jianmu
/
lammps
forked from lijiext/lammps
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Merge branch 'master' into pair_rann 

# Conflicts:
#	cmake/CMakeLists.txt
#	src/Makefile
This commit is contained in:
Axel Kohlmeyer 2021-05-24 12:21:04 -04:00
parent 792b411e46 a0352433c0
commit 61b1126c3d
No known key found for this signature in database
GPG Key ID: D9B44E93BF0C375A
3948 changed files with 110586 additions and 45536 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

1
.gitattributes vendored
View File

@ -1,3 +1,4 @@
.gitattributes export-ignore
.gitignore export-ignore
.github export-ignore
.lgtm.yml export-ignore

16
.github/CODEOWNERS vendored
View File

@ -13,29 +13,37 @@ lib/kim/* @ellio167
lib/mesont/* @iafoss
# whole packages
src/COMPRESS/* @akohlmey
src/COMPRESS/* @rbberger
src/GPU/* @ndtrung81
src/KOKKOS/* @stanmoore1
src/KIM/* @ellio167
src/LATTE/* @cnegre
src/MESSAGE/* @sjplimp
src/MLIAP/* @athomps
src/SNAP/* @athomps
src/SPIN/* @julient31
src/USER-BROWNIAN/* @samueljmcameron
src/USER-CGDNA/* @ohenrich
src/USER-CGSDK/* @akohlmey
src/USER-COLVARS/* @giacomofiorin
src/USER-FEP/* @agiliopadua
src/USER-HDNNP/* @singraber
src/USER-INTEL/* @wmbrownintel
src/USER-MANIFOLD/* @Pakketeretet2
src/USER-MDI/* @taylor-a-barnes
src/USER-MEAMC/* @martok
src/USER-MESONT/* @iafoss
src/USER-MOFFF/* @hheenen
src/USER-MOLFILE/* @akohlmey
src/USER-NETCDF/* @pastewka
src/USER-PACE/* @yury-lysogorskiy
src/USER-PLUMED/* @gtribello
src/USER-PHONON/* @lingtikong
src/USER-PTM/* @pmla
src/USER-OMP/* @akohlmey
src/USER-QMMM/* @akohlmey
src/USER-REAXC/* @hasanmetin
src/USER-REACTION/* @jrgissing
src/USER-SCAFACOS/* @rhalver
src/USER-TALLY/* @akohlmey
src/USER-UEF/* @danicholson
@ -47,7 +55,6 @@ src/GPU/pair_vashishta_gpu.* @andeplane
src/KOKKOS/pair_vashishta_kokkos.* @andeplane
src/MANYBODY/pair_vashishta_table.* @andeplane
src/MANYBODY/pair_atm.* @sergeylishchuk
src/USER-REACTION/fix_bond_react.* @jrgissing
src/USER-MISC/*_grem.* @dstelter92
src/USER-MISC/compute_stress_mop*.* @RomainVermorel
@ -122,6 +129,8 @@ tools/emacs/* @HaoZeke
tools/singularity/* @akohlmey @rbberger
tools/code_standard/* @rbberger
tools/valgrind/* @akohlmey
tools/swig/* @akohlmey
tools/offline/* @rbberger
# tests
unittest/* @akohlmey @rbberger
@ -130,7 +139,7 @@ unittest/* @akohlmey @rbberger
cmake/* @junghans @rbberger
cmake/Modules/Packages/USER-COLVARS.cmake @junghans @rbberger @giacomofiorin
cmake/Modules/Packages/KIM.cmake @junghans @rbberger @ellio167
cmake/presets/*.cmake @junghans @rbberger @akohlmey
cmake/presets/*.cmake @akohlmey
# python
python/* @rbberger
@ -142,6 +151,7 @@ fortran/* @akohlmey
doc/utils/*/* @rbberger
doc/Makefile @rbberger
doc/README @rbberger
examples/plugin/* @akohlmey
# for releases
src/version.h @sjplimp

6
.github/CONTRIBUTING.md vendored
View File

@ -26,11 +26,11 @@ __
## I don't want to read this whole thing I just have a question!
> **Note:** Please do not file an issue to ask a general question about LAMMPS, its features, how to use specific commands, or how perform simulations or analysis in LAMMPS. Instead post your question to the ['lammps-users' mailing list](https://lammps.sandia.gov/mail.html). You do not need to be subscribed to post to the list (but a mailing list subscription avoids having your post delayed until it is approved by a mailing list moderator). Most posts to the mailing list receive a response within less than 24 hours. Before posting to the mailing list, please read the [mailing list guidelines](https://lammps.sandia.gov/guidelines.html). Following those guidelines will help greatly to get a helpful response. Always mention which LAMMPS version you are using.
> **Note:** Please do not file an issue to ask a general question about LAMMPS, its features, how to use specific commands, or how perform simulations or analysis in LAMMPS. Instead post your question to either the ['lammps-users' mailing list](https://lammps.sandia.gov/mail.html) or the [LAMMPS Material Science Discourse forum](https://matsci.org/lammps). You do not need to be subscribed to post to the list (but a mailing list subscription avoids having your post delayed until it is approved by a mailing list moderator). Most posts to the mailing list receive a response within less than 24 hours. Before posting to the mailing list, please read the [mailing list guidelines](https://lammps.sandia.gov/guidelines.html). Following those guidelines will help greatly to get a helpful response. Always mention which LAMMPS version you are using. The LAMMPS forum was recently created as part of a larger effort to build a materials science community and have discussions not just about using LAMMPS. Thus the forum may be also used for discussions that would be off-topic for the mailing list. Those will just have to be moved to a more general category.
## How Can I Contribute?
There are several ways how you can actively contribute to the LAMMPS project: you can discuss compiling and using LAMMPS, and solving LAMMPS related problems with other LAMMPS users on the lammps-users mailing list, you can report bugs or suggest enhancements by creating issues on GitHub (or posting them to the lammps-users mailing list), and you can contribute by submitting pull requests on GitHub or e-mail your code
There are several ways how you can actively contribute to the LAMMPS project: you can discuss compiling and using LAMMPS, and solving LAMMPS related problems with other LAMMPS users on the lammps-users mailing list, you can report bugs or suggest enhancements by creating issues on GitHub (or posting them to the lammps-users mailing list or posting in the LAMMPS Materials Science Discourse forum), and you can contribute by submitting pull requests on GitHub or e-mail your code
to one of the [LAMMPS core developers](https://lammps.sandia.gov/authors.html). As you may see from the aforementioned developer page, the LAMMPS software package includes the efforts of a very large number of contributors beyond the principal authors and maintainers.
### Discussing How To Use LAMMPS
@ -42,6 +42,8 @@ Anyone can browse/search previous questions/answers in the archives. You do not
If you post a message and you are a subscriber, your message will appear immediately. If you are not a subscriber, your message will be moderated, which typically takes one business day. Either way, when someone replies the reply will usually be sent to both, your personal email address and the mailing list. When replying to people, that responded to your post to the list, please always included the mailing list in your replies (i.e. use "Reply All" and **not** "Reply"). Responses will appear on the list in a few minutes, but it can take a few hours for postings and replies to show up in the SourceForge archive. Sending replies also to the mailing list is important, so that responses are archived and people with a similar issue can search for possible solutions in the mailing list archive.
The LAMMPS Materials Science Discourse forum was created recently to facilitate discussion not just about LAMMPS and as part of a larger effort towards building a materials science community. The forum contains a read-only sub-category with the continually updated mailing list archive, so you won't miss anything by joining only the forum and not the mailing list.
### Reporting Bugs
While developers writing code for LAMMPS are careful to test their code, LAMMPS is such a large and complex software, that it is impossible to test for all combinations of features under all normal and not so normal circumstances. Thus bugs do happen, and if you suspect, that you have encountered one, please try to document it and report it as an [Issue](https://github.com/lammps/lammps/issues) on the LAMMPS GitHub project web page. However, before reporting a bug, you need to check whether this is something that may have already been corrected. The [Latest Features and Bug Fixes in LAMMPS](https://lammps.sandia.gov/bug.html) web page lists all significant changes to LAMMPS over the years. It also tells you what the current latest development version of LAMMPS is, and you should test whether your issue still applies to that version.

4
.github/codeql/cpp.yml vendored Normal file
View File

@ -0,0 +1,4 @@
paths:
- src
- lib
- tools

5
.github/codeql/python.yml vendored Normal file
View File

@ -0,0 +1,5 @@
paths:
- python/lammps
queries:
- uses: security-and-quality

8
.github/workflows/codeql-analysis.yml vendored
View File

@ -31,16 +31,18 @@ jobs:
uses: github/codeql-action/init@v1
with:
languages: ${{ matrix.language }}
config-file: ./.github/codeql/${{ matrix.language }}.yml
- name: Create Build Environment
run: cmake -E make_directory ${{github.workspace}}/build
if: ${{ matrix.language == 'cpp' }}
run: mkdir build
- name: Building LAMMPS via CMake
if: ${{ matrix.language == 'cpp' }}
shell: bash
working-directory: ${{github.workspace}}/build
working-directory: build
run: |
cmake -C $GITHUB_WORKSPACE/cmake/presets/most.cmake $GITHUB_WORKSPACE/cmake
cmake -C ../cmake/presets/most.cmake ../cmake
cmake --build . --parallel 2
- name: Perform CodeQL Analysis

32
.github/workflows/unittest-macos.yml vendored
View File

@ -10,6 +10,8 @@ jobs:
name: MacOS Unit Test
if: ${{ github.repository == 'lammps/lammps' }}
runs-on: macos-latest
env:
CCACHE_DIR: ${{ github.workspace }}/.ccache
steps:
- name: Checkout repository
@ -17,20 +19,36 @@ jobs:
with:
fetch-depth: 2
- name: Install ccache
run: brew install ccache
- name: Create Build Environment
run: cmake -E make_directory ${{github.workspace}}/build
run: mkdir build
- name: Set up ccache
uses: actions/cache@v2
with:
path: ${{ env.CCACHE_DIR }}
key: macos-ccache-${{ github.sha }}
restore-keys: macos-ccache-
- name: Building LAMMPS via CMake
shell: bash
working-directory: ${{github.workspace}}/build
working-directory: build
run: |
cmake -C $GITHUB_WORKSPACE/cmake/presets/clang.cmake \
-C $GITHUB_WORKSPACE/cmake/presets/most.cmake \
$GITHUB_WORKSPACE/cmake \
-DENABLE_TESTING=ON -DBUILD_SHARED_LIBS=ON -DLAMMPS_EXCEPTIONS=ON
ccache -z
cmake -C ../cmake/presets/clang.cmake \
-C ../cmake/presets/most.cmake \
-D CMAKE_CXX_COMPILER_LAUNCHER=ccache \
-D CMAKE_C_COMPILER_LAUNCHER=ccache \
-D ENABLE_TESTING=on \
-D BUILD_SHARED_LIBS=on \
-D LAMMPS_EXCEPTIONS=on \
../cmake
cmake --build . --parallel 2
ccache -s
- name: Run Tests
working-directory: ${{github.workspace}}/build
working-directory: build
shell: bash
run: ctest -V

14
.lgtm.yml Normal file
View File

@ -0,0 +1,14 @@
extraction:
cpp:
configure:
command:
- "mkdir build"
- "cd build"
- "cmake -G Ninja -C ../cmake/presets/minimal.cmake ../cmake"
index:
build_command:
- "cd build"
- "ninja"
python:
python_setup:
version: 3

35
SECURITY.md Normal file
View File

@ -0,0 +1,35 @@
# Security Policy
LAMMPS is designed as a user-level application to conduct computer
simulations for research using classical mechanics. As such LAMMPS
depends to some degrees on users providing correctly formatted input and
LAMMPS needs to read and write files based on uncontrolled user input.
As a parallel application for use in high-performance computing
environments, performance critical steps are also done without checking
data.
LAMMPS also is interfaced to a number of external libraries, including
libraries with experimental research software, that are not validated
and tested by the LAMMPS developers, so it is easy to import bad
behavior from calling functions in one of those libraries.
Thus is is quite easy to crash LAMMPS through malicious input and do all
kinds of filesystem manipulations. And because of that LAMMPS should
**NEVER** be compiled or **run** as superuser, either from a "root" or
"administrator" account directly or indirectly via "sudo" or "su".
Therefore what could be seen as a security vulnerability is usually
either a user mistake or a bug in the code. Bugs can be reported in
the LAMMPS project
[issue tracker on GitHub](https://github.com/lammps/lammps/issues).
# Version Updates
LAMMPS follows continuous release development model. We aim to keep all
release versions (stable or patch) fully functional and employ a variety
of automatic testing procedures to detect failures of existing
functionality from adding new features before releases are made. Thus
bugfixes and updates are only integrated into the current development
branch and thus the next (patch) release and users are recommended to
update regularly.

82
cmake/CMakeLists.txt
View File

@ -7,6 +7,11 @@ cmake_minimum_required(VERSION 3.10)
if(POLICY CMP0074)
cmake_policy(SET CMP0074 NEW)
endif()
# set policy to silence warnings about missing executable permissions in
# pythonx.y-config when cross-compiling. review occasionally if it may be set to NEW
if (POLICY CMP0109)
cmake_policy(SET CMP0109 OLD)
endif()
########################################
project(lammps CXX)
@ -104,6 +109,12 @@ endif()
option(BUILD_TOOLS "Build and install LAMMPS tools (msi2lmp, binary2txt, chain)" OFF)
option(BUILD_LAMMPS_SHELL "Build and install the LAMMPS shell" OFF)
# allow enabling clang-tidy for C++ files
set(ENABLE_CLANG_TIDY OFF CACHE BOOL "Include clang-tidy processing when compiling")
if(ENABLE_CLANG_TIDY)
set(CMAKE_CXX_CLANG_TIDY "clang-tidy;-checks=*-header-filter=.*" CACHE STRING "")
endif()
include(GNUInstallDirs)
file(GLOB ALL_SOURCES ${LAMMPS_SOURCE_DIR}/[^.]*.cpp)
file(GLOB MAIN_SOURCES ${LAMMPS_SOURCE_DIR}/main.cpp)
@ -121,10 +132,10 @@ set(STANDARD_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS DIPOLE
PLUGIN QEQ REPLICA RIGID SHOCK SPIN SNAP SRD KIM PYTHON MSCG MPIIO VORONOI
USER-ADIOS USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-MESODPD USER-CGSDK
USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD
USER-LB USER-MANIFOLD USER-MEAMC USER-MESONT USER-MGPT USER-MISC USER-MOFFF
USER-LB USER-MANIFOLD USER-MDI USER-MEAMC USER-MESONT USER-MGPT USER-MISC USER-MOFFF
USER-MOLFILE USER-NETCDF USER-PHONON USER-PLUMED USER-PTM USER-QTB
USER-RANN USER-REACTION USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH
USER-TALLY USER-UEF USER-VTK USER-QUIP USER-QMMM USER-YAFF USER-PACE)
USER-TALLY USER-UEF USER-VTK USER-QUIP USER-QMMM USER-YAFF USER-PACE USER-BROWNIAN)
set(SUFFIX_PACKAGES CORESHELL GPU KOKKOS OPT USER-INTEL USER-OMP)
@ -245,69 +256,6 @@ if(BUILD_OMP)
target_link_libraries(lammps PRIVATE OpenMP::OpenMP_CXX)
endif()
# Compiler specific features for testing
if(${CMAKE_CXX_COMPILER_ID} STREQUAL "GNU")
option(ENABLE_COVERAGE "Enable collecting code coverage data" OFF)
mark_as_advanced(ENABLE_COVERAGE)
if(ENABLE_COVERAGE)
if(CMAKE_VERSION VERSION_LESS 3.13)
if(CMAKE_CXX_FLAGS)
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} --coverage")
else()
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_${CMAKE_BUILD_TYPE}_FLAGS} --coverage")
endif()
else()
target_compile_options(lammps PUBLIC --coverage)
target_link_options(lammps PUBLIC --coverage)
endif()
endif()
endif()
#######################################
# add custom target for IWYU analysis
#######################################
set(ENABLE_IWYU OFF CACHE BOOL "Add 'iwyu' build target to call the include-what-you-use tool")
mark_as_advanced(ENABLE_IWYU)
if(ENABLE_IWYU)
set(CMAKE_EXPORT_COMPILE_COMMANDS ON)
find_program(IWYU_EXE NAMES include-what-you-use iwyu)
find_program(IWYU_TOOL NAMES iwyu_tool iwyu-tool iwyu_tool.py)
if (IWYU_EXE AND IWYU_TOOL)
add_custom_target(
iwyu
${IWYU_TOOL} -o clang -p ${CMAKE_CURRENT_BINARY_DIR} -- -Xiwyu --mapping_file=${CMAKE_CURRENT_SOURCE_DIR}/iwyu/iwyu-extra-map.imp
COMMENT "Running IWYU")
add_dependencies(iwyu lammps)
else()
message(FATAL_ERROR "To use IWYU you need the include-what-you-use/iwyu executable"
"and the iwyu-tool/iwyu_tool script installed in your PATH")
endif()
endif()
set(ENABLE_SANITIZER "none" CACHE STRING "Select a code sanitizer option (none (default), address, leak, thread, undefined)")
mark_as_advanced(ENABLE_SANITIZER)
set(ENABLE_SANITIZER_VALUES none address leak thread undefined)
set_property(CACHE ENABLE_SANITIZER PROPERTY STRINGS ${ENABLE_SANITIZER_VALUES})
validate_option(ENABLE_SANITIZER ENABLE_SANITIZER_VALUES)
string(TOLOWER ${ENABLE_SANITIZER} ENABLE_SANITIZER)
if(NOT ENABLE_SANITIZER STREQUAL "none")
if((${CMAKE_CXX_COMPILER_ID} STREQUAL "GNU") OR (${CMAKE_CXX_COMPILER_ID} STREQUAL "Clang"))
if(CMAKE_VERSION VERSION_LESS 3.13)
if(CMAKE_CXX_FLAGS)
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fsanitize=${ENABLE_SANITIZER}")
else()
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_${CMAKE_BUILD_TYPE}_FLAGS} -fsanitize=${ENABLE_SANITIZER}")
endif()
else()
target_compile_options(lammps PUBLIC -fsanitize=${ENABLE_SANITIZER})
target_link_options(lammps PUBLIC -fsanitize=${ENABLE_SANITIZER})
endif()
else()
message(WARNING "ENABLE_SANITIZER option not supported by ${CMAKE_CXX_COMPILER_ID} compilers. Ignoring.")
set(ENABLE_SANITIZER "none")
endif()
endif()
if(PKG_MSCG OR PKG_USER-ATC OR PKG_USER-AWPMD OR PKG_USER-QUIP OR PKG_LATTE)
enable_language(C)
find_package(LAPACK)
@ -387,8 +335,8 @@ else()
set(CUDA_REQUEST_PIC)
endif()
foreach(PKG_WITH_INCL KSPACE PYTHON MLIAP VORONOI USER-COLVARS USER-MOLFILE USER-NETCDF USER-PLUMED USER-QMMM
USER-QUIP USER-SCAFACOS USER-SMD USER-VTK KIM LATTE MESSAGE MSCG COMPRESS USER-PACE)
foreach(PKG_WITH_INCL KSPACE PYTHON MLIAP VORONOI USER-COLVARS USER-MDI USER-MOLFILE USER-NETCDF USER-PLUMED
USER-QMMM USER-QUIP USER-SCAFACOS USER-SMD USER-VTK KIM LATTE MESSAGE MSCG COMPRESS USER-PACE)
if(PKG_${PKG_WITH_INCL})
include(Packages/${PKG_WITH_INCL})
endif()

4
cmake/Modules/Documentation.cmake
View File

@ -55,8 +55,8 @@ if(BUILD_DOC)
COMMAND ${DOCENV_BINARY_DIR}/pip $ENV{PIP_OPTIONS} install -r ${DOC_BUILD_DIR}/requirements.txt --upgrade
)
set(MATHJAX_URL "https://github.com/mathjax/MathJax/archive/3.1.2.tar.gz" CACHE STRING "URL for MathJax tarball")
set(MATHJAX_MD5 "a4a6a093a89bc2ccab1452d766b98e53" CACHE STRING "MD5 checksum of MathJax tarball")
set(MATHJAX_URL "https://github.com/mathjax/MathJax/archive/3.1.3.tar.gz" CACHE STRING "URL for MathJax tarball")
set(MATHJAX_MD5 "d1c98c746888bfd52ca8ebc10704f92f" CACHE STRING "MD5 checksum of MathJax tarball")
mark_as_advanced(MATHJAX_URL)
# download mathjax distribution and unpack to folder "mathjax"

3
cmake/Modules/GenerateOpenCLHeader.cmake Normal file
View File

@ -0,0 +1,3 @@
# utility script to call WriteOpenCLHeader function
include(${SOURCE_DIR}/Modules/OpenCLUtils.cmake)
WriteOpenCLHeader(${VARNAME} ${HEADER_FILE} ${SOURCE_FILES})

