ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

Merge branch 'master' into type-labels

Browse Source
This commit is contained in:
Steve Plimpton
2021-11-01 08:33:21 -06:00
parent 67ae6eb7b6 4a048e3f57
commit 2436893215
644 changed files with 28176 additions and 4989 deletions
Download Patch File Download Diff File Expand all files Collapse all files

2
.github/CODEOWNERS vendored
View File

@ -83,7 +83,7 @@ src/library.* @sjplimp
src/main.cpp @sjplimp src/main.cpp @sjplimp
src/min_*.* @sjplimp src/min_*.* @sjplimp
src/memory.* @sjplimp src/memory.* @sjplimp
src/modify.* @sjplimp src/modify.* @sjplimp @stanmoore1
src/molecule.* @sjplimp src/molecule.* @sjplimp
src/my_page.h @sjplimp src/my_page.h @sjplimp
src/my_pool_chunk.h @sjplimp src/my_pool_chunk.h @sjplimp

2
.github/workflows/codeql-analysis.yml vendored
View File

@ -3,7 +3,7 @@ name: "CodeQL Code Analysis"
on: on:
push: push:
branches: [master] branches: [develop]
jobs: jobs:
analyze: analyze:

33
.github/workflows/compile-msvc.yml vendored Normal file
View File

@ -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
View File

@ -3,7 +3,7 @@ name: "Unittest for MacOS"
on: on:
push: push:
branches: [master] branches: [develop]
jobs: jobs:
build: build:

7
.gitignore vendored
View File

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

63
cmake/CMakeLists.txt
View File

@ -81,22 +81,40 @@ check_for_autogen_files(${LAMMPS_SOURCE_DIR})
include(CheckIncludeFileCXX) include(CheckIncludeFileCXX)
# set required compiler flags and compiler/CPU arch specific optimizations # set required compiler flags and compiler/CPU arch specific optimizations
if((CMAKE_CXX_COMPILER_ID STREQUAL "Intel") OR (CMAKE_CXX_COMPILER_ID STREQUAL "IntelLLVM")) if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -restrict") if(CMAKE_SYSTEM_NAME STREQUAL "Windows")
if(CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.3 OR CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.4) if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
set(CMAKE_TUNE_DEFAULT "-xCOMMON-AVX512") set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /Qrestrict")
endif()
if(CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.3 OR CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.4)
set(CMAKE_TUNE_DEFAULT "/QxCOMMON-AVX512")
else()
set(CMAKE_TUNE_DEFAULT "/QxHost")
endif()
else() else()
set(CMAKE_TUNE_DEFAULT "-xHost") set(CMAKE_CXX_FLAGS "${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()
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) 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_STANDARD_REQUIRED ON)
set(CMAKE_CXX_EXTENSIONS OFF CACHE BOOL "Use compiler extensions") 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) if(MSVC)
add_compile_options(/Zc:__cplusplus) add_compile_options(/Zc:__cplusplus)
add_compile_options(/wd4244)
add_compile_options(/wd4267)
add_compile_definitions(_CRT_SECURE_NO_WARNINGS)
endif() endif()
# export all symbols when building a .dll file on windows # 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>) target_include_directories(mpi_stubs PUBLIC $<BUILD_INTERFACE:${LAMMPS_SOURCE_DIR}/STUBS>)
if(BUILD_SHARED_LIBS) if(BUILD_SHARED_LIBS)
target_link_libraries(lammps PRIVATE mpi_stubs) 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_include_directories(lammps INTERFACE $<BUILD_INTERFACE:${LAMMPS_SOURCE_DIR}/STUBS>)
target_compile_definitions(lammps INTERFACE $<INSTALL_INTERFACE:LAMMPS_LIB_NO_MPI>) target_compile_definitions(lammps INTERFACE $<INSTALL_INTERFACE:LAMMPS_LIB_NO_MPI>)
else() else()
@ -468,9 +491,12 @@ foreach(HEADER cmath)
endif(NOT FOUND_${HEADER}) endif(NOT FOUND_${HEADER})
endforeach(HEADER) endforeach(HEADER)
set(MATH_LIBRARIES "m" CACHE STRING "math library") # make the standard math library overrideable and autodetected (for systems that don't have it)
mark_as_advanced( MATH_LIBRARIES ) find_library(STANDARD_MATH_LIB m DOC "Standard Math library")
target_link_libraries(lammps PRIVATE ${MATH_LIBRARIES}) mark_as_advanced(STANDARD_MATH_LIB)
if(STANDARD_MATH_LIB)
target_link_libraries(lammps PRIVATE ${STANDARD_MATH_LIB})
endif()
###################################### ######################################
# Generate Basic Style files # Generate Basic Style files
@ -591,15 +617,12 @@ foreach(PKG_WITH_INCL CORESHELL QEQ OPENMP DPD-SMOOTH KOKKOS OPT INTEL GPU)
endforeach() endforeach()
if(PKG_PLUGIN) if(PKG_PLUGIN)
if(BUILD_SHARED_LIBS) target_compile_definitions(lammps PRIVATE -DLMP_PLUGIN)
target_compile_definitions(lammps PRIVATE -DLMP_PLUGIN) endif()
else()
message(WARNING "Plugin loading will not work unless BUILD_SHARED_LIBS is enabled") # link with -ldl or equivalent for plugin loading; except on Windows
endif() if(NOT ${CMAKE_SYSTEM_NAME} STREQUAL "Windows")
# link with -ldl or equivalent for plugin loading; except on Windows target_link_libraries(lammps PRIVATE ${CMAKE_DL_LIBS})
if(NOT ${CMAKE_SYSTEM_NAME} STREQUAL "Windows")
target_link_libraries(lammps PRIVATE ${CMAKE_DL_LIBS})
endif()
endif() endif()
###################################################################### ######################################################################
@ -608,7 +631,7 @@ endif()
# and after everything else that is compiled locally # and after everything else that is compiled locally
###################################################################### ######################################################################
if(CMAKE_SYSTEM_NAME STREQUAL "Windows") if(CMAKE_SYSTEM_NAME STREQUAL "Windows")
target_link_libraries(lammps PRIVATE -lwsock32 -lpsapi) target_link_libraries(lammps PRIVATE "wsock32;psapi")
endif() endif()
###################################################### ######################################################

55
cmake/CMakeSettings.json Normal file
View File

@ -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
View File

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

2
cmake/Modules/LAMMPSUtils.cmake
View File

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

2
cmake/Modules/Packages/KOKKOS.cmake
View File

@ -1,7 +1,7 @@
######################################################################## ########################################################################
# As of version 3.3.0 Kokkos requires C++14 # As of version 3.3.0 Kokkos requires C++14
if(CMAKE_CXX_STANDARD LESS 14) if(CMAKE_CXX_STANDARD LESS 14)
set(CMAKE_CXX_STANDARD 14) message(FATAL_ERROR "The KOKKOS package requires the C++ standard to be set to at least C++14")
endif() endif()
######################################################################## ########################################################################
# consistency checks and Kokkos options/settings required by LAMMPS # consistency checks and Kokkos options/settings required by LAMMPS

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}) option(DOWNLOAD_EIGEN3 "Download Eigen3 instead of using an already installed one)" ${DOWNLOAD_EIGEN3_DEFAULT})
if(DOWNLOAD_EIGEN3) if(DOWNLOAD_EIGEN3)
message(STATUS "Eigen3 download requested - we will build our own") message(STATUS "Eigen3 download requested - we will build our own")
set(EIGEN3_URL "https://gitlab.com/libeigen/eigen/-/archive/3.3.9/eigen-3.3.9.tar.gz" CACHE STRING "URL for Eigen3 tarball")
set(EIGEN3_MD5 "609286804b0f79be622ccf7f9ff2b660" CACHE STRING "MD5 checksum of Eigen3 tarball") set(EIGEN3_URL "${LAMMPS_THIRDPARTY_URL}/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_URL)
mark_as_advanced(EIGEN3_MD5) mark_as_advanced(EIGEN3_MD5)
include(ExternalProject) include(ExternalProject)

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 "a2ac3315c41a1a4a5c912bcb1bc9c5cc" CACHE STRING "MD5 checksum of PACE evaluator library tarball")
set(PACELIB_MD5 "4db54962fbd6adcf8c18d46e1798ceb5" CACHE STRING "MD5 checksum of PACE evaluator library tarball")
mark_as_advanced(PACELIB_URL) mark_as_advanced(PACELIB_URL)
mark_as_advanced(PACELIB_MD5) mark_as_advanced(PACELIB_MD5)
# download library sources to build folder # 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 # uncompress downloaded sources
execute_process( execute_process(
@ -14,12 +14,19 @@ execute_process(
WORKING_DIRECTORY ${CMAKE_BINARY_DIR} WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
) )
file(GLOB PACE_EVALUATOR_INCLUDE_DIR ${CMAKE_BINARY_DIR}/lammps-user-pace-*/USER-PACE) file(GLOB lib-pace ${CMAKE_BINARY_DIR}/lammps-user-pace-*)
file(GLOB PACE_EVALUATOR_SOURCES ${CMAKE_BINARY_DIR}/lammps-user-pace-*/USER-PACE/*.cpp) add_subdirectory(${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) list(FILTER PACE_EVALUATOR_SOURCES EXCLUDE REGEX pair_pace.cpp)
add_library(pace STATIC ${PACE_EVALUATOR_SOURCES}) add_library(pace STATIC ${PACE_EVALUATOR_SOURCES})
set_target_properties(pace PROPERTIES CXX_EXTENSIONS ON OUTPUT_NAME lammps_pace${LAMMPS_MACHINE}) set_target_properties(pace PROPERTIES CXX_EXTENSIONS ON OUTPUT_NAME lammps_pace${LAMMPS_MACHINE})
target_include_directories(pace PUBLIC ${PACE_EVALUATOR_INCLUDE_DIR}) target_include_directories(pace PUBLIC ${PACE_EVALUATOR_INCLUDE_DIR} ${YAML_CPP_INCLUDE_DIR})
target_link_libraries(lammps PRIVATE pace)
target_link_libraries(pace PRIVATE yaml-cpp-pace)
target_link_libraries(lammps PRIVATE pace)

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) get_filename_component(MSI2LMP_SOURCE_DIR ${LAMMPS_TOOLS_DIR}/msi2lmp/src ABSOLUTE)
file(GLOB MSI2LMP_SOURCES ${MSI2LMP_SOURCE_DIR}/[^.]*.c) file(GLOB MSI2LMP_SOURCES ${MSI2LMP_SOURCE_DIR}/[^.]*.c)
add_executable(msi2lmp ${MSI2LMP_SOURCES}) 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(TARGETS msi2lmp DESTINATION ${CMAKE_INSTALL_BINDIR})
install(FILES ${LAMMPS_DOC_DIR}/msi2lmp.1 DESTINATION ${CMAKE_INSTALL_MANDIR}/man1) install(FILES ${LAMMPS_DOC_DIR}/msi2lmp.1 DESTINATION ${CMAKE_INSTALL_MANDIR}/man1)
endif() endif()

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.cpp \
@LAMMPS_SOURCE_DIR@/my_pool_chunk.h \ @LAMMPS_SOURCE_DIR@/my_pool_chunk.h \
@LAMMPS_SOURCE_DIR@/math_eigen.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 # 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 # 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 ## Pull Requests
ALL changes to the LAMMPS code and documentation, however trivial, MUST 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 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 upon patch or stable releases with fast-forward merges based on the
associated tags. Pull requests may also be submitted to (long-running) associated tags. Pull requests may also be submitted to (long-running)
feature branches created by LAMMPS developers inside the LAMMPS project, 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 LAMMPS uses a continuous release development model with incremental
changes, i.e. significant effort is made - including automated pre-merge 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 broken. These tests are run after every update to a pull request. More
extensive and time consuming tests (including regression testing) are 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 releases of LAMMPS every 3-5 weeks at a point, when the LAMMPS
developers feel, that a sufficient amount of changes have happened, and developers feel, that a sufficient amount of changes have happened, and
the post-merge testing has been successful. These patch releases are 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 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 the case of larger change sets or unexpected incompatibilities or side
effects. effects.

