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Merge pull request #2156 from akohlmey/collected-small-changes

Browse Source 
Collected changes for the next patch release
This commit is contained in:
Axel Kohlmeyer
2020-06-15 14:40:27 -04:00
committed by GitHub
parent e083416dd8 0ca7270668
commit c987dfb2c9
195 changed files with 1369 additions and 1036 deletions
Download Patch File Download Diff File Expand all files Collapse all files

5
.github/CODEOWNERS vendored
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@ -10,6 +10,7 @@ lib/molfile/* @akohlmey
lib/qmmm/* @akohlmey lib/qmmm/* @akohlmey
lib/vtk/* @rbberger lib/vtk/* @rbberger
lib/kim/* @ellio167 lib/kim/* @ellio167
lib/mesont/* @iafoss
# whole packages # whole packages
src/COMPRESS/* @akohlmey src/COMPRESS/* @akohlmey
@ -25,6 +26,7 @@ src/USER-COLVARS/* @giacomofiorin
src/USER-INTEL/* @wmbrownintel src/USER-INTEL/* @wmbrownintel
src/USER-MANIFOLD/* @Pakketeretet2 src/USER-MANIFOLD/* @Pakketeretet2
src/USER-MEAMC/* @martok src/USER-MEAMC/* @martok
src/USER-MESONT/* @iafoss
src/USER-MOFFF/* @hheenen src/USER-MOFFF/* @hheenen
src/USER-MOLFILE/* @akohlmey src/USER-MOLFILE/* @akohlmey
src/USER-NETCDF/* @pastewka src/USER-NETCDF/* @pastewka
@ -111,6 +113,7 @@ src/fix_nh.* @athomps
src/info.* @akohlmey @rbberger src/info.* @akohlmey @rbberger
src/timer.* @akohlmey src/timer.* @akohlmey
src/min* @sjplimp @stanmoore1 src/min* @sjplimp @stanmoore1
src/utils.* @akohlmey @rbberger
# tools # tools
tools/msi2lmp/* @akohlmey tools/msi2lmp/* @akohlmey
@ -123,6 +126,8 @@ unittest/* @akohlmey @rbberger
# cmake # cmake
cmake/* @junghans @rbberger cmake/* @junghans @rbberger
cmake/Modules/Packages/USER-COLVARS.cmake @junghans @rbberger @giacomofiorin cmake/Modules/Packages/USER-COLVARS.cmake @junghans @rbberger @giacomofiorin
cmake/Modules/Packages/KIM.cmake @junghans @rbberger @ellio167
cmake/presets/*.cmake @junghans @rbberger @akohlmey
# python # python
python/* @rbberger python/* @rbberger

4
.github/CONTRIBUTING.md vendored
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@ -75,7 +75,9 @@ Here is a checklist of steps you need to follow to submit a single file or user
* Your new source files need to have the LAMMPS copyright, GPL notice, and your name and email address at the top, like other user-contributed LAMMPS source files. They need to create a class that is inside the LAMMPS namespace. If the file is for one of the USER packages, including USER-MISC, then we are not as picky about the coding style (see above). I.e. the files do not need to be in the same stylistic format and syntax as other LAMMPS files, though that would be nice for developers as well as users who try to read your code. * Your new source files need to have the LAMMPS copyright, GPL notice, and your name and email address at the top, like other user-contributed LAMMPS source files. They need to create a class that is inside the LAMMPS namespace. If the file is for one of the USER packages, including USER-MISC, then we are not as picky about the coding style (see above). I.e. the files do not need to be in the same stylistic format and syntax as other LAMMPS files, though that would be nice for developers as well as users who try to read your code.
* You **must** also create or extend a documentation file for each new command or style you are adding to LAMMPS. For simplicity and convenience, the documentation of groups of closely related commands or styles may be combined into a single file. This will be one file for a single-file feature. For a package, it might be several files. These are files in the [reStructuredText](https://docutils.sourceforge.io/rst.html) markup language, that are then converted to HTML and PDF. The tools for this conversion are included in the source distribution, and the translation can be as simple as doing "make html pdf" in the doc folder. Thus the documentation source files must be in the same format and style as other `<name>.rst` files in the lammps/doc/src directory for similar commands and styles; use one or more of them as a starting point. An introduction to reStructuredText can be found at [https://docutils.sourceforge.io/docs/user/rst/quickstart.html](https://docutils.sourceforge.io/docs/user/rst/quickstart.html). The text files can include mathematical expressions and symbol in ".. math::" sections or ":math:" expressions or figures (see doc/JPG for examples), or even additional PDF files with further details (see doc/PDF for examples). The doc page should also include literature citations as appropriate; see the bottom of doc/fix_nh.rst for examples and the earlier part of the same file for how to format the cite itself. The "Restrictions" section of the doc page should indicate that your command is only available if LAMMPS is built with the appropriate USER-MISC or USER-FOO package. See other user package doc files for examples of how to do this. The prerequisite for building the HTML format files are Python 3.x and virtualenv. Please run at least `make html`, `make pdf` and `make spelling` and carefully inspect and proofread the resulting HTML format doc page as well as the output produced to the screen. Make sure that all spelling errors are fixed or the necessary false positives are added to the `doc/utils/sphinx-config/false_positives.txt` file. For new styles, those usually also need to be added to lists on the respective overview pages. This can be checked for also with `make style_check`. * You **must** also create or extend a documentation file for each new command or style you are adding to LAMMPS. For simplicity and convenience, the documentation of groups of closely related commands or styles may be combined into a single file. This will be one file for a single-file feature. For a package, it might be several files. These are files in the [reStructuredText](https://docutils.sourceforge.io/rst.html) markup language, that are then converted to HTML and PDF. The tools for this conversion are included in the source distribution, and the translation can be as simple as doing "make html pdf" in the doc folder. Thus the documentation source files must be in the same format and style as other `<name>.rst` files in the lammps/doc/src directory for similar commands and styles; use one or more of them as a starting point. An introduction to reStructuredText can be found at [https://docutils.sourceforge.io/docs/user/rst/quickstart.html](https://docutils.sourceforge.io/docs/user/rst/quickstart.html). The text files can include mathematical expressions and symbol in ".. math::" sections or ":math:" expressions or figures (see doc/JPG for examples), or even additional PDF files with further details (see doc/PDF for examples). The doc page should also include literature citations as appropriate; see the bottom of doc/fix_nh.rst for examples and the earlier part of the same file for how to format the cite itself. The "Restrictions" section of the doc page should indicate that your command is only available if LAMMPS is built with the appropriate USER-MISC or USER-FOO package. See other user package doc files for examples of how to do this. The prerequisite for building the HTML format files are Python 3.x and virtualenv. Please run at least `make html`, `make pdf` and `make spelling` and carefully inspect and proofread the resulting HTML format doc page as well as the output produced to the screen. Make sure that all spelling errors are fixed or the necessary false positives are added to the `doc/utils/sphinx-config/false_positives.txt` file. For new styles, those usually also need to be added to lists on the respective overview pages. This can be checked for also with `make style_check`.
* For a new package (or even a single command) you should include one or more example scripts demonstrating its use. These should run in no more than a couple minutes, even on a single processor, and not require large data files as input. See directories under examples/USER for examples of input scripts other users provided for their packages. These example inputs are also required for validating memory accesses and testing for memory leaks with valgrind * For a new package (or even a single command) you should include one or more example scripts demonstrating its use. These should run in no more than a couple minutes, even on a single processor, and not require large data files as input. See directories under examples/USER for examples of input scripts other users provided for their packages. These example inputs are also required for validating memory accesses and testing for memory leaks with valgrind
* If there is a paper of yours describing your feature (either the algorithm/science behind the feature itself, or its initial usage, or its implementation in LAMMPS), you can add the citation to the *.cpp source file. See src/USER-EFF/atom_vec_electron.cpp for an example. A LaTeX citation is stored in a variable at the top of the file and a single line of code that references the variable is added to the constructor of the class. Whenever a user invokes your feature from their input script, this will cause LAMMPS to output the citation to a log.cite file and prompt the user to examine the file. Note that you should only use this for a paper you or your group authored. E.g. adding a cite in the code for a paper by Nose and Hoover if you write a fix that implements their integrator is not the intended usage. That kind of citation should just be in the doc page you provide. * For new utility functions or class (i.e. anything that does not depend on a LAMMPS object), new unit tests should be added to the unittest tree.
* When adding a new LAMMPS style, a .yaml file with a test configuration and reference data should be added for the styles where a suitable tester program already exists (e.g. pair styles, bond styles, etc.).
* If there is a paper of yours describing your feature (either the algorithm/science behind the feature itself, or its initial usage, or its implementation in LAMMPS), you can add the citation to the <name>.cpp source file. See src/USER-EFF/atom_vec_electron.cpp for an example. A LaTeX citation is stored in a variable at the top of the file and a single line of code that references the variable is added to the constructor of the class. Whenever a user invokes your feature from their input script, this will cause LAMMPS to output the citation to a log.cite file and prompt the user to examine the file. Note that you should only use this for a paper you or your group authored. E.g. adding a cite in the code for a paper by Nose and Hoover if you write a fix that implements their integrator is not the intended usage. That kind of citation should just be in the doc page you provide.
Finally, as a general rule-of-thumb, the more clear and self-explanatory you make your documentation and README files, and the easier you make it for people to get started, e.g. by providing example scripts, the more likely it is that users will try out your new feature. Finally, as a general rule-of-thumb, the more clear and self-explanatory you make your documentation and README files, and the easier you make it for people to get started, e.g. by providing example scripts, the more likely it is that users will try out your new feature.

1
.github/PULL_REQUEST_TEMPLATE.md vendored
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@ -34,6 +34,7 @@ By submitting this pull request, I agree, that my contribution will be included
- [ ] The added/updated documentation is integrated and tested with the documentation build system - [ ] The added/updated documentation is integrated and tested with the documentation build system
- [ ] The feature has been verified to work with the conventional build system - [ ] The feature has been verified to work with the conventional build system
- [ ] The feature has been verified to work with the CMake based build system - [ ] The feature has been verified to work with the CMake based build system
- [ ] Suitable tests have been added to the unittest tree.
- [ ] A package specific README file has been included or updated - [ ] A package specific README file has been included or updated
- [ ] One or more example input decks are included - [ ] One or more example input decks are included

5
cmake/CMakeLists.txt
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@ -631,6 +631,8 @@ install(
############################################################################### ###############################################################################
if(BUILD_SHARED_LIBS) if(BUILD_SHARED_LIBS)
if(CMAKE_VERSION VERSION_LESS 3.12) if(CMAKE_VERSION VERSION_LESS 3.12)
# adjust so we find Python 3 versions before Python 2 on old systems with old CMake
set(Python_ADDITIONAL_VERSIONS 3.8 3.7 3.6 3.5)
find_package(PythonInterp) # Deprecated since version 3.12 find_package(PythonInterp) # Deprecated since version 3.12
if(PYTHONINTERP_FOUND) if(PYTHONINTERP_FOUND)
set(Python_EXECUTABLE ${PYTHON_EXECUTABLE}) set(Python_EXECUTABLE ${PYTHON_EXECUTABLE})
@ -786,3 +788,6 @@ if(PKG_KSPACE)
endif() endif()
endif() endif()
endif() endif()
if(BUILD_DOC)
message(STATUS "<<< Building HTML Manual >>>")
endif()

37
cmake/Modules/Documentation.cmake
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@ -2,10 +2,19 @@
# Build documentation # Build documentation
############################################################################### ###############################################################################
option(BUILD_DOC "Build LAMMPS HTML documentation" OFF) option(BUILD_DOC "Build LAMMPS HTML documentation" OFF)
if(BUILD_DOC)
find_package(PythonInterp 3 REQUIRED)
set(VIRTUALENV ${PYTHON_EXECUTABLE} -m virtualenv) if(BUILD_DOC)
# Sphinx 3.x requires at least Python 3.5
if(CMAKE_VERSION VERSION_LESS 3.12)
find_package(PythonInterp 3.5 REQUIRED)
set(VIRTUALENV ${PYTHON_EXECUTABLE} -m virtualenv -p ${PYTHON_EXECUTABLE})
else()
find_package(Python3 REQUIRED COMPONENTS Interpreter)
if(Python3_VERSION VERSION_LESS 3.5)
message(FATAL_ERROR "Python 3.5 and up is required to build the HTML documentation")
endif()
set(VIRTUALENV ${Python3_EXECUTABLE} -m virtualenv -p ${Python3_EXECUTABLE})
endif()
file(GLOB DOC_SOURCES ${LAMMPS_DOC_DIR}/src/[^.]*.rst) file(GLOB DOC_SOURCES ${LAMMPS_DOC_DIR}/src/[^.]*.rst)
@ -25,11 +34,10 @@ if(BUILD_DOC)
) )
# download mathjax distribution and unpack to folder "mathjax" # download mathjax distribution and unpack to folder "mathjax"
file(DOWNLOAD "https://github.com/mathjax/MathJax/archive/3.0.5.tar.gz" if(NOT EXISTS ${CMAKE_CURRENT_BINARY_DIR}/mathjax/es5)
"${CMAKE_CURRENT_BINARY_DIR}/mathjax.tar.gz" file(DOWNLOAD "https://github.com/mathjax/MathJax/archive/3.0.5.tar.gz"
EXPECTED_MD5 5d9d3799cce77a1a95eee6be04eb68e7) "${CMAKE_CURRENT_BINARY_DIR}/mathjax.tar.gz"
EXPECTED_MD5 5d9d3799cce77a1a95eee6be04eb68e7)
if(NOT EXISTS ${CMAKE_CURRENT_BINARY_DIR}/mathjax)
execute_process(COMMAND ${CMAKE_COMMAND} -E tar xzf mathjax.tar.gz WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}) execute_process(COMMAND ${CMAKE_COMMAND} -E tar xzf mathjax.tar.gz WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})
file(GLOB MATHJAX_VERSION_DIR ${CMAKE_CURRENT_BINARY_DIR}/MathJax-*) file(GLOB MATHJAX_VERSION_DIR ${CMAKE_CURRENT_BINARY_DIR}/MathJax-*)
execute_process(COMMAND ${CMAKE_COMMAND} -E rename ${MATHJAX_VERSION_DIR} ${CMAKE_CURRENT_BINARY_DIR}/mathjax) execute_process(COMMAND ${CMAKE_COMMAND} -E rename ${MATHJAX_VERSION_DIR} ${CMAKE_CURRENT_BINARY_DIR}/mathjax)
@ -37,11 +45,18 @@ if(BUILD_DOC)
file(MAKE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/html/_static/mathjax) file(MAKE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/html/_static/mathjax)
file(COPY ${CMAKE_CURRENT_BINARY_DIR}/mathjax/es5 DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/html/_static/mathjax/) file(COPY ${CMAKE_CURRENT_BINARY_DIR}/mathjax/es5 DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/html/_static/mathjax/)
# for increased browser compatibility
if(NOT EXISTS ${CMAKE_CURRENT_BINARY_DIR}/html/_static/polyfill.js)
file(DOWNLOAD "https://polyfill.io/v3/polyfill.min.js?features=es6"
"${CMAKE_CURRENT_BINARY_DIR}/html/_static/polyfill.js")
endif()
# note, this may run in parallel with other tasks, so we must not use multiple processes here # note, this may run in parallel with other tasks, so we must not use multiple processes here
add_custom_command( add_custom_command(
OUTPUT html OUTPUT html
DEPENDS ${DOC_SOURCES} docenv requirements.txt DEPENDS ${DOC_SOURCES} docenv requirements.txt
COMMAND ${DOCENV_BINARY_DIR}/sphinx-build -b html -c ${LAMMPS_DOC_DIR}/utils/sphinx-config -d ${CMAKE_BINARY_DIR}/doctrees ${LAMMPS_DOC_DIR}/src html COMMAND ${DOCENV_BINARY_DIR}/sphinx-build -b html -c ${LAMMPS_DOC_DIR}/utils/sphinx-config -d ${CMAKE_BINARY_DIR}/doctrees ${LAMMPS_DOC_DIR}/src html
COMMAND ${CMAKE_COMMAND} -E create_symlink Manual.html ${CMAKE_CURRENT_BINARY_DIR}/html/index.html
) )
# copy selected image files to html output tree # copy selected image files to html output tree
@ -56,17 +71,17 @@ if(BUILD_DOC)
set(HTML_IMAGE_TARGETS "") set(HTML_IMAGE_TARGETS "")
foreach(_IMG ${HTML_EXTRA_IMAGES}) foreach(_IMG ${HTML_EXTRA_IMAGES})
string(PREPEND _IMG JPG/) string(PREPEND _IMG JPG/)
list(APPEND HTML_IMAGE_TARGETS "html/${_IMG}") list(APPEND HTML_IMAGE_TARGETS "${CMAKE_CURRENT_BINARY_DIR}/html/${_IMG}")
add_custom_command( add_custom_command(
OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/html/${_IMG} OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/html/${_IMG}
DEPENDS ${LAMMPS_DOC_DIR}/src/${_IMG} html/JPG DEPENDS ${LAMMPS_DOC_DIR}/src/${_IMG} ${CMAKE_CURRENT_BINARY_DIR}/html/JPG
COMMAND ${CMAKE_COMMAND} -E copy ${LAMMPS_DOC_DIR}/src/${_IMG} ${CMAKE_BINARY_DIR}/html/${_IMG} COMMAND ${CMAKE_COMMAND} -E copy ${LAMMPS_DOC_DIR}/src/${_IMG} ${CMAKE_BINARY_DIR}/html/${_IMG}
) )
endforeach() endforeach()
add_custom_target( add_custom_target(
doc ALL doc ALL
DEPENDS html html/_static/mathjax/es5 ${HTML_IMAGE_TARGETS} DEPENDS html ${CMAKE_CURRENT_BINARY_DIR}/html/_static/mathjax/es5 ${HTML_IMAGE_TARGETS}
SOURCES ${LAMMPS_DOC_DIR}/utils/requirements.txt ${DOC_SOURCES} SOURCES ${LAMMPS_DOC_DIR}/utils/requirements.txt ${DOC_SOURCES}
) )