4
cmake/Modules/OpenCLLoader.cmake
View File

@ -1,6 +1,6 @@
message(STATUS "Downloading and building OpenCL loader library")
set(OPENCL_LOADER_URL "${LAMMPS_THIRDPARTY_URL}/opencl-loader-2020.12.18.tar.gz" CACHE STRING "URL for OpenCL loader tarball")
set(OPENCL_LOADER_MD5 "011cdcbd41030be94f3fced6d763a52a" CACHE STRING "MD5 checksum of OpenCL loader tarball")
set(OPENCL_LOADER_URL "${LAMMPS_THIRDPARTY_URL}/opencl-loader-2021.05.02.tar.gz" CACHE STRING "URL for OpenCL loader tarball")
set(OPENCL_LOADER_MD5 "29180b05056578afda92f0d394c3a373" CACHE STRING "MD5 checksum of OpenCL loader tarball")
mark_as_advanced(OPENCL_LOADER_URL)
mark_as_advanced(OPENCL_LOADER_MD5)

20
cmake/Modules/OpenCLUtils.cmake
View File

@ -1,10 +1,8 @@
function(GenerateOpenCLHeader varname outfile files)
message("Creating ${outfile}...")
function(WriteOpenCLHeader varname outfile files)
file(WRITE ${outfile} "const char * ${varname} = \n")
math(EXPR ARG_END "${ARGC}-1")
separate_arguments(files)
foreach(IDX RANGE 2 ${ARG_END})
list(GET ARGV ${IDX} filename)
foreach(filename ${files})
file(READ ${filename} content)
string(REGEX REPLACE "\\s*//[^\n]*\n" "\n" content "${content}")
string(REGEX REPLACE "\\\\" "\\\\\\\\" content "${content}")
@ -15,4 +13,16 @@ function(GenerateOpenCLHeader varname outfile files)
endforeach()
file(APPEND ${outfile} ";\n")
endfunction(WriteOpenCLHeader)
function(GenerateOpenCLHeader varname outfile files)
list(REMOVE_AT ARGV 0 1)
add_custom_command(OUTPUT ${outfile}
COMMAND ${CMAKE_COMMAND} -D SOURCE_DIR=${CMAKE_CURRENT_SOURCE_DIR}
-D VARNAME=${varname}
-D HEADER_FILE=${outfile}
-D SOURCE_FILES="${ARGV}"
-P ${CMAKE_CURRENT_SOURCE_DIR}/Modules/GenerateOpenCLHeader.cmake
DEPENDS ${ARGV}
COMMENT "Generating ${outfile}...")
endfunction(GenerateOpenCLHeader)

19
cmake/Modules/Packages/GPU.cmake
View File

@ -112,10 +112,10 @@ if(GPU_API STREQUAL "CUDA")
endif()
cuda_compile_fatbin(GPU_GEN_OBJS ${GPU_LIB_CU} OPTIONS ${CUDA_REQUEST_PIC}
-DUNIX -O3 --use_fast_math -Wno-deprecated-gpu-targets -DNV_KERNEL -DUCL_CUDADR ${GPU_CUDA_GENCODE} -D_${GPU_PREC_SETTING})
-DUNIX -O3 --use_fast_math -Wno-deprecated-gpu-targets -DNV_KERNEL -DUCL_CUDADR ${GPU_CUDA_GENCODE} -D_${GPU_PREC_SETTING} -DLAMMPS_${LAMMPS_SIZES})
cuda_compile(GPU_OBJS ${GPU_LIB_CUDPP_CU} OPTIONS ${CUDA_REQUEST_PIC}
-DUNIX -O3 --use_fast_math -Wno-deprecated-gpu-targets -DUCL_CUDADR ${GPU_CUDA_GENCODE} -D_${GPU_PREC_SETTING})
-DUNIX -O3 --use_fast_math -Wno-deprecated-gpu-targets -DUCL_CUDADR ${GPU_CUDA_GENCODE} -D_${GPU_PREC_SETTING} -DLAMMPS_${LAMMPS_SIZES})
foreach(CU_OBJ ${GPU_GEN_OBJS})
get_filename_component(CU_NAME ${CU_OBJ} NAME_WE)
@ -145,7 +145,14 @@ if(GPU_API STREQUAL "CUDA")
target_include_directories(nvc_get_devices PRIVATE ${CUDA_INCLUDE_DIRS})
elseif(GPU_API STREQUAL "OPENCL")
option(USE_STATIC_OPENCL_LOADER "Download and include a static OpenCL ICD loader" ON)
# the static OpenCL loader doesn't seem to work on macOS. use the system provided
# version by default instead (for as long as it will be available)
if("${CMAKE_SYSTEM_NAME}" STREQUAL "Darwin")
set(_opencl_static_default OFF)
else()
set(_opencl_static_default ON)
endif()
option(USE_STATIC_OPENCL_LOADER "Download and include a static OpenCL ICD loader" ${_opencl_static_default})
mark_as_advanced(USE_STATIC_OPENCL_LOADER)
if (USE_STATIC_OPENCL_LOADER)
include(OpenCLLoader)
@ -289,18 +296,18 @@ elseif(GPU_API STREQUAL "HIP")
if(HIP_COMPILER STREQUAL "clang")
add_custom_command(OUTPUT ${CUBIN_FILE}
VERBATIM COMMAND ${HIP_HIPCC_EXECUTABLE} --genco --offload-arch=${HIP_ARCH} -O3 -ffast-math -DUSE_HIP -D_${GPU_PREC_SETTING} -I${LAMMPS_LIB_SOURCE_DIR}/gpu -o ${CUBIN_FILE} ${CU_CPP_FILE}
VERBATIM COMMAND ${HIP_HIPCC_EXECUTABLE} --genco --offload-arch=${HIP_ARCH} -O3 -ffast-math -DUSE_HIP -D_${GPU_PREC_SETTING} -DLAMMPS_${LAMMPS_SIZES} -I${LAMMPS_LIB_SOURCE_DIR}/gpu -o ${CUBIN_FILE} ${CU_CPP_FILE}
DEPENDS ${CU_CPP_FILE}
COMMENT "Generating ${CU_NAME}.cubin")
else()
add_custom_command(OUTPUT ${CUBIN_FILE}
VERBATIM COMMAND ${HIP_HIPCC_EXECUTABLE} --genco -t="${HIP_ARCH}" -f=\"-O3 -ffast-math -DUSE_HIP -D_${GPU_PREC_SETTING} -I${LAMMPS_LIB_SOURCE_DIR}/gpu\" -o ${CUBIN_FILE} ${CU_CPP_FILE}
VERBATIM COMMAND ${HIP_HIPCC_EXECUTABLE} --genco -t="${HIP_ARCH}" -f=\"-O3 -ffast-math -DUSE_HIP -D_${GPU_PREC_SETTING} -DLAMMPS_${LAMMPS_SIZES} -I${LAMMPS_LIB_SOURCE_DIR}/gpu\" -o ${CUBIN_FILE} ${CU_CPP_FILE}
DEPENDS ${CU_CPP_FILE}
COMMENT "Generating ${CU_NAME}.cubin")
endif()
elseif(HIP_PLATFORM STREQUAL "nvcc")
add_custom_command(OUTPUT ${CUBIN_FILE}
VERBATIM COMMAND ${HIP_HIPCC_EXECUTABLE} --fatbin --use_fast_math -DUSE_HIP -D_${GPU_PREC_SETTING} ${HIP_CUDA_GENCODE} -I${LAMMPS_LIB_SOURCE_DIR}/gpu -o ${CUBIN_FILE} ${CU_FILE}
VERBATIM COMMAND ${HIP_HIPCC_EXECUTABLE} --fatbin --use_fast_math -DUSE_HIP -D_${GPU_PREC_SETTING} -DLAMMPS_${LAMMPS_SIZES} ${HIP_CUDA_GENCODE} -I${LAMMPS_LIB_SOURCE_DIR}/gpu -o ${CUBIN_FILE} ${CU_FILE}
DEPENDS ${CU_FILE}
COMMENT "Generating ${CU_NAME}.cubin")
endif()

6
cmake/Modules/Packages/KOKKOS.cmake
View File

@ -37,8 +37,8 @@ if(DOWNLOAD_KOKKOS)
list(APPEND KOKKOS_LIB_BUILD_ARGS "-DCMAKE_CXX_EXTENSIONS=${CMAKE_CXX_EXTENSIONS}")
list(APPEND KOKKOS_LIB_BUILD_ARGS "-DCMAKE_TOOLCHAIN_FILE=${CMAKE_TOOLCHAIN_FILE}")
include(ExternalProject)
set(KOKKOS_URL "https://github.com/kokkos/kokkos/archive/3.3.01.tar.gz" CACHE STRING "URL for KOKKOS tarball")
set(KOKKOS_MD5 "08201d1c7cf5bc458ce0f5b44a629d5a" CACHE STRING "MD5 checksum of KOKKOS tarball")
set(KOKKOS_URL "https://github.com/kokkos/kokkos/archive/3.4.00.tar.gz" CACHE STRING "URL for KOKKOS tarball")
set(KOKKOS_MD5 "c2fdcedb6953e6160c765366f6045abb" CACHE STRING "MD5 checksum of KOKKOS tarball")
mark_as_advanced(KOKKOS_URL)
mark_as_advanced(KOKKOS_MD5)
ExternalProject_Add(kokkos_build
@ -58,7 +58,7 @@ if(DOWNLOAD_KOKKOS)
target_link_libraries(lmp PRIVATE LAMMPS::KOKKOS)
add_dependencies(LAMMPS::KOKKOS kokkos_build)
elseif(EXTERNAL_KOKKOS)
find_package(Kokkos 3.3.01 REQUIRED CONFIG)
find_package(Kokkos 3.4.00 REQUIRED CONFIG)
target_link_libraries(lammps PRIVATE Kokkos::kokkos)
target_link_libraries(lmp PRIVATE Kokkos::kokkos)
else()

8
cmake/Modules/Packages/USER-INTEL.cmake
View File

@ -79,9 +79,11 @@ if(INTEL_ARCH STREQUAL "KNL")
else()
if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
include(CheckCXXCompilerFlag)
foreach(_FLAG -O2 -fp-model fast=2 -no-prec-div -qoverride-limits -qopt-zmm-usage=high -qno-offload -fno-alias -ansi-alias -restrict)
check_cxx_compiler_flag("${_FLAG}" COMPILER_SUPPORTS${_FLAG})
if(COMPILER_SUPPORTS${_FLAG})
foreach(_FLAG -O2 "-fp-model fast=2" -no-prec-div -qoverride-limits -qopt-zmm-usage=high -qno-offload -fno-alias -ansi-alias -restrict)
string(REGEX REPLACE "[ =\"]" "" _FLAGX ${_FLAG})
check_cxx_compiler_flag("${_FLAG}" COMPILER_SUPPORTS${_FLAGX})
if(COMPILER_SUPPORTS${_FLAGX})
separate_arguments(_FLAG UNIX_COMMAND "${_FLAG}")
target_compile_options(lammps PRIVATE ${_FLAG})
endif()
endforeach()

118
cmake/Modules/Packages/USER-MDI.cmake Normal file
View File

@ -0,0 +1,118 @@
find_package(mdi QUIET)
if(${mdi_FOUND})
set(DOWNLOAD_MDI_DEFAULT OFF)
else()
set(DOWNLOAD_MDI_DEFAULT ON)
endif()
option(DOWNLOAD_MDI "Download and compile the MDI library instead of using an already installed one" ${DOWNLOAD_MDI_DEFAULT})
if(DOWNLOAD_MDI)
message(STATUS "MDI download requested - we will build our own")
set(MDI_URL "https://github.com/MolSSI-MDI/MDI_Library/archive/v1.2.9.tar.gz" CACHE STRING "URL for MDI tarball")
set(MDI_MD5 "ddfa46d6ee15b4e59cfd527ec7212184" CACHE STRING "MD5 checksum for MDI tarball")
mark_as_advanced(MDI_URL)
mark_as_advanced(MDI_MD5)
enable_language(C)
# only ON/OFF are allowed for "mpi" flag when building MDI library
# so translate boolean value of BUILD_MPI
# always disable MPI when cross-compiling to Windows.
if((BUILD_MPI) AND NOT((CMAKE_SYSTEM_NAME STREQUAL Windows) AND CMAKE_CROSSCOMPILING))
set(MDI_USE_MPI ON)
else()
set(MDI_USE_MPI OFF)
endif()
# detect if we have python development support and thus can enable python plugins
set(MDI_USE_PYTHON_PLUGINS OFF)
if(CMAKE_VERSION VERSION_LESS 3.12)
find_package(PythonLibs QUIET) # Deprecated since version 3.12
if (PYTHONLIBS_FOUND)
set(MDI_USE_PYTHON_PLUGINS ON)
endif()
else()
find_package(Python QUIET COMPONENTS Development)
if (Python_Development_FOUND)
set(MDI_USE_PYTHON_PLUGINS ON)
endif()
endif()
# download/ build MDI library
# always build static library with -fpic
# support cross-compilation and ninja-build
include(ExternalProject)
ExternalProject_Add(mdi_build
URL ${MDI_URL}
URL_MD5 ${MDI_MD5}
CMAKE_ARGS ${CMAKE_REQUEST_PIC}
-DCMAKE_INSTALL_PREFIX=<INSTALL_DIR>
-DCMAKE_C_COMPILER=${CMAKE_C_COMPILER}
-DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
-DCMAKE_MAKE_PROGRAM=${CMAKE_MAKE_PROGRAM}
-DCMAKE_TOOLCHAIN_FILE=${CMAKE_TOOLCHAIN_FILE}
-Dlanguage=C
-Dlibtype=STATIC
-Dmpi=${MDI_USE_MPI}
-Dpython_plugins=${MDI_USE_PYTHON_PLUGINS}
UPDATE_COMMAND ""
INSTALL_COMMAND ""
BUILD_BYPRODUCTS "<BINARY_DIR>/MDI_Library/libmdi.a"
)
# where is the compiled library?
ExternalProject_get_property(mdi_build BINARY_DIR)
set(MDI_BINARY_DIR "${BINARY_DIR}/MDI_Library")
# workaround for older CMake versions
file(MAKE_DIRECTORY ${MDI_BINARY_DIR})
# create imported target for the MDI library
add_library(LAMMPS::MDI UNKNOWN IMPORTED)
add_dependencies(LAMMPS::MDI mdi_build)
set_target_properties(LAMMPS::MDI PROPERTIES
IMPORTED_LOCATION "${MDI_BINARY_DIR}/libmdi.a"
INTERFACE_INCLUDE_DIRECTORIES ${MDI_BINARY_DIR}
)
set(MDI_DEP_LIBS "")
# if compiling with python plugins we need
# to add python libraries as dependency.
if(MDI_USE_PYTHON_PLUGINS)
if(CMAKE_VERSION VERSION_LESS 3.12)
list(APPEND MDI_DEP_LIBS ${PYTHON_LIBRARIES})
else()
list(APPEND MDI_DEP_LIBS Python::Python)
endif()
endif()
# need to add support for dlopen/dlsym, except when compiling for Windows.
if(NOT ${CMAKE_SYSTEM_NAME} STREQUAL "Windows")
list(APPEND MDI_DEP_LIBS "${CMAKE_DL_LIBS}")
endif()
if(MDI_DEP_LIBS)
set_target_properties(LAMMPS::MDI PROPERTIES
IMPORTED_LINK_INTERFACE_LIBRARIES "${MDI_DEP_LIBS}")
endif()
target_link_libraries(lammps PRIVATE LAMMPS::MDI)
target_link_libraries(lmp PRIVATE LAMMPS::MDI)
else()
find_package(mdi)
if(NOT mdi_FOUND)
message(FATAL_ERROR "MDI library not found. Help CMake to find it "
"by setting mdi_LIBRARY and mdi_INCLUDE_DIR, or set DOWNLOAD_MDI=ON "
"to download and compile it")
endif()
# Link the lammps library against MDI
target_include_directories(lammps PRIVATE ${mdi_INCLUDE_DIR})
target_link_libraries(lammps PRIVATE ${mdi_LIBRARY})
# Link the lammps executable against MDI
target_include_directories(lmp PRIVATE ${mdi_INCLUDE_DIR})
target_link_libraries(lmp PRIVATE ${mdi_LIBRARY})
endif()
target_compile_definitions(lammps PRIVATE -DLMP_USER_MDI)
target_compile_definitions(lmp PRIVATE -DLMP_USER_MDI)

3
cmake/Modules/Packages/USER-PACE.cmake
View File

@ -14,13 +14,12 @@ execute_process(
WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
)
file(GLOB PACE_EVALUATOR_INCLUDE_DIR ${CMAKE_BINARY_DIR}/lammps-user-pace-*/USER-PACE)
file(GLOB PACE_EVALUATOR_SOURCES ${CMAKE_BINARY_DIR}/lammps-user-pace-*/USER-PACE/*.cpp)
list(FILTER PACE_EVALUATOR_SOURCES EXCLUDE REGEX pair_pace.cpp)
add_library(pace STATIC ${PACE_EVALUATOR_SOURCES})
set_target_properties(pace PROPERTIES OUTPUT_NAME pace${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_link_libraries(lammps PRIVATE pace)

73
cmake/Modules/Testing.cmake
View File

@ -56,3 +56,76 @@ if(ENABLE_TESTING)
get_filename_component(LAMMPS_UNITTEST_BIN ${CMAKE_BINARY_DIR}/unittest ABSOLUTE)
add_subdirectory(${LAMMPS_UNITTEST_DIR} ${LAMMPS_UNITTEST_BIN})
endif()
# Compiler specific features for testing
if(${CMAKE_CXX_COMPILER_ID} STREQUAL "GNU")
option(ENABLE_COVERAGE "Enable collecting code coverage data" OFF)
mark_as_advanced(ENABLE_COVERAGE)
if(ENABLE_COVERAGE)
if(CMAKE_VERSION VERSION_LESS 3.13)
if(CMAKE_CXX_FLAGS)
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} --coverage")
else()
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_${CMAKE_BUILD_TYPE}_FLAGS} --coverage")
endif()
else()
target_compile_options(lammps PUBLIC --coverage)
target_link_options(lammps PUBLIC --coverage)
endif()
endif()
endif()
#######################################
# add custom target for IWYU analysis
#######################################
set(ENABLE_IWYU OFF CACHE BOOL "Add 'iwyu' build target to call the include-what-you-use tool")
mark_as_advanced(ENABLE_IWYU)
if(ENABLE_IWYU)
# enforce these settings
set(CMAKE_EXPORT_COMPILE_COMMANDS ON CACHE BOOL "Enable reporting compilation commands to compile_commands.json" FORCE)
if (NOT ((CMAKE_CXX_COMPILER_ID STREQUAL "Clang") OR (CMAKE_CXX_COMPILER_ID STREQUAL "GNU")))
message(FATAL_ERROR "IWYU is only supported with Clang or GNU compilers")
endif()
# detect the "native" header folder so we can include them first
execute_process(COMMAND ${CMAKE_CXX_COMPILER} --print-search-dirs OUTPUT_VARIABLE IWYU_SEARCH_PATHS)
string(REGEX REPLACE ".*libraries: *=([^:]+):.*" "\\1/include" IWYU_EXTRA_INCLUDE_DIR ${IWYU_SEARCH_PATHS})
find_program(IWYU_EXE NAMES include-what-you-use iwyu)
find_program(IWYU_TOOL NAMES iwyu_tool iwyu-tool iwyu_tool.py)
if (IWYU_EXE AND IWYU_TOOL)
add_custom_target(
iwyu
${IWYU_TOOL} -o clang -p ${CMAKE_CURRENT_BINARY_DIR} -- -I${IWYU_EXTRA_INCLUDE_DIR} -Xiwyu --mapping_file=${CMAKE_CURRENT_SOURCE_DIR}/iwyu/iwyu-extra-map.imp
COMMENT "Running IWYU")
add_dependencies(iwyu lammps)
else()
message(FATAL_ERROR "To use IWYU you need the include-what-you-use/iwyu executable"
"and the iwyu-tool/iwyu_tool script installed in your PATH")
endif()
endif()
#######################################
# select code sanitizer options
#######################################
set(ENABLE_SANITIZER "none" CACHE STRING "Select a code sanitizer option (none (default), address, leak, thread, undefined)")
mark_as_advanced(ENABLE_SANITIZER)
set(ENABLE_SANITIZER_VALUES none address leak thread undefined)
set_property(CACHE ENABLE_SANITIZER PROPERTY STRINGS ${ENABLE_SANITIZER_VALUES})
validate_option(ENABLE_SANITIZER ENABLE_SANITIZER_VALUES)
string(TOLOWER ${ENABLE_SANITIZER} ENABLE_SANITIZER)
if(NOT ENABLE_SANITIZER STREQUAL "none")
if((${CMAKE_CXX_COMPILER_ID} STREQUAL "GNU") OR (${CMAKE_CXX_COMPILER_ID} STREQUAL "Clang"))
if(CMAKE_VERSION VERSION_LESS 3.13)
if(CMAKE_CXX_FLAGS)
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fsanitize=${ENABLE_SANITIZER}")
else()
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_${CMAKE_BUILD_TYPE}_FLAGS} -fsanitize=${ENABLE_SANITIZER}")
endif()
else()
target_compile_options(lammps PUBLIC -fsanitize=${ENABLE_SANITIZER})
target_link_options(lammps PUBLIC -fsanitize=${ENABLE_SANITIZER})
endif()
else()
message(WARNING "ENABLE_SANITIZER option not supported by ${CMAKE_CXX_COMPILER_ID} compilers. Ignoring.")
set(ENABLE_SANITIZER "none")
endif()
endif()