2
doc/lammps.1
View File

@ -1,4 +1,4 @@
.TH LAMMPS "29 September 2021" "2021-09-29" .TH LAMMPS "1" "27 October 2021" "2021-10-27"
.SH NAME .SH NAME
.B LAMMPS .B LAMMPS
\- Molecular Dynamics Simulator. \- 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 .SH NAME
.B MSI2LMP .B MSI2LMP
\- Converter for Materials Studio files to LAMMPS \- Converter for Materials Studio files to LAMMPS

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: reduce the storage requirements. Here are some suggestions:
- Create a so-called shallow repository by cloning only the last commit - 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 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 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). 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 the rest the build process will attempt to download and install them into
a python virtual environment and local folders. a python virtual environment and local folders.
A current version of the manual (latest patch release, aka unstable A current version of the manual (latest patch release, that is the state
branch) is is available online at: of the *release* branch) is is available online at:
`https://docs.lammps.org/Manual.html <https://docs.lammps.org/Manual.html>`_. `https://docs.lammps.org/ <https://docs.lammps.org/>`_.
A version of the manual corresponding to the ongoing development (aka master branch) A version of the manual corresponding to the ongoing development (that is
is available online at: `https://docs.lammps.org/latest/ the state of the *develop* branch) is available online at:
<https://docs.lammps.org/latest/>`_ `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 Build using GNU make
-------------------- --------------------

32
doc/src/Build_settings.rst
View File

@ -321,9 +321,7 @@ following settings:
.. code-block:: make .. code-block:: make
LMP_INC = -DLAMMPS_JPEG LMP_INC = -DLAMMPS_JPEG -DLAMMPS_PNG -DLAMMPS_FFMPEG <other LMP_INC settings>
LMP_INC = -DLAMMPS_PNG
LMP_INC = -DLAMMPS_FFMPEG
JPG_INC = -I/usr/local/include # path to jpeglib.h, png.h, zlib.h header files if make cannot find them 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 JPG_PATH = -L/usr/lib # paths to libjpeg.a, libpng.a, libz.a (.so) files if make cannot find them
@ -354,8 +352,10 @@ Read or write compressed files
----------------------------------------- -----------------------------------------
If this option is enabled, large files can be read or written with If this option is enabled, large files can be read or written with
gzip compression by several LAMMPS commands, including compression by ``gzip`` or similar tools by several LAMMPS commands,
:doc:`read_data <read_data>`, :doc:`rerun <rerun>`, and :doc:`dump <dump>`. including :doc:`read_data <read_data>`, :doc:`rerun <rerun>`, and
:doc:`dump <dump>`. Currently supported compression tools are:
``gzip``, ``bzip2``, ``zstd``, and ``lzma``.
.. tabs:: .. tabs::
@ -364,23 +364,23 @@ gzip compression by several LAMMPS commands, including
.. code-block:: bash .. code-block:: bash
-D WITH_GZIP=value # yes or no -D WITH_GZIP=value # yes or no
# default is yes if CMake can find gzip, else no # default is yes if CMake can find the gzip program, else no
-D GZIP_EXECUTABLE=path # path to gzip executable if CMake cannot find it
.. tab:: Traditional make .. tab:: Traditional make
.. code-block:: 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()" This option requires that your operating system fully supports the
function in the standard runtime library and that a ``gzip`` executable can be "popen()" function in the standard runtime library and that a ``gzip``
found by LAMMPS during a run. or other executable can be found by LAMMPS in the standard search path
during a run.
.. note:: .. note::
On some clusters with high-speed networks, using the "fork()" library On clusters with high-speed networks, using the "fork()" library call
call (required by "popen()") can interfere with the fast communication (required by "popen()") can interfere with the fast communication
library and lead to simulations using compressed output or input to library and lead to simulations using compressed output or input to
hang or crash. For selected operations, compressed file I/O is also hang or crash. For selected operations, compressed file I/O is also
available using a compression library instead, which is what the available using a compression library instead, which is what the
@ -452,7 +452,7 @@ those systems:
.. code-block:: make .. code-block:: make
LMP_INC = -DLAMMPS_LONGLONG_TO_LONG LMP_INC = -DLAMMPS_LONGLONG_TO_LONG <other LMP_INC settings>
---------- ----------
@ -479,7 +479,7 @@ e.g. to Python. Of course, the calling code has to be set up to
.. code-block:: make .. code-block:: make
LMP_INC = -DLAMMPS_EXCEPTIONS LMP_INC = -DLAMMPS_EXCEPTIONS <other LMP_INC settings>
.. note:: .. note::
@ -520,7 +520,7 @@ executable, not the library.
.. code-block:: make .. 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 After compilation with this flag set, the LAMMPS executable will stop
and produce a core dump when a division by zero, overflow, illegal math 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:`General remarks <generic>`
* :ref:`Running Linux on Windows <linux>` * :ref:`Running Linux on Windows <linux>`
* :ref:`Using GNU GCC ported to Windows <gnu>` * :ref:`Using GNU GCC ported to Windows <gnu>`
* :ref:`Using Visual Studio <msvc>`
* :ref:`Using a cross-compiler <cross>` * :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 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 (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 virtual machine software and compile and run LAMMPS in a Linux virtual
machine, or - if you have a sufficiently up-to-date Windows 10 machine, or - if you have a sufficiently up-to-date Windows 10 or
installation - consider using the Windows subsystem for Linux. This Windows 11 installation - consider using the Windows subsystem for
optional Windows feature allows you to run the bash shell from Ubuntu Linux. This optional Windows feature allows you to run the bash shell
from within Windows and from there on, you can pretty much use that from Ubuntu from within Windows and from there on, you can pretty much
shell like you are running on an Ubuntu Linux machine (e.g. installing use that shell like you are running on an Ubuntu Linux machine
software via apt-get and more). For more details on that, please see (e.g. installing software via apt-get and more). For more details on
:doc:`this tutorial <Howto_wsl>`. that, please see :doc:`this tutorial <Howto_wsl>`.
.. _gnu: .. _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 yourself, please report them on the lammps-users mailing list, or file
them as an issue or pull request on the LAMMPS GitHub project. 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: .. _cross:
Using a cross-compiler Using a cross-compiler

2
doc/src/Commands_fix.rst
View File

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

1
doc/src/Developer.rst
View File

@ -18,4 +18,5 @@ of time and requests from the LAMMPS user community.
Developer_plugins Developer_plugins
Developer_unittest Developer_unittest
Classes Classes
Developer_platform
Developer_utils Developer_utils

152
doc/src/Developer_platform.rst Normal file
View File

@ -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

25
doc/src/Developer_utils.rst
View File

@ -7,7 +7,9 @@ a collection of convenience functions and utilities that perform common
tasks that are required repeatedly throughout the LAMMPS code like tasks that are required repeatedly throughout the LAMMPS code like
reading or writing to files with error checking or translation of reading or writing to files with error checking or translation of
strings into specific types of numbers with checking for validity. This 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 I/O with status check and similar functions
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
@ -101,6 +103,12 @@ and parsing files or arguments.
.. doxygenfunction:: strdup .. doxygenfunction:: strdup
:project: progguide :project: progguide
.. doxygenfunction:: lowercase
:project: progguide
.. doxygenfunction:: uppercase
:project: progguide
.. doxygenfunction:: trim .. doxygenfunction:: trim
:project: progguide :project: progguide
@ -143,21 +151,6 @@ and parsing files or arguments.
.. doxygenfunction:: is_double .. doxygenfunction:: is_double
:project: progguide :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 Potential file functions
^^^^^^^^^^^^^^^^^^^^^^^^ ^^^^^^^^^^^^^^^^^^^^^^^^

4
doc/src/Developer_write.rst
View File

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

4
doc/src/Examples.rst
View File

@ -80,7 +80,7 @@ Lowercase directories
+-------------+------------------------------------------------------------------+ +-------------+------------------------------------------------------------------+
| friction | frictional contact of spherical asperities between 2d surfaces | | 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 | | 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 | | 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 | | PACKAGES | examples for specific packages and contributed commands |
+------------+--------------------------------------------------------------------------------------------------+ +------------+--------------------------------------------------------------------------------------------------+

133
doc/src/Howto_github.rst
View File

@ -7,11 +7,11 @@ LAMMPS GitHub tutorial
This document describes the process of how to use GitHub to integrate This document describes the process of how to use GitHub to integrate
changes or additions you have made to LAMMPS into the official LAMMPS changes or additions you have made to LAMMPS into the official LAMMPS
distribution. It uses the process of updating this very tutorial as distribution. It uses the process of updating this very tutorial as an
an example to describe the individual steps and options. You need to example to describe the individual steps and options. You need to be
be familiar with git and you may want to have a look at the familiar with git and you may want to have a look at the `git book
`git book <http://git-scm.com/book/>`_ to reacquaint yourself with some <http://git-scm.com/book/>`_ to familiarize yourself with some of the
of the more advanced git features used below. more advanced git features used below.
As of fall 2016, submitting contributions to LAMMPS via pull requests As of fall 2016, submitting contributions to LAMMPS via pull requests
on GitHub is the preferred option for integrating contributed features on GitHub is the preferred option for integrating contributed features
@ -37,15 +37,15 @@ username or e-mail address and password.
**Forking the repository** **Forking the repository**
To get changes into LAMMPS, you need to first fork the `lammps/lammps` 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>`_ 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 .. image:: JPG/tutorial_branch.png
:align: center :align: center
If it is not, use the button to change it to *master*\ . Once it is, use the If it is not, use the button to change it to *develop*. Once it is, use
fork button to create a fork. the fork button to create a fork.
.. image:: JPG/tutorial_fork.png .. image:: JPG/tutorial_fork.png
:align: center :align: center
@ -64,11 +64,12 @@ LAMMPS development.
**Adding changes to your own fork** **Adding changes to your own fork**
Additions to the upstream version of LAMMPS are handled using *feature 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 created, which contains only those modification relevant to one specific
feature. For example, adding a single fix would consist of creating a 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 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** **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 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. default to "lammps". Typical names are "mylammps" or something similar.
You can use this local clone to make changes and You can use this local clone to make changes and test them without
test them without interfering with the repository on GitHub. interfering with the repository on GitHub.
To pull changes from upstream into this copy, you can go to the directory To pull changes from upstream into this copy, you can go to the directory
and use git pull: and use git pull:
@ -103,28 +104,45 @@ and use git pull:
.. code-block:: bash .. code-block:: bash
$ cd mylammps $ cd mylammps
$ git checkout master $ git checkout develop
$ git pull https://github.com/lammps/lammps $ git pull https://github.com/lammps/lammps develop
You can also add this URL as a remote: You can also add this URL as a remote:
.. code-block:: bash .. 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 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 workflow that updated this tutorial, and hence we will call the branch
"github-tutorial-update": "github-tutorial-update":
.. code-block:: bash .. 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 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, repository. Just remember that if you want to start working on another,
unrelated feature, you should switch branches! 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 changes are made**
After everything is done, add the files to the branch and commit them: 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 LAMMPS developers may add labels to your pull request to assign it to
categories (mostly for bookkeeping purposes), but a few of them are categories (mostly for bookkeeping purposes), but a few of them are
important: needs_work, work_in_progress, test-for-regression, and important: *needs_work*, *work_in_progress*, *run_tests*,
full-regression-test. The first two indicate, that your pull request *test_for_regression*, and *ready_for_merge*. The first two indicate,
is not considered to be complete. With "needs_work" the burden is on that your pull request is not considered to be complete. With
exclusively on you; while "work_in_progress" can also mean, that a "needs_work" the burden is on exclusively on you; while
LAMMPS developer may want to add changes. Please watch the comments "work_in_progress" can also mean, that a LAMMPS developer may want to
to the pull requests. The two "test" labels are used to trigger add changes. Please watch the comments to the pull requests. The two
extended tests before the code is merged. This is sometimes done by "test" labels are used to trigger extended tests before the code is
LAMMPS developers, if they suspect that there may be some subtle merged. This is sometimes done by LAMMPS developers, if they suspect
side effects from your changes. It is not done by default, because that there may be some subtle side effects from your changes. It is not
those tests are very time consuming. 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** **Reviews**
As of Summer 2018, a pull request needs at least 1 approving review As of Fall 2021, a pull request needs to pass all automatic tests and at
from a LAMMPS developer with write access to the repository. least 1 approving review from a LAMMPS developer with write access to
In case your changes touch code that certain developers are associated the repository before it is eligible for merging. In case your changes
with, they are auto-requested by the GitHub software. Those associations touch code that certain developers are associated with, they are
are set in the file auto-requested by the GitHub software. Those associations are set in
`.github/CODEOWNERS <https://github.com/lammps/lammps/blob/master/.github/CODEOWNERS>`_ the file `.github/CODEOWNERS
Thus if you want to be automatically notified to review when anybody <https://github.com/lammps/lammps/blob/develop/.github/CODEOWNERS>`_ Thus
changes files or packages, that you have contributed to LAMMPS, you can if you want to be automatically notified to review when anybody changes
add suitable patterns to that file, or a LAMMPS developer may add you. 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, Otherwise, you can also manually request reviews from specific developers,
or LAMMPS developers - in their assessment of your pull request - may 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 After the review, the developer can choose to implement changes directly
or suggest them to you. or suggest them to you.
* Case c) means that the pull request has been assigned to the developer * 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: 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 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, 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. 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 file a pull request in **your** forked GitHub repository to include
branch, that you have submitted as a pull request yourself. In that changes in the branch, that you have submitted as a pull request
case, you can choose to merge their changes back into your branch, yourself. In that case, you can choose to merge their changes back into
possibly make additional changes or corrections and proceed from there. your branch, possibly make additional changes or corrections and proceed
It looks something like this: from there. It looks something like this:
.. image:: JPG/tutorial_reverse_pull_request.png .. image:: JPG/tutorial_reverse_pull_request.png
:align: center :align: center
@ -419,7 +441,7 @@ This merge also shows up on the lammps GitHub page:
**After a merge** **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 .. image:: JPG/tutorial_merged.png
:align: center :align: center
@ -433,8 +455,8 @@ branch!
.. code-block:: bash .. code-block:: bash
$ git checkout master $ git checkout develop
$ git pull master $ git pull https://github.com/lammps/lammps develop
$ git branch -d github-tutorial-update $ git branch -d github-tutorial-update
If you do not pull first, it is not really a problem but git will warn 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 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 know your branch just got merged into LAMMPS upstream. If you
first delete and then pull, everything should still be fine. 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 Finally, if you delete the branch locally, you might want to push this
to your remote(s) as well: to your remote(s) as well:
@ -453,14 +476,14 @@ to your remote(s) as well:
**Recent changes in the workflow** **Recent changes in the workflow**
Some changes to the workflow are not captured in this tutorial. For Some changes to the workflow are not captured in this tutorial. For
example, in addition to the master branch, to which all new features example, in addition to the *develop* branch, to which all new features
should be submitted, there is now also an "unstable" and a "stable" should be submitted, there is also a *release* and a *stable* branch;
branch; these have the same content as "master", but are only updated these have the same content as *develop*, but are only updated after a
after a patch release or stable release was made. patch release or stable release was made. Furthermore, the naming of
Furthermore, the naming of the patches now follow the pattern the patches now follow the pattern "patch_<Day><Month><Year>" to
"patch_<Day><Month><Year>" to simplify comparisons between releases. simplify comparisons between releases. Finally, all patches and
Finally, all patches and submissions are subject to automatic testing submissions are subject to automatic testing and code checks to make
and code checks to make sure they at the very least compile. sure they at the very least compile.
A discussion of the LAMMPS developer GitHub workflow can be found in the file 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
doc/src/Howto_thermostat.rst
View File