12
cmake/Modules/LAMMPSUtils.cmake
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@ -96,9 +96,15 @@ function(FetchPotentials pkgfolder potfolder)
math(EXPR plusone "${blank}+1") math(EXPR plusone "${blank}+1")
string(SUBSTRING ${line} 0 ${blank} pot) string(SUBSTRING ${line} 0 ${blank} pot)
string(SUBSTRING ${line} ${plusone} -1 sum) string(SUBSTRING ${line} ${plusone} -1 sum)
message(STATUS "Checking external potential ${pot} from ${LAMMPS_POTENTIALS_URL}") if(EXISTS ${LAMMPS_POTENTIALS_DIR}/${pot})
file(DOWNLOAD "${LAMMPS_POTENTIALS_URL}/${pot}.${sum}" "${LAMMPS_POTENTIALS_DIR}/${pot}" file(MD5 "${LAMMPS_POTENTIALS_DIR}/${pot}" oldsum)
EXPECTED_HASH MD5=${sum} SHOW_PROGRESS) endif()
if(NOT sum STREQUAL oldsum)
message(STATUS "Checking external potential ${pot} from ${LAMMPS_POTENTIALS_URL}")
file(DOWNLOAD "${LAMMPS_POTENTIALS_URL}/${pot}.${sum}" "${CMAKE_BINARY_DIR}/${pot}"
EXPECTED_HASH MD5=${sum} SHOW_PROGRESS)
file(COPY "${CMAKE_BINARY_DIR}/${pot}" DESTINATION ${LAMMPS_POTENTIALS_DIR})
endif()
endforeach() endforeach()
endif() endif()
endfunction(FetchPotentials) endfunction(FetchPotentials)

29
cmake/Modules/Packages/USER-SCAFACOS.cmake
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@ -14,6 +14,29 @@ endif()
option(DOWNLOAD_SCAFACOS "Download ScaFaCoS library instead of using an already installed one" ${DOWNLOAD_SCAFACOS_DEFAULT}) option(DOWNLOAD_SCAFACOS "Download ScaFaCoS library instead of using an already installed one" ${DOWNLOAD_SCAFACOS_DEFAULT})
if(DOWNLOAD_SCAFACOS) if(DOWNLOAD_SCAFACOS)
message(STATUS "ScaFaCoS download requested - we will build our own") message(STATUS "ScaFaCoS download requested - we will build our own")
# create variables to pass our compiler flags along to the subsystem compile
# need to apply -fallow-argument-mismatch, if the fortran compiler supports it
include(CheckFortranCompilerFlag)
check_fortran_compiler_flag("-fallow-argument-mismatch" GNUFortran_ARGUMENT_MISMATCH_FLAG)
if(GNUFortran_ARGUMENT_MISMATCH_FLAG)
set(APPEND_Fortran_FLAG "-fallow-argument-mismatch")
endif()
if(CMAKE_Fortran_FLAGS)
set(SCAFACOS_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} ${APPEND_Fortran_FLAG}")
else()
set(SCAFACOS_Fortran_FLAGS "${CMAKE_Fortran_${CMAKE_BUILD_TYPE}_FLAGS} ${APPEND_Fortran_FLAG}")
endif()
if(CMAKE_CXX_FLAGS)
set(SCAFACOS_CXX_FLAGS "${CMAKE_CXX_FLAGS}")
else()
set(SCAFACOS_CXX_FLAGS "${CMAKE_CXX_${CMAKE_BUILD_TYPE}_FLAGS}")
endif()
if(CMAKE_C_FLAGS)
set(SCAFACOS_C_FLAGS "${CMAKE_C_FLAGS}")
else()
set(SCAFACOS_C_FLAGS "${CMAKE_C_${CMAKE_BUILD_TYPE}_FLAGS}")
endif()
include(ExternalProject) include(ExternalProject)
ExternalProject_Add(scafacos_build ExternalProject_Add(scafacos_build
URL https://github.com/scafacos/scafacos/releases/download/v1.0.1/scafacos-1.0.1.tar.gz URL https://github.com/scafacos/scafacos/releases/download/v1.0.1/scafacos-1.0.1.tar.gz
@ -22,9 +45,9 @@ if(DOWNLOAD_SCAFACOS)
--enable-fcs-solvers=fmm,p2nfft,direct,ewald,p3m --enable-fcs-solvers=fmm,p2nfft,direct,ewald,p3m
--with-internal-fftw --with-internal-pfft --with-internal-fftw --with-internal-pfft
--with-internal-pnfft ${CONFIGURE_REQUEST_PIC} --with-internal-pnfft ${CONFIGURE_REQUEST_PIC}
FC=${CMAKE_MPI_Fortran_COMPILER} FC=${CMAKE_MPI_Fortran_COMPILER} FCFLAGS=${SCAFACOS_Fortran_FLAGS}
CXX=${CMAKE_MPI_CXX_COMPILER} CXX=${CMAKE_MPI_CXX_COMPILER} CXXFLAGS=${SCAFACOS_CXX_FLAGS}
CC=${CMAKE_MPI_C_COMPILER} CC=${CMAKE_MPI_C_COMPILER} CFLAGS=${SCAFACOS_C_FLAGS}
F77= F77=
BUILD_BYPRODUCTS BUILD_BYPRODUCTS
<INSTALL_DIR>/lib/libfcs.a <INSTALL_DIR>/lib/libfcs.a

17
cmake/presets/download.cmake Normal file
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@ -0,0 +1,17 @@
# 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.
set(ALL_PACKAGES KIM LATTE MSCG VORONOI USER-PLUMED USER-SCAFACOS USER-SMD USER-MESONT)
foreach(PKG ${ALL_PACKAGES})
set(PKG_${PKG} ON CACHE BOOL "" FORCE)
endforeach()
set(DOWNLOAD_KIM ON CACHE BOOL "" FORCE)
set(DOWNLOAD_LATTE 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_PLUMED ON CACHE BOOL "" FORCE)
set(DOWNLOAD_SCAFACOS ON CACHE BOOL "" FORCE)

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

@ -4,7 +4,7 @@ set(WIN_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU
USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK
USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF
USER-FEP USER-INTEL USER-MANIFOLD USER-MEAMC USER-MESODPD USER-FEP USER-INTEL USER-MANIFOLD USER-MEAMC USER-MESODPD
USER-MISC USER-MGPT USER-MOFFF USER-MOLFILE USER-OMP USER-MESONT USER-MISC USER-MGPT USER-MOFFF USER-MOLFILE USER-OMP
USER-PHONON USER-PTM USER-QTB USER-REACTION USER-REAXC USER-PHONON USER-PTM USER-QTB USER-REACTION USER-REAXC
USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF
USER-YAFF) USER-YAFF)

23
doc/src/Build_basics.rst
View File

@ -225,7 +225,7 @@ A few example command lines are:
For compiling with the Clang/LLVM compilers a CMake preset is provided that For compiling with the Clang/LLVM compilers a CMake preset is provided that
can be loaded with `-C ../cmake/presets/clang.cmake`. Similarly, can be loaded with `-C ../cmake/presets/clang.cmake`. Similarly,
`-C ../cmake/presets/intel.cmake` should switch the `-C ../cmake/presets/intel.cmake` should switch the
In addition you can set ``CMAKE_TUNE_FLAGS`` to specifically add In addition you can set ``CMAKE_TUNE_FLAGS`` to specifically add
compiler flags to tune for optimal performance on given hosts. By compiler flags to tune for optimal performance on given hosts. By
@ -372,7 +372,8 @@ it. The build step will also create generic soft links, named
``liblammps.a`` and ``liblammps.so``\ , which point to the specific ``liblammps.a`` and ``liblammps.so``\ , which point to the specific
``liblammps_machine.a/so`` files. ``liblammps_machine.a/so`` files.
**CMake and make info**\ : CMake and make info
^^^^^^^^^^^^^^^^^^^
Note that for creating a shared library, all the libraries it depends on Note that for creating a shared library, all the libraries it depends on
must be compiled to be compatible with shared libraries. This should be must be compiled to be compatible with shared libraries. This should be
@ -462,7 +463,8 @@ tool. The actual translation is then done via make commands.
.. _rst: https://docutils.readthedocs.io/en/sphinx-docs/user/rst/quickstart.html .. _rst: https://docutils.readthedocs.io/en/sphinx-docs/user/rst/quickstart.html
.. _sphinx: https://sphinx-doc.org .. _sphinx: https://sphinx-doc.org
**Documentation make option**\ : Documentation make option
^^^^^^^^^^^^^^^^^^^^^^^^^
The following make commands can be issued in the doc folder of the The following make commands can be issued in the doc folder of the
LAMMPS source distribution. LAMMPS source distribution.
@ -489,7 +491,8 @@ your system.
current LAMMPS version (HTML and PDF files), from the website current LAMMPS version (HTML and PDF files), from the website
`download page <https://lammps.sandia.gov/download.html>`_. `download page <https://lammps.sandia.gov/download.html>`_.
**CMake build option**\ : CMake build option
^^^^^^^^^^^^^^^^^^
It is also possible to create the HTML version of the manual within It is also possible to create the HTML version of the manual within
the :doc:`CMake build directory <Build_cmake>`. The reason for this the :doc:`CMake build directory <Build_cmake>`. The reason for this
@ -512,7 +515,8 @@ Build LAMMPS tools
Some tools described in :doc:`Auxiliary tools <Tools>` can be built directly Some tools described in :doc:`Auxiliary tools <Tools>` can be built directly
using CMake or Make. using CMake or Make.
**CMake build3**\ : CMake build
^^^^^^^^^^^
.. code-block:: bash .. code-block:: bash
@ -521,7 +525,8 @@ using CMake or Make.
The generated binaries will also become part of the LAMMPS installation The generated binaries will also become part of the LAMMPS installation
(see below). (see below).
**Traditional make**\ : Traditional make
^^^^^^^^^^^^^^^^
.. code-block:: bash .. code-block:: bash
@ -545,7 +550,8 @@ a globally visible place on your system, for others to access. Note
that you may need super-user privileges (e.g. sudo) if the directory that you may need super-user privileges (e.g. sudo) if the directory
you want to copy files to is protected. you want to copy files to is protected.
**CMake build**\ : CMake build
^^^^^^^^^^^
.. code-block:: bash .. code-block:: bash
@ -553,7 +559,8 @@ you want to copy files to is protected.
make # perform make after CMake command make # perform make after CMake command
make install # perform the installation into prefix make install # perform the installation into prefix
**Traditional make**\ : Traditional make
^^^^^^^^^^^^^^^^
There is no "install" option in the ``src/Makefile`` for LAMMPS. If There is no "install" option in the ``src/Makefile`` for LAMMPS. If
you wish to do this you will need to first build LAMMPS, then manually you wish to do this you will need to first build LAMMPS, then manually

10
doc/src/Build_development.rst
View File

@ -126,7 +126,7 @@ in the next section.
.. note:: .. note::
This unit test framework is new and still under development. The unit test framework is new and still under development.
The coverage is only minimal and will be expanded over time. The coverage is only minimal and will be expanded over time.
Tests styles of the same kind of style (e.g. pair styles or Tests styles of the same kind of style (e.g. pair styles or
bond styles) are performed with the same executable using bond styles) are performed with the same executable using
@ -237,12 +237,12 @@ and working.
performed with automatically rescaled epsilon to account for performed with automatically rescaled epsilon to account for
additional loss of precision from code optimizations and different additional loss of precision from code optimizations and different
summation orders. summation orders.
- When compiling with aggressive compiler optimization, some tests - When compiling with (aggressive) compiler optimization, some tests
are likely to fail. It is recommended to inspect the individual are likely to fail. It is recommended to inspect the individual
tests in detail to decide whether the specific error for a specific tests in detail to decide, whether the specific error for a specific
property is acceptable (it often is), or this may be an indication property is acceptable (it often is), or this may be an indication
of mis-compiled code (or undesired large of precision due to of mis-compiled code (or an undesired large loss of precision due
reordering of operations). to significant reordering of operations and thus less error cancellation).
Collect and visualize code coverage metrics Collect and visualize code coverage metrics
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