18
cmake/Modules/YAML.cmake
View File

@ -6,15 +6,27 @@ set(YAML_MD5 "bb15429d8fb787e7d3f1c83ae129a999" CACHE STRING "MD5 checksum of li
mark_as_advanced(YAML_URL)
mark_as_advanced(YAML_MD5)
# support cross-compilation to windows
if(CMAKE_CROSSCOMPILING AND (CMAKE_SYSTEM_NAME STREQUAL "Windows"))
if(CMAKE_SYSTEM_PROCESSOR STREQUAL "x86")
set(YAML_CROSS_HOST --host=i686-mingw64)
elseif(CMAKE_SYSTEM_PROCESSOR STREQUAL "x86_64")
set(YAML_CROSS_HOST --host=x86_64-mingw64)
else()
message(FATAL_ERROR "Unsupported cross-compilation "
" for ${CMAKE_SYSTEM_NAME}/${CMAKE_SYSTEM_PROCESSOR}"
" on ${CMAKE_HOST_SYSTEM}/${CMAKE_HOST_SYSTEM_PROCESSOR}")
endif()
endif()
ExternalProject_Add(libyaml
URL ${YAML_URL}
URL_MD5 ${YAML_MD5}
SOURCE_DIR "${CMAKE_BINARY_DIR}/yaml-src"
BINARY_DIR "${CMAKE_BINARY_DIR}/yaml-build"
CONFIGURE_COMMAND <SOURCE_DIR>/configure ${CONFIGURE_REQUEST_PIC}
CXX=${CMAKE_CXX_COMPILER}
CC=${CMAKE_C_COMPILER}
--prefix=<INSTALL_DIR> --disable-shared
CXX=${CMAKE_CXX_COMPILER} CC=${CMAKE_C_COMPILER}
--prefix=<INSTALL_DIR> --disable-shared ${YAML_CROSS_HOST}
BUILD_BYPRODUCTS <INSTALL_DIR>/lib/libyaml${CMAKE_STATIC_LIBRARY_SUFFIX}
TEST_COMMAND "")

2
cmake/Modules/generate_lmpgitversion.cmake
View File

@ -17,7 +17,7 @@ if(GIT_FOUND AND EXISTS ${LAMMPS_DIR}/.git)
ERROR_QUIET
WORKING_DIRECTORY ${LAMMPS_DIR}
OUTPUT_STRIP_TRAILING_WHITESPACE)
execute_process(COMMAND ${GIT_EXECUTABLE} describe --dirty=-modified
execute_process(COMMAND ${GIT_EXECUTABLE} describe --dirty=-modified --always
OUTPUT_VARIABLE temp_git_describe
ERROR_QUIET
WORKING_DIRECTORY ${LAMMPS_DIR}

20
cmake/presets/all_off.cmake
View File

@ -2,16 +2,16 @@
# an existing package selection without losing any other settings
set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU
GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MISC MESSAGE MLIAP
MOLECULE MPIIO MSCG OPT PERI POEMS PYTHON QEQ REPLICA RIGID SHOCK
SNAP SPIN SRD VORONOI
USER-ADIOS USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK
USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP
USER-H5MD USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESODPD
USER-MESONT USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-OMP
USER-PHONON USER-PLUMED USER-PTM USER-QMMM USER-QTB USER-QUIP
USER-REACTION USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ
USER-SPH USER-TALLY USER-UEF USER-VTK USER-YAFF)
GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MESSAGE MISC MLIAP MOLECULE
MPIIO MSCG OPT PERI PLUGIN POEMS PYTHON QEQ REPLICA RIGID SHOCK SNAP SPIN
SRD VORONOI
USER-ADIOS USER-ATC USER-AWPMD USER-BROWNIAN USER-BOCS USER-CGDNA USER-CGSDK
USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD
USER-INTEL USER-LB USER-MANIFOLD USER-MDI USER-MEAMC USER-MESODPD USER-MESONT
USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-OMP USER-PACE
USER-PHONON USER-PLUMED USER-PTM USER-QMMM USER-QTB USER-QUIP USER-REACTION
USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY
USER-UEF USER-VTK USER-YAFF)
foreach(PKG ${ALL_PACKAGES})
set(PKG_${PKG} OFF CACHE BOOL "" FORCE)

20
cmake/presets/all_on.cmake
View File

@ -4,16 +4,16 @@
# with just a working C++ compiler and an MPI library.
set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU
GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MISC MESSAGE MLIAP
MOLECULE MPIIO MSCG OPT PERI POEMS PYTHON QEQ REPLICA RIGID SHOCK
SNAP SPIN SRD VORONOI
USER-ADIOS USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK
USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP
USER-H5MD USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESODPD
USER-MESONT USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-OMP
USER-PHONON USER-PLUMED USER-PTM USER-QMMM USER-QTB USER-QUIP
USER-REACTION USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ
USER-SPH USER-TALLY USER-UEF USER-VTK USER-YAFF)
GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MESSAGE MISC MLIAP MOLECULE
MPIIO MSCG OPT PERI PLUGIN POEMS PYTHON QEQ REPLICA RIGID SHOCK SNAP SPIN
SRD VORONOI
USER-ADIOS USER-ATC USER-AWPMD USER-BROWNIAN USER-BOCS USER-CGDNA USER-CGSDK
USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD
USER-INTEL USER-LB USER-MANIFOLD USER-MDI USER-MEAMC USER-MESODPD USER-MESONT
USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-OMP USER-PACE
USER-PHONON USER-PLUMED USER-PTM USER-QMMM USER-QTB USER-QUIP USER-REACTION
USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY
USER-UEF USER-VTK USER-YAFF)
foreach(PKG ${ALL_PACKAGES})
set(PKG_${PKG} ON CACHE BOOL "" FORCE)

10
cmake/presets/clang.cmake
View File

@ -4,10 +4,18 @@ set(CMAKE_CXX_COMPILER "clang++" CACHE STRING "" FORCE)
set(CMAKE_C_COMPILER "clang" CACHE STRING "" FORCE)
set(CMAKE_CXX_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE)
set(CMAKE_CXX_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
set(CMAKE_CXX_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
set(CMAKE_Fortran_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE)
set(CMAKE_Fortran_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
set(CMAKE_Fortran_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
set(CMAKE_C_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE)
set(CMAKE_C_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
set(CMAKE_C_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
set(MPI_CXX "clang++" CACHE STRING "" FORCE)
set(MPI_CXX_COMPILER "mpicxx" CACHE STRING "" FORCE)
unset(HAVE_OMP_H_INCLUDE CACHE)
unset(HAVE_OMP_H_INCLUDE CACHE)
set(OpenMP_C "clang" CACHE STRING "" FORCE)
set(OpenMP_C_FLAGS "-fopenmp" CACHE STRING "" FORCE)
set(OpenMP_C_LIB_NAMES "omp" CACHE STRING "" FORCE)

8
cmake/presets/download.cmake
View File

@ -1,7 +1,7 @@
# preset that turns on packages with automatic downloads of sources of potentials
# compilation of libraries like Plumed or ScaFaCoS can take a considerable amount of time.
# Preset that turns on packages with automatic downloads of sources or potentials.
# Compilation of libraries like Plumed or ScaFaCoS can take a considerable amount of time.
set(ALL_PACKAGES KIM LATTE MSCG VORONOI USER-PLUMED USER-SCAFACOS USER-SMD USER-MESONT)
set(ALL_PACKAGES KIM LATTE MSCG VORONOI USER-PLUMED USER-SCAFACOS USER-SMD USER-MESONT USER-MDI USER-PACE)
foreach(PKG ${ALL_PACKAGES})
set(PKG_${PKG} ON CACHE BOOL "" FORCE)
@ -9,9 +9,11 @@ endforeach()
set(DOWNLOAD_KIM ON CACHE BOOL "" FORCE)
set(DOWNLOAD_LATTE ON CACHE BOOL "" FORCE)
set(DOWNLOAD_MDI ON CACHE BOOL "" FORCE)
set(DOWNLOAD_MSCG ON CACHE BOOL "" FORCE)
set(DOWNLOAD_VORO ON CACHE BOOL "" FORCE)
set(DOWNLOAD_EIGEN3 ON CACHE BOOL "" FORCE)
set(DOWNLOAD_PACE ON CACHE BOOL "" FORCE)
set(DOWNLOAD_PLUMED ON CACHE BOOL "" FORCE)
set(DOWNLOAD_SCAFACOS ON CACHE BOOL "" FORCE)

12
cmake/presets/intel.cmake
View File

@ -3,10 +3,20 @@
set(CMAKE_CXX_COMPILER "icpc" CACHE STRING "" FORCE)
set(CMAKE_C_COMPILER "icc" CACHE STRING "" FORCE)
set(CMAKE_Fortran_COMPILER "ifort" CACHE STRING "" FORCE)
set(CMAKE_CXX_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE)
set(CMAKE_CXX_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
set(CMAKE_CXX_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
set(CMAKE_Fortran_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE)
set(CMAKE_Fortran_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
set(CMAKE_Fortran_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
set(CMAKE_C_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE)
set(CMAKE_C_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
set(CMAKE_C_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
set(MPI_CXX "icpc" CACHE STRING "" FORCE)
set(MPI_CXX_COMPILER "mpicxx" CACHE STRING "" FORCE)
unset(HAVE_OMP_H_INCLUDE CACHE)
unset(HAVE_OMP_H_INCLUDE CACHE)
set(OpenMP_C "icc" CACHE STRING "" FORCE)
set(OpenMP_C_FLAGS "-qopenmp" CACHE STRING "" FORCE)
set(OpenMP_C_LIB_NAMES "omp" CACHE STRING "" FORCE)

4
cmake/presets/mingw-cross.cmake
View File

@ -1,11 +1,11 @@
set(WIN_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU
GRANULAR KSPACE LATTE MANYBODY MC MISC MLIAP MOLECULE OPT
PERI POEMS QEQ REPLICA RIGID SHOCK SNAP SPIN SRD VORONOI
USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK
USER-ATC USER-AWPMD USER-BOCS USER-BROWNIAN USER-CGDNA USER-CGSDK
USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF
USER-FEP USER-INTEL USER-MANIFOLD USER-MEAMC USER-MESODPD
USER-MESONT USER-MISC USER-MGPT USER-MOFFF USER-MOLFILE USER-OMP
USER-PHONON USER-PTM USER-QTB USER-REACTION USER-REAXC
USER-PACE USER-PHONON USER-PTM USER-QTB USER-REACTION USER-REAXC
USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF
USER-YAFF)

6
cmake/presets/most.cmake
View File

@ -5,9 +5,9 @@
set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE
GRANULAR KSPACE MANYBODY MC MISC MLIAP MOLECULE OPT PERI
PLUGIN POEMS PYTHON QEQ REPLICA RIGID SHOCK SNAP SPIN SRD VORONOI
USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS USER-DIFFRACTION
USER-DPD USER-DRUDE USER-EFF USER-FEP USER-MEAMC USER-MESODPD
USER-MISC USER-MOFFF USER-OMP USER-PHONON USER-REACTION
USER-BROWNIAN USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS
USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-MEAMC
USER-MESODPD USER-MISC USER-MOFFF USER-OMP USER-PHONON USER-REACTION
USER-REAXC USER-SDPD USER-SPH USER-SMD USER-UEF USER-YAFF)
foreach(PKG ${ALL_PACKAGES})

9
cmake/presets/nolib.cmake
View File

@ -1,10 +1,11 @@
# preset that turns off all packages that require some form of external
# library or special compiler (fortran or cuda) or equivalent.
set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MPIIO MSCG PYTHON
VORONOI USER-ADIOS USER-ATC USER-AWPMD USER-H5MD USER-LB
USER-MOLFILE USER-MESONT USER-NETCDF USER-PLUMED USER-QMMM USER-QUIP
USER-SCAFACOS USER-SMD USER-VTK)
set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MESSAGE MPIIO MSCG
PYTHON VORONOI
USER-ADIOS USER-ATC USER-AWPMD USER-H5MD USER-LB USER-MOLFILE USER-MESONT
USER-MDI USER-NETCDF USER-PACE USER-PLUMED USER-QMMM USER-QUIP USER-SCAFACOS
USER-SMD USER-VTK)
foreach(PKG ${PACKAGES_WITH_LIB})
set(PKG_${PKG} OFF CACHE BOOL "" FORCE)

14
cmake/presets/oneapi.cmake
View File

@ -1,12 +1,22 @@
# preset that will enable the LLVM based Intel compilers with support for MPI and OpenMP (on Linux boxes)
# preset that will enable the LLVM based Intel compilers with support for MPI and OpenMP and Fortran (on Linux boxes)
set(CMAKE_CXX_COMPILER "icpx" CACHE STRING "" FORCE)
set(CMAKE_C_COMPILER "icx" CACHE STRING "" FORCE)
set(CMAKE_Fortran_COMPILER "ifx" CACHE STRING "" FORCE)
set(CMAKE_CXX_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE)
set(CMAKE_CXX_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
set(CMAKE_CXX_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
set(CMAKE_Fortran_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE)
set(CMAKE_Fortran_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
set(CMAKE_Fortran_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
set(CMAKE_C_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE)
set(CMAKE_C_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
set(CMAKE_C_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
set(MPI_CXX "icpx" CACHE STRING "" FORCE)
set(MPI_CXX_COMPILER "mpicxx" CACHE STRING "" FORCE)
unset(HAVE_OMP_H_INCLUDE CACHE)
unset(HAVE_OMP_H_INCLUDE CACHE)
set(OpenMP_C "icx" CACHE STRING "" FORCE)
set(OpenMP_C_FLAGS "-qopenmp" CACHE STRING "" FORCE)
set(OpenMP_C_LIB_NAMES "omp" CACHE STRING "" FORCE)

2
doc/Makefile
View File

@ -236,7 +236,7 @@ $(VENV):
)
$(MATHJAX):
@git clone --depth 1 git://github.com/mathjax/MathJax.git $@
@git clone -b 3.1.4 -c advice.detachedHead=0 --depth 1 git://github.com/mathjax/MathJax.git $@
$(TXT2RST) $(ANCHORCHECK): $(VENV)
@( \

2
doc/lammps.1
View File

@ -1,4 +1,4 @@
.TH LAMMPS "8 April 2021" "2021-04-08"
.TH LAMMPS "14 May 2021" "2021-05-14"
.SH NAME
.B LAMMPS
\- Molecular Dynamics Simulator.

22
doc/src/Build_development.rst
View File

@ -28,6 +28,28 @@ variable VERBOSE set to 1:
----------
.. _clang-tidy
Enable static code analysis with clang-tidy
-------------------------------------------
The `clang-tidy tool <https://clang.llvm.org/extra/clang-tidy/>`_ is a
static code analysis tool to diagnose (and potentially fix) typical
programming errors or coding style violations. It has a modular framework
of tests that can be adjusted to help identifying problems before they
become bugs and also assist in modernizing large code bases (like LAMMPS).
It can be enabled for all C++ code with the following CMake flag
.. code-block:: bash
-D ENABLE_CLANG_TIDY=value # value = no (default) or yes
With this flag enabled all source files will be processed twice, first to
be compiled and then to be analyzed. Please note that the analysis can be
significantly more time consuming than the compilation itself.
----------
.. _iwyu_processing:
Report missing and unneeded '#include' statements

40
doc/src/Build_extras.rst
View File

@ -49,6 +49,7 @@ This is the list of packages that may require additional steps.
* :ref:`USER-COLVARS <user-colvars>`
* :ref:`USER-H5MD <user-h5md>`
* :ref:`USER-INTEL <user-intel>`
* :ref:`USER-MDI <user-mdi>`
* :ref:`USER-MESONT <user-mesont>`
* :ref:`USER-MOLFILE <user-molfile>`
* :ref:`USER-NETCDF <user-netcdf>`
@ -467,6 +468,9 @@ They must be specified in uppercase.
* - ARMV8_THUNDERX2
- HOST
- ARMv8 Cavium ThunderX2 CPU
* - A64FX
- HOST
- ARMv8.2 with SVE Support
* - WSM
- HOST
- Intel Westmere CPU (SSE 4.2)
@ -539,6 +543,9 @@ They must be specified in uppercase.
* - AMPERE80
- GPU
- NVIDIA Ampere generation CC 8.0 GPU
* - AMPERE86
- GPU
- NVIDIA Ampere generation CC 8.6 GPU
* - VEGA900
- GPU
- AMD GPU MI25 GFX900
@ -547,12 +554,12 @@ They must be specified in uppercase.
- AMD GPU MI50/MI60 GFX906
* - VEGA908
- GPU
- AMD GPU GFX908
- AMD GPU MI100 GFX908
* - INTEL_GEN
- GPU
- Intel GPUs Gen9+
This list was last updated for version 3.3 of the Kokkos library.
This list was last updated for version 3.4 of the Kokkos library.
.. tabs::
@ -1533,6 +1540,35 @@ TBB and MKL.
----------
.. _user-mdi:
USER-MDI package
-----------------------------
.. tabs::
.. tab:: CMake build
.. code-block:: bash
-D DOWNLOAD_MDI=value # download MDI Library for build, value = no (default) or yes
.. tab:: Traditional make
Before building LAMMPS, you must build the MDI Library in
``lib/mdi``\ . You can do this by executing a command like one
of the following from the ``lib/mdi`` directory:
.. code-block:: bash
$ python Install.py -m gcc # build using gcc compiler
$ python Install.py -m icc # build using icc compiler
The build should produce two files: ``lib/mdi/includelink/mdi.h``
and ``lib/mdi/liblink/libmdi.so``\ .
----------
.. _user-mesont:
USER-MESONT package

1
doc/src/Commands_all.rst
View File

@ -67,6 +67,7 @@ An alphabetic list of all general LAMMPS commands.
* :doc:`lattice <lattice>`
* :doc:`log <log>`
* :doc:`mass <mass>`
* :doc:`mdi/engine <mdi_engine>`
* :doc:`message <message>`
* :doc:`minimize <minimize>`
* :doc:`min_modify <min_modify>`

4
doc/src/Commands_fix.rst
View File

@ -39,6 +39,9 @@ OPT.
* :doc:`ave/time <fix_ave_time>`
* :doc:`aveforce <fix_aveforce>`
* :doc:`balance <fix_balance>`
* :doc:`brownian <fix_brownian>`
* :doc:`brownian/asphere <fix_brownian>`
* :doc:`brownian/sphere <fix_brownian>`
* :doc:`bocs <fix_bocs>`
* :doc:`bond/break <fix_bond_break>`
* :doc:`bond/create <fix_bond_create>`
@ -98,6 +101,7 @@ OPT.
* :doc:`lb/viscous <fix_lb_viscous>`
* :doc:`lineforce <fix_lineforce>`
* :doc:`manifoldforce <fix_manifoldforce>`
* :doc:`mdi/engine <fix_mdi_engine>`
* :doc:`meso/move <fix_meso_move>`
* :doc:`momentum (k) <fix_momentum>`
* :doc:`momentum/chunk <fix_momentum>`

4
doc/src/Commands_pair.rst
View File

@ -87,6 +87,8 @@ OPT.
* :doc:`coul/wolf/cs <pair_cs>`
* :doc:`dpd (gio) <pair_dpd>`
* :doc:`dpd/fdt <pair_dpd_fdt>`
* :doc:`dpd/ext <pair_dpd_ext>`
* :doc:`dpd/ext/tstat <pair_dpd_ext>`
* :doc:`dpd/fdt/energy (k) <pair_dpd_fdt>`
* :doc:`dpd/tstat (go) <pair_dpd>`
* :doc:`dsmc <pair_dsmc>`
@ -169,7 +171,7 @@ OPT.
* :doc:`lj/sdk/coul/long (go) <pair_sdk>`
* :doc:`lj/sdk/coul/msm (o) <pair_sdk>`
* :doc:`lj/sf/dipole/sf (go) <pair_dipole>`
* :doc:`lj/smooth (o) <pair_lj_smooth>`
* :doc:`lj/smooth (go) <pair_lj_smooth>`
* :doc:`lj/smooth/linear (o) <pair_lj_smooth_linear>`
* :doc:`lj/switch3/coulgauss/long <pair_lj_switch3_coulgauss_long>`
* :doc:`lj96/cut (go) <pair_lj96>`