@ -2,8 +2,8 @@ Thermostats
=========== ===========
Thermostatting means controlling the temperature of particles in an MD Thermostatting means controlling the temperature of particles in an MD
simulation. :doc:`Barostatting <Howto_barostat>` means controlling the simulation. :doc:`Barostatting <Howto_barostat>` means controlling
pressure. Since the pressure includes a kinetic component due to the pressure. Since the pressure includes a kinetic component due to
particle velocities, both these operations require calculation of the particle velocities, both these operations require calculation of the
temperature. Typically a target temperature (T) and/or pressure (P) temperature. Typically a target temperature (T) and/or pressure (P)
is specified by the user, and the thermostat or barostat attempts to 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:`pair_style dpd/tstat <pair_dpd>`
:doc:`Fix nvt <fix_nh>` only thermostats the translational velocity of :doc:`Fix nvt <fix_nh>` only thermostats the translational velocity of
particles. :doc:`Fix nvt/sllod <fix_nvt_sllod>` also does this, except particles. :doc:`Fix nvt/sllod <fix_nvt_sllod>` also does this,
that it subtracts out a velocity bias due to a deforming box and except that it subtracts out a velocity bias due to a deforming box
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 and integrates the SLLOD equations of motion. See the :doc:`Howto
velocities but also rotational velocities for spherical and aspherical nemd <Howto_nemd>` page for further details. :doc:`Fix nvt/sphere
particles. <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:: .. note::
@ -40,25 +42,31 @@ particles.
e.g. molecular systems. The latter can be tricky to do correctly. e.g. molecular systems. The latter can be tricky to do correctly.
DPD thermostatting alters pairwise interactions in a manner analogous 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 Any of the thermostatting fixes can be instructed to use custom
computes that remove bias which has two effects: first, the current temperature computes that remove bias which has two effects: first,
calculated temperature, which is compared to the requested target temperature, the current calculated temperature, which is compared to the requested
is calculated with the velocity bias removed; second, the thermostat adjusts target temperature, is calculated with the velocity bias removed;
only the thermal temperature component of the particle's velocities, which are second, the thermostat adjusts only the thermal temperature component
the velocities with the bias removed. The removed bias is then added back of the particle's velocities, which are the velocities with the bias
to the adjusted velocities. See the doc pages for the individual removed. The removed bias is then added back to the adjusted
fixes and for the :doc:`fix_modify <fix_modify>` command for velocities. See the doc pages for the individual fixes and for the
instructions on how to assign a temperature compute to a :doc:`fix_modify <fix_modify>` command for instructions on how to
thermostatting fix. For example, you can apply a thermostat to only assign a temperature compute to a thermostatting fix.
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>`.
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_asphere`
* :doc:`compute_temp_body` * :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_rotate`
* :doc:`compute_temp_sphere` * :doc:`compute_temp_sphere`
.. note:: .. note::
Only the nvt fixes perform time integration, meaning they update 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/sphere <fix_nve_sphere>`
* :doc:`fix nve/asphere <fix_nve_asphere>` * :doc:`fix nve/asphere <fix_nve_asphere>`
Thermodynamic output, which can be setup via the Thermodynamic output, which can be setup via the :doc:`thermo_style
:doc:`thermo_style <thermo_style>` command, often includes temperature <thermo_style>` command, often includes temperature values. As
values. As explained on the page for the explained on the page for the :doc:`thermo_style <thermo_style>`
:doc:`thermo_style <thermo_style>` command, the default temperature is command, the default temperature is setup by the thermo command
setup by the thermo command itself. It is NOT the temperature itself. It is NOT the temperature associated with any thermostatting
associated with any thermostatting fix you have defined or with any fix you have defined or with any compute you have defined that
compute you have defined that calculates a temperature. The doc pages calculates a temperature. The doc pages for the thermostatting fixes
for the thermostatting fixes explain the ID of the temperature compute explain the ID of the temperature compute they create. Thus if you
they create. Thus if you want to view these temperatures, you need to want to view these temperatures, you need to specify them explicitly
specify them explicitly via the :doc:`thermo_style custom <thermo_style>` command. Or you can use the via the :doc:`thermo_style custom <thermo_style>` command. Or you can
:doc:`thermo_modify <thermo_modify>` command to re-define what use the :doc:`thermo_modify <thermo_modify>` command to re-define what
temperature compute is used for default thermodynamic output. temperature compute is used for default thermodynamic output.
---------- ----------

47
doc/src/Install_git.rst
View File

@ -9,7 +9,8 @@ has several advantages:
command. command.
* You can create your own development branches to add code to LAMMPS. * You can create your own development branches to add code to LAMMPS.
* You can submit your new features back to GitHub for inclusion in * 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 You must have `git <git_>`_ installed on your system to use the
commands explained below to communicate with the git servers on 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 As of October 2016, the official home of public LAMMPS development is
on GitHub. The previously advertised LAMMPS git repositories on 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 .. _git: https://git-scm.com
.. _svn: https://help.github.com/en/github/importing-your-projects-to-github/working-with-subversion-on-github .. _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 * **stable** : this branch is updated with every stable release;
* **unstable** : this branch is updated with every patch release updates are always "fast forward" merges from *develop*
* **master** : this branch continuously follows ongoing development * **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 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: create a local copy of the LAMMPS repository with a command like:
.. code-block:: bash .. 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 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 (Note that you actually download all 3 branches; you can switch
between them at any time using "git checkout <branch name>".) 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 Once the command completes, your directory will contain the same files
as if you unpacked a current LAMMPS tarball, with the exception, that as if you unpacked a current LAMMPS tarball, with the exception, that
the HTML documentation files are not included. They can be fetched the HTML documentation files are not included. They can be fetched
from the LAMMPS website by typing ``make fetch`` in the doc directory. 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 Or they can be generated from the content provided in ``doc/src`` by
typing ``make html`` from the doc directory. typing ``make html`` from the ``doc`` directory.
After initial cloning, as bug fixes and new features are added to 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 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 .. code-block:: bash
$ git checkout unstable # not needed if you always stay in this branch $ git checkout release # not needed if you always stay in this branch
$ git checkout stable # use one of these 3 checkout commands $ git checkout stable # use one of these 3 checkout commands
$ git checkout master # to choose the branch to follow $ git checkout develop # to choose the branch to follow
$ git pull $ git pull
Doing a "pull" will not change any files you have added to the LAMMPS 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>`_. 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 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`` 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. check out any other desired branch) first.
Once you have updated your local files with a ``git pull`` (or ``git Once you have updated your local files with a ``git pull`` (or ``git

2
doc/src/Intro_opensource.rst
View File

@ -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 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. 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 .. _lgpl: https://www.gnu.org/licenses/old-licenses/lgpl-2.1.html

2
doc/src/Manual_version.rst
View File

@ -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>`_. 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 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 changes have accumulated *and* the software passes a set of automated
tests, we release it in the next *patch* release, which are made every tests, we release it in the next *patch* release, which are made every
few weeks. Info on patch releases are on `this website page few weeks. Info on patch releases are on `this website page

2
doc/src/Speed.rst
View File

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

4
doc/src/accel_styles.rst
View File

@ -1,7 +1,7 @@
Styles with a *gpu*, *intel*, *kk*, *omp*, or *opt* suffix are Styles with a *gpu*, *intel*, *kk*, *omp*, or *opt* suffix are
functionally the same as the corresponding style without the suffix. functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available 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 page. The accelerated styles take the same arguments and should
produce the same results, except for round-off and precision issues. 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 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. :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. instructions on how to use the accelerated styles effectively.

18
doc/src/angle_charmm.rst
View File

@ -56,23 +56,7 @@ radian\^2.
---------- ----------
Styles with a *gpu*, *intel*, *kk*, *omp*, or *opt* suffix are .. include:: accel_styles.rst
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.
---------- ----------

23
doc/src/atom_style.rst
View File

@ -319,28 +319,9 @@ styles; see the :doc:`Modify <Modify>` doc page.
---------- ----------
Styles with a *kk* suffix are functionally the same as the .. include:: accel_styles.rst
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.
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 Restrictions
"""""""""""" """"""""""""

2
doc/src/fix.rst
View File

@ -166,6 +166,7 @@ page are followed by one or more of (g,i,k,o,t) to indicate which
accelerated styles exist. accelerated styles exist.
* :doc:`accelerate/cos <fix_accelerate_cos>` - apply cosine-shaped acceleration to atoms * :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 <fix_adapt>` - change a simulation parameter over time
* :doc:`adapt/fep <fix_adapt_fep>` - enhanced version of fix adapt * :doc:`adapt/fep <fix_adapt_fep>` - enhanced version of fix adapt
* :doc:`addforce <fix_addforce>` - add a force to each atom * :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:`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:`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:`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 <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:`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 * :doc:`move <fix_move>` - move atoms in a prescribed fashion

118
doc/src/fix_acks2_reaxff.rst Normal file
View File

@ -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
doc/src/fix_atom_swap.rst
View File

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

25
doc/src/fix_langevin.rst
View File

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

25
doc/src/fix_langevin_drude.rst
View File

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

170
doc/src/fix_mol_swap.rst Normal file
View File

@ -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
doc/src/fix_nh.rst
View File