501
doc/src/Build_extras.rst
View File

@ -60,12 +60,13 @@ This is the list of packages that may require additional steps.
.. _compress: .. _compress:
COMPRESS package COMPRESS package
------------------------------- ----------------
To build with this package you must have the zlib compression library To build with this package you must have the zlib compression library
available on your system. available on your system.
**CMake build**\ : CMake build
^^^^^^^^^^^
If CMake cannot find the library, you can set these variables: If CMake cannot find the library, you can set these variables:
@ -74,10 +75,11 @@ If CMake cannot find the library, you can set these variables:
-D ZLIB_INCLUDE_DIR=path # path to zlib.h header file -D ZLIB_INCLUDE_DIR=path # path to zlib.h header file
-D ZLIB_LIBRARIES=path # path to libz.a (.so) file -D ZLIB_LIBRARIES=path # path to libz.a (.so) file
**Traditional make**\ : Traditional make
^^^^^^^^^^^^^^^^
If make cannot find the library, you can edit the file If make cannot find the library, you can edit the file
lib/compress/Makefile.lammps to specify the paths and library ``lib/compress/Makefile.lammps`` to specify the paths and library
name. name.
---------- ----------
@ -91,7 +93,8 @@ To build with this package, you must choose options for precision and
which GPU hardware to build for. The GPU package currently supports which GPU hardware to build for. The GPU package currently supports
three different types of backends: OpenCL, CUDA and HIP. three different types of backends: OpenCL, CUDA and HIP.
**CMake build**\ : CMake build
^^^^^^^^^^^
.. code-block:: bash .. code-block:: bash
@ -159,7 +162,8 @@ and the linker to work correctly.
cmake -D PKG_GPU=on -D GPU_API=HIP -D HIP_ARCH=sm_70 .. cmake -D PKG_GPU=on -D GPU_API=HIP -D HIP_ARCH=sm_70 ..
make -j 4 make -j 4
**Traditional make**\ : Traditional make
^^^^^^^^^^^^^^^^
Before building LAMMPS, you must build the GPU library in ``lib/gpu``\ . Before building LAMMPS, you must build the GPU library in ``lib/gpu``\ .
You can do this manually if you prefer; follow the instructions in You can do this manually if you prefer; follow the instructions in
@ -208,10 +212,10 @@ your machine are not correct, the LAMMPS build will fail, and
.. note:: .. note::
If you re-build the GPU library in lib/gpu, you should always If you re-build the GPU library in ``lib/gpu``, you should always
un-install the GPU package in lammps/src, then re-install it and un-install the GPU package in ``lammps/src``, then re-install it and
re-build LAMMPS. This is because the compilation of files in the GPU re-build LAMMPS. This is because the compilation of files in the GPU
package uses the library settings from the lib/gpu/Makefile.machine package uses the library settings from the ``lib/gpu/Makefile.machine``
used to build the GPU library. used to build the GPU library.
---------- ----------
@ -250,7 +254,8 @@ See the list of all KIM models here: https://openkim.org/browse/models
the KIM API library with all its models, may take a long time (tens of the KIM API library with all its models, may take a long time (tens of
minutes to hours) to build. Of course you only need to do that once.) minutes to hours) to build. Of course you only need to do that once.)
**CMake build**\ : CMake build
^^^^^^^^^^^
.. code-block:: bash .. code-block:: bash
@ -282,7 +287,8 @@ As an alternative, you can specify your own CA cert path by setting the
environment variable ``CURL_CA_BUNDLE`` to the path of your choice. A call environment variable ``CURL_CA_BUNDLE`` to the path of your choice. A call
to the KIM web query would get this value from the environmental variable. to the KIM web query would get this value from the environmental variable.
**Traditional make**\ : Traditional make
^^^^^^^^^^^^^^^^
You can download and build the KIM library manually if you prefer; You can download and build the KIM library manually if you prefer;
follow the instructions in ``lib/kim/README``\ . You can also do it in one follow the instructions in ``lib/kim/README``\ . You can also do it in one
@ -300,7 +306,7 @@ invoke the ``lib/kim/Install.py`` script with the specified args.
$ make lib-kim args="-p /usr/local -a EAM_Dynamo_Ackland_W__MO_141627196590_002" # ditto but add one model or driver $ make lib-kim args="-p /usr/local -a EAM_Dynamo_Ackland_W__MO_141627196590_002" # ditto but add one model or driver
Settings for OpenKIM web queries discussed above need to be applied by adding Settings for OpenKIM web queries discussed above need to be applied by adding
them to the ``LMP_INC`` variable through editing the Makefile.machine you are them to the ``LMP_INC`` variable through editing the ``Makefile.machine`` you are
using. For example: using. For example:
.. code-block:: make .. code-block:: make
@ -605,7 +611,8 @@ LATTE package
To build with this package, you must download and build the LATTE To build with this package, you must download and build the LATTE
library. library.
**CMake build**\ : CMake build
^^^^^^^^^^^
.. code-block:: bash .. code-block:: bash
@ -618,7 +625,8 @@ already on your system (in a location CMake cannot find it),
``LATTE_LIBRARY`` is the filename (plus path) of the LATTE library file, ``LATTE_LIBRARY`` is the filename (plus path) of the LATTE library file,
not the directory the library file is in. not the directory the library file is in.
**Traditional make**\ : Traditional make
^^^^^^^^^^^^^^^^
You can download and build the LATTE library manually if you prefer; You can download and build the LATTE library manually if you prefer;
follow the instructions in ``lib/latte/README``\ . You can also do it in follow the instructions in ``lib/latte/README``\ . You can also do it in
@ -634,11 +642,12 @@ args:
$ make lib-latte args="-b -m gfortran" # download and build in lib/latte and $ make lib-latte args="-b -m gfortran" # download and build in lib/latte and
# copy Makefile.lammps.gfortran to Makefile.lammps # copy Makefile.lammps.gfortran to Makefile.lammps
Note that 3 symbolic (soft) links, "includelink" and "liblink" and Note that 3 symbolic (soft) links, ``includelink`` and ``liblink`` and
"filelink.o", are created in lib/latte to point into the LATTE home ``filelink.o``, are created in ``lib/latte`` to point to required
dir. When LAMMPS itself is built it will use these links. You should folders and files in the LATTE home directory. When LAMMPS itself is
also check that the Makefile.lammps file you create is appropriate for built it will use these links. You should also check that the
the compiler you use on your system to build LATTE. ``Makefile.lammps`` file you create is appropriate for the compiler you
use on your system to build LATTE.
---------- ----------
@ -651,7 +660,8 @@ This package can optionally include support for messaging via sockets,
using the open-source `ZeroMQ library <http://zeromq.org>`_, which must using the open-source `ZeroMQ library <http://zeromq.org>`_, which must
be installed on your system. be installed on your system.
**CMake build**\ : CMake build
^^^^^^^^^^^
.. code-block:: bash .. code-block:: bash
@ -659,7 +669,8 @@ be installed on your system.
-D ZMQ_LIBRARY=path # ZMQ library file (only needed if a custom location) -D ZMQ_LIBRARY=path # ZMQ library file (only needed if a custom location)
-D ZMQ_INCLUDE_DIR=path # ZMQ include directory (only needed if a custom location) -D ZMQ_INCLUDE_DIR=path # ZMQ include directory (only needed if a custom location)
**Traditional make**\ : Traditional make
^^^^^^^^^^^^^^^^
Before building LAMMPS, you must build the CSlib library in Before building LAMMPS, you must build the CSlib library in
``lib/message``\ . You can build the CSlib library manually if you prefer; ``lib/message``\ . You can build the CSlib library manually if you prefer;
@ -674,8 +685,8 @@ simply invoke the ``lib/message/Install.py`` script with the specified args:
$ make lib-message args="-s" # build as serial lib with no ZMQ support $ make lib-message args="-s" # build as serial lib with no ZMQ support
The build should produce two files: ``lib/message/cslib/src/libmessage.a`` The build should produce two files: ``lib/message/cslib/src/libmessage.a``
and ``lib/message/Makefile.lammps``\ . The latter is copied from an and ``lib/message/Makefile.lammps``. The latter is copied from an
existing ``Makefile.lammps.\*`` and has settings to link with the ZeroMQ existing ``Makefile.lammps.*`` and has settings to link with the ZeroMQ
library if requested in the build. library if requested in the build.
---------- ----------
@ -691,7 +702,8 @@ library. Building the MS-CG library requires that the GSL
machine. See the ``lib/mscg/README`` and ``MSCG/Install`` files for machine. See the ``lib/mscg/README`` and ``MSCG/Install`` files for
more details. more details.
**CMake build**\ : CMake build
^^^^^^^^^^^
.. code-block:: bash .. code-block:: bash
@ -706,7 +718,8 @@ filename (plus path) of the MSCG library file, not the directory the
library file is in. ``MSCG_INCLUDE_DIR`` is the directory the MSCG library file is in. ``MSCG_INCLUDE_DIR`` is the directory the MSCG
include file is in. include file is in.
**Traditional make**\ : Traditional make
^^^^^^^^^^^^^^^^
You can download and build the MS-CG library manually if you prefer; You can download and build the MS-CG library manually if you prefer;
follow the instructions in ``lib/mscg/README``\ . You can also do it in one follow the instructions in ``lib/mscg/README``\ . You can also do it in one
@ -734,16 +747,18 @@ not need to edit the ``lib/mscg/Makefile.lammps`` file.
OPT package OPT package
--------------------- ---------------------
**CMake build**\ : CMake build
^^^^^^^^^^^
No additional settings are needed besides ``-D PKG_OPT=yes`` No additional settings are needed besides ``-D PKG_OPT=yes``
**Traditional make**\ : Traditional make
^^^^^^^^^^^^^^^^
The compile flag "-restrict" must be used to build LAMMPS with the OPT The compile flag ``-restrict`` must be used to build LAMMPS with the OPT
package when using Intel compilers. It should be added to the CCFLAGS package when using Intel compilers. It should be added to the CCFLAGS
line of your Makefile.machine. See src/MAKE/OPTIONS/Makefile.opt for line of your ``Makefile.machine``. See
an example. ``src/MAKE/OPTIONS/Makefile.opt`` for an example.
---------- ----------
@ -752,11 +767,13 @@ an example.
POEMS package POEMS package
------------------------- -------------------------
**CMake build**\ : CMake build
^^^^^^^^^^^
No additional settings are needed besides ``-D PKG_OPT=yes`` No additional settings are needed besides ``-D PKG_OPT=yes``
**Traditional make**\ : Traditional make
^^^^^^^^^^^^^^^^
Before building LAMMPS, you must build the POEMS library in ``lib/poems``\ . Before building LAMMPS, you must build the POEMS library in ``lib/poems``\ .
You can do this manually if you prefer; follow the instructions in You can do this manually if you prefer; follow the instructions in
@ -772,8 +789,8 @@ dir, using a command like these, which simply invoke the
$ make lib-poems args="-m icc" # build with Intel icc compiler $ make lib-poems args="-m icc" # build with Intel icc compiler
The build should produce two files: ``lib/poems/libpoems.a`` and The build should produce two files: ``lib/poems/libpoems.a`` and
``lib/poems/Makefile.lammps``\ . The latter is copied from an existing ``lib/poems/Makefile.lammps``. The latter is copied from an existing
``Makefile.lammps.\*`` and has settings needed to build LAMMPS with the ``Makefile.lammps.*`` and has settings needed to build LAMMPS with the
POEMS library (though typically the settings are just blank). If POEMS library (though typically the settings are just blank). If
necessary, you can edit/create a new ``lib/poems/Makefile.machine`` file necessary, you can edit/create a new ``lib/poems/Makefile.machine`` file
for your system, which should define an ``EXTRAMAKE`` variable to specify for your system, which should define an ``EXTRAMAKE`` variable to specify
@ -791,7 +808,8 @@ library available on your system, which needs to be a Python 2.7
version or a Python 3.x version. See ``lib/python/README`` for more version or a Python 3.x version. See ``lib/python/README`` for more
details. details.
**CMake build**\ : CMake build
^^^^^^^^^^^
.. code-block:: bash .. code-block:: bash
@ -804,11 +822,12 @@ PYTHON_EXECUTABLE variable to specify which Python interpreter should
be used. Note note that you will also need to have the development be used. Note note that you will also need to have the development
headers installed for this version, e.g. python2-devel. headers installed for this version, e.g. python2-devel.
**Traditional make**\ : Traditional make
^^^^^^^^^^^^^^^^
The build uses the ``lib/python/Makefile.lammps`` file in the compile/link The build uses the ``lib/python/Makefile.lammps`` file in the compile/link
process to find Python. You should only need to create a new process to find Python. You should only need to create a new
``Makefile.lammps.\*`` file (and copy it to ``Makefile.lammps``\ ) if ``Makefile.lammps.*`` file (and copy it to ``Makefile.lammps``) if
the LAMMPS build fails. the LAMMPS build fails.
---------- ----------
@ -822,7 +841,8 @@ To build with this package, you must download and build the `Voro++ library <vor
.. _voro-home: http://math.lbl.gov/voro++ .. _voro-home: http://math.lbl.gov/voro++
**CMake build**\ : CMake build
^^^^^^^^^^^
.. code-block:: bash .. code-block:: bash
@ -830,19 +850,20 @@ To build with this package, you must download and build the `Voro++ library <vor
-D VORO_LIBRARY=path # Voro++ library file (only needed if at custom location) -D VORO_LIBRARY=path # Voro++ library file (only needed if at custom location)
-D VORO_INCLUDE_DIR=path # Voro++ include directory (only needed if at custom location) -D VORO_INCLUDE_DIR=path # Voro++ include directory (only needed if at custom location)
If DOWNLOAD_VORO is set, the Voro++ library will be downloaded and If ``DOWNLOAD_VORO`` is set, the Voro++ library will be downloaded and
built inside the CMake build directory. If the Voro++ library is built inside the CMake build directory. If the Voro++ library is
already on your system (in a location CMake cannot find it), already on your system (in a location CMake cannot find it),
VORO_LIBRARY is the filename (plus path) of the Voro++ library file, ``VORO_LIBRARY`` is the filename (plus path) of the Voro++ library file,
not the directory the library file is in. VORO_INCLUDE_DIR is the not the directory the library file is in. ``VORO_INCLUDE_DIR`` is the
directory the Voro++ include file is in. directory the Voro++ include file is in.
**Traditional make**\ : Traditional make
^^^^^^^^^^^^^^^^
You can download and build the Voro++ library manually if you prefer; You can download and build the Voro++ library manually if you prefer;
follow the instructions in lib/voronoi/README. You can also do it in follow the instructions in ``lib/voronoi/README``. You can also do it in
one step from the lammps/src dir, using a command like these, which one step from the ``lammps/src`` dir, using a command like these, which
simply invoke the lib/voronoi/Install.py script with the specified simply invoke the ``lib/voronoi/Install.py`` script with the specified
args: args:
.. code-block:: bash .. code-block:: bash
@ -852,10 +873,10 @@ args:
$ make lib-voronoi args="-p $HOME/voro++" # use existing Voro++ installation in $HOME/voro++ $ make lib-voronoi args="-p $HOME/voro++" # use existing Voro++ installation in $HOME/voro++
$ make lib-voronoi args="-b -v voro++0.4.6" # download and build the 0.4.6 version in lib/voronoi/voro++-0.4.6 $ make lib-voronoi args="-b -v voro++0.4.6" # download and build the 0.4.6 version in lib/voronoi/voro++-0.4.6
Note that 2 symbolic (soft) links, "includelink" and "liblink", are Note that 2 symbolic (soft) links, ``includelink`` and ``liblink``, are
created in lib/voronoi to point to the Voro++ src dir. When LAMMPS created in lib/voronoi to point to the Voro++ source dir. When LAMMPS
builds in src it will use these links. You should not need to edit builds in ``src`` it will use these links. You should not need to edit
the lib/voronoi/Makefile.lammps file. the ``lib/voronoi/Makefile.lammps`` file.
---------- ----------
@ -864,23 +885,28 @@ the lib/voronoi/Makefile.lammps file.
USER-ADIOS package USER-ADIOS package
----------------------------------- -----------------------------------
The USER-ADIOS package requires the `ADIOS I/O library <https://github.com/ornladios/ADIOS2>`_, The USER-ADIOS package requires the `ADIOS I/O library
version 2.3.1 or newer. Make sure that you have ADIOS built either with or <https://github.com/ornladios/ADIOS2>`_, version 2.3.1 or newer. Make
without MPI to match if you build LAMMPS with or without MPI. sure that you have ADIOS built either with or without MPI to match if
ADIOS compilation settings for LAMMPS are automatically detected, if the PATH you build LAMMPS with or without MPI. ADIOS compilation settings for
and LD_LIBRARY_PATH environment variables have been updated for the local ADIOS LAMMPS are automatically detected, if the PATH and LD_LIBRARY_PATH
installation and the instructions below are followed for the respective build systems. environment variables have been updated for the local ADIOS installation
and the instructions below are followed for the respective build
systems.
**CMake build**\ : CMake build
^^^^^^^^^^^
.. code-block:: bash .. code-block:: bash
-D ADIOS2_DIR=path # path is where ADIOS 2.x is installed -D ADIOS2_DIR=path # path is where ADIOS 2.x is installed
-D PKG_USER-ADIOS=yes -D PKG_USER-ADIOS=yes
**Traditional make**\ : Traditional make
^^^^^^^^^^^^^^^^
Turn on the USER-ADIOS package before building LAMMPS. If the ADIOS 2.x software is installed in PATH, there is nothing else to do: Turn on the USER-ADIOS package before building LAMMPS. If the ADIOS 2.x
software is installed in PATH, there is nothing else to do:
.. code-block:: bash .. code-block:: bash
@ -901,18 +927,20 @@ USER-ATC package
The USER-ATC package requires the MANYBODY package also be installed. The USER-ATC package requires the MANYBODY package also be installed.
**CMake build**\ : CMake build
^^^^^^^^^^^
No additional settings are needed besides "-D PKG_USER-ATC=yes" No additional settings are needed besides "-D PKG_USER-ATC=yes"
and "-D PKG_MANYBODY=yes". and "-D PKG_MANYBODY=yes".
**Traditional make**\ : Traditional make
^^^^^^^^^^^^^^^^
Before building LAMMPS, you must build the ATC library in lib/atc. Before building LAMMPS, you must build the ATC library in ``lib/atc``.
You can do this manually if you prefer; follow the instructions in You can do this manually if you prefer; follow the instructions in
lib/atc/README. You can also do it in one step from the lammps/src ``lib/atc/README``. You can also do it in one step from the
dir, using a command like these, which simply invoke the ``lammps/src`` dir, using a command like these, which simply invoke the
lib/atc/Install.py script with the specified args: ``lib/atc/Install.py`` script with the specified args:
.. code-block:: bash .. code-block:: bash
@ -921,19 +949,19 @@ lib/atc/Install.py script with the specified args:
$ make lib-atc args="-m mpi" # build with default MPI compiler (settings as with "make mpi") $ make lib-atc args="-m mpi" # build with default MPI compiler (settings as with "make mpi")
$ make lib-atc args="-m icc" # build with Intel icc compiler $ make lib-atc args="-m icc" # build with Intel icc compiler
The build should produce two files: lib/atc/libatc.a and The build should produce two files: ``lib/atc/libatc.a`` and
lib/atc/Makefile.lammps. The latter is copied from an existing ``lib/atc/Makefile.lammps``. The latter is copied from an existing
Makefile.lammps.\* and has settings needed to build LAMMPS with the ATC ``Makefile.lammps.*`` and has settings needed to build LAMMPS with the
library. If necessary, you can edit/create a new ATC library. If necessary, you can edit/create a new
lib/atc/Makefile.machine file for your system, which should define an ``lib/atc/Makefile.machine`` file for your system, which should define
EXTRAMAKE variable to specify a corresponding Makefile.lammps.machine an ``EXTRAMAKE`` variable to specify a corresponding
file. ``Makefile.lammps.<machine>`` file.
Note that the Makefile.lammps file has settings for the BLAS and Note that the Makefile.lammps file has settings for the BLAS and
LAPACK linear algebra libraries. As explained in lib/atc/README these LAPACK linear algebra libraries. As explained in ``lib/atc/README`` these
can either exist on your system, or you can use the files provided in can either exist on your system, or you can use the files provided in
lib/linalg. In the latter case you also need to build the library in ``lib/linalg``. In the latter case you also need to build the library in
lib/linalg with a command like these: ``lib/linalg`` with a command like these:
.. code-block:: bash .. code-block:: bash
@ -947,19 +975,21 @@ lib/linalg with a command like these:
.. _user-awpmd: .. _user-awpmd:
USER-AWPMD package USER-AWPMD package
----------------------------------- ------------------
**CMake build**\ : CMake build
^^^^^^^^^^^
No additional settings are needed besides "-D PKG_USER-AQPMD=yes". No additional settings are needed besides ``-D PKG_USER-AQPMD=yes``.
**Traditional make**\ : Traditional make
^^^^^^^^^^^^^^^^
Before building LAMMPS, you must build the AWPMD library in lib/awpmd. Before building LAMMPS, you must build the AWPMD library in ``lib/awpmd``.
You can do this manually if you prefer; follow the instructions in You can do this manually if you prefer; follow the instructions in
lib/awpmd/README. You can also do it in one step from the lammps/src ``lib/awpmd/README``. You can also do it in one step from the ``lammps/src``
dir, using a command like these, which simply invoke the dir, using a command like these, which simply invoke the
lib/awpmd/Install.py script with the specified args: ``lib/awpmd/Install.py`` script with the specified args:
.. code-block:: bash .. code-block:: bash
@ -968,19 +998,19 @@ lib/awpmd/Install.py script with the specified args:
$ make lib-awpmd args="-m mpi" # build with default MPI compiler (settings as with "make mpi") $ make lib-awpmd args="-m mpi" # build with default MPI compiler (settings as with "make mpi")
$ make lib-awpmd args="-m icc" # build with Intel icc compiler $ make lib-awpmd args="-m icc" # build with Intel icc compiler
The build should produce two files: lib/awpmd/libawpmd.a and The build should produce two files: ``lib/awpmd/libawpmd.a`` and
lib/awpmd/Makefile.lammps. The latter is copied from an existing ``lib/awpmd/Makefile.lammps``. The latter is copied from an existing
Makefile.lammps.\* and has settings needed to build LAMMPS with the ``Makefile.lammps.*`` and has settings needed to build LAMMPS with the
AWPMD library. If necessary, you can edit/create a new AWPMD library. If necessary, you can edit/create a new
lib/awpmd/Makefile.machine file for your system, which should define ``lib/awpmd/Makefile.machine`` file for your system, which should define
an EXTRAMAKE variable to specify a corresponding an ``EXTRAMAKE`` variable to specify a corresponding
Makefile.lammps.machine file. ``Makefile.lammps.<machine>`` file.
Note that the Makefile.lammps file has settings for the BLAS and Note that the ``Makefile.lammps`` file has settings for the BLAS and
LAPACK linear algebra libraries. As explained in lib/awpmd/README LAPACK linear algebra libraries. As explained in ``lib/awpmd/README``
these can either exist on your system, or you can use the files these can either exist on your system, or you can use the files
provided in lib/linalg. In the latter case you also need to build the provided in ``lib/linalg``. In the latter case you also need to build the
library in lib/linalg with a command like these: library in ``lib/linalg`` with a command like these:
.. code-block:: bash .. code-block:: bash
@ -999,36 +1029,26 @@ USER-COLVARS package
This package includes into the LAMMPS distribution the Colvars library, which This package includes into the LAMMPS distribution the Colvars library, which
can be built for the most part with all major versions of the C++ language. can be built for the most part with all major versions of the C++ language.
A few of the most recent features require C++11 support. In particular, the
library is optionally built together with the
`Lepton <https://simtk.org/projects/lepton>`_ library, a copy of which is also
included in the LAMMPS distribution. Lepton implements the
`customFunction <http://colvars.github.io/colvars-refman-lammps/colvars-refman-lammps.html#colvar|customFunction>`_
feature, and requires C++11 support.
See `here <https://colvars.github.io/README-c++11.html>`_ for a detailed list of CMake build
C++11-only features. ^^^^^^^^^^^
**CMake build**\ :
This is the recommended build recipe: no additional settings are normally This is the recommended build recipe: no additional settings are normally
needed besides "-D PKG_USER-COLVARS=yes". needed besides ``-D PKG_USER-COLVARS=yes``.
Building and linking of Lepton (or other C++11-only features) is enabled Traditional make
automatically when compilation is carried out with C++11 support, and disabled ^^^^^^^^^^^^^^^^
otherwise. Optionally, Lepton build may be manually controlled with the flag
"-D COLVARS_LEPTON=yes\|no".
**Traditional make**\ :
Before building LAMMPS, one must build the Colvars library in lib/colvars. Before building LAMMPS, one must build the Colvars library in lib/colvars.
This can be done manually in the same folder by using or adapting one of the This can be done manually in the same folder by using or adapting one of
provided Makefiles: for example, Makefile.g++ for the GNU compiler. the provided Makefiles: for example, ``Makefile.g++`` for the GNU C++
compiler. C++11 compatibility may need to be enabled for some older
compilers (as is done in the example makefile).
In general, it is safer to use build setting consistent with the rest of In general, it is safer to use build setting consistent with the rest of
LAMMPS. This is best carried out from the LAMMPS src directory using a LAMMPS. This is best carried out from the LAMMPS src directory using a
command like these, which simply invoke the lib/colvars/Install.py script with command like these, which simply invoke the ``lib/colvars/Install.py`` script with
the specified args: the specified args:
.. code-block:: bash .. code-block:: bash
@ -1039,7 +1059,7 @@ the specified args:
$ make lib-colvars args="-m g++-debug" # build with GNU g++ compiler and colvars debugging enabled $ make lib-colvars args="-m g++-debug" # build with GNU g++ compiler and colvars debugging enabled
The "machine" argument of the "-m" flag is used to find a Makefile.machine to The "machine" argument of the "-m" flag is used to find a Makefile.machine to
use as build recipe. If it does not already exist in lib/colvars, it will be use as build recipe. If it does not already exist in ``lib/colvars``, it will be
auto-generated by using compiler flags consistent with those parsed from the auto-generated by using compiler flags consistent with those parsed from the
core LAMMPS makefiles. core LAMMPS makefiles.
@ -1050,9 +1070,9 @@ Optional flags may be specified as environment variables:
$ COLVARS_DEBUG=yes make lib-colvars args="-m machine" # Build with debug code (much slower) $ COLVARS_DEBUG=yes make lib-colvars args="-m machine" # Build with debug code (much slower)
$ COLVARS_LEPTON=no make lib-colvars args="-m machine" # Build without Lepton (included otherwise) $ COLVARS_LEPTON=no make lib-colvars args="-m machine" # Build without Lepton (included otherwise)
The build should produce two files: the library lib/colvars/libcolvars.a The build should produce two files: the library ``lib/colvars/libcolvars.a``
(which also includes Lepton objects if enabled) and the specification file (which also includes Lepton objects if enabled) and the specification file
lib/colvars/Makefile.lammps. The latter is auto-generated, and normally does ``lib/colvars/Makefile.lammps``. The latter is auto-generated, and normally does
not need to be edited. not need to be edited.