40
doc/src/Developer_utils.rst
View File

@ -9,14 +9,29 @@ reading or writing to files with error checking or translation of
strings into specific types of numbers with checking for validity. This
reduces redundant implementations and encourages consistent behavior.
I/O with status check
^^^^^^^^^^^^^^^^^^^^^
I/O with status check and similar functions
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
These are wrappers around the corresponding C library calls like
``fgets()`` or ``fread()``. They will check if there were errors
on reading or an unexpected end-of-file state was reached. In that
case, the functions will stop the calculation with an error message,
indicating the name of the problematic file, if possible.
The the first two functions are wrappers around the corresponding C
library calls ``fgets()`` or ``fread()``. They will check if there
were errors on reading or an unexpected end-of-file state was reached.
In that case, the functions will stop with an error message, indicating
the name of the problematic file, if possible unless the *error* argument
is a NULL pointer.
The :cpp:func:`fgets_trunc` function will work similar for ``fgets()``
but it will read in a whole line (i.e. until the end of line or end
of file), but store only as many characters as will fit into the buffer
including a final newline character and the terminating NULL byte.
If the line in the file is longer it will thus be truncated in the buffer.
This function is used by :cpp:func:`read_lines_from_file` to read individual
lines but make certain they follow the size constraints.
The :cpp:func:`read_lines_from_file` function will read the requested
number of lines of a maximum length into a buffer and will return 0
if successful or 1 if not. It also guarantees that all lines are
terminated with a newline character and the entire buffer with a
NULL character.
----------
@ -26,6 +41,12 @@ indicating the name of the problematic file, if possible.
.. doxygenfunction:: sfread
:project: progguide
.. doxygenfunction:: fgets_trunc
:project: progguide
.. doxygenfunction:: read_lines_from_file
:project: progguide
----------
String to number conversions with validity check
@ -164,7 +185,10 @@ Argument processing
Convenience functions
^^^^^^^^^^^^^^^^^^^^^
.. doxygenfunction:: logmesg
.. doxygenfunction:: logmesg(LAMMPS *lmp, const S &format, Args&&... args)
:project: progguide
.. doxygenfunction:: logmesg(LAMMPS *lmp, const std::string &mesg)
:project: progguide
.. doxygenfunction:: getsyserror

2
doc/src/Examples.rst
View File

@ -108,6 +108,8 @@ Lowercase directories
+-------------+------------------------------------------------------------------+
| msst | MSST shock dynamics |
+-------------+------------------------------------------------------------------+
| multi | multi neighboring for systems with large interaction disparities |
+-------------+------------------------------------------------------------------+
| nb3b | use of non-bonded 3-body harmonic pair style |
+-------------+------------------------------------------------------------------+
| neb | nudged elastic band (NEB) calculation for barrier finding |

1
doc/src/Howto.rst
View File

@ -23,6 +23,7 @@ General howto
Howto_library
Howto_couple
Howto_client_server
Howto_mdi
Settings howto
==============

2
doc/src/Howto_drude2.rst
View File

@ -9,6 +9,8 @@ USER-DRUDE package activated. Then, the data file and input scripts
have to be modified to include the Drude dipoles and how to handle
them.
Example input scripts available: examples/USER/drude
----------
**Overview of Drude induced dipoles**

132
doc/src/Howto_mdi.rst Normal file
View File

@ -0,0 +1,132 @@
Using LAMMPS with the MDI library for code coupling
===================================================
.. note::
This Howto doc page will eventually replace the
:doc:`Howto client/server <Howto_client_server>` doc page.
Client/server coupling of two codes is where one code is the "client"
and sends request messages (data) to a "server" code. The server
responds to each request with a reply message. This enables the two
codes to work in tandem to perform a simulation. LAMMPS can act as
either a client or server code; it does this by using the `MolSSI
Driver Interface (MDI) library
<https://molssi-mdi.github.io/MDI_Library/html/index.html>`_,
developed by the `Molecular Sciences Software Institute (MolSSI)
<https://molssi.org>`_.
Alternate methods for code coupling with LAMMPS are described on the
:doc:`Howto couple <Howto_couple>` doc page.
Some advantages of client/server coupling are that the two codes can run
as stand-alone executables; they need not be linked together. Thus
neither code needs to have a library interface. This also makes it easy
to run the two codes on different numbers of processors. If a message
protocol (format and content) is defined for a particular kind of
simulation, then in principle any code which implements the client-side
protocol can be used in tandem with any code which implements the
server-side protocol. Neither code needs to know what specific other
code it is working with.
In MDI nomenclature, a client code is the "driver", and a server code is
an "engine". One driver code can communicate with one or more instances
of one or more engine codes. Driver and engine codes can be written in
any language: C, C++, Fortran, Python, etc.
In addition to allowing driver and engine(s) running to run as
stand-alone executables, MDI also enables a server code to be a
"plugin" to the client code. In this scenario, server code(s) are
compiled as shared libraries, and one (or more) instances of the
server are instantiated by the driver code. If the driver code runs
in parallel, it can split its MPI communicator into multiple
sub-communicators, and launch each plugin engine instance on a
sub-communicator. Driver processors in that sub-communicator exchange
messages with that engine instance, and can also send MPI messages to
other processors in the driver. The driver code can also destroy
engine instances and re-instantiate them.
The way that a driver communicates with an engine is by making
MDI_Send() and MDI_Recv() calls, which are conceptually similar to
MPI_Send() and MPI_Recv() calls. Each send or receive has a string
which identifies the command name, and optionally some data, which can
be a single value or vector of values of any data type. Inside the
MDI library, data is exchanged between the driver and engine via MPI
calls or sockets. This a run-time choice by the user.
-------------
As an example, LAMMPS and the ``pw.x`` command from Quantum Espresso (a
suite of quantum DFT codes), can work together via the MDI library to
perform an ab initio MD (AIMD) simulation, where LAMMPS runs an MD
simulation and sends a message each timestep to ``pw.x`` asking it to
compute quantum forces on the current configuration of atoms. Here is
how the 2 codes are launched to communicate by MPI:
.. code-block:: bash
% mpirun -np 2 lmp_mpi -mdi "-role DRIVER -name d -method MPI" \
-in in.aimd : -np 16 pw.x -in qe.in -mdi "-role ENGINE -name e -method MPI"
In this case LAMMPS runs on 2 processors (MPI tasks), ``pw.x`` runs on 16
processors.
Here is how the 2 codes are launched to communicate by sockets:
.. code-block:: bash
% mpirun -np 2 lmp_mpi -mdi "-role DRIVER -name d -method TCP -port 8021" -in in.aimd
% mpirun -np 16 pw.x -in qe.in -mdi "-role ENGINE -name e -method TCP -port 8021 -hostname localhost"
These commands could be issued in different windows on a desktop
machine. Or in the same window, if the first command is ended with
"&" so as to run in the background. If "localhost" is replaced by an
IP address, ``pw.x`` could be run on another machine on the same network, or
even on another machine across the country.
After both codes initialize themselves to model the same system, this is
what occurs each timestep:
* LAMMPS send a ">COORDS" message to ``pw.x`` with a 3*N vector of current atom coords
* ``pw.x`` receives the message/coords and computes quantum forces on all the atoms
* LAMMPS send a "<FORCES" message to ``pw.x`` and waits for the result
* ``pw.x`` receives the message (after its computation finishes) and sends a 3*N vector of forces
* LAMMPS receives the forces and time integrates to complete a single timestep
-------------
Examples scripts for using LAMMPS as an MDI engine are in the
examples/mdi directory. See the README file in that directory for
instructions on how to run the examples.
.. note::
Work is underway to add commands that allow LAMMPS to be used as an
MDI driver, e.g. for the AIMD example discussed above. Example
scripts for this usage mode will be added the same directory when
available.
If LAMMPS is used as a stand-alone engine it should set up the system
it will be modeling in its input script, then invoke the
:doc:`mdi/engine <mdi_engine>` command. This will put LAMMPS into
"engine mode" where it waits for messages and data from the driver.
When the driver sends an "EXIT" command, LAMMPS will exit engine mode
and the input script will continue.
If LAMMPS is used as a plugin engine it operates the same way, except
that the driver will pass LAMMPS an input script to initialize itself.
Upon receiving the "EXIT" command, LAMMPS will exit engine mode and the
input script will continue. After finishing execution of the input
script, the instance of LAMMPS will be destroyed.
LAMMPS supports the full set of MD-appropriate engine commands defined
by the MDI library. See the :doc:`mdi/engine <mdi_engine>` doc page for
a list of these.
If those commands are not sufficient for a user-developed driver to use
LAMMPS as an engine, then new commands can be easily added. See these
two files which implement the definition of MDI commands and the logic
for responding to them:
* src/MDI/mdi_engine.cpp
* src/MDI/fix_mdi_engine.cpp

12
doc/src/Library_config.rst
View File

@ -15,6 +15,8 @@ This section documents the following functions:
- :cpp:func:`lammps_config_package_count`
- :cpp:func:`lammps_config_package_name`
- :cpp:func:`lammps_config_accelerator`
- :cpp:func:`lammps_has_gpu_device`
- :cpp:func:`lammps_gpu_device_info`
- :cpp:func:`lammps_has_style`
- :cpp:func:`lammps_style_count`
- :cpp:func:`lammps_style_name`
@ -132,6 +134,16 @@ approach.
-----------------------
.. doxygenfunction:: lammps_has_gpu_device
:project: progguide
-----------------------
.. doxygenfunction:: lammps_get_gpu_device_info
:project: progguide
-----------------------
.. doxygenfunction:: lammps_has_style
:project: progguide

13
doc/src/Manual.rst
View File

@ -89,10 +89,15 @@ Programmer Guide
Modify
Developer
*****************
Command Reference
*****************
.. _command_reference:
.. toctree::
:caption: Index
:name: index
:hidden:
:name: reference
:maxdepth: 1
:caption: Command Reference
commands_list
fixes
@ -118,7 +123,7 @@ Indices and tables
.. admonition:: Web Browser Compatibility
The HTML version of the manual makes use of advanced features present
int "modern" web browsers. This can lead to incompatibilities with older
in "modern" web browsers. This can lead to incompatibilities with older
web browsers (released more than 4 years ago) and specific vendor browsers
(e.g. Internet Explorer on Windows; Microsoft Edge works well though)
where parts of the pages are not rendered as expected (e.g. the layout is

73
doc/src/Modify_contribute.rst
View File

@ -10,15 +10,15 @@ Tutorial <Howto_github>` for a demonstration on how to do that. An
alternative is to contact the LAMMPS developers or the indicated
developer of a package or feature directly and send in your contribution
via e-mail, but that can add a significant delay on getting your
contribution included, depending on how busy the developer is you
contact, how complex a task it would be to integrate that code, and how
contribution included, depending on how busy the respective developer
is, how complex a task it would be to integrate that code, and how
many - if any - changes are required before the code can be included.
For any larger modifications or programming project, you are encouraged
to contact the LAMMPS developers ahead of time, in order to discuss
implementation strategies and coding guidelines, that will make it
easier to integrate your contribution and result in less work for
everybody involved. You are also encouraged to search through the list
to contact the LAMMPS developers ahead of time in order to discuss
implementation strategies and coding guidelines. That will make it
easier to integrate your contribution and results in less work for
everybody involved. You are also encouraged to search through the list
of `open issues on GitHub <https://github.com/lammps/lammps/issues>`_
and submit a new issue for a planned feature, so you would not duplicate
the work of others (and possibly get scooped by them) or have your work
@ -34,18 +34,19 @@ installing, or using LAMMPS. Please contact the `lammps-users mailing
list <https://lammps.sandia.gov/mail.html>`_ for those purposes instead.
How quickly your contribution will be integrated depends largely on how
much effort it will cause to integrate and test it, how much it requires
changes to the core codebase, and of how much interest it is to the
larger LAMMPS community. Please see below for a checklist of typical
requirements. Once you have prepared everything, see the :doc:`LAMMPS GitHub
Tutorial <Howto_github>` page for instructions on
how to submit your changes or new files through a GitHub pull
request. If you prefer to submit patches or full files, you should first
make certain, that your code works correctly with the latest patch-level
version of LAMMPS and contains all bug fixes from it. Then create a
gzipped tar file of all changed or added files or a corresponding patch
file using 'diff -u' or 'diff -c' and compress it with gzip. Please only
use gzip compression, as this works well on all platforms.
much effort it will cause to integrate and test it, how many and what
kind of changes it requires to the core codebase, and of how much
interest it is to the larger LAMMPS community. Please see below for a
checklist of typical requirements. Once you have prepared everything,
see the :doc:`LAMMPS GitHub Tutorial <Howto_github>` page for
instructions on how to submit your changes or new files through a GitHub
pull request. If you prefer to submit patches or full files, you should
first make certain, that your code works correctly with the latest
patch-level version of LAMMPS and contains all bug fixes from it. Then
create a gzipped tar file of all changed or added files or a
corresponding patch file using 'diff -u' or 'diff -c' and compress it
with gzip. Please only use gzip compression, as this works well and is
available on all platforms.
If the new features/files are broadly useful we may add them as core
files to LAMMPS or as part of a :doc:`standard package <Packages_standard>`. Else we will add them as a
@ -57,9 +58,12 @@ added to the LAMMPS distribution. All the standard and user packages
are listed and described on the :doc:`Packages details <Packages_details>` doc page.
Note that by providing us files to release, you are agreeing to make
them open-source, i.e. we can release them under the terms of the GPL,
used as a license for the rest of LAMMPS. See the :doc:`LAMMPS license
<Intro_opensource>` doc page for details.
them open-source, i.e. we can release them under the terms of the GPL
(version 2), used as a license for the rest of LAMMPS. And as part of
a LGPL (version 2.1) distribution that we make available to developers
on request only and with files that are authorized for that kind of
distribution removed (e.g. interface to FFTW). See the
:doc:`LAMMPS license <Intro_opensource>` doc page for details.
With user packages and files, all we are really providing (aside from
the fame and fortune that accompanies having your name in the source
@ -112,7 +116,7 @@ packages in the src directory for examples. If you are uncertain, please ask.
your contribution(s) to be added to main LAMMPS code or one of its
standard packages, it needs to be written in a style compatible with
other LAMMPS source files. This means: 2-character indentation per
level, **no tabs**\ , no lines over 80 characters. I/O is done via
level, **no tabs**\ , no lines over 100 characters. I/O is done via
the C-style stdio library (mixing of stdio and iostreams is generally
discouraged), class header files should not import any system headers
outside of <cstdio>, STL containers should be avoided in headers,
@ -131,6 +135,31 @@ packages in the src directory for examples. If you are uncertain, please ask.
LAMMPS source files, including the use of the error class for error
and warning messages.
* To simplify reformatting contributed code in a way that is compatible
with the LAMMPS formatting styles, you can use clang-format (version 8
or later). The LAMMPS distribution includes a suitable ``.clang-format``
file which will be applied if you run ``clang-format -i some_file.cpp``
on your files inside the LAMMPS src tree. Please only reformat files
that you have contributed. For header files containing a
``SomeStyle(keyword, ClassName)`` macros it is required to have this
macro embedded with a pair of ``// clang-format off``, ``// clang-format on``
commends and the line must be terminated with a semi-colon (;).
Example:
.. code-block:: c++
#ifdef COMMAND_CLASS
// clang-format off
CommandStyle(run,Run);
// clang-format on
#else
#ifndef LMP_RUN_H
[...]
You may also use ``// clang-format on/off`` throughout your file
to protect sections of the file from being reformatted.
* If you want your contribution to be added as a user-contributed
feature, and it's a single file (actually a \*.cpp and \*.h file) it can
rapidly be added to the USER-MISC directory. Send us the one-line

46
doc/src/Packages_details.rst
View File

@ -69,6 +69,7 @@ page gives those details.
* :ref:`USER-ATC <PKG-USER-ATC>`
* :ref:`USER-AWPMD <PKG-USER-AWPMD>`
* :ref:`USER-BOCS <PKG-USER-BOCS>`
* :ref:`USER-BROWNIAN <PKG-USER-BROWNIAN>`
* :ref:`USER-CGDNA <PKG-USER-CGDNA>`
* :ref:`USER-CGSDK <PKG-USER-CGSDK>`
* :ref:`USER-COLVARS <PKG-USER-COLVARS>`
@ -81,6 +82,7 @@ page gives those details.
* :ref:`USER-INTEL <PKG-USER-INTEL>`
* :ref:`USER-LB <PKG-USER-LB>`
* :ref:`USER-MANIFOLD <PKG-USER-MANIFOLD>`
* :ref:`USER-MDI <PKG-USER-MDI>`
* :ref:`USER-MEAMC <PKG-USER-MEAMC>`
* :ref:`USER-MESODPD <PKG-USER-MESODPD>`
* :ref:`USER-MESONT <PKG-USER-MESONT>`
@ -445,7 +447,7 @@ time via the "-sf kk" or "-suffix kk" :doc:`command-line switches <Run_options>`
:ref:`USER-INTEL <PKG-USER-INTEL>`, and :ref:`USER-OMP <PKG-USER-OMP>` packages, which
have styles optimized for CPUs, KNLs, and GPUs.
You must have a C++11 compatible compiler to use this package.
You must have a C++14 compatible compiler to use this package.
KOKKOS makes extensive use of advanced C++ features, which can
expose compiler bugs, especially when compiling for maximum
performance at high optimization levels. Please see the file
@ -1266,6 +1268,26 @@ Example inputs are in the examples/USER/bocs folder.
----------
.. _PKG-USER-BROWNIAN:
USER-BROWNIAN package
---------------------
**Contents:**
This package provides :doc:`fix brownian, fix brownian/sphere, and
fix brownian/asphere <fix_brownian>` as well as
:doc:`fix propel/self <fix_propel_self>` which allow to do Brownian
Dynamics time integration of point, spherical and aspherical particles
and also support self-propelled particles.
**Authors:** Sam Cameron (University of Bristol),
Stefan Paquay (while at Brandeis University) (initial version of fix propel/self)
Example inputs are in the examples/USER/brownian folder.
----------
.. _PKG-USER-CGDNA:
USER-CGDNA package
@ -1770,6 +1792,28 @@ Waltham, MA, USA)
----------
.. _PKG-USER-MDI:
USER-MDI package
----------------
**Contents:**
A LAMMPS command and fix to allow client-server coupling of LAMMPS to
other atomic or molecular simulation codes via the `MolSSI Driver Interface
(MDI) library <https://molssi-mdi.github.io/MDI_Library/html/index.html>`_.
**Author:** Taylor Barnes - MolSSI, taylor.a.barnes at gmail.com
**Supporting info:**
* src/USER-MDI/README
* :doc:`mdi/engine <mdi_engine>`
* :doc:`fix mdi/engine <fix_mdi_engine>`
* examples/USER/mdi
----------
.. _PKG-USER-MEAMC:
USER-MEAMC package

4
doc/src/Packages_user.rst
View File

@ -39,6 +39,8 @@ package:
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-BOCS <PKG-USER-BOCS>` | BOCS bottom up coarse graining | :doc:`fix bocs <fix_bocs>` | USER/bocs | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-BROWNIAN <PKG-USER-BROWNIAN>` | Brownian dynamics and self-propelled particles | :doc:`fix brownian <fix_brownian>`, :doc:`fix propel/self <fix_propel_self>` | USER/brownian | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-CGDNA <PKG-USER-CGDNA>` | coarse-grained DNA force fields | src/USER-CGDNA/README | USER/cgdna | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-CGSDK <PKG-USER-CGSDK>` | SDK coarse-graining model | :doc:`pair_style lj/sdk <pair_sdk>` | USER/cgsdk | no |
@ -63,6 +65,8 @@ package:
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-MANIFOLD <PKG-USER-MANIFOLD>` | motion on 2d surfaces | :doc:`fix manifoldforce <fix_manifoldforce>` | USER/manifold | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-MDI <PKG-USER-MDI>` | client-server coupling | :doc:`MDI Howto <Howto_mdi>` | USER/mdi | ext |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-MEAMC <PKG-USER-MEAMC>` | modified EAM potential (C++) | :doc:`pair_style meam/c <pair_meamc>` | meamc | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-MESODPD <PKG-USER-MESODPD>` | mesoscale DPD models | :doc:`pair_style edpd <pair_mesodpd>` | USER/mesodpd | no |