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

30
doc/src/fix_npt_asphere.rst
View File

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

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

27
doc/src/fix_npt_cauchy.rst
View File

@ -400,19 +400,20 @@ temperature or pressure during thermodynamic output via the
compute-ID. It also means that changing attributes of *thermo_temp* compute-ID. It also means that changing attributes of *thermo_temp*
or *thermo_press* will have no effect on this fix. or *thermo_press* will have no effect on this fix.
Like other fixes that perform thermostatting, fix npt/cauchy can Like other fixes that perform thermostatting, this fix can be used
be used with :doc:`compute commands <compute>` that calculate a with :doc:`compute commands <compute>` that remove a "bias" from the
temperature after removing a "bias" from the atom velocities. atom velocities. E.g. to apply the thermostat only to atoms within a
E.g. removing the center-of-mass velocity from a group of atoms or spatial :doc:`region <region>`, or to remove the center-of-mass
only calculating temperature on the x-component of velocity or only velocity from a group of atoms, or to remove the x-component of
calculating temperature for atoms in a geometric region. This is not velocity from the calculation.
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 This is not done by default, but only if the :doc:`fix_modify
a bias term. See the doc pages for individual :doc:`compute commands <compute>` to determine which ones include a bias. In <fix_modify>` command is used to assign a temperature compute to this
this case, the thermostat works in the following manner: the current fix that includes such a bias term. See the doc pages for individual
temperature is calculated taking the bias into account, bias is :doc:`compute temp commands <compute>` to determine which ones include
removed from each atom, thermostatting is performed on the remaining a bias. In this case, the thermostat works in the following manner:
thermal degrees of freedom, and the bias is added back in. 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. *thermo_temp* or *thermo_press* will have no effect on this fix.
Like other fixes that perform thermostatting, this fix can be used Like other fixes that perform thermostatting, this fix can be used
with :doc:`compute commands <compute>` that calculate a temperature with :doc:`compute commands <compute>` that remove a "bias" from the
after removing a "bias" from the atom velocities. E.g. removing the atom velocities. E.g. to apply the thermostat only to atoms within a
center-of-mass velocity from a group of atoms or only calculating spatial :doc:`region <region>`, or to remove the center-of-mass
temperature on the x-component of velocity or only calculating velocity from a group of atoms, or to remove the x-component of
temperature for atoms in a geometric region. This is not done by velocity from the calculation.
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 This is not done by default, but only if the :doc:`fix_modify
term. See the doc pages for individual :doc:`compute commands <compute>` to determine which ones include a bias. In <fix_modify>` command is used to assign a temperature compute to this
this case, the thermostat works in the following manner: the current fix that includes such a bias term. See the doc pages for individual
temperature is calculated taking the bias into account, bias is :doc:`compute temp commands <compute>` to determine which ones include
removed from each atom, thermostatting is performed on the remaining a bias. In this case, the thermostat works in the following manner:
thermal degrees of freedom, and the bias is added back in. 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. effect on this fix.
Like other fixes that perform thermostatting, this fix can be used Like other fixes that perform thermostatting, this fix can be used
with :doc:`compute commands <compute>` that calculate a temperature with :doc:`compute commands <compute>` that remove a "bias" from the
after removing a "bias" from the atom velocities. E.g. removing the atom velocities. E.g. to apply the thermostat only to atoms within a
center-of-mass velocity from a group of atoms or only calculating spatial :doc:`region <region>`, or to remove the center-of-mass
temperature on the x-component of velocity or only calculating velocity from a group of atoms, or to remove the x-component of
temperature for atoms in a geometric region. This is not done by velocity from the calculation.
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 This is not done by default, but only if the :doc:`fix_modify
term. See the doc pages for individual :doc:`compute commands <compute>` to determine which ones include a bias. In <fix_modify>` command is used to assign a temperature compute to this
this case, the thermostat works in the following manner: the current fix that includes such a bias term. See the doc pages for individual
temperature is calculated taking the bias into account, bias is :doc:`compute temp commands <compute>` to determine which ones include
removed from each atom, thermostatting is performed on the remaining a bias. In this case, the thermostat works in the following manner:
thermal degrees of freedom, and the bias is added back in. 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. effect on this fix.
Like other fixes that perform thermostatting, this fix can be used Like other fixes that perform thermostatting, this fix can be used
with :doc:`compute commands <compute>` that calculate a temperature with :doc:`compute commands <compute>` that remove a "bias" from the
after removing a "bias" from the atom velocities. E.g. removing the atom velocities. E.g. to apply the thermostat only to atoms within a
center-of-mass velocity from a group of atoms or only calculating spatial :doc:`region <region>`, or to remove the center-of-mass
temperature on the x-component of velocity or only calculating velocity from a group of atoms, or to remove the x-component of
temperature for atoms in a geometric region. This is not done by velocity from the calculation.
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 This is not done by default, but only if the :doc:`fix_modify
term. See the doc pages for individual :doc:`compute commands <compute>` to determine which ones include a bias. In <fix_modify>` command is used to assign a temperature compute to this
this case, the thermostat works in the following manner: the current fix that includes such a bias term. See the doc pages for individual
temperature is calculated taking the bias into account, bias is :doc:`compute temp commands <compute>` to determine which ones include
removed from each atom, thermostatting is performed on the remaining a bias. In this case, the thermostat works in the following manner:
thermal degrees of freedom, and the bias is added back in. 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 This thermostat is used for a simulation box that is changing size
and/or shape, for example in a non-equilibrium MD (NEMD) simulation. 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 The size/shape change is induced by use of the :doc:`fix deform
can be thought of as having a "streaming" velocity. This <fix_deform>` command, so each point in the simulation box can be
position-dependent streaming velocity is subtracted from each atom's thought of as having a "streaming" velocity. This position-dependent
actual velocity to yield a thermal velocity which is used for streaming velocity is subtracted from each atom's actual velocity to
temperature computation and thermostatting. For example, if the box yield a thermal velocity which is used for temperature computation and
is being sheared in x, relative to y, then points at the bottom of the thermostatting. For example, if the box is being sheared in x,
box (low y) have a small x velocity, while points at the top of the relative to y, then points at the bottom of the box (low y) have a
box (hi y) have a large x velocity. These velocities do not small x velocity, while points at the top of the box (hi y) have a
contribute to the thermal "temperature" of the atom. large x velocity. These velocities do not contribute to the thermal
"temperature" of the atom.
.. note:: .. note::
@ -60,13 +61,15 @@ contribute to the thermal "temperature" of the atom.
consistent. consistent.
The SLLOD equations of motion, originally proposed by Hoover and Ladd The SLLOD equations of motion, originally proposed by Hoover and Ladd
(see :ref:`(Evans and Morriss) <Evans3>`), were proven to be equivalent to (see :ref:`(Evans and Morriss) <Evans3>`), were proven to be
Newton's equations of motion for shear flow by :ref:`(Evans and Morriss) <Evans3>`. They were later shown to generate the desired equivalent to Newton's equations of motion for shear flow by
velocity gradient and the correct production of work by stresses for :ref:`(Evans and Morriss) <Evans3>`. They were later shown to generate
all forms of homogeneous flow by :ref:`(Daivis and Todd) <Daivis>`. As the desired velocity gradient and the correct production of work by
implemented in LAMMPS, they are coupled to a Nose/Hoover chain stresses for all forms of homogeneous flow by :ref:`(Daivis and Todd)
thermostat in a velocity Verlet formulation, closely following the <Daivis>`. As implemented in LAMMPS, they are coupled to a
implementation used for the :doc:`fix nvt <fix_nh>` command. Nose/Hoover chain thermostat in a velocity Verlet formulation, closely
following the implementation used for the :doc:`fix nvt <fix_nh>`
command.
.. note:: .. note::
@ -94,27 +97,28 @@ underscore + "temp", and the group for the new compute is the same as
the fix group. the fix group.
Note that this is NOT the compute used by thermodynamic output (see Note that this is NOT the compute used by thermodynamic output (see
the :doc:`thermo_style <thermo_style>` command) with ID = *thermo_temp*. the :doc:`thermo_style <thermo_style>` command) with ID =
This means you can change the attributes of this fix's temperature *thermo_temp*. This means you can change the attributes of this fix's
(e.g. its degrees-of-freedom) via the temperature (e.g. its degrees-of-freedom) via the :doc:`compute_modify
:doc:`compute_modify <compute_modify>` command or print this temperature <compute_modify>` command or print this temperature during
during thermodynamic output via the :doc:`thermo_style custom <thermo_style>` command using the appropriate compute-ID. thermodynamic output via the :doc:`thermo_style custom <thermo_style>`
It also means that changing attributes of *thermo_temp* will have no command using the appropriate compute-ID. It also means that changing
effect on this fix. attributes of *thermo_temp* will have no effect on this fix.
Like other fixes that perform thermostatting, this fix can be used Like other fixes that perform thermostatting, this fix can be used
with :doc:`compute commands <compute>` that calculate a temperature with :doc:`compute commands <compute>` that remove a "bias" from the
after removing a "bias" from the atom velocities. E.g. removing the atom velocities. E.g. to apply the thermostat only to atoms within a
center-of-mass velocity from a group of atoms or only calculating spatial :doc:`region <region>`, or to remove the center-of-mass
temperature on the x-component of velocity or only calculating velocity from a group of atoms, or to remove the x-component of
temperature for atoms in a geometric region. This is not done by velocity from the calculation.
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 This is not done by default, but only if the :doc:`fix_modify
term. See the doc pages for individual :doc:`compute commands <compute>` to determine which ones include a bias. In <fix_modify>` command is used to assign a temperature compute to this
this case, the thermostat works in the following manner: the current fix that includes such a bias term. See the doc pages for individual
temperature is calculated taking the bias into account, bias is :doc:`compute temp commands <compute>` to determine which ones include
removed from each atom, thermostatting is performed on the remaining a bias. In this case, the thermostat works in the following manner:
thermal degrees of freedom, and the bias is added back in. 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. effect on this fix.
Like other fixes that perform thermostatting, this fix can be used Like other fixes that perform thermostatting, this fix can be used
with :doc:`compute commands <compute>` that calculate a temperature with :doc:`compute commands <compute>` that remove a "bias" from the
after removing a "bias" from the atom velocities. E.g. removing the atom velocities. E.g. to apply the thermostat only to atoms within a
center-of-mass velocity from a group of atoms or only calculating spatial :doc:`region <region>`, or to remove the center-of-mass
temperature on the x-component of velocity or only calculating velocity from a group of atoms, or to remove the x-component of
temperature for atoms in a geometric region. This is not done by velocity from the calculation.
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 This is not done by default, but only if the :doc:`fix_modify
term. See the doc pages for individual :doc:`compute commands <compute>` to determine which ones include a bias. In <fix_modify>` command is used to assign a temperature compute to this
this case, the thermostat works in the following manner: the current fix that includes such a bias term. See the doc pages for individual
temperature is calculated taking the bias into account, bias is :doc:`compute temp commands <compute>` to determine which ones include
removed from each atom, thermostatting is performed on the remaining a bias. In this case, the thermostat works in the following manner:
thermal degrees of freedom, and the bias is added back in. 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 LAMMPS was built with that package. See the :doc:`Build package
<Build_package>` page for more info. <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 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 images of the same atom. Hence, it should not be used for
periodic cell dimensions less than 10 angstroms. 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 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 a unique molecule. The chemical formula of each species is given in
the first line. 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 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, format. A gzipped dump file will be about 3x smaller than the text version,
but will also take longer to write. 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 Nstart = start averaging on this timestep
*file* arg = filename *file* arg = filename
filename = name of file to output time averages to filename = name of file to output time averages to
*overwrite* arg = none = overwrite output file with only latest output
Examples 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 an index (0,1,2...) to account for situations with multiple diffraction
intensity outputs. 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 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 .. include:: accel_styles.rst
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.
The region keyword is also supported by Kokkos, but a Kokkos-enabled .. note::
region must be used. See the region :doc:`region <region>` command for
more information.
These accelerated styles are part of the r Kokkos package. They are The region keyword is supported by Kokkos, but a Kokkos-enabled
only enabled if LAMMPS was built with that package. See the :doc:`Build package <Build_package>` page for more info. region must be used. See the region :doc:`region <region>` command for
more information.
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.
---------- ----------