---------- ----------
@ -1099,12 +1119,14 @@ try a different one, switch to a different build system, consider a
global PLUMED installation or consider downloading PLUMED during the global PLUMED installation or consider downloading PLUMED during the
LAMMPS build. LAMMPS build.
**CMake build**\ : CMake build
^^^^^^^^^^^
When the "-D PKG_USER-PLUMED" flag is included in the cmake command you When the ``-D PKG_USER-PLUMED=yes`` flag is included in the cmake
must ensure that GSL is installed in locations that are specified in command you must ensure that GSL is installed in locations that are
your environment. There are then two additional commands that control specified in your environment. There are then two additional variables
the manner in which PLUMED is obtained and linked into LAMMPS. that control the manner in which PLUMED is obtained and linked into
LAMMPS.
.. code-block:: bash .. code-block:: bash
@ -1114,21 +1136,22 @@ the manner in which PLUMED is obtained and linked into LAMMPS.
If DOWNLOAD_PLUMED is set to "yes", the PLUMED library will be If DOWNLOAD_PLUMED is set to "yes", the PLUMED library will be
downloaded (the version of PLUMED that will be downloaded is hard-coded downloaded (the version of PLUMED that will be downloaded is hard-coded
to a vetted version of PLUMED, usually a recent stable release version) to a vetted version of PLUMED, usually a recent stable release version)
and built inside the CMake build directory. If DOWNLOAD_PLUMED is set and built inside the CMake build directory. If ``DOWNLOAD_PLUMED`` is
to "no" (the default), CMake will try to detect and link to an installed set to "no" (the default), CMake will try to detect and link to an
version of PLUMED. For this to work, the PLUMED library has to be installed version of PLUMED. For this to work, the PLUMED library has
installed into a location where the pkg-config tool can find it or the to be installed into a location where the ``pkg-config`` tool can find
PKG_CONFIG_PATH environment variable has to be set up accordingly. it or the PKG_CONFIG_PATH environment variable has to be set up
PLUMED should be installed in such a location if you compile it using accordingly. PLUMED should be installed in such a location if you
the default make; make install commands. compile it using the default make; make install commands.
The PLUMED_MODE setting determines the linkage mode for the PLUMED The ``PLUMED_MODE`` setting determines the linkage mode for the PLUMED
library. The allowed values for this flag are "static" (default), library. The allowed values for this flag are "static" (default),
"shared", or "runtime". For a discussion of PLUMED linkage modes, "shared", or "runtime". For a discussion of PLUMED linkage modes,
please see above. When DOWNLOAD_PLUMED is enabled the static linkage please see above. When ``DOWNLOAD_PLUMED`` is enabled the static
mode is recommended. linkage mode is recommended.
**Traditional make**\ : Traditional make
^^^^^^^^^^^^^^^^
PLUMED needs to be installed before the USER-PLUMED package is installed PLUMED needs to be installed before the USER-PLUMED package is installed
so that LAMMPS can find the right settings when compiling and linking so that LAMMPS can find the right settings when compiling and linking
@ -1149,9 +1172,9 @@ from the src folder through the following make args:
$ make lib-plumed args="-p /usr/local -m shared" # use existing PLUMED installation in $ make lib-plumed args="-p /usr/local -m shared" # use existing PLUMED installation in
# /usr/local and use shared linkage mode # /usr/local and use shared linkage mode
Note that 2 symbolic (soft) links, "includelink" and "liblink" are Note that 2 symbolic (soft) links, ``includelink`` and ``liblink`` are
created in lib/plumed that point to the location of the PLUMED build to created in lib/plumed that point to the location of the PLUMED build to
use. A new file lib/plumed/Makefile.lammps is also created with settings use. A new file ``lib/plumed/Makefile.lammps`` is also created with settings
suitable for LAMMPS to compile and link PLUMED using the desired linkage suitable for LAMMPS to compile and link PLUMED using the desired linkage
mode. After this step is completed, you can install the USER-PLUMED mode. After this step is completed, you can install the USER-PLUMED
package and compile LAMMPS in the usual manner: package and compile LAMMPS in the usual manner:
@ -1186,9 +1209,10 @@ To build with this package you must have the HDF5 software package
installed on your system, which should include the h5cc compiler and installed on your system, which should include the h5cc compiler and
the HDF5 library. the HDF5 library.
**CMake build**\ : CMake build
^^^^^^^^^^^
No additional settings are needed besides "-D PKG_USER-H5MD=yes". No additional settings are needed besides ``-D PKG_USER-H5MD=yes``.
This should auto-detect the H5MD library on your system. Several This should auto-detect the H5MD library on your system. Several
advanced CMake H5MD options exist if you need to specify where it is advanced CMake H5MD options exist if you need to specify where it is
@ -1196,26 +1220,27 @@ installed. Use the ccmake (terminal window) or cmake-gui (graphical)
tools to see these options and set them interactively from their user tools to see these options and set them interactively from their user
interfaces. interfaces.
**Traditional make**\ : Traditional make
^^^^^^^^^^^^^^^^
Before building LAMMPS, you must build the CH5MD library in lib/h5md. Before building LAMMPS, you must build the CH5MD library in
You can do this manually if you prefer; follow the instructions in ``lib/h5md``. You can do this manually if you prefer; follow the
lib/h5md/README. You can also do it in one step from the lammps/src instructions in ``lib/h5md/README``. You can also do it in one step
dir, using a command like these, which simply invoke the from the ``lammps/src`` dir, using a command like these, which simply
lib/h5md/Install.py script with the specified args: invoke the ``lib/h5md/Install.py`` script with the specified args:
.. code-block:: bash .. code-block:: bash
$ make lib-h5md # print help message $ make lib-h5md # print help message
$ make lib-h5md args="-m h5cc" # build with h5cc compiler $ make lib-h5md args="-m h5cc" # build with h5cc compiler
The build should produce two files: lib/h5md/libch5md.a and The build should produce two files: ``lib/h5md/libch5md.a`` and
lib/h5md/Makefile.lammps. The latter is copied from an existing ``lib/h5md/Makefile.lammps``. The latter is copied from an existing
Makefile.lammps.\* and has settings needed to build LAMMPS with the ``Makefile.lammps.*`` and has settings needed to build LAMMPS with the
system HDF5 library. If necessary, you can edit/create a new system HDF5 library. If necessary, you can edit/create a new
lib/h5md/Makefile.machine file for your system, which should define an ``lib/h5md/Makefile.machine`` file for your system, which should define
EXTRAMAKE variable to specify a corresponding Makefile.lammps.machine an EXTRAMAKE variable to specify a corresponding
file. ``Makefile.lammps.<machine>`` file.
---------- ----------
@ -1230,7 +1255,8 @@ also typically :ref:`install the USER-OMP package <user-omp>`, as it can be
used in tandem with the USER-INTEL package to good effect, as explained used in tandem with the USER-INTEL package to good effect, as explained
on the :doc:`Speed intel <Speed_intel>` doc page. on the :doc:`Speed intel <Speed_intel>` doc page.
**CMake build**\ : CMake build
^^^^^^^^^^^
.. code-block:: bash .. code-block:: bash
@ -1249,11 +1275,12 @@ Best performance is achieved with Intel hardware, Intel compilers, as well as
the Intel TBB and MKL libraries. However, the code also compiles, links, and the Intel TBB and MKL libraries. However, the code also compiles, links, and
runs with other compilers and without TBB and MKL. runs with other compilers and without TBB and MKL.
**Traditional make**\ : Traditional make
^^^^^^^^^^^^^^^^
Choose which hardware to compile for in Makefile.machine via the Choose which hardware to compile for in Makefile.machine via the
following settings. See src/MAKE/OPTIONS/Makefile.intel_cpu\* and following settings. See ``src/MAKE/OPTIONS/Makefile.intel_cpu*`` and
Makefile.knl files for examples. and src/USER-INTEL/README for ``Makefile.knl`` files for examples. and ``src/USER-INTEL/README`` for
additional information. additional information.
For CPUs: For CPUs:
@ -1320,7 +1347,8 @@ define an ``EXTRAMAKE`` variable to specify a corresponding
USER-MOLFILE package USER-MOLFILE package
--------------------------------------- ---------------------------------------
**CMake build**\ : CMake build
^^^^^^^^^^^
.. code-block:: bash .. code-block:: bash
@ -1335,13 +1363,14 @@ folder of the local VMD installation in use. LAMMPS ships with a
couple of default header files that correspond to a popular VMD couple of default header files that correspond to a popular VMD
version, usually the latest release. version, usually the latest release.
**Traditional make**\ : Traditional make
^^^^^^^^^^^^^^^^
The lib/molfile/Makefile.lammps file has a setting for a dynamic The ``lib/molfile/Makefile.lammps`` file has a setting for a dynamic
loading library libdl.a that is typically present on all systems. It loading library libdl.a that is typically present on all systems. It
is required for LAMMPS to link with this package. If the setting is is required for LAMMPS to link with this package. If the setting is
not valid for your system, you will need to edit the Makefile.lammps not valid for your system, you will need to edit the Makefile.lammps
file. See lib/molfile/README and lib/molfile/Makefile.lammps for file. See ``lib/molfile/README`` and ``lib/molfile/Makefile.lammps`` for
details. It is also possible to configure a different folder with details. It is also possible to configure a different folder with
the VMD molfile plugin header files. LAMMPS ships with a couple of the VMD molfile plugin header files. LAMMPS ships with a couple of
default headers, but these are not compatible with all VMD versions, default headers, but these are not compatible with all VMD versions,
@ -1358,22 +1387,24 @@ USER-NETCDF package
To build with this package you must have the NetCDF library installed To build with this package you must have the NetCDF library installed
on your system. on your system.
**CMake build**\ : CMake build
^^^^^^^^^^^
No additional settings are needed besides "-D PKG_USER-NETCDF=yes". No additional settings are needed besides ``-D PKG_USER-NETCDF=yes``.
This should auto-detect the NETCDF library if it is installed on your This should auto-detect the NETCDF library if it is installed on your
system at standard locations. Several advanced CMake NETCDF options system at standard locations. Several advanced CMake NETCDF options
exist if you need to specify where it was installed. Use the ccmake exist if you need to specify where it was installed. Use the ``ccmake``
(terminal window) or cmake-gui (graphical) tools to see these options (terminal window) or ``cmake-gui`` (graphical) tools to see these
and set them interactively from their user interfaces. options and set them interactively from their user interfaces.
**Traditional make**\ : Traditional make
^^^^^^^^^^^^^^^^
The lib/netcdf/Makefile.lammps file has settings for NetCDF include The ``lib/netcdf/Makefile.lammps`` file has settings for NetCDF include
and library files which LAMMPS needs to build with this package. If and library files which LAMMPS needs to build with this package. If
the settings are not valid for your system, you will need to edit the the settings are not valid for your system, you will need to edit the
Makefile.lammps file. See lib/netcdf/README for details. ``Makefile.lammps`` file. See ``lib/netcdf/README`` for details.
---------- ----------
@ -1382,18 +1413,20 @@ Makefile.lammps file. See lib/netcdf/README for details.
USER-OMP package USER-OMP package
------------------------------- -------------------------------
**CMake build**\ : CMake build
^^^^^^^^^^^
No additional settings are required besides "-D PKG_USER-OMP=yes". If No additional settings are required besides ``-D PKG_USER-OMP=yes``. If
CMake detects OpenMP support, the USER-OMP code will be compiled with CMake detects OpenMP support, the USER-OMP code will be compiled with
multi-threading support enabled, otherwise as optimized serial code. multi-threading support enabled, otherwise as optimized serial code.
**Traditional make**\ : Traditional make
^^^^^^^^^^^^^^^^
To enable multi-threading support in the USER-OMP package (and other To enable multi-threading support in the USER-OMP package (and other
styles supporting OpenMP) the following compile and link flags must styles supporting OpenMP) the following compile and link flags must be
be added to your Makefile.machine file. added to your Makefile.machine file. See
See src/MAKE/OPTIONS/Makefile.omp for an example. ``src/MAKE/OPTIONS/Makefile.omp`` for an example.
.. parsed-literal:: .. parsed-literal::
@ -1403,8 +1436,7 @@ See src/MAKE/OPTIONS/Makefile.omp for an example.
LINKFLAGS: -qopenmp # for Intel compilers on Linux LINKFLAGS: -qopenmp # for Intel compilers on Linux
For other platforms and compilers, please consult the documentation For other platforms and compilers, please consult the documentation
about OpenMP support for your compiler. Please see the note about about OpenMP support for your compiler.
how to address compatibility :ref:`issues with the 'default(none)' directive <default-none-issues>` of some compilers.
---------- ----------
@ -1414,19 +1446,20 @@ USER-QMMM package
--------------------------------- ---------------------------------
For using LAMMPS to do QM/MM simulations via the USER-QMMM package you For using LAMMPS to do QM/MM simulations via the USER-QMMM package you
need to build LAMMPS as a library. A LAMMPS executable with fix qmmm need to build LAMMPS as a library. A LAMMPS executable with :doc:`fix
included can be built, but will not be able to do a QM/MM simulation qmmm <fix_qmmm>` included can be built, but will not be able to do a
on as such. You must also build a QM code - currently only Quantum QM/MM simulation on as such. You must also build a QM code - currently
ESPRESSO (QE) is supported - and create a new executable which links only Quantum ESPRESSO (QE) is supported - and create a new executable
LAMMPS and the QM code together. Details are given in the which links LAMMPS and the QM code together. Details are given in the
lib/qmmm/README file. It is also recommended to read the instructions ``lib/qmmm/README`` file. It is also recommended to read the
for :doc:`linking with LAMMPS as a library <Build_link>` for instructions for :doc:`linking with LAMMPS as a library <Build_link>`
background information. This requires compatible Quantum Espresso for background information. This requires compatible Quantum Espresso
and LAMMPS versions. The current interface and makefiles have last and LAMMPS versions. The current interface and makefiles have last been
been verified to work in February 2020 with Quantum Espresso versions verified to work in February 2020 with Quantum Espresso versions 6.3 to
6.3 to 6.5. 6.5.
**CMake build**\ : CMake build
^^^^^^^^^^^
When using CMake, building a LAMMPS library is required and it is When using CMake, building a LAMMPS library is required and it is
recommended to build a shared library, since any libraries built from recommended to build a shared library, since any libraries built from
@ -1443,17 +1476,18 @@ would be:
After completing the LAMMPS build and also configuring and compiling After completing the LAMMPS build and also configuring and compiling
Quantum ESPRESSO with external library support (via "make couple"), Quantum ESPRESSO with external library support (via "make couple"),
go back to the lib/qmmm folder and follow the instructions on the go back to the ``lib/qmmm` folder and follow the instructions on the
README file to build the combined LAMMPS/QE QM/MM executable README file to build the combined LAMMPS/QE QM/MM executable
(pwqmmm.x) in the lib/qmmm folder. You need to make certain, that (pwqmmm.x) in the ``lib/qmmm`` folder. You need to make certain, that
**Traditional make**\ : Traditional make
^^^^^^^^^^^^^^^^
Before building LAMMPS, you must build the QMMM library in lib/qmmm. Before building LAMMPS, you must build the QMMM library in ``lib/qmmm``.
You can do this manually if you prefer; follow the first two steps You can do this manually if you prefer; follow the first two steps
explained in lib/qmmm/README. You can also do it in one step from the explained in ``lib/qmmm/README``. You can also do it in one step from
lammps/src dir, using a command like these, which simply invoke the the ``lammps/src`` dir, using a command like these, which simply invoke
lib/qmmm/Install.py script with the specified args: the ``lib/qmmm/Install.py`` script with the specified args:
.. code-block:: bash .. code-block:: bash
@ -1462,18 +1496,18 @@ lib/qmmm/Install.py script with the specified args:
$ make lib-qmmm args="-m mpi" # build with default MPI compiler (settings as in "make mpi") $ make lib-qmmm args="-m mpi" # build with default MPI compiler (settings as in "make mpi")
$ make lib-qmmm args="-m gfortran" # build with GNU Fortran compiler $ make lib-qmmm args="-m gfortran" # build with GNU Fortran compiler
The build should produce two files: lib/qmmm/libqmmm.a and The build should produce two files: ``lib/qmmm/libqmmm.a`` and
lib/qmmm/Makefile.lammps. The latter is copied from an existing ``lib/qmmm/Makefile.lammps``. The latter is copied from an existing
Makefile.lammps.\* and has settings needed to build LAMMPS with the ``Makefile.lammps.*`` and has settings needed to build LAMMPS with the
QMMM library (though typically the settings are just blank). If QMMM library (though typically the settings are just blank). If
necessary, you can edit/create a new lib/qmmm/Makefile.machine file necessary, you can edit/create a new ``lib/qmmm/Makefile.<machine>`` file
for your system, which should define an EXTRAMAKE variable to specify for your system, which should define an ``EXTRAMAKE`` variable to
a corresponding Makefile.lammps.machine file. specify a corresponding ``Makefile.lammps.<machine>`` file.
You can then install QMMM package and build LAMMPS in the usual You can then install QMMM package and build LAMMPS in the usual
manner. After completing the LAMMPS build and compiling Quantum manner. After completing the LAMMPS build and compiling Quantum
ESPRESSO with external library support (via "make couple"), go back to ESPRESSO with external library support (via "make couple"), go back to
the lib/qmmm folder and follow the instructions in the README file to the ``lib/qmmm`` folder and follow the instructions in the README file to
build the combined LAMMPS/QE QM/MM executable (pwqmmm.x) in the build the combined LAMMPS/QE QM/MM executable (pwqmmm.x) in the
lib/qmmm folder. lib/qmmm folder.
@ -1488,26 +1522,28 @@ To build with this package, you must download and build the QUIP
library. It can be obtained from GitHub. For support of GAP library. It can be obtained from GitHub. For support of GAP
potentials, additional files with specific licensing conditions need potentials, additional files with specific licensing conditions need
to be downloaded and configured. See step 1 and step 1.1 in the to be downloaded and configured. See step 1 and step 1.1 in the
lib/quip/README file for details on how to do this. ``lib/quip/README`` file for details on how to do this.
**CMake build**\ : CMake build
^^^^^^^^^^^
.. code-block:: bash .. code-block:: bash
-D QUIP_LIBRARY=path # path to libquip.a (only needed if a custom location) -D QUIP_LIBRARY=path # path to libquip.a (only needed if a custom location)
CMake will not download and build the QUIP library. But once you have CMake will not download and build the QUIP library. But once you have
done that, a CMake build of LAMMPS with "-D PKG_USER-QUIP=yes" should done that, a CMake build of LAMMPS with ``-D PKG_USER-QUIP=yes`` should
work. Set QUIP_LIBRARY if CMake cannot find the QUIP library. work. Set QUIP_LIBRARY if CMake cannot find the QUIP library.
**Traditional make**\ : Traditional make
^^^^^^^^^^^^^^^^
The download/build procedure for the QUIP library, described in The download/build procedure for the QUIP library, described in
lib/quip/README file requires setting two environment variables, ``lib/quip/README`` file requires setting two environment variables,
QUIP_ROOT and QUIP_ARCH. These are accessed by the QUIP_ROOT and QUIP_ARCH. These are accessed by the
lib/quip/Makefile.lammps file which is used when you compile and link lib/quip/Makefile.lammps file which is used when you compile and link
LAMMPS with this package. You should only need to edit LAMMPS with this package. You should only need to edit
Makefile.lammps if the LAMMPS build can not use its settings to ``Makefile.lammps`` if the LAMMPS build can not use its settings to
successfully build on your system. successfully build on your system.
---------- ----------
@ -1517,11 +1553,13 @@ successfully build on your system.
USER-SCAFACOS package USER-SCAFACOS package
----------------------------------------- -----------------------------------------
To build with this package, you must download and build the `ScaFaCoS Coulomb solver library <scafacos-home_>`_ To build with this package, you must download and build the `ScaFaCoS
Coulomb solver library <scafacos-home_>`_
.. _scafacos-home: http://www.scafacos.de .. _scafacos-home: http://www.scafacos.de
**CMake build**\ : CMake build
^^^^^^^^^^^
.. code-block:: bash .. code-block:: bash
@ -1536,22 +1574,23 @@ SCAFACOS_LIBRARY is the filename (plus path) of the ScaFaCoS library
file, not the directory the library file is in. SCAFACOS_INCLUDE_DIR file, not the directory the library file is in. SCAFACOS_INCLUDE_DIR
is the directory the ScaFaCoS include file is in. is the directory the ScaFaCoS include file is in.
**Traditional make**\ : Traditional make
^^^^^^^^^^^^^^^^
You can download and build the ScaFaCoS library manually if you You can download and build the ScaFaCoS library manually if you
prefer; follow the instructions in lib/scafacos/README. You can also prefer; follow the instructions in ``lib/scafacos/README``. You can also
do it in one step from the lammps/src dir, using a command like these, do it in one step from the ``lammps/src`` dir, using a command like these,
which simply invoke the lib/scafacos/Install.py script with the which simply invoke the ``lib/scafacos/Install.py`` script with the
specified args: specified args:
make lib-scafacos # print help message make lib-scafacos # print help message
make lib-scafacos args="-b" # download and build in lib/scafacos/scafacos-<version> make lib-scafacos args="-b" # download and build in lib/scafacos/scafacos-<version>
make lib-scafacos args="-p $HOME/scafacos # use existing ScaFaCoS installation in $HOME/scafacos make lib-scafacos args="-p $HOME/scafacos # use existing ScaFaCoS installation in $HOME/scafacos
Note that 2 symbolic (soft) links, "includelink" and "liblink", are Note that 2 symbolic (soft) links, ``includelink`` and ``liblink``, are
created in lib/scafacos to point to the ScaFaCoS src dir. When LAMMPS created in ``lib/scafacos`` to point to the ScaFaCoS src dir. When LAMMPS
builds in src it will use these links. You should not need to edit builds in src it will use these links. You should not need to edit
the lib/scafacos/Makefile.lammps file. the ``lib/scafacos/Makefile.lammps`` file.
---------- ----------
@ -1563,24 +1602,26 @@ USER-SMD package
To build with this package, you must download the Eigen3 library. To build with this package, you must download the Eigen3 library.
Eigen3 is a template library, so you do not need to build it. Eigen3 is a template library, so you do not need to build it.
**CMake build**\ : CMake build
^^^^^^^^^^^
.. code-block:: bash .. code-block:: bash
-D DOWNLOAD_EIGEN3 # download Eigen3, value = no (default) or yes -D DOWNLOAD_EIGEN3 # download Eigen3, value = no (default) or yes
-D EIGEN3_INCLUDE_DIR=path # path to Eigen library (only needed if a custom location) -D EIGEN3_INCLUDE_DIR=path # path to Eigen library (only needed if a custom location)
If DOWNLOAD_EIGEN3 is set, the Eigen3 library will be downloaded and If ``DOWNLOAD_EIGEN3`` is set, the Eigen3 library will be downloaded and
inside the CMake build directory. If the Eigen3 library is already on inside the CMake build directory. If the Eigen3 library is already on
your system (in a location CMake cannot find it), EIGEN3_INCLUDE_DIR your system (in a location CMake cannot find it), ``EIGEN3_INCLUDE_DIR``
is the directory the Eigen3++ include file is in. is the directory the Eigen3++ include file is in.
**Traditional make**\ : Traditional make
^^^^^^^^^^^^^^^^
You can download the Eigen3 library manually if you prefer; follow the You can download the Eigen3 library manually if you prefer; follow the
instructions in lib/smd/README. You can also do it in one step from instructions in ``lib/smd/README``. You can also do it in one step from
the lammps/src dir, using a command like these, which simply invoke the ``lammps/src`` dir, using a command like these, which simply invoke
the lib/smd/Install.py script with the specified args: the ``lib/smd/Install.py`` script with the specified args:
.. code-block:: bash .. code-block:: bash
@ -1588,9 +1629,9 @@ the lib/smd/Install.py script with the specified args:
$ make lib-smd args="-b" # download to lib/smd/eigen3 $ make lib-smd args="-b" # download to lib/smd/eigen3
$ make lib-smd args="-p /usr/include/eigen3" # use existing Eigen installation in /usr/include/eigen3 $ make lib-smd args="-p /usr/include/eigen3" # use existing Eigen installation in /usr/include/eigen3
Note that a symbolic (soft) link named "includelink" is created in Note that a symbolic (soft) link named ``includelink`` is created in
lib/smd to point to the Eigen dir. When LAMMPS builds it will use ``lib/smd`` to point to the Eigen dir. When LAMMPS builds it will use
this link. You should not need to edit the lib/smd/Makefile.lammps this link. You should not need to edit the ``lib/smd/Makefile.lammps``
file. file.
---------- ----------
@ -1603,21 +1644,23 @@ USER-VTK package
To build with this package you must have the VTK library installed on To build with this package you must have the VTK library installed on
your system. your system.
**CMake build**\ : CMake build
^^^^^^^^^^^
No additional settings are needed besides "-D PKG_USER-VTK=yes". No additional settings are needed besides ``-D PKG_USER-VTK=yes``.
This should auto-detect the VTK library if it is installed on your This should auto-detect the VTK library if it is installed on your
system at standard locations. Several advanced VTK options exist if system at standard locations. Several advanced VTK options exist if
you need to specify where it was installed. Use the ccmake (terminal you need to specify where it was installed. Use the ``ccmake`` (terminal
window) or cmake-gui (graphical) tools to see these options and set window) or ``cmake-gui`` (graphical) tools to see these options and set
them interactively from their user interfaces. them interactively from their user interfaces.
**Traditional make**\ : Traditional make
^^^^^^^^^^^^^^^^
The lib/vtk/Makefile.lammps file has settings for accessing VTK files The ``lib/vtk/Makefile.lammps`` file has settings for accessing VTK files
and its library, which LAMMPS needs to build with this package. If and its library, which LAMMPS needs to build with this package. If
the settings are not valid for your system, check if one of the other the settings are not valid for your system, check if one of the other
lib/vtk/Makefile.lammps.\* files is compatible and copy it to ``lib/vtk/Makefile.lammps.*`` files is compatible and copy it to
Makefile.lammps. If none of the provided files work, you will need to Makefile.lammps. If none of the provided files work, you will need to
edit the Makefile.lammps file. See lib/vtk/README for details. edit the ``Makefile.lammps`` file. See ``lib/vtk/README`` for details.

