix that includes such a bias term. See the doc pages for individual
:doc:`compute temp commands <compute>` to determine which ones include
a bias. In this case, the thermostat works in the following manner:
bias is removed from each atom, thermostatting is performed on the
remaining thermal degrees of freedom, and the bias is added back in.
----------

25
doc/src/fix_nvt_sphere.rst
View File

@ -86,18 +86,19 @@ It also means that changing attributes of *thermo_temp* will have no
effect on this fix.
Like other fixes that perform thermostatting, this fix can be used
with :doc:`compute commands <compute>` that calculate a temperature
after removing a "bias" from the atom velocities. E.g. removing the
center-of-mass velocity from a group of atoms or only calculating
temperature on the x-component of velocity or only calculating
temperature for atoms in a geometric region. This is not done by
default, but only if the :doc:`fix_modify <fix_modify>` command is used
to assign a temperature compute to this fix that includes such a bias
term. See the doc pages for individual :doc:`compute commands <compute>` to determine which ones include a bias. In
this case, the thermostat works in the following manner: the current
temperature is calculated taking the bias into account, bias is
removed from each atom, thermostatting is performed on the remaining
thermal degrees of freedom, and the bias is added back in.
with :doc:`compute commands <compute>` that remove a "bias" from the
atom velocities. E.g. to apply the thermostat only to atoms within a
spatial :doc:`region <region>`, or to remove the center-of-mass
velocity from a group of atoms, or to remove the x-component of
velocity from the calculation.
This is not done by default, but only if the :doc:`fix_modify
<fix_modify>` command is used to assign a temperature compute to this
fix that includes such a bias term. See the doc pages for individual
:doc:`compute temp commands <compute>` to determine which ones include
a bias. In this case, the thermostat works in the following manner:
bias is removed from each atom, thermostatting is performed on the
remaining thermal degrees of freedom, and the bias is added back in.
----------

5
doc/src/fix_qeq.rst
View File

@ -230,7 +230,10 @@ 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.
The qeq fixes are not compatible with the GPU and USER-INTEL packages.
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>`.
Related commands
""""""""""""""""

6
doc/src/fix_qeq_reaxff.rst
View File

@ -116,6 +116,12 @@ This fix does not correctly handle interactions involving multiple
periodic images of the same atom. Hence, it should not be used for
periodic cell dimensions less than 10 angstroms.
This fix may be used in combination with :doc:`fix efield <fix_efield>`
and will apply the external electric field during charge equilibration,
but there may be only one fix efield instance used, it may only use a
constant electric field, and the electric field vector may only have
components in non-periodic directions.
Related commands
""""""""""""""""

11
doc/src/fix_reaxff_species.rst
View File

@ -56,6 +56,17 @@ number of molecules of each species. In this context, "species" means
a unique molecule. The chemical formula of each species is given in
the first line.
.. warning::
In order to compute averaged data, it is required that there are no
neighbor list rebuilds between the *Nfreq* steps. For that reason, fix
*reaxff/species* may change your neighbor list settings. There will
be a warning message showing the new settings. Having an *Nfreq*
setting that is larger than what is required for correct computation
of the ReaxFF force field interactions can thus lead to incorrect
results. For typical ReaxFF calculations a value of 100 is already
quite large.
If the filename ends with ".gz", the output file is written in gzipped
format. A gzipped dump file will be about 3x smaller than the text version,
but will also take longer to write.

5
doc/src/fix_saed_vtk.rst
View File

@ -28,7 +28,6 @@ Syntax
Nstart = start averaging on this timestep
*file* arg = filename
filename = name of file to output time averages to
*overwrite* arg = none = overwrite output file with only latest output
Examples
""""""""
@ -161,10 +160,6 @@ the *file* keyword and this string is appended with _N.vtk where N is
an index (0,1,2...) to account for situations with multiple diffraction
intensity outputs.
The *overwrite* keyword will continuously overwrite the output file
with the latest output, so that it only contains one timestep worth of
output. This option can only be used with the *ave running* setting.
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""

23
doc/src/fix_setforce.rst
View File

@ -89,26 +89,13 @@ precession vectors instead of the forces.
----------
Styles with a *gpu*, *intel*, *kk*, *omp*, or *opt* suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
page. The accelerated styles take the same arguments and should
produce the same results, except for round-off and precision issues.
.. include:: accel_styles.rst
The region keyword is also supported by Kokkos, but a Kokkos-enabled
region must be used. See the region :doc:`region <region>` command for
more information.
.. note::
These accelerated styles are part of the r Kokkos package. They are
only enabled if LAMMPS was built with that package. See the :doc:`Build package <Build_package>` page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
:doc:`suffix <suffix>` command in your input script.
See the :doc:`Speed packages <Speed_packages>` page for more
instructions on how to use the accelerated styles effectively.
The region keyword is supported by Kokkos, but a Kokkos-enabled
region must be used. See the region :doc:`region <region>` command for
more information.
----------