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. effect on this fix.
Like other fixes that perform thermostatting, this fix can be used Like other fixes that perform thermostatting, this fix can be used
with :doc:`compute commands <compute>` that calculate a temperature with :doc:`compute commands <compute>` that remove a "bias" from the
after removing a "bias" from the atom velocities. E.g. removing the atom velocities. E.g. to apply the thermostat only to atoms within a
center-of-mass velocity from a group of atoms or only calculating spatial :doc:`region <region>`, or to remove the center-of-mass
temperature on the x-component of velocity or only calculating velocity from a group of atoms, or to remove the x-component of
temperature for atoms in a geometric region. This is not done by velocity from the calculation.
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 This is not done by default, but only if the :doc:`fix_modify
term. See the doc pages for individual :doc:`compute commands <compute>` to determine which ones include a bias. In <fix_modify>` command is used to assign a temperature compute to this
this case, the thermostat works in the following manner: the current fix that includes such a bias term. See the doc pages for individual
temperature is calculated taking the bias into account, bias is :doc:`compute temp commands <compute>` to determine which ones include
removed from each atom, thermostatting is performed on the remaining a bias. In this case, the thermostat works in the following manner:
thermal degrees of freedom, and the bias is added back in. 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 It also means that changing attributes of *thermo_temp* will have no
effect on this fix. effect on this fix.
Like other fixes that perform thermostatting, these fixes can be used Like other fixes that perform thermostatting, this fix can be used
with :doc:`compute commands <compute>` that calculate a temperature with :doc:`compute commands <compute>` that remove a "bias" from the
after removing a "bias" from the atom velocities. E.g. removing the atom velocities. E.g. to apply the thermostat only to atoms within a
center-of-mass velocity from a group of atoms or only calculating spatial :doc:`region <region>`, or to remove the center-of-mass
temperature on the x-component of velocity or only calculating velocity from a group of atoms, or to remove the x-component of
temperature for atoms in a geometric region. This is not done by velocity from the calculation.
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 This is not done by default, but only if the :doc:`fix_modify
term. See the doc pages for individual :doc:`compute commands <compute>` to determine which ones include a bias. In <fix_modify>` command is used to assign a temperature compute to this
this case, the thermostat works in the following manner: the current fix that includes such a bias term. See the doc pages for individual
temperature is calculated taking the bias into account, bias is :doc:`compute temp commands <compute>` to determine which ones include
removed from each atom, thermostatting is performed on the remaining a bias. In this case, the thermostat works in the following manner:
thermal degrees of freedom, and the bias is added back in. 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 An important feature of these thermostats is that they have an
associated effective energy that is a constant of motion. associated effective energy that is a constant of motion. The
The effective energy is the total energy (kinetic + potential) plus effective energy is the total energy (kinetic + potential) plus the
the accumulated kinetic energy changes due to the thermostat. The accumulated kinetic energy changes due to the thermostat. The latter
latter quantity is the global scalar computed by these fixes. This quantity is the global scalar computed by these fixes. This feature is
feature is useful to check the integration of the equations of motion useful to check the integration of the equations of motion against
against discretization errors. In other words, the conservation of discretization errors. In other words, the conservation of the
the effective energy can be used to choose an appropriate integration effective energy can be used to choose an appropriate integration
:doc:`timestep <timestep>`. This is similar to the usual paradigm of :doc:`timestep <timestep>`. This is similar to the usual paradigm of
checking the conservation of the total energy in the microcanonical checking the conservation of the total energy in the microcanonical
ensemble. 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. attributes of *thermo_temp* will have no effect on this fix.
Like other fixes that perform thermostatting, this fix can be used Like other fixes that perform thermostatting, this fix can be used
with :doc:`compute commands <compute>` that calculate a temperature with :doc:`compute commands <compute>` that remove a "bias" from the
after removing a "bias" from the atom velocities. E.g. removing the atom velocities. E.g. to apply the thermostat only to atoms within a
center-of-mass velocity from a group of atoms or only calculating spatial :doc:`region <region>`, or to remove the center-of-mass
temperature on the x-component of velocity or only calculating velocity from a group of atoms, or to remove the x-component of
temperature for atoms in a geometric region. This is not done by velocity from the calculation.
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 This is not done by default, but only if the :doc:`fix_modify
bias term. See the doc pages for individual :doc:`compute commands <fix_modify>` command is used to assign a temperature compute to this
<compute>` to determine which ones include a bias. In this case, the fix that includes such a bias term. See the doc pages for individual
thermostat works in the following manner: the current temperature is :doc:`compute temp commands <compute>` to determine which ones include
calculated taking the bias into account, bias is removed from each a bias. In this case, the thermostat works in the following manner:
atom, thermostatting is performed on the remaining thermal degrees of bias is removed from each atom, thermostatting is performed on the
freedom, and the bias is added back in. 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 Like other fixes that perform thermostatting, this fix can be used
be used with :doc:`compute commands <compute>` that calculate a with :doc:`compute commands <compute>` that remove a "bias" from the
temperature after removing a "bias" from the atom velocities. atom velocities. E.g. to apply the thermostat only to atoms within a
This is not done by default, but only if the :doc:`fix_modify <fix_modify>` command spatial :doc:`region <region>`, or to remove the center-of-mass
is used to assign a temperature compute to this fix that includes such velocity from a group of atoms, or to remove the x-component of
a bias term. See the doc pages for individual :doc:`compute commands <compute>` to determine which ones include a bias. In velocity from the calculation.
this case, the thermostat works in the following manner: the current
temperature is calculated taking the bias into account, bias is This is not done by default, but only if the :doc:`fix_modify
removed from each atom, thermostatting is performed on the remaining <fix_modify>` command is used to assign a temperature compute to this
thermal DOF, and the bias is added back in. 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:: .. note::
However, not all temperature compute commands are valid to be used with these fixes. However, not all temperature compute commands are valid to be used
Precisely, only temperature compute that does not modify the DOF of the group can be used. with these fixes. Precisely, only temperature compute that does
E.g. :doc:`compute temp/ramp <compute_temp_ramp>` and :doc:`compute viscosity/cos <compute_viscosity_cos>` not modify the DOF of the group can be used. E.g. :doc:`compute
compute the kinetic energy after remove a velocity gradient without affecting the DOF of the group, temp/ramp <compute_temp_ramp>` and :doc:`compute viscosity/cos
then they can be invoked in this way. <compute_viscosity_cos>` compute the kinetic energy after remove a
In contrast, :doc:`compute temp/partial <compute_temp_partial>` may remove the DOF at one or more dimensions, velocity gradient without affecting the DOF of the group, then they
therefore it cannot be used with these fixes. 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.
---------- ----------

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 .. include:: accel_styles.rst
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.
---------- ----------

39
doc/src/kspace_style.rst
View File

@ -414,33 +414,26 @@ relative RMS error.
---------- ----------
Styles with a *gpu*, *intel*, *kk*, *omp*, or *opt* suffix are .. include:: accel_styles.rst
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.
More specifically, the *pppm/gpu* style performs charge assignment and .. note::
force interpolation calculations on the GPU. These processes are
performed either in single or double precision, depending on whether
the -DFFT_SINGLE setting was specified in your low-level Makefile, as
discussed above. The FFTs themselves are still calculated on the CPU.
If *pppm/gpu* is used with a GPU-enabled pair style, part of the PPPM
calculation can be performed concurrently on the GPU while other
calculations for non-bonded and bonded force calculation are performed
on the CPU.
The *pppm/kk* style performs charge assignment and force interpolation For the GPU package, the *pppm/gpu* style performs charge assignment
calculations, along with the FFTs themselves, on the GPU or (optionally) threaded and force interpolation calculations on the GPU. These processes
on the CPU when using OpenMP and FFTW3. are performed either in single or double precision, depending on
whether the -DFFT_SINGLE setting was specified in your low-level
Makefile, as discussed above. The FFTs themselves are still
calculated on the CPU. If *pppm/gpu* is used with a GPU-enabled
pair style, part of the PPPM calculation can be performed
concurrently on the GPU while other calculations for non-bonded and
bonded force calculation are performed on the CPU.
These accelerated styles are part of the GPU, INTEL, KOKKOS, .. note::
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.
See the :doc:`Speed packages <Speed_packages>` page for more For the KOKKOS package, the *pppm/kk* style performs charge
instructions on how to use the accelerated styles effectively. assignment and force interpolation calculations, along with the FFTs
themselves, on the GPU or (optionally) threaded on the CPU when
using OpenMP and FFTW3.
---------- ----------

2
doc/src/package.rst
View File

@ -166,7 +166,7 @@ intel", or "package omp" command with default settings.
set, either to default values or to specified settings. I.e. settings set, either to default values or to specified settings. I.e. settings
from previous invocations do not persist across multiple invocations. from previous invocations do not persist across multiple invocations.
See the :doc:`Speed packages <Speed_packages>` page for more details See the :doc:`Accelerator packages <Speed_packages>` page for more details
about using the various accelerator packages for speeding up LAMMPS about using the various accelerator packages for speeding up LAMMPS
simulations. simulations.

16
doc/src/pair_agni.rst
View File

@ -67,21 +67,7 @@ and input files are provided in the examples/PACKAGES/agni directory.
---------- ----------
Styles with *omp* suffix is functionally the same as the corresponding .. include:: accel_styles.rst
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 style takes
the same arguments and should produce the same results, except for
round-off and precision issues.
The accelerated style is part of the OPENMP. 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 style 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.
---------- ----------

33
doc/src/pair_hybrid.rst
View File

@ -383,30 +383,19 @@ coefficients to 0.0.
---------- ----------
Styles with a *gpu*, *intel*, *kk*, *omp*, or *opt* suffix are .. include:: accel_styles.rst
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. Pair style *hybrid/scaled* does (currently) not support the
*gpu*, *omp*, *kk*, or *intel* suffix.
Since the *hybrid*, *hybrid/overlay*, *hybrid/scaled* styles delegate .. note::
computation to the individual sub-styles, the suffix versions of the
*hybrid* and *hybrid/overlay* styles are used to propagate the
corresponding suffix to all sub-styles, if those versions
exist. Otherwise the non-accelerated version will be used.
The individual accelerated sub-styles are part of the GPU, KOKKOS, Since the *hybrid*, *hybrid/overlay*, *hybrid/scaled* styles
INTEL, OPENMP, and OPT packages, respectively. They are only delegate computation to the individual sub-styles, the suffix
enabled if LAMMPS was built with those packages. See the :doc:`Build versions of the *hybrid* and *hybrid/overlay* styles are used to
package <Build_package>` page for more info. propagate the corresponding suffix to all sub-styles, if those
versions exist. Otherwise the non-accelerated version will be used.
You can specify the accelerated styles explicitly in your input script The individual accelerated sub-styles are part of the GPU, KOKKOS,
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 INTEL, OPENMP, and OPT packages, respectively. They are only
:doc:`suffix <suffix>` command in your input script. enabled if LAMMPS was built with those packages. See the
:doc:`Build package <Build_package>` page for more info.
See the :doc:`Speed packages <Speed_packages>` page for more
instructions on how to use the accelerated styles effectively.
---------- ----------

11
doc/src/pair_reaxff.rst
View File

@ -20,7 +20,7 @@ Syntax
.. parsed-literal:: .. parsed-literal::
keyword = *checkqeq* or *lgvdw* or *safezone* or *mincap* or *minhbonds* keyword = *checkqeq* or *lgvdw* or *safezone* or *mincap* or *minhbonds*
*checkqeq* value = *yes* or *no* = whether or not to require qeq/reaxff fix *checkqeq* value = *yes* or *no* = whether or not to require qeq/reaxff or acks2/reaxff fix
*enobonds* value = *yes* or *no* = whether or not to tally energy of atoms with no bonds *enobonds* value = *yes* or *no* = whether or not to tally energy of atoms with no bonds
*lgvdw* value = *yes* or *no* = whether or not to use a low gradient vdW correction *lgvdw* value = *yes* or *no* = whether or not to use a low gradient vdW correction
*safezone* = factor used for array allocation *safezone* = factor used for array allocation
@ -119,7 +119,8 @@ The ReaxFF parameter files provided were created using a charge
equilibration (QEq) model for handling the electrostatic interactions. equilibration (QEq) model for handling the electrostatic interactions.
Therefore, by default, LAMMPS requires that either the Therefore, by default, LAMMPS requires that either the
:doc:`fix qeq/reaxff <fix_qeq_reaxff>` or the :doc:`fix qeq/reaxff <fix_qeq_reaxff>` or the
:doc:`fix qeq/shielded <fix_qeq>` command be used with :doc:`fix qeq/shielded <fix_qeq>` or :doc:`fix acks2/reaxff <fix_acks2_reaxff>`
command be used with
*pair_style reaxff* when simulating a ReaxFF model, to equilibrate *pair_style reaxff* when simulating a ReaxFF model, to equilibrate
the charges each timestep. the charges each timestep.
@ -128,7 +129,8 @@ for the QEq fixes, allowing a simulation to be run without charge
equilibration. In this case, the static charges you assign to each equilibration. In this case, the static charges you assign to each
atom will be used for computing the electrostatic interactions in atom will be used for computing the electrostatic interactions in
the system. See the :doc:`fix qeq/reaxff <fix_qeq_reaxff>` or the system. See the :doc:`fix qeq/reaxff <fix_qeq_reaxff>` or
:doc:`fix qeq/shielded <fix_qeq>` command documentation for more details. :doc:`fix qeq/shielded <fix_qeq>` or :doc:`fix acks2/reaxff <fix_acks2_reaxff>`
command documentation for more details.
Using the optional keyword *lgvdw* with the value *yes* turns on the Using the optional keyword *lgvdw* with the value *yes* turns on the
low-gradient correction of ReaxFF for long-range London Dispersion, low-gradient correction of ReaxFF for long-range London Dispersion,
@ -352,7 +354,8 @@ Related commands
"""""""""""""""" """"""""""""""""
:doc:`pair_coeff <pair_coeff>`, :doc:`fix qeq/reaxff <fix_qeq_reaxff>`, :doc:`pair_coeff <pair_coeff>`, :doc:`fix qeq/reaxff <fix_qeq_reaxff>`,
:doc:`fix reaxff/bonds <fix_reaxff_bonds>`, :doc:`fix reaxff/species <fix_reaxff_species>` :doc:`fix acks2/reaxff <fix_acks2_reaxff>`, :doc:`fix reaxff/bonds <fix_reaxff_bonds>`,
:doc:`fix reaxff/species <fix_reaxff_species>`
Default Default
""""""" """""""