88
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@ -1,12 +1,12 @@
Link LAMMPS as a library to another code Link LAMMPS as a library to another code
======================================== ========================================
LAMMPS is designed as a library of C++ objects and can thus be LAMMPS is designed as a library of C++ objects that can be
integrated into other applications including Python scripts. integrated into other applications including Python scripts.
The files ``src/library.cpp`` and ``src/library.h`` define a The files ``src/library.cpp`` and ``src/library.h`` define a
C-style API for using LAMMPS as a library. See the :doc:`Howto C-style API for using LAMMPS as a library. See the :doc:`Howto
library <Howto_library>` doc page for a description of the interface library <Howto_library>` page for a description of the interface
and how to extend it for your needs. and how to use it for your needs.
The :doc:`Build basics <Build_basics>` doc page explains how to build The :doc:`Build basics <Build_basics>` doc page explains how to build
LAMMPS as either a shared or static library. This results in a file LAMMPS as either a shared or static library. This results in a file
@ -31,18 +31,18 @@ the suffix ``.so.0`` (or some other number).
communicator with a subset of MPI ranks to the function creating the communicator with a subset of MPI ranks to the function creating the
LAMMPS instance. LAMMPS instance.
---------- Link with LAMMPS as a static library
------------------------------------
**Link with LAMMPS as a static library**\ :
The calling application can link to LAMMPS as a static library with The calling application can link to LAMMPS as a static library with
compilation and link commands as in the examples shown below. These compilation and link commands as in the examples shown below. These
are examples for a code written in C in the file *caller.c*. are examples for a code written in C in the file ``caller.c``.
The benefit of linking to a static library is, that the resulting The benefit of linking to a static library is, that the resulting
executable is independent of that library since all required executable is independent of that library since all required
executable code from the library is copied into the calling executable. executable code from the library is copied into the calling executable.
*CMake build*\ : CMake build
^^^^^^^^^^^
This assumes that LAMMPS has been configured without setting a This assumes that LAMMPS has been configured without setting a
``LAMMPS_MACHINE`` name, installed with "make install", and the ``LAMMPS_MACHINE`` name, installed with "make install", and the
@ -55,7 +55,8 @@ The commands to compile and link a coupled executable are then:
mpicc -c -O $(pkgconf liblammps --cflags) caller.c mpicc -c -O $(pkgconf liblammps --cflags) caller.c
mpicxx -o caller caller.o -$(pkgconf liblammps --libs) mpicxx -o caller caller.o -$(pkgconf liblammps --libs)
*Traditional make*\ : Traditional make
^^^^^^^^^^^^^^^^
This assumes that LAMMPS has been compiled in the folder This assumes that LAMMPS has been compiled in the folder
``${HOME}/lammps/src`` with "make mpi". The commands to compile and link ``${HOME}/lammps/src`` with "make mpi". The commands to compile and link
@ -83,20 +84,20 @@ LAMMPS library without any optional packages that depend on libraries
need to include all flags, libraries, and paths for the coupled need to include all flags, libraries, and paths for the coupled
executable, that are also required to link the LAMMPS executable. executable, that are also required to link the LAMMPS executable.
*CMake build*\ : CMake build
^^^^^^^^^^^
When using CMake, additional libraries with sources in the lib folder When using CMake, additional libraries with sources in the lib folder
are built, but not included in ``liblammps.a`` and (currently) not are built, but not included in ``liblammps.a`` and (currently) not
installed with "make install" and not included in the *pkgconfig* installed with ``make install`` and not included in the ``pkgconfig``
configuration file. They can be found in the top level build folder, configuration file. They can be found in the top level build folder,
but you have to determine the necessary link flags manually. It is but you have to determine the necessary link flags manually. It is
therefore recommended to either use the traditional make procedure to therefore recommended to either use the traditional make procedure to
build and link with a static library or build and link with a shared build and link with a static library or build and link with a shared
library instead. library instead.
.. TODO: this needs to be updated to reflect that latest CMake changes after they are complete. Traditional make
^^^^^^^^^^^^^^^^
*Traditional make*\ :
After you have compiled a static LAMMPS library using the conventional After you have compiled a static LAMMPS library using the conventional
build system for example with "make mode=static serial". And you also build system for example with "make mode=static serial". And you also
@ -110,10 +111,10 @@ change to:
g++ -o caller caller.o -L${HOME}/lammps/lib/poems \ g++ -o caller caller.o -L${HOME}/lammps/lib/poems \
-L${HOME}/lammps/src/STUBS -L${HOME}/lammps/src -llammps_serial -lpoems -lmpi_stubs -L${HOME}/lammps/src/STUBS -L${HOME}/lammps/src -llammps_serial -lpoems -lmpi_stubs
Note, that you need to link with "g++" instead of "gcc", since the Note, that you need to link with ``g++`` instead of ``gcc`` even if you have
LAMMPS library is C++ code. You can display the currently applied written your code in C, since LAMMPS itself is C++ code. You can display the
settings for building LAMMPS for the "serial" machine target by using currently applied settings for building LAMMPS for the "serial" machine target
the command: by using the command:
.. code-block:: bash .. code-block:: bash
@ -123,25 +124,24 @@ Which should output something like:
.. code-block:: bash .. code-block:: bash
# Compiler: # Compiler:
CXX=g++ CXX=g++
# Linker: # Linker:
LD=g++ LD=g++
# Compilation: # Compilation:
CXXFLAGS=-g -O3 -DLAMMPS_GZIP -DLAMMPS_MEMALIGN=64 -I${HOME}/compile/lammps/lib/poems -I${HOME}/compile/lammps/src/STUBS CXXFLAGS=-g -O3 -DLAMMPS_GZIP -DLAMMPS_MEMALIGN=64 -I${HOME}/compile/lammps/lib/poems -I${HOME}/compile/lammps/src/STUBS
# Linking: # Linking:
LDFLAGS=-g -O LDFLAGS=-g -O
# Libraries: # Libraries:
LDLIBS=-L${HOME}/compile/lammps/src -llammps_serial -L${HOME}/compile/lammps/lib/poems -L${HOME}/compile/lammps/src/STUBS -lpoems -lmpi_stubs LDLIBS=-L${HOME}/compile/lammps/src -llammps_serial -L${HOME}/compile/lammps/lib/poems -L${HOME}/compile/lammps/src/STUBS -lpoems -lmpi_stubs
From this you can gather the necessary paths and flags. With From this you can gather the necessary paths and flags. With
makefiles for other *machine* configurations you need to do the makefiles for other *machine* configurations you need to do the
equivalent and replace "serial" with the corresponding *machine* name equivalent and replace "serial" with the corresponding "machine" name
of the makefile. of the makefile.
---------- Link with LAMMPS as a shared library
------------------------------------
**Link with LAMMPS as a shared library**\ :
When linking to LAMMPS built as a shared library, the situation becomes When linking to LAMMPS built as a shared library, the situation becomes
much simpler, as all dependent libraries and objects are either included much simpler, as all dependent libraries and objects are either included
@ -151,7 +151,8 @@ linking the calling executable. Only the *-I* flags are needed. So the
example case from above of the serial version static LAMMPS library with example case from above of the serial version static LAMMPS library with
the POEMS package installed becomes: the POEMS package installed becomes:
*CMake build*\ : CMake build
^^^^^^^^^^^
The commands with a shared LAMMPS library compiled with the CMake The commands with a shared LAMMPS library compiled with the CMake
build process are the same as for the static library. build process are the same as for the static library.
@ -161,10 +162,11 @@ build process are the same as for the static library.
mpicc -c -O $(pkgconf liblammps --cflags) caller.c mpicc -c -O $(pkgconf liblammps --cflags) caller.c
mpicxx -o caller caller.o -$(pkgconf --libs) mpicxx -o caller caller.o -$(pkgconf --libs)
*Traditional make*\ : Traditional make
^^^^^^^^^^^^^^^^
The commands with a shared LAMMPS library compiled with the The commands with a shared LAMMPS library compiled with the
traditional make build using "make mode=shared serial" becomes: traditional make build using ``make mode=shared serial`` becomes:
.. code-block:: bash .. code-block:: bash
@ -231,29 +233,3 @@ If a required library is missing, you would get a 'not found' entry:
libc.so.6 => /usr/lib64/libc.so.6 (0x00007fb7c7b5d000) libc.so.6 => /usr/lib64/libc.so.6 (0x00007fb7c7b5d000)
/lib64/ld-linux-x86-64.so.2 (0x00007fb7c80a2000) /lib64/ld-linux-x86-64.so.2 (0x00007fb7c80a2000)
----------
**Calling the LAMMPS library**\ :
Either flavor of library (static or shared) allows one or more LAMMPS
objects to be instantiated from the calling program. When used from a
C++ program, most of the symbols and functions in LAMMPS are wrapped
in a ``LAMMPS_NS`` namespace; you can safely use any of its classes and
methods from within the calling code, as needed, and you will not incur
conflicts with functions and variables in your code that share the name.
This, however, does not extend to all additional libraries bundled with
LAMMPS in the lib folder and some of the low-level code of some packages.
To be compatible with C, Fortran, Python programs, the library has a simple
C-style interface, provided in ``src/library.cpp`` and ``src/library.h``.
See the :doc:`Python library <Python_library>` doc page for a
description of the Python interface to LAMMPS, which wraps the C-style
interface from a shared library through the `ctypes python module <ctypes_>`_.
See the sample codes in ``examples/COUPLE/simple`` for examples of C++ and
C and Fortran codes that invoke LAMMPS through its library interface.
Other examples in the COUPLE directory use coupling ideas discussed on
the :doc:`Howto couple <Howto_couple>` doc page.
.. _ctypes: https://docs.python.org/3/library/ctypes.html