25
doc/src/fix_temp_berendsen.rst
View File

@ -102,18 +102,19 @@ It also means that changing attributes of *thermo_temp* will have no
effect on this fix.
Like other fixes that perform thermostatting, this fix can be used
with :doc:`compute commands <compute>` that calculate a temperature
after removing a "bias" from the atom velocities. E.g. removing the
center-of-mass velocity from a group of atoms or only calculating
temperature on the x-component of velocity or only calculating
temperature for atoms in a geometric region. This is not done by
default, but only if the :doc:`fix_modify <fix_modify>` command is used
to assign a temperature compute to this fix that includes such a bias
term. See the doc pages for individual :doc:`compute commands <compute>` to determine which ones include a bias. In
this case, the thermostat works in the following manner: the current
temperature is calculated taking the bias into account, bias is
removed from each atom, thermostatting is performed on the remaining
thermal degrees of freedom, and the bias is added back in.
with :doc:`compute commands <compute>` that remove a "bias" from the
atom velocities. E.g. to apply the thermostat only to atoms within a
spatial :doc:`region <region>`, or to remove the center-of-mass
velocity from a group of atoms, or to remove the x-component of
velocity from the calculation.
This is not done by default, but only if the :doc:`fix_modify
<fix_modify>` command is used to assign a temperature compute to this
fix that includes such a bias term. See the doc pages for individual
:doc:`compute temp commands <compute>` to determine which ones include
a bias. In this case, the thermostat works in the following manner:
bias is removed from each atom, thermostatting is performed on the
remaining thermal degrees of freedom, and the bias is added back in.
----------

41
doc/src/fix_temp_csvr.rst
View File

@ -110,28 +110,29 @@ during thermodynamic output via the :doc:`thermo_style custom <thermo_style>` co
It also means that changing attributes of *thermo_temp* will have no
effect on this fix.
Like other fixes that perform thermostatting, these fixes can be used
with :doc:`compute commands <compute>` that calculate a temperature
after removing a "bias" from the atom velocities. E.g. removing the
center-of-mass velocity from a group of atoms or only calculating
temperature on the x-component of velocity or only calculating
temperature for atoms in a geometric region. This is not done by
default, but only if the :doc:`fix_modify <fix_modify>` command is used
to assign a temperature compute to this fix that includes such a bias
term. See the doc pages for individual :doc:`compute commands <compute>` to determine which ones include a bias. In
this case, the thermostat works in the following manner: the current
temperature is calculated taking the bias into account, bias is
removed from each atom, thermostatting is performed on the remaining
thermal degrees of freedom, and the bias is added back in.
Like other fixes that perform thermostatting, this fix can be used
with :doc:`compute commands <compute>` that remove a "bias" from the
atom velocities. E.g. to apply the thermostat only to atoms within a
spatial :doc:`region <region>`, or to remove the center-of-mass
velocity from a group of atoms, or to remove the x-component of
velocity from the calculation.
This is not done by default, but only if the :doc:`fix_modify
<fix_modify>` command is used to assign a temperature compute to this
fix that includes such a bias term. See the doc pages for individual
:doc:`compute temp commands <compute>` to determine which ones include
a bias. In this case, the thermostat works in the following manner:
bias is removed from each atom, thermostatting is performed on the
remaining thermal degrees of freedom, and the bias is added back in.
An important feature of these thermostats is that they have an
associated effective energy that is a constant of motion.
The effective energy is the total energy (kinetic + potential) plus
the accumulated kinetic energy changes due to the thermostat. The
latter quantity is the global scalar computed by these fixes. This
feature is useful to check the integration of the equations of motion
against discretization errors. In other words, the conservation of
the effective energy can be used to choose an appropriate integration
associated effective energy that is a constant of motion. The
effective energy is the total energy (kinetic + potential) plus the
accumulated kinetic energy changes due to the thermostat. The latter
quantity is the global scalar computed by these fixes. This feature is
useful to check the integration of the equations of motion against
discretization errors. In other words, the conservation of the
effective energy can be used to choose an appropriate integration
:doc:`timestep <timestep>`. This is similar to the usual paradigm of
checking the conservation of the total energy in the microcanonical
ensemble.