26
doc/src/pair_sw.rst
View File

@ -159,28 +159,14 @@ taken from the ij and ik pairs (:math:`\sigma`, *a*, :math:`\gamma`)
---------- ----------
Styles with a *gpu*, *intel*, *kk*, *omp*, or *opt* suffix are .. include:: accel_styles.rst
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, .. note::
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 When using the INTEL package with this style, there is an additional
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 5 to 10 percent performance improvement when the Stillinger-Weber
:doc:`suffix <suffix>` command in your input script. parameters p and q are set to 4 and 0 respectively. These
parameters are common for modeling silicon and water.
When using the INTEL package with this style, there is an
additional 5 to 10 percent performance improvement when the
Stillinger-Weber parameters p and q are set to 4 and 0 respectively.
These parameters are common for modeling silicon and water.
See the :doc:`Speed packages <Speed_packages>` page for more
instructions on how to use the accelerated styles effectively.
---------- ----------

6
doc/src/plugin.rst
View File

@ -65,10 +65,8 @@ only enabled if LAMMPS was built with that package.
See the :doc:`Build package <Build_package>` page for See the :doc:`Build package <Build_package>` page for
more info. Plugins are not available on Windows. more info. Plugins are not available on Windows.
For the loading of plugins to work the LAMMPS library must be If plugins access functions or classes from a package, LAMMPS must
:ref:`compiled as a shared library <library>`. If plugins have been compiled with that package included.
access functions or classes from a package, LAMMPS must have
been compiled with that package included.
Plugins are dependent on the LAMMPS binary interface (ABI) Plugins are dependent on the LAMMPS binary interface (ABI)
and particularly the MPI library used. So they are not guaranteed and particularly the MPI library used. So they are not guaranteed

23
doc/src/region.rst
View File

@ -371,26 +371,13 @@ sub-regions can be defined with the *open* keyword.
---------- ----------
Styles with a *gpu*, *intel*, *kk*, *omp*, or *opt* suffix are .. include:: accel_styles.rst
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.
The code using the region (such as a fix or compute) must also be supported .. note::
by Kokkos or no acceleration will occur. Currently, only *block* style
regions are supported by Kokkos.
These accelerated styles are part of the Kokkos package. They are Currently, only *block* style regions are supported by Kokkos. The
only enabled if LAMMPS was built with that package. See the :doc:`Build package <Build_package>` page for more info. code using the region (such as a fix or compute) must also be
supported by Kokkos or no acceleration will occur.
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.
---------- ----------

22
doc/src/run_style.rst
View File

@ -125,12 +125,13 @@ screen.0 by default; see the :doc:`-plog and -pscreen command-line switches <Run
for the second partition will not contain thermodynamic output beyond the for the second partition will not contain thermodynamic output beyond the
first timestep of the run. first timestep of the run.
See the :doc:`Speed packages <Speed_packages>` page for performance See the :doc:`Accelerator packages <Speed_packages>` page for
details of the speed-up offered by the *verlet/split* style. One performance details of the speed-up offered by the *verlet/split*
important performance consideration is the assignment of logical style. One important performance consideration is the assignment of
processors in the 2 partitions to the physical cores of a parallel logical processors in the 2 partitions to the physical cores of a
machine. The :doc:`processors <processors>` command has options to parallel machine. The :doc:`processors <processors>` command has
support this, and strategies are discussed in :doc:`Section 5 <Speed>` of the manual. options to support this, and strategies are discussed in :doc:`Section
5 <Speed>` of the manual.
---------- ----------
@ -295,10 +296,10 @@ except for round-off and precision issues.
You can specify *respa/omp* explicitly in your input script, or you You can specify *respa/omp* explicitly in your input script, or you
can use the :doc:`-suffix command-line switch <Run_options>` when 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 invoke LAMMPS, or you can use the :doc:`suffix <suffix>` command in
input script. 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. instructions on how to use the accelerated styles effectively.
---------- ----------
@ -308,7 +309,8 @@ Restrictions
The *verlet/split* style can only be used if LAMMPS was built with the The *verlet/split* style can only be used if LAMMPS was built with the
REPLICA package. Correspondingly the *respa/omp* style is available REPLICA package. Correspondingly the *respa/omp* style is available
only if the OPENMP package was included. See the :doc:`Build package <Build_package>` page for more info. only if the OPENMP package was included. See the :doc:`Build package
<Build_package>` page for more info.
Whenever using rRESPA, the user should experiment with trade-offs in Whenever using rRESPA, the user should experiment with trade-offs in
speed and accuracy for their system, and verify that they are speed and accuracy for their system, and verify that they are

4
doc/utils/check-styles.py
View File

@ -254,7 +254,7 @@ for command_type, entries in index.items():
print("Total number of style index entries:", total_index) print("Total number of style index entries:", total_index)
skip_fix = ('python', 'NEIGH_HISTORY/omp','qeq/reax','reax/c/bonds','reax/c/species') skip_fix = ('python', 'NEIGH_HISTORY/omp','acks2/reax','qeq/reax','reax/c/bonds','reax/c/species')
skip_pair = ('meam/c','lj/sf','reax/c') skip_pair = ('meam/c','lj/sf','reax/c')
counter = 0 counter = 0
@ -282,7 +282,7 @@ if counter:
counter = 0 counter = 0
counter += check_style_index("compute", compute, index["compute"]) counter += check_style_index("compute", compute, index["compute"])
counter += check_style_index("fix", fix, index["fix"], skip=['python','qeq/reax','reax/c/bonds','reax/c/species']) counter += check_style_index("fix", fix, index["fix"], skip=['python','acks2/reax','qeq/reax','reax/c/bonds','reax/c/species'])
counter += check_style_index("angle_style", angle, index["angle_style"]) counter += check_style_index("angle_style", angle, index["angle_style"])
counter += check_style_index("bond_style", bond, index["bond_style"]) counter += check_style_index("bond_style", bond, index["bond_style"])
counter += check_style_index("dihedral_style", dihedral, index["dihedral_style"]) counter += check_style_index("dihedral_style", dihedral, index["dihedral_style"])

12
doc/utils/requirements.txt
View File

@ -1,7 +1,7 @@
Sphinx==4.0.3 Sphinx
sphinxcontrib-spelling==7.2.1 sphinxcontrib-spelling
git+git://github.com/akohlmey/sphinx-fortran@parallel-read git+git://github.com/akohlmey/sphinx-fortran@parallel-read
sphinx_tabs==3.2.0 sphinx_tabs
breathe==4.31.0 breathe
Pygments==2.10.0 Pygments
six==1.16.0 six

14
doc/utils/sphinx-config/false_positives.txt
View File

@ -19,6 +19,7 @@ accuracies
ach ach
ackland ackland
Ackland Ackland
acks
acolor acolor
acos acos
Acta Acta
@ -77,6 +78,7 @@ allocators
allosws allosws
AlO AlO
Alonso Alonso
Alperen
alphak alphak
alphashrink alphashrink
amap amap
@ -685,6 +687,7 @@ diagonalized
diagonalizers diagonalizers
diagonalizing diagonalizing
Diallo Diallo
diblock
Dickel Dickel
diel diel
differentiable differentiable
@ -1135,6 +1138,7 @@ Germann
Germano Germano
gerolf gerolf
Gerolf Gerolf
getrusage
Gershgorin Gershgorin
getter getter
gettimeofday gettimeofday
@ -1222,6 +1226,7 @@ Guo
gw gw
gyromagnetic gyromagnetic
gz gz
gzip
gzipped gzipped
Haak Haak
Hafskjold Hafskjold
@ -1252,6 +1257,7 @@ hbond
hcp hcp
hdnnp hdnnp
HDNNP HDNNP
Hearn
heatconduction heatconduction
Hebbeker Hebbeker
Hebenstreit Hebenstreit
@ -1278,6 +1284,7 @@ hgrid
hhmrr hhmrr
Hibbs Hibbs
Higdon Higdon
hiID
Hijazi Hijazi
Hilger Hilger
Hinestrosa Hinestrosa
@ -1774,6 +1781,7 @@ Loewen
logfile logfile
logfreq logfreq
logicals logicals
loID
Lomdahl Lomdahl
Lond Lond
lookup lookup
@ -1809,6 +1817,7 @@ lyon
Lysogorskiy Lysogorskiy
Lyulin Lyulin
lz lz
lzma
Maaravi Maaravi
MACHDYN MACHDYN
machdyn machdyn
@ -2762,6 +2771,7 @@ REAXFF
ReaxFF ReaxFF
reaxff reaxff
rebo rebo
recurse
recursing recursing
Ree Ree
refactored refactored
@ -3076,6 +3086,7 @@ Spearot
specular specular
spellcheck spellcheck
Spellmeyer Spellmeyer
Speybroeck
sph sph
SPH SPH
Spickermann Spickermann
@ -3441,6 +3452,7 @@ usec
uSemiParallel uSemiParallel
userguide userguide
username username
usleep
usr usr
util util
utils utils
@ -3488,6 +3500,7 @@ Verlag
verlet verlet
Verlet Verlet
versa versa
Verstraelen
ves ves
vflag vflag
vhi vhi
@ -3554,6 +3567,7 @@ vzcm
vzi vzi
Waals Waals
Wadley Wadley
Waroquier
wallstyle wallstyle
walltime walltime
Waltham Waltham

0
examples/MC/README → examples/MC-LOOP/README
View File

0
examples/MC/in.mc → examples/MC-LOOP/in.mc
View File

0
examples/MC/log.13Oct16.mc.g++.1 → examples/MC-LOOP/log.13Oct16.mc.g++.1
View File

4
examples/README
View File

@ -75,7 +75,6 @@ eim: NaCl using the EIM potential
ellipse: ellipsoidal particles in spherical solvent, 2d system ellipse: ellipsoidal particles in spherical solvent, 2d system
flow: Couette and Poiseuille flow in a 2d channel flow: Couette and Poiseuille flow in a 2d channel
friction: frictional contact of spherical asperities between 2d surfaces friction: frictional contact of spherical asperities between 2d surfaces
gcmc: Grand Canonical MC with fix gcmc, Widom insertion with fix widom
gjf: use of fix langevin Gronbech-Jensen/Farago option gjf: use of fix langevin Gronbech-Jensen/Farago option
granregion: use of fix wall/region/gran as boundary on granular particles granregion: use of fix wall/region/gran as boundary on granular particles
hugoniostat: Hugoniostat shock dynamics hugoniostat: Hugoniostat shock dynamics
@ -83,6 +82,7 @@ hyper: global and local hyperdynamics of diffusion on Pt surface
indent: spherical indenter into a 2d solid indent: spherical indenter into a 2d solid
kim: use of potentials in Knowledge Base for Interatomic Models (KIM) kim: use of potentials in Knowledge Base for Interatomic Models (KIM)
latte: use of LATTE density-functional tight-binding quantum code latte: use of LATTE density-functional tight-binding quantum code
mc: MC package models: GCMC, Widom, fix mol/swap
meam: MEAM test for SiC and shear (same as shear examples) meam: MEAM test for SiC and shear (same as shear examples)
melt: rapid melt of 3d LJ system melt: rapid melt of 3d LJ system
message: client/server coupling of 2 codes message: client/server coupling of 2 codes
@ -167,7 +167,7 @@ The KAPPA directory has example scripts for computing the thermal
conductivity (kappa) of a LJ liquid using 5 different methods. See conductivity (kappa) of a LJ liquid using 5 different methods. See
the KAPPA/README file for more info. the KAPPA/README file for more info.
The MC directory has an example script for using LAMMPS as an The MC-LOOP directory has an example script for using LAMMPS as an
energy-evaluation engine in a iterative Monte Carlo energy-relaxation energy-evaluation engine in a iterative Monte Carlo energy-relaxation
loop. loop.