19
doc/src/Run_options.rst
View File

@ -10,6 +10,7 @@ letter abbreviation can be used:
* :ref:`-i or -in <file>`
* :ref:`-k or -kokkos <run-kokkos>`
* :ref:`-l or -log <log>`
* :ref:`-mdi <mdi>`
* :ref:`-m or -mpicolor <mpicolor>`
* :ref:`-c or -cite <cite>`
* :ref:`-nc or -nocite <nocite>`
@ -196,9 +197,23 @@ Option -plog will override the name of the partition log files file.N.
----------
.. _mdi:
**-mdi 'multiple flags'**
This flag is only recognized and used when LAMMPS has support for the MolSSI
Driver Interface (MDI) included as part of the :ref:`USER-MDI <PKG-USER-MDI>`
package. This flag is specific to the MDI library and controls how LAMMPS
interacts with MDI. There are usually multiple flags that have to follow it
and those have to be placed in quotation marks. For more information about
how to launch LAMMPS in MDI client/server mode please refer to the
:doc:`MDI Howto <Howto_mdi>`.
----------
.. _mpicolor:
**-mpicolor** color
**-mpicolor color**
If used, this must be the first command-line argument after the LAMMPS
executable name. It is only used when LAMMPS is launched by an mpirun
@ -223,7 +238,7 @@ links with from the lib/message directory. See the
.. _cite:
**-cite style or file name**
**-cite style** or **file name**
Select how and where to output a reminder about citing contributions
to the LAMMPS code that were used during the run. Available styles are

98
doc/src/Tools.rst
View File

@ -94,6 +94,7 @@ Miscellaneous tools
* :ref:`kate <kate>`
* :ref:`LAMMPS shell <lammps_shell>`
* :ref:`LAMMPS magic patterns for file(1) <magic>`
* :ref:`Offline build tool <offline>`
* :ref:`singularity <singularity_tool>`
* :ref:`SWIG interface <swig>`
* :ref:`vim <vim>`
@ -756,6 +757,103 @@ See the README file in the tools/msi2lmp folder for more information.
----------
.. _offline:
Scripts for building LAMMPS when offline
----------------------------------------
In some situations it might be necessary to build LAMMPS on a system
without direct internet access. The scripts in ``tools/offline`` folder
allow you to pre-load external dependencies for both the documentation
build and for building LAMMPS with CMake.
It does so by
#. downloading necessary ``pip`` packages,
#. cloning ``git`` repositories
#. downloading tarballs
to a designated cache folder.
As of April 2021, all of these downloads make up around 600MB. By
default, the offline scripts will download everything into the
``$HOME/.cache/lammps`` folder, but this can be changed by setting the
``LAMMPS_CACHING_DIR`` environment variable.
Once the caches have been initialized, they can be used for building the
LAMMPS documentation or compiling LAMMPS using CMake on an offline
system.
The ``use_caches.sh`` script must be sourced into the current shell
to initialize the offline build environment. Note that it must use
the same ``LAMMPS_CACHING_DIR``. This script does the following:
#. Set up environment variables that modify the behavior of both,
``pip`` and ``git``
#. Start a simple local HTTP server using Python to host files for CMake
Afterwards, it will print out instruction on how to modify the CMake
command line to make sure it uses the local HTTP server.
To undo the environment changes and shutdown the local HTTP server,
run the ``deactivate_caches`` command.
Examples
^^^^^^^^
For all of the examples below, you first need to create the cache, which
requires an internet connection.
.. code-block:: bash
./tools/offline/init_caches.sh
Afterwards, you can disconnect or copy the contents of the
``LAMMPS_CACHING_DIR`` folder to an offline system.
Documentation Build
^^^^^^^^^^^^^^^^^^^
The documentation build will create a new virtual environment that
typically first installs dependencies from ``pip``. With the offline
environment loaded, these installations will instead grab the necessary
packages from your local cache.
.. code-block:: bash
# if LAMMPS_CACHING_DIR is different from default, make sure to set it first
# export LAMMPS_CACHING_DIR=path/to/folder
source tools/offline/use_caches.sh
cd doc/
make html
deactivate_caches
CMake Build
^^^^^^^^^^^
When compiling certain packages with external dependencies, the CMake
build system will download necessary files or sources from the web. For
more flexibility the CMake configuration allows users to specify the URL
of each of these dependencies. What the ``init_caches.sh`` script does
is create a CMake "preset" file, which sets the URLs for all of the known
dependencies and redirects the download to the local cache.
.. code-block:: bash
# if LAMMPS_CACHING_DIR is different from default, make sure to set it first
# export LAMMPS_CACHING_DIR=path/to/folder
source tools/offline/use_caches.sh
mkdir build
cd build
cmake -D LAMMPS_DOWNLOADS_URL=${HTTP_CACHE_URL} -C "${LAMMPS_HTTP_CACHE_CONFIG}" -C ../cmake/presets/most.cmake ../cmake
make -j 8
deactivate_caches
----------
.. _phonon:
phonon tool

1
doc/src/angle_table.rst
View File

@ -69,7 +69,6 @@ parenthesized comments):
HAM (keyword is the first text on line)
N 181 FP 0 0 EQ 90.0 (N, FP, EQ parameters)
(blank line)
N 181 FP 0 0 (N, FP parameters)
1 0.0 200.5 2.5 (index, angle, energy, derivative)
2 1.0 198.0 2.5
...

58
doc/src/comm_modify.rst
View File

@ -11,13 +11,17 @@ Syntax
comm_modify keyword value ...
* zero or more keyword/value pairs may be appended
* keyword = *mode* or *cutoff* or *cutoff/multi* or *group* or *vel*
* keyword = *mode* or *cutoff* or *cutoff/multi* or *multi/reduce* or *group* or *vel*
.. parsed-literal::
*mode* value = *single* or *multi* = communicate atoms within a single or multiple distances
*mode* value = *single*, *multi*, or *multi/old* = communicate atoms within a single or multiple distances
*cutoff* value = Rcut (distance units) = communicate atoms from this far away
*cutoff/multi* type value
*cutoff/multi* collection value
collection = atom collection or collection range (supports asterisk notation)
value = Rcut (distance units) = communicate atoms for selected types from this far away
*reduce/multi* arg = none = reduce number of communicated ghost atoms for multi style
*cutoff/multi/old* type value
type = atom type or type range (supports asterisk notation)
value = Rcut (distance units) = communicate atoms for selected types from this far away
*group* value = group-ID = only communicate atoms in the group
@ -28,9 +32,9 @@ Examples
.. code-block:: LAMMPS
comm_modify mode multi
comm_modify mode multi reduce/multi
comm_modify mode multi group solvent
comm_modift mode multi cutoff/multi 1 10.0 cutoff/multi 2*4 15.0
comm_modify mode multi cutoff/multi 1 10.0 cutoff/multi 2*4 15.0
comm_modify vel yes
comm_modify mode single cutoff 5.0 vel yes
comm_modify cutoff/multi * 0.0
@ -62,12 +66,18 @@ sub-domain. The distance is by default the maximum of the neighbor
cutoff across all atom type pairs.
For many systems this is an efficient algorithm, but for systems with
widely varying cutoffs for different type pairs, the *multi* mode can
be faster. In this case, each atom type is assigned its own distance
widely varying cutoffs for different type pairs, the *multi* or *multi/old* mode can
be faster. In *multi*, each atom is assigned to a collection which should
correspond to a set of atoms with similar interaction cutoffs.
In this case, each atom collection is assigned its own distance
cutoff for communication purposes, and fewer atoms will be
communicated. See the :doc:`neighbor multi <neighbor>` command for a
neighbor list construction option that may also be beneficial for
simulations of this kind.
communicated. in *multi/old*, a similar technique is used but atoms
are grouped by atom type. See the :doc:`neighbor multi <neighbor>` and
:doc:`neighbor multi/old <neighbor>` commands for
neighbor list construction options that may also be beneficial for
simulations of this kind. The *multi* communication mode is only compatible
with the *multi* neighbor style. The *multi/old* communication mode is comparable
with both the *multi* and *multi/old* neighbor styles.
The *cutoff* keyword allows you to extend the ghost cutoff distance
for communication mode *single*\ , which is the distance from the borders
@ -87,12 +97,26 @@ warning is printed, if this bond based estimate is larger than the
communication cutoff used.
The *cutoff/multi* option is equivalent to *cutoff*\ , but applies to
communication mode *multi* instead. Since in this case the communication
cutoffs are determined per atom type, a type specifier is needed and
cutoff for one or multiple types can be extended. Also ranges of types
using the usual asterisk notation can be given. For granular pair styles,
the default cutoff is set to the sum of the current maximum atomic radii
for each type.
communication mode *multi* instead. Since the communication cutoffs are
determined per atom collections, a collection specifier is needed and
cutoff for one or multiple collections can be extended. Also ranges of
collections using the usual asterisk notation can be given. Collections
are indexed from 1 to N where N is the total number of collections.
Note that the arguments for *cutoff/multi* are parsed right before each
simulation to account for potential changes in the number of
collections. Custom cutoffs are preserved between runs but if
collections are redefined, one may want to re-specify the communication
cutoffs. For granular pair styles,the default cutoff is set to the sum
of the current maximum atomic radii for each collection. The
*cutoff/multi/old* option is similar to *cutoff/multi* except it
operates on atom types as opposed to collections.
The *reduce/multi* option applies to *multi* and sets the communication
cutoff for a particle equal to the maximum interaction distance between particles
in the same collection. This reduces the number of
ghost atoms that need to be communicated. This method is only compatible with the
*multi* neighbor style and requires a half neighbor list and Newton on.
See the :doc:`neighbor multi <neighbor>` command for more information.
These are simulation scenarios in which it may be useful or even
necessary to set a ghost cutoff > neighbor cutoff:
@ -123,7 +147,7 @@ ghost cutoff should be set.
In the last scenario, a :doc:`fix <fix>` or :doc:`compute <compute>` or
:doc:`pairwise potential <pair_style>` needs to calculate with ghost
atoms beyond the normal pairwise cutoff for some computation it
performs (e.g. locate neighbors of ghost atoms in a multibody pair
performs (e.g. locate neighbors of ghost atoms in a manybody pair
potential). Setting the ghost cutoff appropriately can insure it will
find the needed atoms.

1
doc/src/commands_list.rst
View File

@ -59,6 +59,7 @@ Commands
lattice
log
mass
mdi_engine
message
min_modify
min_spin

2
doc/src/compute_fep.rst
View File

@ -48,6 +48,8 @@ Examples
compute 1 all fep 298 pair lj/cut epsilon 1 * v_delta pair lj/cut sigma 1 * v_delta volume yes
compute 1 all fep 300 atom charge 2 v_delta
Example input scripts available: examples/USER/fep
Description
"""""""""""

2
doc/src/compute_temp_drude.rst
View File

@ -20,6 +20,8 @@ Examples
compute TDRUDE all temp/drude
Example input scripts available: examples/USER/drude
Description
"""""""""""

4
doc/src/fix.rst
View File

@ -182,6 +182,9 @@ accelerated styles exist.
* :doc:`ave/time <fix_ave_time>` - compute/output global time-averaged quantities
* :doc:`aveforce <fix_aveforce>` - add an averaged force to each atom
* :doc:`balance <fix_balance>` - perform dynamic load-balancing
* :doc:`brownian <fix_brownian>` - overdamped translational brownian motion
* :doc:`brownian/asphere <fix_brownian>` - overdamped translational and rotational brownian motion for ellipsoids
* :doc:`brownian/sphere <fix_brownian>` - overdamped translational and rotational brownian motion for spheres
* :doc:`bocs <fix_bocs>` - NPT style time integration with pressure correction
* :doc:`bond/break <fix_bond_break>` - break bonds on the fly
* :doc:`bond/create <fix_bond_create>` - create bonds on the fly
@ -241,6 +244,7 @@ accelerated styles exist.
* :doc:`lb/viscous <fix_lb_viscous>` -
* :doc:`lineforce <fix_lineforce>` - constrain atoms to move in a line
* :doc:`manifoldforce <fix_manifoldforce>` - restrain atoms to a manifold during minimization
* :doc:`mdi/engine <fix_mdi_engine>` - connect LAMMPS to external programs via the MolSSI Driver Interface (MDI)
* :doc:`meso/move <fix_meso_move>` - move mesoscopic SPH/SDPD particles in a prescribed fashion
* :doc:`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

3
doc/src/fix_adapt_fep.rst
View File

@ -56,6 +56,9 @@ Examples
fix 1 all adapt/fep 1 pair lj/cut epsilon * * v_scale1 coul/cut scale 3 3 v_scale2 scale yes reset yes
fix 1 all adapt/fep 10 atom diameter 1 v_size
Example input scripts available: examples/USER/fep
Description
"""""""""""

43
doc/src/fix_bond_react.rst
View File

@ -328,8 +328,8 @@ keyword 'ChiralIDs' lists the atom IDs of chiral atoms whose
handedness should be enforced. The fifth optional section begins with
the keyword 'Constraints' and lists additional criteria that must be
satisfied in order for the reaction to occur. Currently, there are
five types of constraints available, as discussed below: 'distance',
'angle', 'dihedral', 'arrhenius', and 'rmsd'.
six types of constraints available, as discussed below: 'distance',
'angle', 'dihedral', 'arrhenius', 'rmsd', and 'custom'.
A sample map file is given below:
@ -500,6 +500,45 @@ example, the molecule fragment could consist of only the backbone
atoms of a polymer chain. This constraint can be used to enforce a
specific relative position and orientation between reacting molecules.
The constraint of type 'custom' has the following syntax:
.. parsed-literal::
custom *varstring*
where 'custom' is the required keyword, and *varstring* is a
variable expression. The expression must be a valid equal-style
variable formula that can be read by the :doc:`variable <variable>` command,
after any special reaction functions are evaluated. If the resulting
expression is zero, the reaction is prevented from occurring;
otherwise, it is permitted to occur. There are two special reaction
functions available, 'rxnsum' and 'rxnave'. These functions operate
over the atoms in a given reaction site, and have one mandatory
argument and one optional argument. The mandatory argument is the
identifier for an atom-style variable. The second, optional argument
is the name of a molecule fragment in the pre-reaction template, and
can be used to operate over a subset of atoms in the reaction site.
The 'rxnsum' function sums the atom-style variable over the reaction
site, while the 'rxnave' returns the average value. For example, a
constraint on the total potential energy of atoms involved in the
reaction can be imposed as follows:
.. code-block:: LAMMPS
compute 1 all pe/atom # in LAMMPS input script
variable my_pe atom c_1 # in LAMMPS input script
.. code-block:: LAMMPS
custom "rxnsum(v_my_pe) > 100" # in Constraints section of map file
The above example prevents the reaction from occurring unless the
total potential energy of the reaction site is above 100. The variable
expression can be interpreted as the probability of the reaction
occurring by using an inequality and the 'random(x,y,z)' function
available as an equal-style variable input, similar to the 'arrhenius'
constraint above.
By default, all constraints must be satisfied for the reaction to
occur. In other words, constraints are evaluated as a series of
logical values using the logical AND operator "&&". More complex logic

216
doc/src/fix_brownian.rst Normal file
View File

@ -0,0 +1,216 @@
.. index:: fix brownian
.. index:: fix brownian/sphere
.. index:: fix brownian/asphere
fix brownian command
===========================
fix brownian/sphere command
===========================
fix brownian/sphere command
===========================
Syntax
""""""
.. parsed-literal::
fix ID group-ID style_name temp seed keyword args
* ID, group-ID are documented in :doc:`fix <fix>` command
* style_name = *brownian* or *brownian/sphere* or *brownian/asphere*
* temp = temperature
* seed = random number generator seed
* one or more keyword/value pairs may be appended
* keyword = *rng* or *dipole* or *gamma_r_eigen* or *gamma_t_eigen* or *gamma_r* or *gamma_t*
.. parsed-literal::
*rng* value = *uniform* or *gaussian* or *none*
*uniform* = use uniform random number generator
*gaussian* = use gaussian random number generator
*none* = turn off noise
*dipole* value = *mux* and *muy* and *muz* for *brownian/asphere*
*mux*, *muy*, and *muz* = update orientation of dipole having direction (*mux*,*muy*,*muz*) in body frame of rigid body
*gamma_r_eigen* values = *gr1* and *gr2* and *gr3* for *brownian/asphere*
*gr1*, *gr2*, and *gr3* = diagonal entries of body frame rotational friction tensor
*gamma_r* values = *gr* for *brownian/sphere*
*gr* = magnitude of the (isotropic) rotational friction tensor
*gamma_t_eigen* values = *gt1* and *gt2* and *gt3* for *brownian/asphere*
*gt1*, *gt2*, and *gt3* = diagonal entries of body frame translational friction tensor
*gamma_t* values = *gt* for *brownian* and *brownian/sphere*
*gt* = magnitude of the (isotropic) translational friction tensor
Examples
""""""""
.. code-block:: LAMMPS
fix 1 all brownian 1.0 12908410 gamma_t 1.0
fix 1 all brownian 1.0 12908410 gamma_t 3.0 rng gaussian
fix 1 all brownian/sphere 1.0 1294019 gamma_t 3.0 gamma_r 1.0
fix 1 all brownian/sphere 1.0 19581092 gamma_t 1.0 gamma_r 0.3 rng none
fix 1 all brownian/asphere 1.0 1294019 gamma_t_eigen 1.0 2.0 3.0 gamma_r_eigen 4.0 7.0 8.0 rng gaussian
fix 1 all brownian/asphere 1.0 1294019 gamma_t_eigen 1.0 2.0 3.0 gamma_r_eigen 4.0 7.0 8.0 dipole 1.0 0.0 0.0
Description
"""""""""""
Perform Brownian Dynamics time integration to update position, velocity,
dipole orientation (for spheres) and quaternion orientation (for
ellipsoids, with optional dipole update as well) of all particles in the
fix group in each timestep. Brownian Dynamics uses Newton's laws of
motion in the limit that inertial forces are negligible compared to
viscous forces. The stochastic equation of motion for the center of mass
positions is
.. math::
d\mathbf{r} = \mathbf{\gamma}_t^{-1}\mathbf{F}dt+\sqrt{2k_BT}\mathbf{\gamma}_t^{-1/2}d\mathbf{W}_t,
in the lab-frame (i.e. :math:`\mathbf{\gamma}_t` is not diagonal, but
only depends on orientation and so the noise is still additive).
The rotational motion for the spherical and ellipsoidal particles is not
as simple an expression, but is chosen to replicate the Boltzmann
distribution for the case of conservative torques (see :ref:`(Ilie)
<Ilie1>` or :ref:`(Delong) <Delong1>`).
For the style *brownian*, only the positions of the particles are
updated. This is therefore suitable for point particle simulations.
For the style *brownian/sphere*, the positions of the particles are
updated, and a dipole slaved to the spherical orientation is also
updated. This style therefore requires the hybrid atom style
:doc:`atom_style dipole <atom_style>` and :doc:`atom_style sphere
<atom_style>`.
For the style *brownian/asphere*, the center of mass positions and the
quaternions of ellipsoidal particles are updated. This fix style is
suitable for equations of motion where the rotational and translational
friction tensors can be diagonalized in a certain (body) reference frame.
---------
.. note::
This integrator does not by default assume a relationship between the
rotational and translational friction tensors, though such a relationship
should exist in the case of no-slip boundary conditions between the particles and
the surrounding (implicit) solvent. E.g. in the case of spherical particles,
the condition :math:`\gamma_t=3\gamma_r/\sigma^2` must be explicitly
accounted for by setting *gamma_t* to 3x and *gamma_r* to x (where
:math:`\sigma` is the spherical diameter). A similar (though more complex)
relationship holds for ellipsoids and rod-like particles.
---------
.. note::
Temperature computation using the :doc:`compute temp <compute_temp>`
will not correctly compute temperature of these overdamped dynamics
since we are explicitly neglecting inertial effects.
Furthermore, this time integrator does not add the stochastic terms or
viscous terms to the force and/or torques. Rather, they are just added
in to the equations of motion to update the degrees of freedom.
---------
If the *rng* keyword is used with the *uniform* value, then the noise
is generated from a uniform distribution (see
:ref:`(Dunweg) <Dunweg7>` for why this works). This is the same method
of noise generation as used in :doc:`fix_langevin <fix_langevin>`.
If the *rng* keyword is used with the *gaussian* value, then the noise
is generated from a gaussian distribution. Typically this added
complexity is unnecessary, and one should be fine using the *uniform*
value for reasons argued in :ref:`(Dunweg) <Dunweg7>`.
If the *rng* keyword is used with the *none* value, then the noise
terms are set to zero.
The *gamma_t* keyword sets the (isotropic) translational viscous damping.
Required for (and only compatible with) *brownian* and *brownian/sphere*.
The units of *gamma_t* are mass/time.
The *gamma_r* keyword sets the (isotropic) rotational viscous damping.
Required for (and only compatible with) *brownian/sphere*.
The units of *gamma_r* are mass*length**2/time.
The *gamma_r_eigen*, and *gamma_t_eigen* keywords are the eigenvalues of
the rotational and viscous damping tensors (having the same units as
their isotropic counterparts). Required for (and only compatible with)
*brownian/asphere*. For a 2D system, the first two values of *gamma_r_eigen*
must be inf (only rotation in xy plane), and the third value of *gamma_t_eigen*
must be inf (only diffusion in xy plane).
If the *dipole* keyword is used, then the dipole moments of the particles
are updated as described above. Only compatible with *brownian/asphere*
(as *brownian/sphere* updates dipoles automatically).
----------
.. note::
For style *brownian/asphere*, the components *gamma_t_eigen* =(x,x,x) and
*gamma_r_eigen* = (y,y,y), the dynamics will replicate those of the
*brownian/sphere* style with *gamma_t* = x and *gamma_r* = y.
----------
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
No information about this fix is written to :doc:`binary restart files <restart>`.
No global or per-atom quantities are stored
by this fix for access by various :doc:`output commands <Howto_output>`.
No parameter of this fix can be used with the *start/stop* keywords of
the :doc:`run <run>` command. This fix is not invoked during
:doc:`energy minimization <minimize>`.
Restrictions
""""""""""""
The style *brownian/sphere* fix requires that atoms store torque and angular velocity (omega)
as defined by the :doc:`atom_style sphere <atom_style>` command.
The style *brownian/asphere* fix requires that atoms store torque and quaternions
as defined by the :doc:`atom_style ellipsoid <atom_style>` command.
If the *dipole* keyword is used, they must also store a dipole moment
as defined by the :doc:`atom_style dipole <atom_style>` command.
This fix is part of the USER-BROWNIAN 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 propel/self <fix_propel_self>`,
:doc:`fix langevin <fix_langevin>`, :doc:`fix nve/sphere <fix_nve_sphere>`,
Default
"""""""
The default for *rng* is *uniform*. The default for the rotational and translational friction
tensors are the identity tensor.
----------
.. _Ilie1:
**(Ilie)** Ilie, Briels, den Otter, Journal of Chemical Physics, 142, 114103 (2015).
.. _Delong1:
**(Delong)** Delong, Usabiaga, Donev, Journal of Chemical Physics. 143, 144107 (2015)
.. _Dunweg7:
**(Dunweg)** Dunweg and Paul, Int J of Modern Physics C, 2, 817-27 (1991).