26
doc/src/fix_temp_rescale.rst
View File

@ -109,19 +109,19 @@ command using the appropriate compute-ID. It also means that changing
attributes of *thermo_temp* will have no effect on this fix.
Like other fixes that perform thermostatting, this fix can be used
with :doc:`compute commands <compute>` that calculate a temperature
after removing a "bias" from the atom velocities. E.g. removing the
center-of-mass velocity from a group of atoms or only calculating
temperature on the x-component of velocity or only calculating
temperature for atoms in a geometric region. This is not done by
default, but only if the :doc:`fix_modify <fix_modify>` command is
used to assign a temperature compute to this fix that includes such a
bias term. See the doc pages for individual :doc:`compute commands
<compute>` to determine which ones include a bias. In this case, the
thermostat works in the following manner: the current temperature is
calculated taking the bias into account, bias is removed from each
atom, thermostatting is performed on the remaining thermal degrees of
freedom, and the bias is added back in.
with :doc:`compute commands <compute>` that remove a "bias" from the
atom velocities. E.g. to apply the thermostat only to atoms within a
spatial :doc:`region <region>`, or to remove the center-of-mass
velocity from a group of atoms, or to remove the x-component of
velocity from the calculation.
This is not done by default, but only if the :doc:`fix_modify
<fix_modify>` command is used to assign a temperature compute to this
fix that includes such a bias term. See the doc pages for individual
:doc:`compute temp commands <compute>` to determine which ones include
a bias. In this case, the thermostat works in the following manner:
bias is removed from each atom, thermostatting is performed on the
remaining thermal degrees of freedom, and the bias is added back in.
----------

40
doc/src/fix_tgnh_drude.rst
View File

@ -187,26 +187,32 @@ barostatting.
----------
Like other fixes that perform thermostatting, these fixes can
be used with :doc:`compute commands <compute>` that calculate a
temperature after removing a "bias" from the atom velocities.
This is not done by default, but only if the :doc:`fix_modify <fix_modify>` command
is used to assign a temperature compute to this fix that includes such
a bias term. See the doc pages for individual :doc:`compute commands <compute>` to determine which ones include a bias. In
this case, the thermostat works in the following manner: the current
temperature is calculated taking the bias into account, bias is
removed from each atom, thermostatting is performed on the remaining
thermal DOF, and the bias is added back in.
Like other fixes that perform thermostatting, this fix can be used
with :doc:`compute commands <compute>` that remove a "bias" from the
atom velocities. E.g. to apply the thermostat only to atoms within a
spatial :doc:`region <region>`, or to remove the center-of-mass
velocity from a group of atoms, or to remove the x-component of
velocity from the calculation.
This is not done by default, but only if the :doc:`fix_modify
<fix_modify>` command is used to assign a temperature compute to this
fix that includes such a bias term. See the doc pages for individual
:doc:`compute temp commands <compute>` to determine which ones include
a bias. In this case, the thermostat works in the following manner:
bias is removed from each atom, thermostatting is performed on the
remaining thermal degrees of freedom, and the bias is added back in.
.. note::
However, not all temperature compute commands are valid to be used with these fixes.
Precisely, only temperature compute that does not modify the DOF of the group can be used.
E.g. :doc:`compute temp/ramp <compute_temp_ramp>` and :doc:`compute viscosity/cos <compute_viscosity_cos>`
compute the kinetic energy after remove a velocity gradient without affecting the DOF of the group,
then they can be invoked in this way.
In contrast, :doc:`compute temp/partial <compute_temp_partial>` may remove the DOF at one or more dimensions,
therefore it cannot be used with these fixes.
However, not all temperature compute commands are valid to be used
with these fixes. Precisely, only temperature compute that does
not modify the DOF of the group can be used. E.g. :doc:`compute
temp/ramp <compute_temp_ramp>` and :doc:`compute viscosity/cos
<compute_viscosity_cos>` compute the kinetic energy after remove a
velocity gradient without affecting the DOF of the group, then they
can be invoked in this way. In contrast, :doc:`compute
temp/partial <compute_temp_partial>` may remove the DOF at one or
more dimensions, therefore it cannot be used with these fixes.
----------

2
doc/src/group.rst
View File

@ -38,7 +38,7 @@ Syntax
*intersect* args = two or more group IDs
*dynamic* args = parent-ID keyword value ...
one or more keyword/value pairs may be appended
keyword = *region* or *var* or *every*
keyword = *region* or *var* or *property* or *every*
*region* value = region-ID
*var* value = name of variable
*property* value = name of custom integer or floating point vector

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20
doc/src/improper_harmonic.rst
View File

@ -64,25 +64,7 @@ radian\^2.
----------
Styles with a *gpu*, *intel*, *kk*, *omp*, or *opt* suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
page. The accelerated styles take the same arguments and should
produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, INTEL, KOKKOS,
OPENMP and OPT packages, respectively. They are only enabled if
LAMMPS was built with those packages. See the :doc:`Build package
<Build_package>` page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the :doc:`-suffix
command-line switch <Run_options>` when you invoke LAMMPS, or you can
use the :doc:`suffix <suffix>` command in your input script.
See the :doc:`Speed packages <Speed_packages>` page for more
instructions on how to use the accelerated styles effectively.
.. include:: accel_styles.rst
----------

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