0
examples/gcmc/CO2.txt → examples/mc/CO2.txt
View File

0
examples/gcmc/H2O.txt → examples/mc/H2O.txt
View File

11733
examples/mc/data.bead Normal file
View File

File diff suppressed because it is too large Load Diff

0
examples/gcmc/data.spce → examples/mc/data.spce
View File

0
examples/gcmc/data.widom.lj → examples/mc/data.widom.lj
View File

0
examples/gcmc/in.gcmc.co2 → examples/mc/in.gcmc.co2
View File

0
examples/gcmc/in.gcmc.h2o → examples/mc/in.gcmc.h2o
View File

0
examples/gcmc/in.gcmc.lj → examples/mc/in.gcmc.lj
View File

44
examples/mc/in.mixed Normal file
View File

@ -0,0 +1,44 @@
# test script for fix mol/swap
# initial system is 50/50 chains of type 1 and type 2
# b/c epsilon12 is set to 1.02 (weakly same as 1/1 or 1/2) the
# system will stay in equilibrium as a mix of both chain types
# fix mol/swap helps this happen quickly
# see the last 2 columns of thermo output for counts of 2 chain types
units lj
atom_style angle
neighbor 0.36 bin
neigh_modify delay 0
pair_style lj/cut 1.1224620483
bond_style fene
angle_style cosine
special_bonds lj 0.0 1.0 1.0
read_data data.bead
pair_coeff * * 1.0 1.0 1.1224620483
pair_coeff 1 2 1.02 1.0 1.1224620483
bond_coeff 1 30.0 1.5 1.0 1.0
angle_coeff 1 1.500
pair_modify shift yes
variable vt1 atom type==1
variable vt2 atom type==2
group g1 dynamic all var vt1 every 100
group g2 dynamic all var vt2 every 100
variable count1 equal count(g1)
variable count2 equal count(g2)
timestep 0.010
fix 1 all langevin 1.0 1.0 100.0 702547
fix 2 all nve
fix 3 all mol/swap 100 1 1 2 482794 1.0
compute p all pressure thermo_temp
thermo 1000
thermo_style custom step temp etotal press f_3[1] f_3[2] v_count1 v_count2
run 50000

44
examples/mc/in.pure Normal file
View File

@ -0,0 +1,44 @@
# test script for fix mol/swap
# initial system is 50/50 chains of type 1 and type 2
# b/c epsilon12 is set to 1.1 (stronger than 1/1 or 2/2) the
# system will go to equilibrium as mostly one type or the other
# fix mol/swap helps this happen quickly
# see the last 2 columns of thermo output for counts of 2 chain types
units lj
atom_style angle
neighbor 0.36 bin
neigh_modify delay 0
pair_style lj/cut 1.1224620483
bond_style fene
angle_style cosine
special_bonds lj 0.0 1.0 1.0
read_data data.bead
pair_coeff * * 1.0 1.0 1.1224620483
pair_coeff 1 2 1.1 1.0 1.1224620483
bond_coeff 1 30.0 1.5 1.0 1.0
angle_coeff 1 1.500
pair_modify shift yes
variable vt1 atom type==1
variable vt2 atom type==2
group g1 dynamic all var vt1 every 100
group g2 dynamic all var vt2 every 100
variable count1 equal count(g1)
variable count2 equal count(g2)
timestep 0.010
fix 1 all langevin 1.0 1.0 100.0 702547
fix 2 all nve
fix 3 all mol/swap 100 1 1 2 482794 1.0
compute p all pressure thermo_temp
thermo 1000
thermo_style custom step temp etotal press f_3[1] f_3[2] v_count1 v_count2
run 50000

0
examples/gcmc/in.widom.lj → examples/mc/in.widom.lj
View File

0
examples/gcmc/in.widom.spce → examples/mc/in.widom.spce
View File

164
examples/mc/log.13Oct21.mixed.g++.4 Normal file
View File

@ -0,0 +1,164 @@
LAMMPS (29 Sep 2021)
# test script for fix mol/swap
# initial system is 50/50 chains of type 1 and type 2
# b/c epsilon12 is set to 1.02 (weakly same as 1/1 or 1/2) the
# system will stay in equilibrium as a mix of both chain types
# fix mol/swap helps this happen quickly
# see the last 2 columns of thermo output for counts of 2 chain types
units lj
atom_style angle
neighbor 0.36 bin
neigh_modify delay 0
pair_style lj/cut 1.1224620483
bond_style fene
angle_style cosine
special_bonds lj 0.0 1.0 1.0
read_data data.bead
Reading data file ...
orthogonal box = (-8.2115700 -8.2115700 -8.2115700) to (8.2115700 8.2115700 8.2115700)
1 by 2 by 2 MPI processor grid
reading atoms ...
4000 atoms
scanning bonds ...
1 = max bonds/atom
scanning angles ...
1 = max angles/atom
reading bonds ...
3900 bonds
reading angles ...
3800 angles
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 1 1
special bond factors coul: 0 0 0
2 = max # of 1-2 neighbors
2 = max # of 1-3 neighbors
4 = max # of 1-4 neighbors
6 = max # of special neighbors
special bonds CPU = 0.001 seconds
read_data CPU = 0.028 seconds
pair_coeff * * 1.0 1.0 1.1224620483
pair_coeff 1 2 1.02 1.0 1.1224620483
bond_coeff 1 30.0 1.5 1.0 1.0
angle_coeff 1 1.500
pair_modify shift yes
variable vt1 atom type==1
variable vt2 atom type==2
group g1 dynamic all var vt1 every 100
dynamic group g1 defined
group g2 dynamic all var vt2 every 100
dynamic group g2 defined
variable count1 equal count(g1)
variable count2 equal count(g2)
timestep 0.010
fix 1 all langevin 1.0 1.0 100.0 702547
fix 2 all nve
fix 3 all mol/swap 100 1 1 2 482794 1.0
compute p all pressure thermo_temp
thermo 1000
thermo_style custom step temp etotal press f_3[1] f_3[2] v_count1 v_count2
run 50000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.482462
ghost atom cutoff = 1.482462
binsize = 0.74123102, bins = 23 23 23
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
WARNING: Communication cutoff 1.4824620483 is shorter than a bond length based estimate of 1.815. This may lead to errors. (../comm.cpp:728)
Per MPI rank memory allocation (min/avg/max) = 5.313 | 5.314 | 5.314 Mbytes
Step Temp TotEng Press f_3[1] f_3[2] v_count1 v_count2
0 0 21.451627 5.079399 0 0 2000 2000
1000 0.49011138 21.59359 4.2337989 10 10 2000 2000
2000 0.55288866 21.724374 4.4596786 20 20 2080 1920
3000 0.59299724 21.844178 4.6112243 30 29 2280 1720
4000 0.64746348 21.964318 4.9463669 40 39 2280 1720
5000 0.67853936 22.053147 5.1950218 50 48 2320 1680
6000 0.70751144 22.147453 5.0636869 60 58 2240 1760
7000 0.73570064 22.233705 5.4872622 70 68 2160 1840
8000 0.7677554 22.312938 5.4283736 80 77 2360 1640
9000 0.78493237 22.383155 5.8547233 90 87 2440 1560
10000 0.80634514 22.449402 5.8785731 100 96 2400 1600
11000 0.82563194 22.475286 5.8193738 110 104 2400 1600
12000 0.81684024 22.527492 6.0323967 120 114 2320 1680
13000 0.84497155 22.567888 6.0488755 130 122 2240 1760
14000 0.85452242 22.606908 6.1983634 140 132 2080 1920
15000 0.88109242 22.654336 6.1408279 150 141 1960 2040
16000 0.88925915 22.707597 6.1560975 160 150 2000 2000
17000 0.91598439 22.762791 6.1071728 170 160 2000 2000
18000 0.92453211 22.778304 6.3330693 180 170 2240 1760
19000 0.92839551 22.797316 6.2917909 190 180 2000 2000
20000 0.93054033 22.819289 6.091701 200 189 2200 1800
21000 0.93955351 22.844135 6.5833013 210 198 2000 2000
22000 0.94454858 22.856272 6.5661753 220 207 2200 1800
23000 0.95446407 22.878735 6.5957294 230 216 2160 1840
24000 0.94748257 22.894539 6.6187447 240 226 1920 2080
25000 0.95732202 22.912292 6.4795471 250 236 1680 2320
26000 0.96970172 22.908988 6.537366 260 245 1720 2280
27000 0.96032166 22.924899 6.6238248 270 255 1960 2040
28000 0.96197769 22.9358 6.8926097 280 264 1920 2080
29000 0.98745595 22.964694 6.5839025 290 271 2040 1960
30000 0.99264869 22.947884 6.3893499 300 280 1920 2080
31000 0.96953069 22.957927 6.6616047 310 289 1800 2200
32000 0.99955117 22.963979 6.5958456 320 298 1680 2320
33000 0.97090103 22.969029 6.9087296 330 307 1800 2200
34000 0.99818457 22.988477 6.6471994 340 316 1920 2080
35000 0.9965288 22.992883 6.9691785 350 325 2040 1960
36000 0.99533174 22.983774 6.6585089 360 334 2000 2000
37000 0.98819278 22.995387 6.618802 370 344 2080 1920
38000 0.99598576 22.991892 6.7536669 380 354 2080 1920
39000 0.99312702 22.989239 6.4028165 390 364 2080 1920
40000 1.0035821 23.001944 6.9307671 400 374 1920 2080
41000 0.99914733 23.00134 6.6251677 410 383 1880 2120
42000 0.98054536 22.981781 6.5918554 420 393 1880 2120
43000 0.99413829 23.008 6.7390795 430 403 1720 2280
44000 0.98867961 23.00521 6.8505543 440 412 1600 2400
45000 0.99626811 23.019995 6.827741 450 421 1640 2360
46000 1.0186043 23.020759 6.6195562 460 430 1680 2320
47000 1.0121335 23.019271 6.6022102 470 439 1800 2200
48000 0.99883756 23.013973 6.5255522 480 448 1920 2080
49000 0.99425223 23.022708 6.609746 490 458 2240 1760
50000 0.99505489 23.012641 6.4592863 500 468 2240 1760
Loop time of 19.4175 on 4 procs for 50000 steps with 4000 atoms
Performance: 2224796.830 tau/day, 2574.996 timesteps/s
95.0% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.5467 | 2.6684 | 2.7896 | 6.3 | 13.74
Bond | 2.3037 | 2.4117 | 2.5085 | 5.3 | 12.42
Neigh | 7.3597 | 7.3633 | 7.3673 | 0.1 | 37.92
Comm | 3.0482 | 3.2694 | 3.4997 | 10.2 | 16.84
Output | 0.0014609 | 0.0017069 | 0.0021793 | 0.7 | 0.01
Modify | 2.9624 | 3.0581 | 3.1424 | 4.7 | 15.75
Other | | 0.6447 | | | 3.32
Nlocal: 1000.00 ave 1013 max 986 min
Histogram: 1 0 0 1 0 0 0 1 0 1
Nghost: 1186.25 ave 1198 max 1178 min
Histogram: 2 0 0 0 0 0 1 0 0 1
Neighs: 4927.00 ave 5028 max 4790 min
Histogram: 1 0 0 0 0 1 0 1 0 1
Total # of neighbors = 19708
Ave neighs/atom = 4.9270000
Ave special neighs/atom = 5.7000000
Neighbor list builds = 10721
Dangerous builds = 0
Total wall time: 0:00:19