29
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@ -45,7 +45,8 @@ packages:
The mechanism for including packages is simple but different for CMake The mechanism for including packages is simple but different for CMake
versus make. versus make.
**CMake build**\ : CMake build
^^^^^^^^^^^
.. code-block:: csh .. code-block:: csh
@ -72,7 +73,8 @@ once with CMake.
invoke cmake. CMake will give an error if that is not the case, invoke cmake. CMake will give an error if that is not the case,
indicating how you can un-install all packages in the src dir. indicating how you can un-install all packages in the src dir.
**Traditional make**\ : Traditional make
^^^^^^^^^^^^^^^^
.. code-block:: bash .. code-block:: bash
@ -108,7 +110,8 @@ once with make.
within the same command. You can include or exclude multiple packages within the same command. You can include or exclude multiple packages
in a single make command, e.g. make yes-colloid no-manybody. in a single make command, e.g. make yes-colloid no-manybody.
**CMake and make info**\ : CMake and make info
^^^^^^^^^^^^^^^^^^^
Any package can be included or excluded in a LAMMPS build, independent Any package can be included or excluded in a LAMMPS build, independent
of all other packages. However, some packages include files derived of all other packages. However, some packages include files derived
@ -132,7 +135,7 @@ src directory.
.. _cmake_presets: .. _cmake_presets:
**CMake shortcuts for installing many packages**\ : CMake presets for installing many packages
Instead of specifying all the CMake options via the command-line, Instead of specifying all the CMake options via the command-line,
CMake allows initializing its settings cache using script files. CMake allows initializing its settings cache using script files.
@ -148,13 +151,14 @@ one of them as a starting point and customize it to your needs.
.. code-block:: bash .. code-block:: bash
cmake -C ../cmake/presets/minimal.cmake [OPTIONS] ../cmake # enable just a few core packages cmake -C ../cmake/presets/minimal.cmake [OPTIONS] ../cmake # enable just a few core packages
cmake -C ../cmake/presets/most.cmake [OPTIONS] ../cmake # enable most packages cmake -C ../cmake/presets/most.cmake [OPTIONS] ../cmake # enable most packages
cmake -C ../cmake/presets/nolib.cmake [OPTIONS] ../cmake # disable packages that do require extra libraries or tools cmake -C ../cmake/presets/download.cmake [OPTIONS] ../cmake # enable packages which download sources or potential files
cmake -C ../cmake/presets/clang.cmake [OPTIONS] ../cmake # change settings to use the Clang compilers by default cmake -C ../cmake/presets/nolib.cmake [OPTIONS] ../cmake # disable packages that do require extra libraries or tools
cmake -C ../cmake/presets/intel.cmake [OPTIONS] ../cmake # change settings to use the Intel compilers by default cmake -C ../cmake/presets/clang.cmake [OPTIONS] ../cmake # change settings to use the Clang compilers by default
cmake -C ../cmake/presets/all_on.cmake [OPTIONS] ../cmake # enable all packages cmake -C ../cmake/presets/intel.cmake [OPTIONS] ../cmake # change settings to use the Intel compilers by default
cmake -C ../cmake/presets/all_off.cmake [OPTIONS] ../cmake # disable all packages cmake -C ../cmake/presets/all_on.cmake [OPTIONS] ../cmake # enable all packages
cmake -C ../cmake/presets/all_off.cmake [OPTIONS] ../cmake # disable all packages
mingw64-cmake -C ../cmake/presets/mingw-cross.cmake [OPTIONS] ../cmake # compile with MinGW cross compilers mingw64-cmake -C ../cmake/presets/mingw-cross.cmake [OPTIONS] ../cmake # compile with MinGW cross compilers
.. note:: .. note::
@ -184,7 +188,8 @@ one of them as a starting point and customize it to your needs.
---------- ----------
**Make shortcuts for installing many packages**\ : Make shortcuts for installing many packages
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
The following commands are useful for managing package source files The following commands are useful for managing package source files
and their installation when building LAMMPS via traditional make. and their installation when building LAMMPS via traditional make.