2
doc/src/fix_drude.rst
View File

@ -22,6 +22,8 @@ Examples
fix 1 all drude 1 1 0 1 0 2 2 2
fix 1 all drude C C N C N D D D
Example input scripts available: examples/USER/drude
Description
"""""""""""

2
doc/src/fix_drude_transform.rst
View File

@ -25,6 +25,8 @@ Examples
fix 3 all drude/transform/direct
fix 1 all drude/transform/inverse
Example input scripts available: examples/USER/drude
Description
"""""""""""

5
doc/src/fix_grem.rst
View File

@ -92,6 +92,11 @@ The :doc:`thermo_modify <thermo_modify>` *press* option is supported
by this fix to add the rescaled kinetic pressure as part of
:doc:`thermodynamic output <thermo_style>`.
This fix computes a global scalar which can be accessed by various
:doc:`output commands <Howto_output>`. The scalar is the effective
temperature :math:`T_{eff}`. The scalar value calculated by this
fix is "intensive".
Restrictions
""""""""""""

2
doc/src/fix_langevin_drude.rst
View File

@ -35,6 +35,8 @@ Examples
fix 3 all langevin/drude 300.0 100.0 19377 1.0 20.0 83451
fix 1 all langevin/drude 298.15 100.0 19377 5.0 10.0 83451 zero yes
Example input scripts available: examples/USER/drude
Description
"""""""""""

59
doc/src/fix_mdi_engine.rst Normal file
View File

@ -0,0 +1,59 @@
.. index:: fix mdi/engine
fix mdi/engine command
======================
Syntax
""""""
.. parsed-literal::
fix ID group-ID mdi/engine
* ID, group-ID are documented in :doc:`fix <fix>` command
* mdi/engine = style name of this fix command
Examples
""""""""
.. code-block:: LAMMPS
fix 1 all mdi/engine
Description
"""""""""""
This fix is used along with the :doc:`mdi/engine <mdi_engine>` command
to enable LAMMPS to use the `MDI Library
<https://molssi-mdi.github.io/MDI_Library/html/index.html>`_ to run as
an MDI engine. The fix provides hooks that enable MDI driver codes to
communicate with LAMMPS at various points within a LAMMPS timestep.
It is not generally necessary to add this fix to a LAMMPS input file,
even when using the :doc:`mdi/engine <mdi_engine>` command. If the
:doc:`mdi/engine <mdi_engine>` command is executed and this fix is not
present, it will automatically be added and applied as a new fix for
all atoms for the duration of the command. Thus it is only necessary
to add this fix to an input file when you want to modify the group-ID
or the ordering of this fix relative to other fixes in the input script.
For more information about running LAMMPS as an MDI engine, see the
:doc:`mdi/engine <mdi_engine>` command and the :doc:`Howto mdi
<Howto_mdi>` doc page.
Restrictions
""""""""""""
This command is part of the USER-MDI 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:`mdi/engine <mdi_engine>`
Default
"""""""
none

16
doc/src/fix_precession_spin.rst
View File

@ -125,10 +125,10 @@ axis along the :math:`(1 1 1)`-type cube diagonals). :math:`K_2^c >
diagonals. See chapter 2 of :ref:`(Skomski) <Skomski1>` for more
details on cubic anisotropies.
Style *stt* is used to simulate the interaction between the spins and
Style *stt* is used to simulate the interaction between the spins and
a spin-transfer torque.
See equation (7) of :ref:`(Chirac) <Chirac1>` for more details about the
implemented spin-transfer torque term.
See equation (7) of :ref:`(Chirac) <Chirac1>` for more details about the
implemented spin-transfer torque term.
In all cases, the choice of :math:`(x y z)` only imposes the vector
directions for the forces. Only the direction of the vector is
@ -139,12 +139,12 @@ Those styles can be combined within one single command line.
.. note::
The norm of all vectors defined with the precession/spin command
The norm of all vectors defined with the precession/spin command
have to be non-zero. For example, defining
"fix 1 all precession/spin zeeman 0.1 0.0 0.0 0.0" would result
in an error message.
in an error message.
Since those vector components are used to compute the inverse of the
field (or anisotropy) vector norm, setting a zero-vector would result
field (or anisotropy) vector norm, setting a zero-vector would result
in a division by zero.
----------
@ -197,6 +197,6 @@ Oxford University Press.
.. _Chirac1:
**(Chirac)** Chirac, Théophile, et al. Ultrafast antiferromagnetic
switching in NiO induced by spin transfer torques.
**(Chirac)** Chirac, Theophile, et al. Ultrafast antiferromagnetic
switching in NiO induced by spin transfer torques.
Physical Review B 102.13 (2020): 134415.

183
doc/src/fix_propel_self.rst
View File

@ -8,52 +8,121 @@ Syntax
.. parsed-literal::
fix ID group-ID propel/self mode magnitude keyword values ...
fix ID group-ID propel/self mode magnitude keyword values
* ID, group-ID are documented in :doc:`fix <fix>` command
* propel/self = style name of this fix command
* mode = velocity or quat
* magnitude = magnitude of the active force
* one or more keyword/value pairs may be appended to args
* keyword = *types*
* mode = *dipole* or *velocity* or *quat*
* magnitude = magnitude of self-propulsion force
* zero or one keyword/value pairs may be appended
* keyword = *qvector*
.. parsed-literal::
*qvector* value = direction of force in ellipsoid frame
*sx*, *sy*, *sz* = components of *qvector*
*types* values = one or more atom types
Examples
""""""""
.. code-block:: LAMMPS
fix active_group all propel/self velocity 1.0
fix constant_velocity all viscous 1.0
fix active_group all propel/self quat 1.0
fix active all propel/self quat 1.0 types 1 2 4
fix active all propel/self dipole 40.0
fix active all propel/self velocity 10.0
fix active all propel/self quat 15.7 qvector 1.0 0.0 0.0
Description
"""""""""""
Adds a force of a constant magnitude to each atom in the group. The nature in
which the force is added depends on the mode.
Add a force to each atom in the group due to a self-propulsion force. The
force is given by
For *mode* = *velocity*, the active force acts along the velocity vector of
each atom. This can be interpreted as a velocity-dependent friction,
such as proposed by :ref:`(Erdmann) <Erdmann>`.
.. math::
For *mode* = *quat* the force is applied along the axis obtained
by rotating the x-axis along the atom's quaternion. In other words, the
force is along the x-axis in the atom's body frame. This mode requires
all atoms in the group to have a quaternion, so atom_style should
either be ellipsoid or body. In combination with Langevin thermostat
for translation and rotation in the overdamped regime, the quaternion
mode corresponds to the active Brownian particle model introduced by
:ref:`(Henkes) <Henkes>`, :ref:`(Bialke) <Bialke>` and :ref:`(Fily)
<Fily>`.
F_i = f_P e_i
By default, this fix is applied to all atoms in the group. You can
override this behavior by specifying the atom types the fix should work
on through the *types* keyword.
where *i* is the particle the force is being applied to, :math:`f_P`
is the magnitude of the force, and :math:`e_i` is the vector direction
of the force. The specification of :math:`e_i` is based on which of the
three keywords (*dipole* or *velocity* or *quat*) one selects.
For mode *dipole*, :math:`e_i` is just equal to
the dipole vectors of the atoms in the group. Therefore, if the dipoles
are not unit vectors, the :math:`e_i` will not be unit vectors.
.. note::
If another command changes the magnitude of the dipole, this force will
change accordingly (since :math:`|e_i|` will change, which is physically
equivalent to re-scaling :math:`f_P` while keeping :math:`|e_i|` constant),
and no warning will be provided by LAMMPS. This is almost never what you
want, so ensure you are not changing dipole magnitudes with another LAMMPS
fix or pair style. Furthermore, self-propulsion forces (almost) always
set :math:`e_i` to be a unit vector for all times, so it's best to set
all the dipole magnitudes to 1.0 unless you have a good reason not to
(see the :doc:`set <set>` command on how to do this).
For mode *velocity*, :math:`e_i` points in the direction
of the current velocity (a unit-vector). This can be interpreted as a
velocity-dependent friction, as proposed by e.g. :ref:`(Erdmann) <Erdmann1>`.
For mode *quat*, :math:`e_i` points in the direction of a unit
vector, oriented in the coordinate frame of the ellipsoidal particles,
which defaults to point along the x-direction. This default behavior
can be changed by via the *quatvec* keyword.
The optional *quatvec* keyword specifies the direction of self-propulsion
via a unit vector (sx,sy,sz). The arguments *sx*, *sy*, and *sz*, are
defined within the coordinate frame of the atom's
ellipsoid. For instance, for an ellipsoid with long axis along
its x-direction, if one wanted the self-propulsion force to also
be along this axis, set *sx* equal to 1 and *sy*, *sz* both equal
to zero. This keyword may only be specified for mode *quat*.
.. note::
In using keyword *quatvec*, the three arguments *sx*,
*sy*, and *sz* will be automatically normalized to components
of a unit vector internally to avoid users having to explicitly
do so themselves. Therefore, in mode *quat*, the vectors :math:`e_i`
will always be of unit length.
Along with adding a force contribution, this fix can also
contribute to the virial (pressure) of the system, defined as
:math:`f_P \sum_i <e_i . r_i>/(d V)`, where :math:`r_i` is the
*unwrapped* coordinate of particle i in the case of periodic
boundary conditions. See :ref:`(Winkler) <Winkler1>` for a
discussion of this active pressure contribution.
For modes *dipole* and *quat*, this fix is by default
included in pressure computations.
For mode *velocity*, this fix is by default not included
in pressure computations.
.. note::
In contrast to equilibrium systems, pressure of active systems
in general depends on the geometry of the container.
The active pressure contribution as calculated in this fix
is only valid for certain boundary conditions (spherical
walls, rectangular walls, or periodic boundary conditions).
For other geometries, the pressure must be measured via
explicit calculation of the force per unit area on a wall,
and so one must not calculate it using this fix.
(Use :doc:`fix_modify <fix_modify>` as described below
to turn off the virial contribution of this fix). Again,
see :ref:`(Winkler) <Winkler1>` for discussion of why this
is the case.
Furthermore, when dealing with active systems, the temperature
is no longer well defined. Therefore, one should ensure that
the *virial* flag is used in the
:doc:`compute pressure <compute_pressure>` command (turning
off temperature contributions).
----------
@ -62,40 +131,48 @@ Restart, fix_modify, output, run start/stop, minimize info
No information about this fix is written to :doc:`binary restart files <restart>`.
This fix is not imposed during minimization.
The :doc:`fix_modify <fix_modify>` *virial* option is supported by this
fix to add the contribution due to the added forces on atoms to the
system's virial as part of :doc:`thermodynamic output <thermo_style>`.
The default is *virial yes* for keywords *dipole* and *quat*. The
default is *virial no* for keyword *velocity*.
No parameter of this fix can be used with the *start/stop* keywords of
the :doc:`run <run>` command.
Restrictions
""""""""""""
In quat mode, this fix makes use of per-atom quaternions to take
into account the fact that the orientation can rotate and hence the
direction of the active force can change. The quat mode
of this fix only works with atom_style ellipsoid.
With keyword *dipole*, this fix only works when the DIPOLE package is enabled.
See the :doc:`Build package <Build_package>` doc page for more info.
This fix is part of the USER-BROWNIAN 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 setforce <fix_setforce>`, :doc:`fix addforce <fix_addforce>`
.. _Erdmann:
**(Erdmann)** U. Erdmann , W. Ebeling, L. Schimansky-Geier, and F. Schweitzer,
Eur. Phys. J. B 15, 105-113, 2000.
.. _Henkes:
**(Henkes)** Henkes, S, Fily, Y., and Marchetti, M. C. Phys. Rev. E, 84, 040301(R), 2011.
.. _Bialke:
**(Bialke)** J. Bialke, T. Speck, and H Loewen, Phys. Rev. Lett. 108, 168301, 2012.
.. _Fily:
**(Fily)** Y. Fily and M.C. Marchetti, Phys. Rev. Lett. 108, 235702, 2012.
:doc:`fix efield <fix_efield>` , :doc:`fix setforce <fix_setforce>`,
:doc:`fix addforce <fix_addforce>`
Default
"""""""
types
none
----------
.. _Erdmann1:
**(Erdmann)** U. Erdmann , W. Ebeling, L. Schimansky-Geier, and F. Schweitzer,
Eur. Phys. J. B 15, 105-113, 2000.
.. _Winkler1:
**(Winkler)** Winkler, Wysocki, and Gompper, Soft Matter, 11, 6680 (2015).

2
doc/src/fix_tgnh_drude.rst
View File

@ -62,6 +62,8 @@ Examples
fix 2 jello tgnpt/drude temp 300.0 300.0 100.0 1.0 20.0 tri 5.0 5.0 1000.0
fix 2 ice tgnpt/drude temp 250.0 250.0 100.0 1.0 20.0 x 1.0 1.0 0.5 y 2.0 2.0 0.5 z 3.0 3.0 0.5 yz 0.1 0.1 0.5 xz 0.2 0.2 0.5 xy 0.3 0.3 0.5 nreset 1000
Example input scripts available: examples/USER/drude
Description
"""""""""""

88
doc/src/mdi_engine.rst Normal file
View File

@ -0,0 +1,88 @@
.. index:: mdi/engine
mdi_engine command
==================
Syntax
""""""
.. parsed-literal::
mdi_engine
Description
"""""""""""
This command is used to have LAMMPS act as a server with another
client code to effectively couple the two codes together in
client/server mode.
More specifically, this command causes LAMMPS to begin using the `MDI
Library <https://molssi-mdi.github.io/MDI_Library/html/index.html>`_
to run as an MDI engine (server), responding to commands made by an
external MDI driver code (client). See the :doc:`Howto mdi
<Howto_mdi>` doc page for more information about how LAMMPS can work
as both an MDI driver or engine.
General information about launching codes that communicate using the
MDI Library can be found in the `corresponding page
<https://molssi-mdi.github.io/MDI_Library/html/library_page.html#library_launching_sec>`_
of the MDI Library's documentation.
----------
This command should typically be used in an input script after LAMMPS
has setup the system it is going to model in collaboration with the
driver code. Depending on how the driver code tells the LAMMPS engine
to exit, other commands can be executed after this command, but
typically it should be used at the end of the LAMMPS input script.
To act as a MD-based MDI engine, this is the list of MDI commands from
a driver code which LAMMPS currently recognizes. See more details
about these commands in the `MDI library documentation
<https://molssi-mdi.github.io/MDI_Library/html/mdi_standard.html>`_
.. NOTE: Taylor - is this the best link for this info? Can we flesh this
.. out with the full list of supported commands? Maybe the distinction
.. of what "node" the commands refer to is not needed in this table?
.. list-table::
:widths: 20 80
:header-rows: 1
* - Command name
- Action
* - >NATOMS
- Driver sends the number of atoms in the system
* - <NATOMS
- Driver requests the number of atoms in the system
* - <COORDS
- Driver requests 3*N double-precision atom coordinates
* - >FORCES
- Driver sends 3*N double-precision atom forces
* - <COORDS
- Driver requests 3*N double-precision atom forces
* - EXIT
- Driver tells the engine (LAMMPS) to exit engine mode
If these commands are not sufficient to support what a driver which
you write needs, additional commands can be defined by simply using a
new command name not in this list. Code to support the new command
needs to be added to the USER-MDI package within LAMMPS; see its
src/USER-MDI/mdi_engine.cpp and fix_mdi_engine.cpp files.
Restrictions
""""""""""""
This command is part of the USER-MDI 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 mdi/engine <fix_mdi_engine>`
Default
"""""""
None

40
doc/src/neigh_modify.rst
View File

@ -14,7 +14,7 @@ Syntax
.. parsed-literal::
keyword = *delay* or *every* or *check* or *once* or *cluster* or *include* or *exclude* or *page* or *one* or *binsize*
keyword = *delay* or *every* or *check* or *once* or *cluster* or *include* or *exclude* or *page* or *one* or *binsize* or *collection/type* or *collection/interval*
*delay* value = N
N = delay building until this many steps since last build
*every* value = M
@ -47,6 +47,12 @@ Syntax
N = max number of neighbors of one atom
*binsize* value = size
size = bin size for neighbor list construction (distance units)
*collection/type* values = N arg1 ... argN
N = number of custom collections
arg = N separate lists of types (see below)
*collection/interval* values = N arg1 ... argN
N = number of custom collections
arg = N separate cutoffs for intervals (see below)
Examples
""""""""
@ -58,6 +64,8 @@ Examples
neigh_modify exclude group frozen frozen check no
neigh_modify exclude group residue1 chain3
neigh_modify exclude molecule/intra rigid
neigh_modify collection/type 2 1*2,5 3*4
neigh_modify collection/interval 2 1.0 10.0
Description
"""""""""""
@ -188,8 +196,9 @@ atom can have.
The *binsize* option allows you to specify what size of bins will be
used in neighbor list construction to sort and find neighboring atoms.
By default, for :doc:`neighbor style bin <neighbor>`, LAMMPS uses bins
that are 1/2 the size of the maximum pair cutoff. For :doc:`neighbor style multi <neighbor>`, the bins are 1/2 the size of the minimum pair
cutoff. Typically these are good values for minimizing the time for
that are 1/2 the size of the maximum pair cutoff. For :doc:`neighbor style multi <neighbor>`,
the bins are 1/2 the size of the collection interaction cutoff.
Typically these are good values for minimizing the time for
neighbor list construction. This setting overrides the default.
If you make it too big, there is little overhead due to
looping over bins, but more atoms are checked. If you make it too
@ -197,6 +206,31 @@ small, the optimal number of atoms is checked, but bin overhead goes
up. If you set the binsize to 0.0, LAMMPS will use the default
binsize of 1/2 the cutoff.
The *collection/type* option allows you to define collections of atom
types, used by the *multi* neighbor mode. By grouping atom types with
similar physical size or interaction cutoff lengths, one may be able
to improve performance by reducing
overhead. You must first specify the number of collections N to be
defined followed by N lists of types. Each list consists of a series of type
ranges separated by commas. The range can be specified as a
single numeric value, or a wildcard asterisk can be used to specify a range
of values. This takes the form "\*" or "\*n" or "n\*" or "m\*n". For
example, if M = the number of atom types, then an asterisk with no numeric
values means all types from 1 to M. A leading asterisk means all types
from 1 to n (inclusive). A trailing asterisk means all types from n to M
(inclusive). A middle asterisk means all types from m to n (inclusive).
Note that all atom types must be included in exactly one of the N collections.
The *collection/interval* option provides a similar capability. This
command allows a user to define collections by specifying a series of
cutoff intervals. LAMMPS will automatically sort atoms into these
intervals based on their type-dependent cutoffs or their finite size.
You must first specify the number of collections N to be defined
followed by N values representing the upper cutoff of each interval.
This command is particularly useful for granular pair styles where the
interaction distance of particles depends on their radius and may not
depend on their atom type.
Restrictions
""""""""""""

39
doc/src/neighbor.rst
View File

@ -11,7 +11,7 @@ Syntax
neighbor skin style
* skin = extra distance beyond force cutoff (distance units)
* style = *bin* or *nsq* or *multi*
* style = *bin* or *nsq* or *multi* or *multi/old*
Examples
""""""""
@ -55,14 +55,31 @@ For the *bin* style, the bin size is set to 1/2 of
the largest cutoff distance between any pair of atom types and a
single set of bins is defined to search over for all atom types. This
can be inefficient if one pair of types has a very long cutoff, but
other type pairs have a much shorter cutoff. For style *multi* the
bin size is set to 1/2 of the shortest cutoff distance and multiple
sets of bins are defined to search over for different atom types.
other type pairs have a much shorter cutoff. The *multi* style uses
different sized bins for collections of different sized particles, where
"size" may mean the physical size of the particle or its cutoff
distance for interacting with other particles. Different
sets of bins are then used to construct the neighbor lists as as further
described by Shire, Hanley, and Stratford :ref:`(Shire) <bytype-Shire>`.
This imposes some extra setup overhead, but the searches themselves
may be much faster for the short-cutoff cases.
See the :doc:`comm_modify mode multi <comm_modify>` command for a
communication option that may also be beneficial for simulations of
this kind.
may be much faster. By default, each atom type defines a separate
collection of particles. For systems where two or more atom types
have the same size (either physical size or cutoff distance), the
definition of collections can be customized, which can result in less
overhead and faster performance. See the :doc:`neigh_modify <neigh_modify>`
command for how to define custom collections. Whether the collection
definition is customized or not, also see the
:doc:`comm_modify mode multi <comm_modify>` command for communication
options that further improve performance in a manner consistent with
neighbor style multi.
An alternate style, *multi/old*, sets the bin size to 1/2 of the shortest
cutoff distance and multiple sets of bins are defined to search over for
different atom types. This algorithm used to be the default *multi*
algorithm in LAMMPS but was found to be significantly slower than the new
approach. For now we are keeping the old option in case there are use cases
where multi/old outperforms the new multi style.
The :doc:`neigh_modify <neigh_modify>` command has additional options
that control how often neighbor lists are built and which pairs are
@ -90,3 +107,9 @@ Default
| 0.001 bin for units = si, skin = 0.001 meters = 1.0 mm
| 0.1 bin for units = cgs, skin = 0.1 cm = 1.0 mm
|
----------
.. _bytype-Shire:
**(Shire)** Shire, Hanley and Stratford, Comp Part Mech, (2020).