164
examples/mc/log.13Oct21.pure.g++.4 Normal file
View File

@ -0,0 +1,164 @@
LAMMPS (29 Sep 2021)
# test script for fix mol/swap
# initial system is 50/50 chains of type 1 and type 2
# b/c epsilon12 is set to 1.1 (stronger than 1/1 or 2/2) the
# system will go to equilibrium as mostly one type or the other
# fix mol/swap helps this happen quickly
# see the last 2 columns of thermo output for counts of 2 chain types
units lj
atom_style angle
neighbor 0.36 bin
neigh_modify delay 0
pair_style lj/cut 1.1224620483
bond_style fene
angle_style cosine
special_bonds lj 0.0 1.0 1.0
read_data data.bead
Reading data file ...
orthogonal box = (-8.2115700 -8.2115700 -8.2115700) to (8.2115700 8.2115700 8.2115700)
1 by 2 by 2 MPI processor grid
reading atoms ...
4000 atoms
scanning bonds ...
1 = max bonds/atom
scanning angles ...
1 = max angles/atom
reading bonds ...
3900 bonds
reading angles ...
3800 angles
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 1 1
special bond factors coul: 0 0 0
2 = max # of 1-2 neighbors
2 = max # of 1-3 neighbors
4 = max # of 1-4 neighbors
6 = max # of special neighbors
special bonds CPU = 0.001 seconds
read_data CPU = 0.034 seconds
pair_coeff * * 1.0 1.0 1.1224620483
pair_coeff 1 2 1.1 1.0 1.1224620483
bond_coeff 1 30.0 1.5 1.0 1.0
angle_coeff 1 1.500
pair_modify shift yes
variable vt1 atom type==1
variable vt2 atom type==2
group g1 dynamic all var vt1 every 100
dynamic group g1 defined
group g2 dynamic all var vt2 every 100
dynamic group g2 defined
variable count1 equal count(g1)
variable count2 equal count(g2)
timestep 0.010
fix 1 all langevin 1.0 1.0 100.0 702547
fix 2 all nve
fix 3 all mol/swap 100 1 1 2 482794 1.0
compute p all pressure thermo_temp
thermo 1000
thermo_style custom step temp etotal press f_3[1] f_3[2] v_count1 v_count2
run 50000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.482462
ghost atom cutoff = 1.482462
binsize = 0.74123102, bins = 23 23 23
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
WARNING: Communication cutoff 1.4824620483 is shorter than a bond length based estimate of 1.815. This may lead to errors. (../comm.cpp:728)
Per MPI rank memory allocation (min/avg/max) = 5.313 | 5.314 | 5.314 Mbytes
Step Temp TotEng Press f_3[1] f_3[2] v_count1 v_count2
0 0 21.4699 5.230121 0 0 2000 2000
1000 0.50228459 21.61044 4.3659303 10 9 1960 2040
2000 0.55721903 21.75955 4.5695439 20 17 1960 2040
3000 0.61139287 21.892943 4.6514755 30 26 2240 1760
4000 0.65767189 22.002303 5.1854503 40 33 2280 1720
5000 0.69383416 22.110271 5.3803498 50 41 2280 1720
6000 0.72692038 22.205887 5.1756569 60 49 2280 1720
7000 0.77151336 22.306777 5.5743555 70 56 2240 1760
8000 0.78606858 22.37036 5.7745208 80 64 2560 1440
9000 0.79363653 22.420931 5.7369418 90 71 2680 1320
10000 0.82352629 22.488759 6.0238896 100 76 2720 1280
11000 0.83867685 22.534887 6.1263771 110 82 2800 1200
12000 0.85335127 22.590281 6.1499954 120 86 2800 1200
13000 0.86430985 22.632068 6.1654016 130 89 2760 1240
14000 0.88057592 22.680253 6.2162735 140 94 2800 1200
15000 0.89326694 22.719731 6.4789839 150 97 2760 1240
16000 0.90667644 22.737367 6.214481 160 101 2760 1240
17000 0.91190336 22.758572 6.2293336 170 105 2600 1400
18000 0.93182455 22.782019 6.2865382 180 111 2680 1320
19000 0.93002139 22.797048 6.5579988 190 117 2600 1400
20000 0.92396243 22.796108 6.6207461 200 122 2800 1200
21000 0.92949808 22.802813 6.3753268 210 125 2920 1080
22000 0.93415719 22.807112 6.4696121 220 130 3040 960
23000 0.9214833 22.82116 6.4146288 230 131 3080 920
24000 0.95693685 22.839738 6.4035728 240 135 2920 1080
25000 0.95421851 22.865199 6.4510751 250 138 2880 1120
26000 0.95476555 22.878082 6.4652888 260 145 3000 1000
27000 0.95773535 22.880671 6.757952 270 149 3000 1000
28000 0.95405332 22.896053 6.7425175 280 155 3080 920
29000 0.95955713 22.904144 6.6672832 290 161 3240 760
30000 0.95521498 22.886699 6.6197941 300 164 3360 640
31000 0.96431176 22.91094 6.6373887 310 168 3440 560
32000 0.96592495 22.903679 6.4245884 320 172 3520 480
33000 0.96457971 22.922681 6.6987987 330 175 3480 520
34000 0.96541889 22.92116 6.5992755 340 178 3600 400
35000 0.96892691 22.923361 6.7973298 350 178 3600 400
36000 0.97267726 22.923431 6.6577403 360 179 3640 360
37000 0.97514714 22.939979 6.4028068 370 183 3640 360
38000 0.98638599 22.952022 6.6518868 380 183 3640 360
39000 0.97864891 22.962534 6.3906837 390 184 3680 320
40000 0.9933016 22.975785 6.6819613 400 185 3720 280
41000 0.9861477 22.977271 6.6747347 410 187 3800 200
42000 0.98157369 22.963129 6.830028 420 187 3800 200
43000 0.98202452 22.966947 6.5257905 430 187 3800 200
44000 0.99540503 22.971262 6.5546513 440 187 3800 200
45000 0.98433653 22.978028 6.4316725 450 189 3800 200
46000 0.97912775 22.981328 6.9139851 460 189 3800 200
47000 0.9791927 22.981131 6.6417971 470 190 3840 160
48000 0.99601024 22.998536 6.6756953 480 191 3880 120
49000 0.99589958 22.998489 6.9262843 490 191 3880 120
50000 0.99294715 23.00399 6.6976013 500 192 3920 80
Loop time of 19.5161 on 4 procs for 50000 steps with 4000 atoms
Performance: 2213556.537 tau/day, 2561.987 timesteps/s
95.0% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.6256 | 2.7183 | 2.8265 | 5.2 | 13.93
Bond | 2.3363 | 2.4406 | 2.5197 | 4.8 | 12.51
Neigh | 7.382 | 7.3884 | 7.3936 | 0.2 | 37.86
Comm | 3.014 | 3.2136 | 3.3994 | 9.4 | 16.47
Output | 0.0014574 | 0.0017086 | 0.0020613 | 0.5 | 0.01
Modify | 3.0282 | 3.1295 | 3.2034 | 4.1 | 16.04
Other | | 0.624 | | | 3.20
Nlocal: 1000.00 ave 1011 max 993 min
Histogram: 2 0 0 0 0 1 0 0 0 1
Nghost: 1187.25 ave 1202 max 1179 min
Histogram: 2 0 0 1 0 0 0 0 0 1
Neighs: 4939.25 ave 5067 max 4850 min
Histogram: 1 0 0 2 0 0 0 0 0 1
Total # of neighbors = 19757
Ave neighs/atom = 4.9392500
Ave special neighs/atom = 5.7000000
Neighbor list builds = 10714
Dangerous builds = 0
Total wall time: 0:00:19

0
examples/gcmc/log.27Nov18.gcmc.h2o.g++.1 → examples/mc/log.27Nov18.gcmc.h2o.g++.1
View File

0
examples/gcmc/log.27Nov18.gcmc.lj.g++.1 → examples/mc/log.27Nov18.gcmc.lj.g++.1
View File

0
examples/gcmc/log.27Nov18.gcmc.lj.g++.4 → examples/mc/log.27Nov18.gcmc.lj.g++.4
View File

0
examples/gcmc/log.30Jun20.widom.lj.g++.1 → examples/mc/log.30Jun20.widom.lj.g++.1
View File

0
examples/gcmc/log.30Jun20.widom.lj.g++.4 → examples/mc/log.30Jun20.widom.lj.g++.4
View File

0
examples/gcmc/log.30Jun20.widom.spce.g++.1 → examples/mc/log.30Jun20.widom.spce.g++.1
View File

0
examples/gcmc/log.31Mar21.gcmc.co2.g++.1 → examples/mc/log.31Mar21.gcmc.co2.g++.1
View File

33
examples/plugins/CMakeLists.txt
View File

@ -14,6 +14,15 @@ endif()
project(plugins VERSION 1.0 LANGUAGES CXX) project(plugins VERSION 1.0 LANGUAGES CXX)
# 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()
# NOTE: the next line should be commented out when used outside of the LAMMPS package # NOTE: the next line should be commented out when used outside of the LAMMPS package
get_filename_component(LAMMPS_SOURCE_DIR ${PROJECT_SOURCE_DIR}/../../src ABSOLUTE) get_filename_component(LAMMPS_SOURCE_DIR ${PROJECT_SOURCE_DIR}/../../src ABSOLUTE)
set(LAMMPS_HEADER_DIR ${LAMMPS_SOURCE_DIR} CACHE PATH "Location of LAMMPS headers") set(LAMMPS_HEADER_DIR ${LAMMPS_SOURCE_DIR} CACHE PATH "Location of LAMMPS headers")
@ -32,15 +41,10 @@ set(CMAKE_CXX_STANDARD 11)
set(CMAKE_CXX_STANDARD_REQUIRED ON) set(CMAKE_CXX_STANDARD_REQUIRED ON)
# Need -restrict with Intel compilers # Need -restrict with Intel compilers
if((CMAKE_CXX_COMPILER_ID STREQUAL "Intel") OR (CMAKE_CXX_COMPILER_ID STREQUAL "IntelLLVM")) if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -restrict") set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -restrict")
endif() endif()
# bail out on windows
if(CMAKE_SYSTEM_NAME STREQUAL Windows)
message(FATAL_ERROR "LAMMPS plugins are currently not supported on Windows")
endif()
set(CMAKE_MODULE_PATH ${CMAKE_SOURCE_DIR}) set(CMAKE_MODULE_PATH ${CMAKE_SOURCE_DIR})
include(CheckIncludeFileCXX) include(CheckIncludeFileCXX)
include(LAMMPSInterfaceCXX) include(LAMMPSInterfaceCXX)
@ -62,12 +66,21 @@ add_library(zero2plugin MODULE zero2plugin.cpp pair_zero2.cpp bond_zero2.cpp
angle_zero2.cpp dihedral_zero2.cpp improper_zero2.cpp) angle_zero2.cpp dihedral_zero2.cpp improper_zero2.cpp)
target_link_libraries(zero2plugin PRIVATE lammps) target_link_libraries(zero2plugin PRIVATE lammps)
set_target_properties(morse2plugin nve2plugin helloplugin zero2plugin PROPERTIES set_target_properties(morse2plugin nve2plugin helloplugin zero2plugin PROPERTIES PREFIX "")
PREFIX ""
LINK_FLAGS "-rdynamic")
# MacOS seems to need this # MacOS seems to need this
if(CMAKE_SYSTEM_NAME STREQUAL Darwin) if(CMAKE_SYSTEM_NAME STREQUAL Darwin)
set_target_properties(morse2plugin nve2plugin helloplugin zero2plugin
PROPERTIES LINK_FLAGS "-Wl,-undefined,dynamic_lookup")
elseif(CMAKE_SYSTEM_NAME STREQUAL "Windows")
# tell CMake to export all symbols to a .dll on Windows with special case for MinGW cross-compilers
set_target_properties(morse2plugin nve2plugin helloplugin zero2plugin
PROPERTIES WINDOWS_EXPORT_ALL_SYMBOLS TRUE)
if(CMAKE_CROSSCOMPILING)
set_target_properties(morse2plugin nve2plugin helloplugin zero2plugin
PROPERTIES LINK_FLAGS "-Wl,--export-all-symbols")
endif()
else()
set_target_properties(morse2plugin nve2plugin helloplugin zero2plugin PROPERTIES set_target_properties(morse2plugin nve2plugin helloplugin zero2plugin PROPERTIES
LINK_FLAGS "-Wl,-undefined,dynamic_lookup") LINK_FLAGS "-rdynamic")
endif() endif()

Some files were not shown because too many files have changed in this diff Show More