82
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@ -44,7 +44,8 @@ require use of an FFT library to compute 1d FFTs. The KISS FFT
library is included with LAMMPS but other libraries can be faster. library is included with LAMMPS but other libraries can be faster.
LAMMPS can use them if they are available on your system. LAMMPS can use them if they are available on your system.
**CMake variables**\ : CMake build
^^^^^^^^^^^
.. code-block:: bash .. code-block:: bash
@ -74,7 +75,12 @@ to assist:
-D FFT_MKL_THREADS=on # enable using threaded FFTs with MKL libraries -D FFT_MKL_THREADS=on # enable using threaded FFTs with MKL libraries
-D MKL_LIBRARIES=path -D MKL_LIBRARIES=path
**Makefile.machine settings**\ : Traditional make
^^^^^^^^^^^^^^^^
To change the FFT library to be used and its options, you have to edit
your machine Makefile. Below are examples how the makefile variables
could be changed.
.. code-block:: make .. code-block:: make
@ -104,7 +110,8 @@ As with CMake, you do not need to set paths in ``FFT_INC`` or ``FFT_PATH``, if
the compiler can find the FFT header and library files in its default search path. the compiler can find the FFT header and library files in its default search path.
You must specify ``FFT_LIB`` with the appropriate FFT libraries to include in the link. You must specify ``FFT_LIB`` with the appropriate FFT libraries to include in the link.
**CMake and make info**\ : CMake build
^^^^^^^^^^^
The `KISS FFT library <http://kissfft.sf.net>`_ is included in the LAMMPS The `KISS FFT library <http://kissfft.sf.net>`_ is included in the LAMMPS
distribution. It is portable across all platforms. Depending on the size distribution. It is portable across all platforms. Depending on the size
@ -127,7 +134,7 @@ download it from `www.fftw.org <http://www.fftw.org>`_. LAMMPS requires
version 3.X; the legacy version 2.1.X is no longer supported. version 3.X; the legacy version 2.1.X is no longer supported.
Building FFTW for your box should be as simple as ``./configure; make; Building FFTW for your box should be as simple as ``./configure; make;
make install``\ . The install command typically requires root privileges make install``. The install command typically requires root privileges
(e.g. invoke it via sudo), unless you specify a local directory with (e.g. invoke it via sudo), unless you specify a local directory with
the "--prefix" option of configure. Type ``./configure --help`` to see the "--prefix" option of configure. Type ``./configure --help`` to see
various options. various options.
@ -169,20 +176,25 @@ ARRAY mode.
.. _size: .. _size:
Size of LAMMPS data types Size of LAMMPS integer types
------------------------------------ ------------------------------------
LAMMPS has a few integer data types which can be defined as 4-byte or LAMMPS has a few integer data types which can be defined as either
8-byte integers. The default setting of "smallbig" is almost always 4-byte (= 32-bit) or 8-byte (= 64-bit) integers at compile time.
adequate. The default setting of "smallbig" is almost always adequate.
**CMake variable**\ : CMake build
^^^^^^^^^^^
.. code-block:: bash .. code-block:: bash
-D LAMMPS_SIZES=value # smallbig (default) or bigbig or smallsmall -D LAMMPS_SIZES=value # smallbig (default) or bigbig or smallsmall
**Makefile.machine setting**\ : Traditional build
^^^^^^^^^^^^^^^^^
If you want a setting different from the default, you need to edit your
machine Makefile.
.. code-block:: make .. code-block:: make
@ -190,7 +202,8 @@ adequate.
The default setting is ``-DLAMMPS_SMALLBIG`` if nothing is specified The default setting is ``-DLAMMPS_SMALLBIG`` if nothing is specified
**CMake and make info**\ : CMake and make info
^^^^^^^^^^^^^^^^^^^
The default "smallbig" setting allows for simulations with: The default "smallbig" setting allows for simulations with:
@ -251,7 +264,8 @@ PNG image files. Likewise the :doc:`dump movie <dump_image>` command
outputs movie files in MPEG format. Using these options requires the outputs movie files in MPEG format. Using these options requires the
following settings: following settings:
**CMake variables**\ : CMake build
^^^^^^^^^^^
.. code-block:: bash .. code-block:: bash
@ -276,7 +290,8 @@ variables:
-D ZLIB_LIBRARIES=path # path to libz.a (.so) file -D ZLIB_LIBRARIES=path # path to libz.a (.so) file
-D FFMPEG_EXECUTABLE=path # path to ffmpeg executable -D FFMPEG_EXECUTABLE=path # path to ffmpeg executable
**Makefile.machine settings**\ : Traditional make
^^^^^^^^^^^^^^^^
.. code-block:: make .. code-block:: make
@ -295,7 +310,8 @@ with a list of graphics libraries to include in the link. You must
insure ffmpeg is in a directory where LAMMPS can find it at runtime, insure ffmpeg is in a directory where LAMMPS can find it at runtime,
that is a directory in your PATH environment variable. that is a directory in your PATH environment variable.
**CMake and make info**\ : CMake and make info
^^^^^^^^^^^^^^^^^^^
Using ``ffmpeg`` to output movie files requires that your machine Using ``ffmpeg`` to output movie files requires that your machine
supports the "popen" function in the standard runtime library. supports the "popen" function in the standard runtime library.
@ -318,7 +334,8 @@ If this option is enabled, large files can be read or written with
gzip compression by several LAMMPS commands, including gzip compression by several LAMMPS commands, including
:doc:`read_data <read_data>`, :doc:`rerun <rerun>`, and :doc:`dump <dump>`. :doc:`read_data <read_data>`, :doc:`rerun <rerun>`, and :doc:`dump <dump>`.
**CMake variables**\ : CMake build
^^^^^^^^^^^
.. code-block:: bash .. code-block:: bash
@ -326,13 +343,15 @@ gzip compression by several LAMMPS commands, including
# default is yes if CMake can find gzip, else no # default is yes if CMake can find gzip, else no
-D GZIP_EXECUTABLE=path # path to gzip executable if CMake cannot find it -D GZIP_EXECUTABLE=path # path to gzip executable if CMake cannot find it
**Makefile.machine setting**\ : Traditional make
^^^^^^^^^^^^^^^^
.. code-block:: make .. code-block:: make
LMP_INC = -DLAMMPS_GZIP LMP_INC = -DLAMMPS_GZIP
**CMake and make info**\ : CMake and make info
^^^^^^^^^^^^^^^^^^^
This option requires that your machine supports the "popen()" function This option requires that your machine supports the "popen()" function
in the standard runtime library and that a gzip executable can be in the standard runtime library and that a gzip executable can be
@ -363,7 +382,8 @@ pointers that are aligned to 16-byte boundaries. Using SSE vector
instructions efficiently, however, requires memory blocks being instructions efficiently, however, requires memory blocks being
aligned on 64-byte boundaries. aligned on 64-byte boundaries.
**CMake variable**\ : CMake build
^^^^^^^^^^^
.. code-block:: bash .. code-block:: bash
@ -374,7 +394,8 @@ and revert to using the malloc() C-library function instead. When
compiling LAMMPS for Windows systems, malloc() will always be used compiling LAMMPS for Windows systems, malloc() will always be used
and this setting ignored. and this setting ignored.
**Makefile.machine setting**\ : Traditional make
^^^^^^^^^^^^^^^^
.. code-block:: make .. code-block:: make
@ -398,13 +419,15 @@ types, the following setting will be needed. It converts "long long"
to a "long" data type, which should be the desired 8-byte integer on to a "long" data type, which should be the desired 8-byte integer on
those systems: those systems:
**CMake variable**\ : CMake build
^^^^^^^^^^^
.. code-block:: bash .. code-block:: bash
-D LAMMPS_LONGLONG_TO_LONG=value # yes or no (default) -D LAMMPS_LONGLONG_TO_LONG=value # yes or no (default)
**Makefile.machine setting**\ : Traditional make
^^^^^^^^^^^^^^^^
.. code-block:: make .. code-block:: make
@ -420,17 +443,26 @@ Exception handling when using LAMMPS as a library
This setting is useful when external codes drive LAMMPS as a library. This setting is useful when external codes drive LAMMPS as a library.
With this option enabled, LAMMPS errors do not kill the calling code. With this option enabled, LAMMPS errors do not kill the calling code.
Instead, the call stack is unwound and control returns to the caller, Instead, the call stack is unwound and control returns to the caller,
e.g. to Python. Of course the calling code has to be set up to e.g. to Python. Of course, the calling code has to be set up to
*catch* exceptions from within LAMMPS. *catch* exceptions thrown from within LAMMPS.
**CMake variable**\ : CMake build
^^^^^^^^^^^
.. code-block:: bash .. code-block:: bash
-D LAMMPS_EXCEPTIONS=value # yes or no (default) -D LAMMPS_EXCEPTIONS=value # yes or no (default)
**Makefile.machine setting**\ : Traditional make
^^^^^^^^^^^^^^^^
.. code-block:: make .. code-block:: make
LMP_INC = -DLAMMPS_EXCEPTIONS LMP_INC = -DLAMMPS_EXCEPTIONS
.. note::
When LAMMPS is running in parallel, it is not always possible to
cleanly recover from an exception since not all parallel ranks may
throw an exception and thus other MPI ranks may get stuck waiting for
messages from the ones with errors.

6
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@ -31,9 +31,9 @@ does something different than this sequence:
run 100 run 100
In the first case, the specified timestep (0.5 fs) is used for two In the first case, the specified timestep (0.5 fs) is used for two
simulations of 100 timesteps each. In the 2nd case, the default simulations of 100 timesteps each. In the second case, the default
timestep (1.0 fs) is used for the 1st 100 step simulation and a 0.5 fs timestep (1.0 fs) is used for the first 100 step simulation and a 0.5 fs
timestep is used for the 2nd one. timestep is used for the second one.
(2) Some commands are only valid when they follow other commands. For (2) Some commands are only valid when they follow other commands. For
example you cannot set the temperature of a group of atoms until atoms example you cannot set the temperature of a group of atoms until atoms

2
doc/src/Commands_pair.rst
View File

@ -78,7 +78,7 @@ OPT.
* :doc:`coul/long/soft (o) <pair_fep_soft>` * :doc:`coul/long/soft (o) <pair_fep_soft>`
* :doc:`coul/msm (o) <pair_coul>` * :doc:`coul/msm (o) <pair_coul>`
* :doc:`coul/slater/cut <pair_coul_slater>` * :doc:`coul/slater/cut <pair_coul_slater>`
* :doc:`coul/slater/long <pair_coul_slater>` * :doc:`coul/slater/long <pair_coul_slater>`
* :doc:`coul/shield <pair_coul_shield>` * :doc:`coul/shield <pair_coul_shield>`
* :doc:`coul/streitz <pair_coul>` * :doc:`coul/streitz <pair_coul>`
* :doc:`coul/wolf (ko) <pair_coul>` * :doc:`coul/wolf (ko) <pair_coul>`

2
doc/src/Developer/developer.tex
View File

@ -142,7 +142,7 @@ follows:
minimize. minimize.
\item The Special class walks the bond topology of a molecular system \item The Special class walks the bond topology of a molecular system
to find 1st, 2nd, 3rd neighbors of each atom. It is invoked by to find first, second, third neighbors of each atom. It is invoked by
several commands, like read\_data, read\_restart, and replicate. several commands, like read\_data, read\_restart, and replicate.
\item The Atom class stores all per-atom arrays. More precisely, they \item The Atom class stores all per-atom arrays. More precisely, they

18
doc/src/Errors_debug.rst
View File

@ -23,7 +23,7 @@ We use it to show how to identify the origin of a segmentation fault.
double *special_lj = force->special_lj; double *special_lj = force->special_lj;
int newton_pair = force->newton_pair; int newton_pair = force->newton_pair;
+ double comx = 0.0; + double comx = 0.0;
inum = list->inum; inum = list->inum;
ilist = list->ilist; ilist = list->ilist;
@@ -134,8 +135,10 @@ void PairLJCut::compute(int eflag, int vflag) @@ -134,8 +135,10 @@ void PairLJCut::compute(int eflag, int vflag)
@ -31,7 +31,7 @@ We use it to show how to identify the origin of a segmentation fault.
} }
} }
- } - }
+ comx += atom->rmass[i]*x[i][0]; /* BUG */ + comx += atom->rmass[i]*x[i][0]; /* BUG */
+ } + }
+ printf("comx = %g\n",comx); + printf("comx = %g\n",comx);
@ -42,7 +42,7 @@ After recompiling LAMMPS and running the input you should get something like thi
.. code-block: .. code-block:
$ ./lmp -in in.melt $ ./lmp -in in.melt
LAMMPS (19 Mar 2020) LAMMPS (19 Mar 2020)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
using 1 OpenMP thread(s) per MPI task using 1 OpenMP thread(s) per MPI task
@ -98,11 +98,11 @@ drop back to the GDB prompt.
Unit style : lj Unit style : lj
Current step : 0 Current step : 0
Time step : 0.005 Time step : 0.005
Program received signal SIGSEGV, Segmentation fault. Program received signal SIGSEGV, Segmentation fault.
0x00000000006653ab in LAMMPS_NS::PairLJCut::compute (this=0x829740, eflag=1, vflag=<optimized out>) at /home/akohlmey/compile/lammps/src/pair_lj_cut.cpp:139 0x00000000006653ab in LAMMPS_NS::PairLJCut::compute (this=0x829740, eflag=1, vflag=<optimized out>) at /home/akohlmey/compile/lammps/src/pair_lj_cut.cpp:139
139 comx += atom->rmass[i]*x[i][0]; /* BUG */ 139 comx += atom->rmass[i]*x[i][0]; /* BUG */
(gdb) (gdb)
Now typing the command "where" will show the stack of functions starting from Now typing the command "where" will show the stack of functions starting from
the current function back to "main()". the current function back to "main()".
@ -119,7 +119,7 @@ the current function back to "main()".
#4 0x0000000000410ad3 in LAMMPS_NS::Input::execute_command (this=0x7d1410) at /home/akohlmey/compile/lammps/src/input.cpp:864 #4 0x0000000000410ad3 in LAMMPS_NS::Input::execute_command (this=0x7d1410) at /home/akohlmey/compile/lammps/src/input.cpp:864
#5 0x00000000004111fb in LAMMPS_NS::Input::file (this=0x7d1410) at /home/akohlmey/compile/lammps/src/input.cpp:229 #5 0x00000000004111fb in LAMMPS_NS::Input::file (this=0x7d1410) at /home/akohlmey/compile/lammps/src/input.cpp:229
#6 0x000000000040933a in main (argc=<optimized out>, argv=<optimized out>) at /home/akohlmey/compile/lammps/src/main.cpp:65 #6 0x000000000040933a in main (argc=<optimized out>, argv=<optimized out>) at /home/akohlmey/compile/lammps/src/main.cpp:65
(gdb) (gdb)
You can also print the value of variables and see if there is anything You can also print the value of variables and see if there is anything
unexpected. Segmentation faults, for example, commonly happen when a unexpected. Segmentation faults, for example, commonly happen when a
@ -189,12 +189,12 @@ the console are not mixed.
.. code-block:: .. code-block::
$ valgrind ./lmp -in in.melt $ valgrind ./lmp -in in.melt
==1933642== Memcheck, a memory error detector ==1933642== Memcheck, a memory error detector
==1933642== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==1933642== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al.
==1933642== Using Valgrind-3.15.0 and LibVEX; rerun with -h for copyright info ==1933642== Using Valgrind-3.15.0 and LibVEX; rerun with -h for copyright info
==1933642== Command: ./lmp -in in.melt ==1933642== Command: ./lmp -in in.melt
==1933642== ==1933642==
LAMMPS (19 Mar 2020) LAMMPS (19 Mar 2020)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
using 1 OpenMP thread(s) per MPI task using 1 OpenMP thread(s) per MPI task
@ -228,7 +228,7 @@ the console are not mixed.
==1933642== by 0x4111FA: LAMMPS_NS::Input::file() (input.cpp:229) ==1933642== by 0x4111FA: LAMMPS_NS::Input::file() (input.cpp:229)
==1933642== by 0x409339: main (main.cpp:65) ==1933642== by 0x409339: main (main.cpp:65)
==1933642== Address 0x0 is not stack'd, malloc'd or (recently) free'd ==1933642== Address 0x0 is not stack'd, malloc'd or (recently) free'd
==1933642== ==1933642==
As you can see, the stack trace information is similar to that obtained As you can see, the stack trace information is similar to that obtained
from GDB. In addition you get a more specific hint about what cause the from GDB. In addition you get a more specific hint about what cause the

22
doc/src/Errors_messages.rst
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@ -381,7 +381,7 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
are defined. are defined.
*Bond atom missing in box size check* *Bond atom missing in box size check*
The 2nd atoms needed to compute a particular bond is missing on this The second atom needed to compute a particular bond is missing on this
processor. Typically this is because the pairwise cutoff is set too processor. Typically this is because the pairwise cutoff is set too
short or the bond has blown apart and an atom is too far away. short or the bond has blown apart and an atom is too far away.
@ -391,7 +391,7 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
the atoms are too far apart to make a valid bond. the atoms are too far apart to make a valid bond.
*Bond atom missing in image check* *Bond atom missing in image check*
The 2nd atom in a particular bond is missing on this processor. The second atom in a particular bond is missing on this processor.
Typically this is because the pairwise cutoff is set too short or the Typically this is because the pairwise cutoff is set too short or the
bond has blown apart and an atom is too far away. bond has blown apart and an atom is too far away.
@ -401,12 +401,12 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
are too far apart to make a valid bond. are too far apart to make a valid bond.
*Bond atoms %d %d missing on proc %d at step %ld* *Bond atoms %d %d missing on proc %d at step %ld*
The 2nd atom needed to compute a particular bond is missing on this The second atom needed to compute a particular bond is missing on this
processor. Typically this is because the pairwise cutoff is set too processor. Typically this is because the pairwise cutoff is set too
short or the bond has blown apart and an atom is too far away. short or the bond has blown apart and an atom is too far away.
*Bond atoms missing on proc %d at step %ld* *Bond atoms missing on proc %d at step %ld*
The 2nd atom needed to compute a particular bond is missing on this The second atom needed to compute a particular bond is missing on this
processor. Typically this is because the pairwise cutoff is set too processor. Typically this is because the pairwise cutoff is set too
short or the bond has blown apart and an atom is too far away. short or the bond has blown apart and an atom is too far away.
@ -1374,7 +1374,7 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
template does not qualify. template does not qualify.
*Cannot use fix box/relax on a 2nd non-periodic dimension* *Cannot use fix box/relax on a 2nd non-periodic dimension*
When specifying an off-diagonal pressure component, the 2nd of the two When specifying an off-diagonal pressure component, the second of the two
dimensions must be periodic. E.g. if the xy component is specified, dimensions must be periodic. E.g. if the xy component is specified,
then the y dimension must be periodic. then the y dimension must be periodic.
@ -1388,7 +1388,7 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
also keyword tri or xy, this is wrong. also keyword tri or xy, this is wrong.
*Cannot use fix box/relax with tilt factor scaling on a 2nd non-periodic dimension* *Cannot use fix box/relax with tilt factor scaling on a 2nd non-periodic dimension*
When specifying scaling on a tilt factor component, the 2nd of the two When specifying scaling on a tilt factor component, the second of the two
dimensions must be periodic. E.g. if the xy component is specified, dimensions must be periodic. E.g. if the xy component is specified,
then the y dimension must be periodic. then the y dimension must be periodic.
@ -1429,7 +1429,7 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
This would be changing the same box dimension twice. This would be changing the same box dimension twice.
*Cannot use fix nvt/npt/nph on a 2nd non-periodic dimension* *Cannot use fix nvt/npt/nph on a 2nd non-periodic dimension*
When specifying an off-diagonal pressure component, the 2nd of the two When specifying an off-diagonal pressure component, the second of the two
dimensions must be periodic. E.g. if the xy component is specified, dimensions must be periodic. E.g. if the xy component is specified,
then the y dimension must be periodic. then the y dimension must be periodic.
@ -1447,13 +1447,13 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
Self-explanatory. Self-explanatory.
*Cannot use fix nvt/npt/nph with xy scaling when y is non-periodic dimension* *Cannot use fix nvt/npt/nph with xy scaling when y is non-periodic dimension*
The 2nd dimension in the barostatted tilt factor must be periodic. The second dimension in the barostatted tilt factor must be periodic.
*Cannot use fix nvt/npt/nph with xz scaling when z is non-periodic dimension* *Cannot use fix nvt/npt/nph with xz scaling when z is non-periodic dimension*
The 2nd dimension in the barostatted tilt factor must be periodic. The second dimension in the barostatted tilt factor must be periodic.
*Cannot use fix nvt/npt/nph with yz scaling when z is non-periodic dimension* *Cannot use fix nvt/npt/nph with yz scaling when z is non-periodic dimension*
The 2nd dimension in the barostatted tilt factor must be periodic. The second dimension in the barostatted tilt factor must be periodic.
*Cannot use fix pour rigid and not molecule* *Cannot use fix pour rigid and not molecule*
Self-explanatory. Self-explanatory.
@ -7192,7 +7192,7 @@ keyword to allow for additional bonds to be formed
does not exist. does not exist.
*Replacing a fix, but new style != old style* *Replacing a fix, but new style != old style*
A fix ID can be used a 2nd time, but only if the style matches the A fix ID can be used a second time, but only if the style matches the
previous fix. In this case it is assumed you with to reset a fix's previous fix. In this case it is assumed you with to reset a fix's
parameters. This error may mean you are mistakenly re-using a fix ID parameters. This error may mean you are mistakenly re-using a fix ID
when you do not intend to. when you do not intend to.