1
doc/src/pair_coul_tt.rst
View File

@ -29,6 +29,7 @@ Examples
pair_coeff 1 2 coul/tt 4.0 1.0 4 12.0
pair_coeff 1 3* coul/tt 4.5 1.0 4
Example input scripts available: examples/USER/drude
Description
"""""""""""

138
doc/src/pair_dpd_ext.rst Normal file
View File

@ -0,0 +1,138 @@
.. index:: pair_style dpd/ext
.. index:: pair_style dpd/ext/tstat
pair_style dpd/ext command
==========================
pair_style dpd/ext/tstat command
================================
Syntax
""""""
.. code-block:: LAMMPS
pair_style dpd/ext T cutoff seed
pair_style dpd/ext/tstat Tstart Tstop cutoff seed
* T = temperature (temperature units)
* Tstart,Tstop = desired temperature at start/end of run (temperature units)
* cutoff = global cutoff for DPD interactions (distance units)
* seed = random # seed (positive integer)
Examples
""""""""
.. code-block:: LAMMPS
pair_style dpd/ext 1.0 2.5 34387
pair_coeff 1 1 25.0 4.5 4.5 0.5 0.5 1.2
pair_coeff 1 2 40.0 4.5 4.5 0.5 0.5 1.2
pair_style dpd/ext/tstat 1.0 1.0 2.5 34387
pair_coeff 1 1 4.5 4.5 0.5 0.5 1.2
pair_coeff 1 2 4.5 4.5 0.5 0.5 1.2
Description
"""""""""""
The style *dpd/ext* computes an extended force field for dissipative particle dynamics (DPD) following the exposition in :ref:`(Groot) <Groot>`, :ref:`(Junghans) <Junghans>`.
Style *dpd/ext/tstat* invokes an extended DPD thermostat on pairwise interactions, equivalent to the non-conservative portion of the extended DPD force field. To use *dpd/ext/tstat* as a thermostat for another pair style, use the :doc:`pair_style hybrid/overlay <pair_hybrid>` command to compute both the desired pair interaction and the thermostat for each pair of particles.
For the style *dpd/ext*\ , the force on atom I due to atom J is given as a sum
of 3 terms
.. math::
\mathbf{f} = & f^C + f^D + f^R \qquad \qquad r < r_c \\
f^C = & A_{ij} w(r) \hat{\mathbf{r}}_{ij} \\
f^D = & - \gamma_{\parallel} w_{\parallel}^2(r) (\hat{\mathbf{r}}_{ij} \cdot \mathbf{v}_{ij}) \hat{\mathbf{r}}_{ij} - \gamma_{\perp} w_{\perp}^2 (r) ( \mathbf{I} - \hat{\mathbf{r}}_{ij} \hat{\mathbf{r}}_{ij}^{\rm T} ) \mathbf{v}_{ij} \\
f^R = & \sigma_{\parallel} w_{\parallel}(r) \frac{\alpha}{\sqrt{\Delta t}} \hat{\mathbf{r}}_{ij} + \sigma_{\perp} w_{\perp} (r) ( \mathbf{I} - \hat{\mathbf{r}}_{ij} \hat{\mathbf{r}}_{ij}^{\rm T} ) \frac{\mathbf{\xi}_{ij}}{\sqrt{\Delta t}}\\
w(r) = & 1 - r/r_c \\
where :math:`\mathbf{f}^C` is a conservative force, :math:`\mathbf{f}^D` is a dissipative force, and :math:`\mathbf{f}^R` is a random force. :math:`A_{ij}` is the maximum repulsion between the two atoms, :math:`\hat{\mathbf{r}}_{ij}` is a unit vector in the direction :math:`\mathbf{r}_i - \mathbf{r}_j`, :math:`\mathbf{v}_{ij} = \mathbf{v}_i - \mathbf{v}_j` is the vector difference in velocities of the two atoms, :math:`\alpha` and :math:`\mathbf{\xi}_{ij}` are Gaussian random numbers with zero mean and unit variance, :math:`\Delta t` is the timestep, :math:`w (r) = 1 - r / r_c` is a weight function for the conservative interactions that varies between 0 and 1, :math:`r_c` is the corresponding cutoff, :math:`w_{\alpha} ( r ) = ( 1 - r / \bar{r}_c )^{s_{\alpha}}`, :math:`\alpha \equiv ( \parallel, \perp )`, are weight functions with coefficients :math:`s_\alpha` that vary between 0 and 1, :math:`\bar{r}_c` is the corresponding cutoff, :math:`\mathbf{I}` is the unit matrix, :math:`\sigma_{\alpha} = \sqrt{2 k T \gamma_{\alpha}}`, where :math:`k` is the Boltzmann constant and :math:`T` is the temperature in the pair\_style command.
For the style *dpd/ext/tstat*\ , the force on atom I due to atom J is the same as the above equation, except that the conservative :math:`\mathbf{f}^C` term is dropped. Also, during the run, T is set each timestep to a ramped value from Tstart to Tstop.
For the style *dpd/ext*\ , the pairwise energy associated with style *dpd/ext* is only due to the conservative force term :math:`\mathbf{f}^C`, and is shifted to be zero at the cutoff distance :math:`r_c`. The pairwise virial is calculated using all three terms. There is no pairwise energy for style *dpd/ext/tstat*, but the last two terms of the formula contribute the virial.
For the style *dpd/ext/tstat*, the force on atom I due to atom J is the same as the above equation, except that the conservative :math:`\mathbf{f}^C` term is dropped. Also, during the run, T is set each timestep to a ramped value from Tstart to Tstop.
For the style *dpd/ext*\ , the pairwise energy associated with style *dpd/ext* is only due to the conservative force term :math:`\mathbf{f}^C`, and is shifted to be zero at the cutoff distance :math:`r_c`. The pairwise virial is calculated using all three terms. There is no pairwise energy for style *dpd/ext/tstat*, but the last two terms of the formula contribute the virial.
For the style *dpd/ext*, the following coefficients must be defined for each pair of atoms types via the :doc:`pair_coeff <pair_coeff>` command as in the examples above:
* A (force units)
* :math:`\gamma_{\perp}` (force/velocity units)
* :math:`\gamma_{\parallel}` (force/velocity units)
* :math:`s_{\perp}` (unitless)
* :math:`s_{\parallel}` (unitless)
* :math:`r_c` (distance units)
The last coefficient is optional. If not specified, the global DPD cutoff is used. Note that :math:`\sigma`'s are set equal to :math:`\sqrt{2 k T \gamma}`, where :math:`T` is the temperature set by the :doc:`pair_style <pair_style>` command so it does not need to be specified.
For the style *dpd/ext/tstat*, the coefficients defined for each pair of atoms types via the :doc:`pair_coeff <pair_coeff>` command is the same, except that A is not included.
.. note::
If you are modeling DPD polymer chains, you may want to use the :doc:`pair_style srp <pair_srp>` command in conjunction with these pair styles. It is a soft segmental repulsive potential (SRP) that can prevent DPD polymer chains from crossing each other.
.. note::
The virial calculation for pressure when using this pair style includes all the components of force listed above, including the random force.
----------
**Mixing, shift, table, tail correction, restart, rRESPA info**\ :
The style *dpd/ext* does not support mixing. Thus, coefficients for all I,J pairs must be specified explicitly.
The pair styles do not support the :doc:`pair_modify <pair_modify>` shift option for the energy of the pair interaction. Note that as discussed above, the energy due to the conservative :math:`\mathbf{f}^C` term is already shifted to be zero at the cutoff distance :math:`r_c`.
The :doc:`pair_modify <pair_modify>` table option is not relevant for the style *dpd/ext*.
The style *dpd/ext* does not support the :doc:`pair_modify <pair_modify>` tail option for adding long-range tail corrections to energy and pressure.
The pair styles can only be used via the pair keyword of the :doc:`run_style respa <run_style>` command. They do not support the *inner*\ , *middle*\ , and *outer*\ keywords.
The style *dpd/ext/tstat* can ramp its target temperature over multiple runs, using the start and stop keywords of the :doc:`run <run>` command. See the :doc:`run <run>` command for details of how to do this.
----------
Restrictions
""""""""""""
The default frequency for rebuilding neighbor lists is every 10 steps (see the :doc:`neigh_modify <neigh_modify>` command). This may be too infrequent for style *dpd/ext* simulations since particles move rapidly and can overlap by large amounts. If this setting yields a non-zero number of \say{dangerous} reneighborings (printed at the end of a simulation), you should experiment with forcing reneighboring more often and see if system energies/trajectories change.
The pair styles require to use the :doc:`comm_modify vel yes <comm_modify>` command so that velocities are stored by ghost atoms.
The pair styles will not restart exactly when using the :doc:`read_restart <read_restart>` command, though they should provide statistically similar results. This is because the forces they compute depend on atom velocities. See the :doc:`read_restart <read_restart>` command for more details.
Related commands
""""""""""""""""
:doc:`pair_style dpd <pair_dpd>`, :doc:`pair_coeff <pair_coeff>`, :doc:`fix nvt <fix_nh>`, :doc:`fix langevin <fix_langevin>`, :doc:`pair_style srp <pair_srp>`
**Default:** none
----------
.. _Groot:
**(Groot)** Groot and Warren, J Chem Phys, 107, 4423-35 (1997).
.. _Junghans:
**(Junghans)** Junghans, Praprotnik and Kremer, Soft Matter 4, 156, 1119-1128 (2008).

2
doc/src/pair_fep_soft.rst
View File

@ -182,6 +182,8 @@ Examples
pair_coeff * * 100.0 2.0 1.5 1.0
pair_coeff 1 1 100.0 2.0 1.5 1.0 3.0
Example input scripts available: examples/USER/fep
Description
"""""""""""

12
doc/src/pair_hybrid.rst
View File

@ -257,7 +257,7 @@ then overrides them with 0.0 only for CHARMM:
.. code-block:: LAMMPS
special_bonds amber
pair_hybrid lj/charmm/coul/long 8.0 10.0 lj/cut/coul/long 10.0
pair_style hybrid lj/charmm/coul/long 8.0 10.0 lj/cut/coul/long 10.0
pair_modify pair lj/charmm/coul/long special lj/coul 0.0 0.0 0.0
The this input achieves the same effect:
@ -265,7 +265,7 @@ The this input achieves the same effect:
.. code-block:: LAMMPS
special_bonds 0.0 0.0 0.1
pair_hybrid lj/charmm/coul/long 8.0 10.0 lj/cut/coul/long 10.0
pair_style hybrid lj/charmm/coul/long 8.0 10.0 lj/cut/coul/long 10.0
pair_modify pair lj/cut/coul/long special lj 0.0 0.0 0.5
pair_modify pair lj/cut/coul/long special coul 0.0 0.0 0.83333333
pair_modify pair lj/charmm/coul/long special lj/coul 0.0 0.0 0.0
@ -279,7 +279,7 @@ effectively *lj/coul 0.0 0.0 0.5* as required for OPLS/AA:
.. code-block:: LAMMPS
special_bonds lj/coul 1e-20 1e-20 0.5
pair_hybrid tersoff lj/cut/coul/long 12.0
pair_style hybrid tersoff lj/cut/coul/long 12.0
pair_modify pair tersoff special lj/coul 1.0 1.0 1.0
For use with the various :doc:`compute \*/tally <compute_tally>`
@ -417,7 +417,11 @@ assigned automatically to the sub-style defined for both I,I and J,J and
its coefficients generated by the mixing rule used by that sub-style.
For the *hybrid/overlay* and *hybrid/scaled* style, there is an
additional requirement that both the I,I and J,J pairs are assigned to a
single sub-style. See the :doc:`pair_modify <pair_modify>` command for
single sub-style. If this requirement is not met, no I,J coeffs will be
generated, even if the sub-styles support mixing, and I,J pair
coefficients must be explicitly defined.
See the :doc:`pair_modify <pair_modify>` command for
details of mixing rules. See the See the doc page for the sub-style to
see if allows for mixing.

16
doc/src/pair_lj_cut_tip4p.rst
View File

@ -145,6 +145,22 @@ specified since a Coulombic cutoff cannot be specified for an individual I,J
type pair. All type pairs use the same global Coulombic cutoff specified in
the pair_style command.
.. warning::
Because of how these pair styles implement the coulomb interactions
by implicitly defining a fourth site for the negative charge
of the TIP4P and similar water models, special care must be taken
when using these pair styles with other computations that also use
charges. Unless they are specially set up to also handle the implicit
definition of the 4th site, results are likely incorrect. Example:
:doc:`compute dipole/chunk <compute_dipole_chunk>`. For the same
reason, when using one of these pair styles with
:doc:`pair_style hybrid <pair_hybrid>`, **all** coulomb interactions
should be handled by a single sub-style with TIP4P support. All other
instances and styles will "see" the M point charges at the position
of the Oxygen atom and thus compute incorrect forces and energies.
LAMMPS will print a warning when it detects one of these issues.
----------
A version of these styles with a soft core, *lj/cut/tip4p/long/soft*\ , suitable

3
doc/src/pair_lj_smooth.rst
View File

@ -1,10 +1,11 @@
.. index:: pair_style lj/smooth
.. index:: pair_style lj/smooth/gpu
.. index:: pair_style lj/smooth/omp
pair_style lj/smooth command
============================
Accelerator Variants: *lj/smooth/omp*
Accelerator Variants: *lj/smooth/gpu*, *lj/smooth/omp*
Syntax
""""""

2
doc/src/pair_style.rst
View File

@ -150,6 +150,8 @@ accelerated styles exist.
* :doc:`coul/wolf <pair_coul>` - Coulomb via Wolf potential
* :doc:`coul/wolf/cs <pair_cs>` - Coulomb via Wolf potential with core/shell adjustments
* :doc:`dpd <pair_dpd>` - dissipative particle dynamics (DPD)
* :doc:`dpd/ext <pair_dpd_ext>` - generalized force field for DPD
* :doc:`dpd/ext/tstat <pair_dpd_ext>` - pair-wise DPD thermostatting with generalized force field
* :doc:`dpd/fdt <pair_dpd_fdt>` - DPD for constant temperature and pressure
* :doc:`dpd/fdt/energy <pair_dpd_fdt>` - DPD for constant energy and enthalpy
* :doc:`dpd/tstat <pair_dpd>` - pair-wise DPD thermostatting

2
doc/src/pair_thole.rst
View File

@ -42,6 +42,8 @@ Examples
pair_style lj/cut/thole/long 2.6 12.0
Example input scripts available: examples/USER/drude
Description
"""""""""""

3
doc/src/read_data.rst
View File

@ -223,6 +223,9 @@ The structure of the data file is important, though many settings and
sections are optional or can come in any order. See the examples
directory for sample data files for different problems.
The file will be read line by line, but there is a limit of 254
characters per line and characters beyond that limit will be ignored.
A data file has a header and a body. The header appears first. The
first line of the header is always skipped; it typically contains a
description of the file. Then lines are read one at a time. Lines

46
doc/src/thermo_modify.rst
View File

@ -11,12 +11,13 @@ Syntax
thermo_modify keyword value ...
* one or more keyword/value pairs may be listed
* keyword = *lost* or *lost/bond* or *norm* or *flush* or *line* or *format* or *temp* or *press*
* keyword = *lost* or *lost/bond* or *warn* or *norm* or *flush* or *line* or *format* or *temp* or *press*
.. parsed-literal::
*lost* value = *error* or *warn* or *ignore*
*lost/bond* value = *error* or *warn* or *ignore*
*warn* value = *ignore* or *reset* or *default* or a number
*norm* value = *yes* or *no*
*flush* value = *yes* or *no*
*line* value = *one* or *multi*
@ -75,6 +76,43 @@ are drifting out of the box through a fixed boundary condition (see
the :doc:`boundary <boundary>` command). In this case one atom may be
deleted before the rest of the molecule is, on a later timestep.
The *warn* keyword allows you to control whether LAMMPS will print
warning messages and how many of them. Most warning messages are only
printed by MPI rank 0. They are usually pointing out important issues
that should be investigated, but LAMMPS cannot determine for
certain whether they are an indication of an error.
Some warning messages are printed during a run (or immediately before)
each time a specific MPI rank encounters the issue, e.g. bonds that are
stretched too far or dihedrals in extreme configurations. These number
of these can quickly blow up the size of the log file and screen output.
Thus a limit of 100 warning messages is applied by default. The warning
count is applied to the entire input unless reset with a ``thermo_modify
warn reset`` command. If there are more warnings than the limit, LAMMPS
will print one final warning that it will not print any additional
warning messages.
.. note::
The warning limit is enforced on either the per-processor count or
the total count across all processors. For efficiency reasons,
however, the total count is only updated at steps with thermodynamic
output. Thus when running on a large number of processors in
parallel, the total number of warnings printed can be significantly
larger than the given limit.
Any number after the keyword *warn* will change the warning limit
accordingly. With the value *ignore* all warnings will be suppressed,
with the value *always* no limit will be applied and warnings will
always be printed, with the value *reset* the internal warning counter
will be reset to zero, and with the value *default*, the counter is
reset and the limit set to 100. An example usage of either *reset* or
*default* would be to re-enable warnings that were disabled or have
reached the limit during equilibration, where the warnings would be
acceptable while the system is still adjusting, but then change
to all warnings for the production run, where they would indicate
problems that would require a closer look at what is causing them.
The *norm* keyword determines whether various thermodynamic output
values are normalized by the number of atoms or not, depending on
whether it is set to *yes* or *no*\ . Different unit styles have
@ -183,9 +221,9 @@ Related commands
Default
"""""""
The option defaults are lost = error, norm = yes for unit style of
*lj*\ , norm = no for unit style of *real* and *metal*\ , flush = no,
and temp/press = compute IDs defined by thermo_style.
The option defaults are lost = error, warn = 100, norm = yes for unit
style of *lj*\ , norm = no for unit style of *real* and *metal*\ ,
flush = no, and temp/press = compute IDs defined by thermo_style.
The defaults for the line and format options depend on the thermo
style. For styles "one" and "custom", the line and format defaults

14
doc/src/variable.rst
View File

@ -363,12 +363,14 @@ variable, as discussed below.
The rules for formatting the file are as follows. Each time a set of
per-atom values is read, a non-blank line is searched for in the file.
A comment character "#" can be used anywhere on a line; text starting
with the comment character is stripped. Blank lines are skipped. The
first "word" of a non-blank line, delimited by white-space, is read as
the count N of per-atom lines to immediately follow. N can be the
total number of atoms in the system, or only a subset. The next N
lines have the following format
The file is read line by line but only up to 254 characters are used.
The rest are ignored. A comment character "#" can be used anywhere
on a line and all text following and the "#" character are ignored;
text starting with the comment character is stripped. Blank lines
are skipped. The first "word" of a non-blank line, delimited by
white-space, is read as the count N of per-atom lines to immediately
follow. N can be the total number of atoms in the system, or only a
subset. The next N lines have the following format
.. parsed-literal::

1
doc/utils/requirements.txt
View File

@ -4,3 +4,4 @@ git+git://github.com/akohlmey/sphinx-fortran@parallel-read
sphinx_tabs
breathe
Pygments
six

4
doc/utils/sphinx-config/_static/css/lammps.css
View File

@ -35,6 +35,10 @@ hr {
display: none;
}
#command-reference.section h2 {
display: none;
}
.ui.tabular.menu .item {
padding-right: 1em;
padding-left: 1em;

2
doc/utils/sphinx-config/conf.py.in
View File

@ -241,7 +241,7 @@ html_show_sourcelink = False
# Output file base name for HTML help builder.
htmlhelp_basename = 'LAMMPSdoc'
html_add_permalinks = ''
html_permalinks = True
if 'epub' in sys.argv:
html_math_renderer = 'imgmath'

29
doc/utils/sphinx-config/false_positives.txt
View File

@ -47,6 +47,7 @@ Agnolin
Ai
Aidan
aij
aimd
airebo
Aj
ajs
@ -101,6 +102,7 @@ anisotropic
anisotropies
anisotropy
ansi
antiferromagnetic
antiquewhite
Antisymmetrized
antisymmetry
@ -195,6 +197,7 @@ Ballenegger
Bammann
Banna
Barashev
barnes
barostat
Barostats
barostatted
@ -311,6 +314,7 @@ br
Branduardi
Branicio
brennan
Briels
Brien
Brilliantov
Broadwell
@ -625,6 +629,7 @@ delflag
Dellago
delocalization
delocalized
Delong
delr
deltaHf
Dendrimer
@ -708,6 +713,7 @@ dodgerblue
dof
doi
Donadio
Donev
dotc
Doty
doxygen
@ -1023,6 +1029,7 @@ fmag
fmass
fmm
fmt
fmtlib
fmx
fmy
fmz
@ -1141,6 +1148,7 @@ GMock
gneb
GNEB
Goldfarb
Gompper
Gonzalez-Melchor
googlemail
googletest
@ -1201,6 +1209,7 @@ Halver
Hamaker
Hamel
Hammerschmidt
Hanley
haptic
Hara
Harpertown
@ -1263,6 +1272,7 @@ holonomic
Homebrew
hooke
Hookean
hostname
hotpink
Houlle
howto
@ -1319,6 +1329,7 @@ ijk
ijkl
ik
Ikeshoji
Ilie
ilmenau
Ilmenau
ilp
@ -1721,6 +1732,7 @@ Lmpsdata
lmptype
LMT
ln
localhost
localTemp
localvectors
Loewen
@ -1851,6 +1863,8 @@ mc
McLachlan
md
mdf
MDI
mdi
mdpd
mDPD
meam
@ -2177,6 +2191,7 @@ nimpropers
nimpropertypes
Nimpropertype
Ninteger
NiO
Nissila
nist
nitride
@ -2188,6 +2203,7 @@ nl
nlayers
nlen
Nlines
nlines
nlo
nlocal
Nlocal
@ -2279,6 +2295,7 @@ Ntype
ntypes
Ntypes
nucleotides
nullptr
num
numa
numactl
@ -2538,6 +2555,7 @@ ppn
pppm
prd
Prakash
Praprotnik
pre
Pre
prec
@ -2832,6 +2850,8 @@ Runge
runtime
Rutuparna
rx
rxnave
rxnsum
ry
rz
Ryckaert
@ -3103,6 +3123,7 @@ Swinburne
Swol
Swope
Sx
sx
sy
Sy
symplectic
@ -3112,6 +3133,7 @@ sysdim
Syst
systemd
Sz
sz
Tabbernor
tabinner
Tadmor
@ -3130,6 +3152,7 @@ Tanmoy
Tartakovsky
taskset
taubi
taylor
tb
tchain
Tchain
@ -3163,6 +3186,7 @@ th
thb
thei
Theodorou
Theophile
Theor
thermalization
thermalize
@ -3315,6 +3339,7 @@ Uleft
uloop
Ulomek
ulsph
Ultrafast
uMech
umin
Umin
@ -3350,6 +3375,7 @@ upenn
upto
Urbakh
Urbana
Usabiaga
usec
uSemiParallel
userguide
@ -3494,6 +3520,7 @@ Wikipedia
Wildcard
wildcard
wildcards
Winkler
Wirnsberger
wirtes
witin
@ -3505,6 +3532,7 @@ Worley
Wriggers
Wuppertal
Wurtzite
Wysocki
www
wx
Wx
@ -3595,6 +3623,7 @@ ZBL
Zc
zcm
Zeeman
zeeman
Zemer
Zepeda
zflag

2
examples/ASPHERE/box/in.box
View File

@ -67,7 +67,7 @@ delete_atoms overlap 1.0 small big
reset_timestep 0
neighbor 0.3 bin
neighbor 0.3 multi
neigh_modify delay 0 every 1 check yes
comm_modify mode multi group big vel yes

2
examples/ASPHERE/box/in.box.mp
View File

@ -67,7 +67,7 @@ delete_atoms overlap 1.0 small big
reset_timestep 0
neighbor 0.3 bin
neighbor 0.3 multi
neigh_modify delay 0 every 1 check yes
comm_modify mode multi group big vel yes

2
examples/ASPHERE/dimer/in.dimer
View File

@ -61,7 +61,7 @@ delete_atoms overlap 0.5 small big
reset_timestep 0
neighbor 0.3 bin
neighbor 0.3 multi
neigh_modify delay 0 every 1 check yes
comm_modify mode multi group big vel yes

2
examples/ASPHERE/dimer/in.dimer.mp
View File

@ -61,7 +61,7 @@ delete_atoms overlap 0.5 small big
reset_timestep 0
neighbor 0.3 bin
neighbor 0.3 multi
neigh_modify delay 0 every 1 check yes
comm_modify mode multi group big vel yes

2
examples/ASPHERE/ellipsoid/in.ellipsoid
View File

@ -72,7 +72,7 @@ delete_atoms overlap 1.6 small big
reset_timestep 0
neighbor 0.3 bin
neighbor 0.3 multi
neigh_modify delay 0 every 1 check yes
comm_modify mode multi group big vel yes

2
examples/ASPHERE/ellipsoid/in.ellipsoid.mp
View File

@ -72,7 +72,7 @@ delete_atoms overlap 1.6 small big
reset_timestep 0
neighbor 0.3 bin
neighbor 0.3 multi
neigh_modify delay 0 every 1 check yes
comm_modify mode multi group big vel yes

2
examples/ASPHERE/line/in.line.srd
View File

@ -34,7 +34,7 @@ reset_timestep 0
velocity small create 1.44 87287 loop geom
neighbor 0.3 bin
neighbor 0.3 multi
neigh_modify delay 0 every 1 check yes
neigh_modify exclude molecule/intra big include big

2
examples/ASPHERE/poly/in.poly
View File

@ -70,7 +70,7 @@ delete_atoms overlap 1.0 small big
reset_timestep 0
neighbor 0.3 bin
neighbor 0.3 multi
neigh_modify delay 0 every 1 check yes
comm_modify mode multi group big vel yes

2
examples/ASPHERE/poly/in.poly.mp
View File

@ -70,7 +70,7 @@ delete_atoms overlap 1.0 small big
reset_timestep 0
neighbor 0.3 bin
neighbor 0.3 multi
neigh_modify delay 0 every 1 check yes
comm_modify mode multi group big vel yes

2
examples/ASPHERE/star/in.star
View File

@ -67,7 +67,7 @@ delete_atoms overlap 0.5 small big
reset_timestep 0
neighbor 0.3 bin
neighbor 0.3 multi
neigh_modify delay 0 every 1 check yes
comm_modify mode multi group big vel yes

2
examples/ASPHERE/star/in.star.mp
View File

@ -67,7 +67,7 @@ delete_atoms overlap 0.5 small big
reset_timestep 0
neighbor 0.3 bin
neighbor 0.3 multi
neigh_modify delay 0 every 1 check yes
comm_modify mode multi group big vel yes

2
examples/ASPHERE/tri/in.tri.srd
View File

@ -33,7 +33,7 @@ reset_timestep 0
velocity small create 1.44 87287 loop geom
neighbor 0.3 bin
neighbor 0.3 multi
neigh_modify delay 0 every 1 check yes
neigh_modify exclude molecule/intra big include big

53
examples/USER/brownian/2d_velocity/in2d.velocity Normal file
View File

@ -0,0 +1,53 @@
##### 2d overdamped brownian dynamics with self-propulsion force in direction of velocity. #####
variable gamma_t equal 1.0
variable temp equal 1.0
variable seed equal 1974019
variable fp equal 4.0
variable params string ${gamma_t}_${temp}_${fp}
units lj
dimension 2
newton off
lattice sq 0.4
region box block -16 16 -16 16 -0.2 0.2
create_box 1 box
create_atoms 1 box
mass * 1.0
velocity all create 1.0 1 loop geom
neighbor 1.0 bin
neigh_modify every 1 delay 1 check yes
pair_style none
fix step all brownian ${temp} ${seed} gamma_t ${gamma_t}
fix vel all propel/self velocity ${fp}
fix 2 all enforce2d
fix_modify vel virial yes
compute press all pressure NULL virial
thermo_style custom step temp epair c_press
#equilibration
timestep 0.0000000001
thermo 500
run 5000
reset_timestep 0
#initialisation for the main run
# MSD
compute msd all msd
thermo_style custom step ke pe c_msd[*] c_press
timestep 0.00001
thermo 1000
# main run
run 12000

151
examples/USER/brownian/2d_velocity/log.11May2021.in2d_velocity.g++.1 Normal file
View File

@ -0,0 +1,151 @@
LAMMPS (8 Apr 2021)
using 1 OpenMP thread(s) per MPI task
##### 2d overdamped brownian dynamics with self-propulsion force in direction of velocity. #####
variable gamma_t equal 1.0
variable temp equal 1.0
variable seed equal 1974019
variable fp equal 4.0
variable params string ${gamma_t}_${temp}_${fp}
variable params string 1_${temp}_${fp}
variable params string 1_1_${fp}
variable params string 1_1_4
units lj
dimension 2
newton off
lattice sq 0.4
Lattice spacing in x,y,z = 1.5811388 1.5811388 1.5811388
region box block -16 16 -16 16 -0.2 0.2
create_box 1 box
Created orthogonal box = (-25.298221 -25.298221 -0.31622777) to (25.298221 25.298221 0.31622777)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 1024 atoms
create_atoms CPU = 0.001 seconds
mass * 1.0
velocity all create 1.0 1 loop geom
neighbor 1.0 bin
neigh_modify every 1 delay 1 check yes
pair_style none
fix step all brownian ${temp} ${seed} gamma_t ${gamma_t}
fix step all brownian 1 ${seed} gamma_t ${gamma_t}
fix step all brownian 1 1974019 gamma_t ${gamma_t}
fix step all brownian 1 1974019 gamma_t 1
fix vel all propel/self velocity ${fp}
fix vel all propel/self velocity 4
fix 2 all enforce2d
fix_modify vel virial yes
compute press all pressure NULL virial
thermo_style custom step temp epair c_press
#equilibration
timestep 0.0000000001
thermo 500
run 5000
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2141)
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:167)
Per MPI rank memory allocation (min/avg/max) = 2.289 | 2.289 | 2.289 Mbytes
Step Temp E_pair c_press
0 1 0 -0.18336111
500 2.0519273e+10 0 -0.048238222
1000 1.9821717e+10 0 -0.4711053
1500 1.9697609e+10 0 -0.13539588
2000 2.0209443e+10 0 0.0094958039
2500 1.9591299e+10 0 0.40117118
3000 2.089566e+10 0 -0.036548251
3500 1.978692e+10 0 0.28282578
4000 2.0657848e+10 0 0.17618064
4500 2.0837353e+10 0 -0.080724651
5000 2.0348316e+10 0 -0.17471195
Loop time of 0.575164 on 1 procs for 5000 steps with 1024 atoms
Performance: 0.075 tau/day, 8693.168 timesteps/s
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0036819 | 0.0036819 | 0.0036819 | 0.0 | 0.64
Output | 0.00027752 | 0.00027752 | 0.00027752 | 0.0 | 0.05
Modify | 0.51999 | 0.51999 | 0.51999 | 0.0 | 90.41
Other | | 0.05121 | | | 8.90
Nlocal: 1024.00 ave 1024 max 1024 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 65.0000 ave 65 max 65 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0.00000 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0.0000000
Neighbor list builds = 0
Dangerous builds = 0
reset_timestep 0
#initialisation for the main run
# MSD
compute msd all msd
thermo_style custom step ke pe c_msd[*] c_press
timestep 0.00001
thermo 1000
# main run
run 12000
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:167)
Per MPI rank memory allocation (min/avg/max) = 2.664 | 2.664 | 2.664 Mbytes
Step KinEng PotEng c_msd[1] c_msd[2] c_msd[3] c_msd[4] c_press
0 2.0328444e+10 0 0 0 0 0 -0.17471195
1000 197017.59 0 0.018147562 0.019839233 0 0.037986796 -0.71897807
2000 197030.23 0 0.03909867 0.041721342 0 0.080820011 -0.30051929
3000 201997.2 0 0.065694399 0.06235257 0 0.12804697 -0.85167039
4000 199927.76 0 0.085698715 0.080328815 0 0.16602753 0.18493117
5000 198665.7 0 0.10896054 0.097021266 0 0.2059818 -0.090735406
6000 199277.78 0 0.13081111 0.11724814 0 0.24805925 -0.18189034
7000 199850.54 0 0.14721838 0.13806858 0 0.28528696 0.11334674
8000 191577.11 0 0.16582149 0.15935853 0 0.32518002 -0.73284569
9000 197331.29 0 0.17995704 0.18652927 0 0.3664863 -0.015558407
10000 197048.17 0 0.2034106 0.20329856 0 0.40670916 0.36985211
11000 200105.54 0 0.21809835 0.21966463 0 0.43776298 0.36437
12000 203180.39 0 0.23810386 0.23666184 0 0.47476569 -0.072006034
Loop time of 1.37465 on 1 procs for 12000 steps with 1024 atoms
Performance: 7542.303 tau/day, 8729.517 timesteps/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0.00012231 | 0.00012231 | 0.00012231 | 0.0 | 0.01
Comm | 0.0024607 | 0.0024607 | 0.0024607 | 0.0 | 0.18
Output | 0.00068665 | 0.00068665 | 0.00068665 | 0.0 | 0.05
Modify | 1.2479 | 1.2479 | 1.2479 | 0.0 | 90.78
Other | | 0.1235 | | | 8.98
Nlocal: 1024.00 ave 1024 max 1024 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0.00000 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0.00000 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0.0000000
Neighbor list builds = 15
Dangerous builds = 0
Total wall time: 0:00:01

151
examples/USER/brownian/2d_velocity/log.11May2021.in2d_velocity.g++.4 Normal file
View File

@ -0,0 +1,151 @@
LAMMPS (8 Apr 2021)
using 1 OpenMP thread(s) per MPI task
##### 2d overdamped brownian dynamics with self-propulsion force in direction of velocity. #####
variable gamma_t equal 1.0
variable temp equal 1.0
variable seed equal 1974019
variable fp equal 4.0
variable params string ${gamma_t}_${temp}_${fp}
variable params string 1_${temp}_${fp}
variable params string 1_1_${fp}
variable params string 1_1_4
units lj
dimension 2
newton off
lattice sq 0.4
Lattice spacing in x,y,z = 1.5811388 1.5811388 1.5811388
region box block -16 16 -16 16 -0.2 0.2
create_box 1 box
Created orthogonal box = (-25.298221 -25.298221 -0.31622777) to (25.298221 25.298221 0.31622777)
2 by 2 by 1 MPI processor grid
create_atoms 1 box
Created 1024 atoms
create_atoms CPU = 0.001 seconds
mass * 1.0
velocity all create 1.0 1 loop geom
neighbor 1.0 bin
neigh_modify every 1 delay 1 check yes
pair_style none
fix step all brownian ${temp} ${seed} gamma_t ${gamma_t}
fix step all brownian 1 ${seed} gamma_t ${gamma_t}
fix step all brownian 1 1974019 gamma_t ${gamma_t}
fix step all brownian 1 1974019 gamma_t 1
fix vel all propel/self velocity ${fp}
fix vel all propel/self velocity 4
fix 2 all enforce2d
fix_modify vel virial yes
compute press all pressure NULL virial
thermo_style custom step temp epair c_press
#equilibration
timestep 0.0000000001
thermo 500
run 5000
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2141)
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:167)
Per MPI rank memory allocation (min/avg/max) = 2.289 | 2.289 | 2.289 Mbytes
Step Temp E_pair c_press
0 1 0 -0.18336111
500 1.9862591e+10 0 -0.32013566
1000 2.0093184e+10 0 -0.36609742
1500 1.9562283e+10 0 -0.53349351
2000 1.9903977e+10 0 0.63783249
2500 2.0260128e+10 0 0.30046413
3000 1.9948065e+10 0 -0.63093105
3500 1.9507486e+10 0 0.48762848
4000 2.0049087e+10 0 0.40289309
4500 1.9975813e+10 0 0.57649363
5000 2.0129291e+10 0 -0.41288352
Loop time of 0.238949 on 4 procs for 5000 steps with 1024 atoms
Performance: 0.181 tau/day, 20924.952 timesteps/s
92.6% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0080078 | 0.024718 | 0.031782 | 6.2 | 10.34
Output | 0.0001812 | 0.00029999 | 0.00063467 | 0.0 | 0.13
Modify | 0.13401 | 0.14401 | 0.15438 | 2.4 | 60.27
Other | | 0.06992 | | | 29.26
Nlocal: 256.000 ave 256 max 256 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 33.0000 ave 33 max 33 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 0.00000 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0.0000000
Neighbor list builds = 0
Dangerous builds = 0
reset_timestep 0
#initialisation for the main run
# MSD
compute msd all msd
thermo_style custom step ke pe c_msd[*] c_press
timestep 0.00001
thermo 1000
# main run
run 12000
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:167)
Per MPI rank memory allocation (min/avg/max) = 2.664 | 2.664 | 2.664 Mbytes
Step KinEng PotEng c_msd[1] c_msd[2] c_msd[3] c_msd[4] c_press
0 2.0109634e+10 0 0 0 0 0 -0.41288352
1000 195711.46 0 0.020076462 0.020523099 0 0.040599561 -0.32125126
2000 203263.85 0 0.039242992 0.039661282 0 0.078904274 0.11008705
3000 197417.54 0 0.064938128 0.057716419 0 0.12265455 0.16967601
4000 200505.97 0 0.086511225 0.074975267 0 0.16148649 0.31338473
5000 199373.77 0 0.10583263 0.098175658 0 0.20400829 0.34205791
6000 192881.14 0 0.12152088 0.11706037 0 0.23858125 -0.27870467
7000 203045.3 0 0.1383248 0.13629503 0 0.27461983 -0.046936646
8000 198544.08 0 0.16064738 0.1582206 0 0.31886798 -0.18803452
9000 205450.74 0 0.17926529 0.1829047 0 0.36216999 0.47191228
10000 200371.73 0 0.20084273 0.20365189 0 0.40449463 0.093098262
11000 202911.93 0 0.21569236 0.22221715 0 0.43790952 -0.38430031
12000 192590.04 0 0.24041439 0.24114487 0 0.48155926 -0.1677052
Loop time of 0.443026 on 4 procs for 12000 steps with 1024 atoms
Performance: 23402.683 tau/day, 27086.439 timesteps/s
97.7% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 3.2663e-05 | 3.3855e-05 | 3.4809e-05 | 0.0 | 0.01
Comm | 0.0030291 | 0.0030628 | 0.0030825 | 0.0 | 0.69
Output | 0.00027895 | 0.00051624 | 0.001184 | 0.0 | 0.12
Modify | 0.31607 | 0.33372 | 0.37391 | 4.0 | 75.33
Other | | 0.1057 | | | 23.86
Nlocal: 256.000 ave 259 max 253 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Nghost: 0.00000 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 0.00000 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0.0000000
Neighbor list builds = 15
Dangerous builds = 0
Total wall time: 0:00:00

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