8
doc/src/Errors_warnings.rst
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@ -43,17 +43,17 @@ Doc page with :doc:`ERROR messages <Errors_messages>`
Self-explanatory. Self-explanatory.
*Bond atom missing in box size check* *Bond atom missing in box size check*
The 2nd atoms needed to compute a particular bond is missing on this The second atom needed to compute a particular bond is missing on this
processor. Typically this is because the pairwise cutoff is set too processor. Typically this is because the pairwise cutoff is set too
short or the bond has blown apart and an atom is too far away. short or the bond has blown apart and an atom is too far away.
*Bond atom missing in image check* *Bond atom missing in image check*
The 2nd atom in a particular bond is missing on this processor. The second atom in a particular bond is missing on this processor.
Typically this is because the pairwise cutoff is set too short or the Typically this is because the pairwise cutoff is set too short or the
bond has blown apart and an atom is too far away. bond has blown apart and an atom is too far away.
*Bond atoms missing at step %ld* *Bond atoms missing at step %ld*
The 2nd atom needed to compute a particular bond is missing on this The second atom needed to compute a particular bond is missing on this
processor. Typically this is because the pairwise cutoff is set too processor. Typically this is because the pairwise cutoff is set too
short or the bond has blown apart and an atom is too far away. short or the bond has blown apart and an atom is too far away.
@ -486,7 +486,7 @@ This will most likely cause errors in kinetic fluctuations.
a new style. a new style.
*No Kspace calculation with verlet/split* *No Kspace calculation with verlet/split*
The 2nd partition performs a kspace calculation so the kspace_style The second partition performs a kspace calculation so the kspace_style
command must be used. command must be used.
*No automatic unit conversion to XTC file format conventions possible for units lj* *No automatic unit conversion to XTC file format conventions possible for units lj*

2
doc/src/Examples.rst
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@ -163,7 +163,7 @@ Here is how you can run and visualize one of the sample problems:
Running the simulation produces the files *dump.indent* and Running the simulation produces the files *dump.indent* and
*log.lammps*\ . You can visualize the dump file of snapshots with a *log.lammps*\ . You can visualize the dump file of snapshots with a
variety of 3rd-party tools highlighted on the variety of third-party tools highlighted on the
`Visualization <https://lammps.sandia.gov/viz.html>`_ page of the LAMMPS `Visualization <https://lammps.sandia.gov/viz.html>`_ page of the LAMMPS
web site. web site.

2
doc/src/Howto_chunk.rst
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@ -197,7 +197,7 @@ compress individual polymer chains (molecules) in a mixture, is
explained on the :doc:`compute chunk/spread/atom <compute_chunk_spread_atom>` command doc page. explained on the :doc:`compute chunk/spread/atom <compute_chunk_spread_atom>` command doc page.
(7) An example for using one set of per-chunk values for molecule (7) An example for using one set of per-chunk values for molecule
chunks, to create a 2nd set of micelle-scale chunks (clustered chunks, to create a second set of micelle-scale chunks (clustered
molecules, due to hydrophobicity), is explained on the :doc:`compute chunk/reduce <compute_reduce_chunk>` command doc page. molecules, due to hydrophobicity), is explained on the :doc:`compute chunk/reduce <compute_reduce_chunk>` command doc page.
(8) An example for using one set of per-chunk values (dipole moment (8) An example for using one set of per-chunk values (dipole moment

32
doc/src/Howto_cmake.rst
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@ -114,19 +114,19 @@ summary screen will look like this:
-- Detecting CXX compiler ABI info - done -- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features -- Detecting CXX compile features
-- Detecting CXX compile features - done -- Detecting CXX compile features - done
-- Found Git: /usr/bin/git (found version "2.25.2") -- Found Git: /usr/bin/git (found version "2.25.2")
-- Running check for auto-generated files from make-based build system -- Running check for auto-generated files from make-based build system
-- Found MPI_CXX: /usr/lib64/mpich/lib/libmpicxx.so (found version "3.1") -- Found MPI_CXX: /usr/lib64/mpich/lib/libmpicxx.so (found version "3.1")
-- Found MPI: TRUE (found version "3.1") -- Found MPI: TRUE (found version "3.1")
-- Looking for C++ include omp.h -- Looking for C++ include omp.h
-- Looking for C++ include omp.h - found -- Looking for C++ include omp.h - found
-- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5")
-- Found OpenMP: TRUE (found version "4.5") -- Found OpenMP: TRUE (found version "4.5")
-- Found JPEG: /usr/lib64/libjpeg.so (found version "62") -- Found JPEG: /usr/lib64/libjpeg.so (found version "62")
-- Found PNG: /usr/lib64/libpng.so (found version "1.6.37") -- Found PNG: /usr/lib64/libpng.so (found version "1.6.37")
-- Found ZLIB: /usr/lib64/libz.so (found version "1.2.11") -- Found ZLIB: /usr/lib64/libz.so (found version "1.2.11")
-- Found GZIP: /usr/bin/gzip -- Found GZIP: /usr/bin/gzip
-- Found FFMPEG: /usr/bin/ffmpeg -- Found FFMPEG: /usr/bin/ffmpeg
-- Performing Test COMPILER_SUPPORTS-ffast-math -- Performing Test COMPILER_SUPPORTS-ffast-math
-- Performing Test COMPILER_SUPPORTS-ffast-math - Success -- Performing Test COMPILER_SUPPORTS-ffast-math - Success
-- Performing Test COMPILER_SUPPORTS-march=native -- Performing Test COMPILER_SUPPORTS-march=native
@ -143,7 +143,7 @@ summary screen will look like this:
* JPEG * JPEG
* PNG * PNG
* ZLIB * ZLIB
-- <<< Build configuration >>> -- <<< Build configuration >>>
Build type: RelWithDebInfo Build type: RelWithDebInfo
Install path: /home/akohlmey/.local Install path: /home/akohlmey/.local
@ -157,7 +157,7 @@ summary screen will look like this:
Options: -ffast-math;-march=native Options: -ffast-math;-march=native
-- <<< Linker flags: >>> -- <<< Linker flags: >>>
-- Executable name: lmp -- Executable name: lmp
-- Static library flags: -- Static library flags:
-- <<< MPI flags >>> -- <<< MPI flags >>>
-- MPI includes: /usr/include/mpich-x86_64 -- MPI includes: /usr/include/mpich-x86_64
-- MPI libraries: /usr/lib64/mpich/lib/libmpicxx.so;/usr/lib64/mpich/lib/libmpi.so; -- MPI libraries: /usr/lib64/mpich/lib/libmpicxx.so;/usr/lib64/mpich/lib/libmpi.so;
@ -291,7 +291,7 @@ Some common CMake variables
.. list-table:: .. list-table::
:header-rows: 1 :header-rows: 1
* - Variable * - Variable
- Description - Description
* - ``CMAKE_INSTALL_PREFIX`` * - ``CMAKE_INSTALL_PREFIX``
@ -313,13 +313,13 @@ Some common CMake variables
- Fortran compiler to be used for compilation (default: system specific, ``gfortran`` on Linux) - Fortran compiler to be used for compilation (default: system specific, ``gfortran`` on Linux)
* - ``CXX_COMPILER_LAUNCHER`` * - ``CXX_COMPILER_LAUNCHER``
- tool to launch the C++ compiler, e.g. ``ccache`` or ``distcc`` for faster compilation (default: empty) - tool to launch the C++ compiler, e.g. ``ccache`` or ``distcc`` for faster compilation (default: empty)
Some common LAMMPS specific variables Some common LAMMPS specific variables
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
.. list-table:: .. list-table::
:header-rows: 1 :header-rows: 1
* - Variable * - Variable
- Description - Description
* - ``BUILD_MPI`` * - ``BUILD_MPI``
@ -438,7 +438,7 @@ the target name to the command. Example: ``cmake --build . --target all`` or
* - ``clean`` * - ``clean``
- remove all generated files - remove all generated files
Choosing generators Choosing generators
------------------- -------------------

2
doc/src/Howto_coreshell.rst
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@ -119,7 +119,7 @@ non-polarized ions (ions without an attached satellite particle). The
groups, one for the core atoms, another for the shell atoms. groups, one for the core atoms, another for the shell atoms.
Non-polarized ions which might also be included in the treated system Non-polarized ions which might also be included in the treated system
should not be included into either of these groups, they are taken should not be included into either of these groups, they are taken
into account by the *group-ID* (2nd argument) of the compute. The into account by the *group-ID* (second argument) of the compute. The
groups can be defined using the :doc:`group *type*\ <group>` command. groups can be defined using the :doc:`group *type*\ <group>` command.
Note that to perform thermostatting using this definition of Note that to perform thermostatting using this definition of
temperature, the :doc:`fix modify temp <fix_modify>` command should be temperature, the :doc:`fix modify temp <fix_modify>` command should be

2
doc/src/Howto_multiple.rst
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@ -91,4 +91,4 @@ With these modifications, the 8 simulations of each script would run
on the 3 partitions one after the other until all were finished. on the 3 partitions one after the other until all were finished.
Initially, 3 simulations would be started simultaneously, one on each Initially, 3 simulations would be started simultaneously, one on each
partition. When one finished, that partition would then start partition. When one finished, that partition would then start
the 4th simulation, and so forth, until all 8 were completed. the fourth simulation, and so forth, until all 8 were completed.

2
doc/src/Howto_restart.rst
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@ -28,7 +28,7 @@ scripts are based on. If that script had the line
added to it, it would produce 2 binary restart files (tmp.restart.50 added to it, it would produce 2 binary restart files (tmp.restart.50
and tmp.restart.100) as it ran. and tmp.restart.100) as it ran.
This script could be used to read the 1st restart file and re-run the This script could be used to read the first restart file and re-run the
last 50 timesteps: last 50 timesteps:
.. code-block:: LAMMPS .. code-block:: LAMMPS

6
doc/src/Howto_triclinic.rst
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@ -85,7 +85,7 @@ where *V* is the volume of the box, **X** is the original vector quantity and
**x** is the vector in the LAMMPS basis. **x** is the vector in the LAMMPS basis.
There is no requirement that a triclinic box be periodic in any There is no requirement that a triclinic box be periodic in any
dimension, though it typically should be in at least the 2nd dimension dimension, though it typically should be in at least the second dimension
of the tilt (y in xy) if you want to enforce a shift in periodic of the tilt (y in xy) if you want to enforce a shift in periodic
boundary conditions across that boundary. Some commands that work boundary conditions across that boundary. Some commands that work
with triclinic boxes, e.g. the :doc:`fix deform <fix_deform>` and :doc:`fix npt <fix_nh>` commands, require periodicity or non-shrink-wrap with triclinic boxes, e.g. the :doc:`fix deform <fix_deform>` and :doc:`fix npt <fix_nh>` commands, require periodicity or non-shrink-wrap
@ -120,7 +120,7 @@ The 9 parameters, as well as lx,ly,lz, can be output via the
To avoid extremely tilted boxes (which would be computationally To avoid extremely tilted boxes (which would be computationally
inefficient), LAMMPS normally requires that no tilt factor can skew inefficient), LAMMPS normally requires that no tilt factor can skew
the box more than half the distance of the parallel box length, which the box more than half the distance of the parallel box length, which
is the 1st dimension in the tilt factor (x for xz). This is required is the first dimension in the tilt factor (x for xz). This is required
both when the simulation box is created, e.g. via the both when the simulation box is created, e.g. via the
:doc:`create_box <create_box>` or :doc:`read_data <read_data>` commands, :doc:`create_box <create_box>` or :doc:`read_data <read_data>` commands,
as well as when the box shape changes dynamically during a simulation, as well as when the box shape changes dynamically during a simulation,
@ -137,7 +137,7 @@ limit during a dynamics run (e.g. via the :doc:`fix deform <fix_deform>`
command), then the box is "flipped" to an equivalent shape with a tilt command), then the box is "flipped" to an equivalent shape with a tilt
factor within the bounds, so the run can continue. See the :doc:`fix deform <fix_deform>` doc page for further details. factor within the bounds, so the run can continue. See the :doc:`fix deform <fix_deform>` doc page for further details.
One exception to this rule is if the 1st dimension in the tilt One exception to this rule is if the first dimension in the tilt
factor (x for xy) is non-periodic. In that case, the limits on the factor (x for xy) is non-periodic. In that case, the limits on the
tilt factor are not enforced, since flipping the box in that dimension tilt factor are not enforced, since flipping the box in that dimension
does not change the atom positions due to non-periodicity. In this does not change the atom positions due to non-periodicity. In this

2
doc/src/Intro_nonfeatures.rst
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@ -34,7 +34,7 @@ Here are suggestions on how to perform these tasks:
molecular builder that will generate complex molecular models. See molecular builder that will generate complex molecular models. See
the :doc:`Tools <Tools>` doc page for details on tools packaged with the :doc:`Tools <Tools>` doc page for details on tools packaged with
LAMMPS. The `Pre/post processing page <http:/lammps.sandia.gov/prepost.html>`_ of the LAMMPS website LAMMPS. The `Pre/post processing page <http:/lammps.sandia.gov/prepost.html>`_ of the LAMMPS website
describes a variety of 3rd party tools for this task. Furthermore, describes a variety of third party tools for this task. Furthermore,
some LAMMPS internal commands allow to reconstruct, or selectively add some LAMMPS internal commands allow to reconstruct, or selectively add
topology information, as well as provide the option to insert molecule topology information, as well as provide the option to insert molecule
templates instead of atoms for building bulk molecular systems. templates instead of atoms for building bulk molecular systems.

3
doc/src/Manual.rst
View File

@ -32,11 +32,12 @@ a brief description of the basic code structure of LAMMPS.
---------- ----------
Once you are familiar with LAMMPS, you may want to bookmark :doc:`this page <Commands>` since it gives quick access to a doc page for Once you are familiar with LAMMPS, you may want to bookmark :doc:`this page <Commands_all>` since it gives quick access to a doc page for
every LAMMPS command. every LAMMPS command.
.. _lws: https://lammps.sandia.gov .. _lws: https://lammps.sandia.gov
.. _user_documentation:
.. toctree:: .. toctree::
:maxdepth: 2 :maxdepth: 2
:numbered: 3 :numbered: 3

177
doc/src/Manual_build.rst
View File

@ -1,60 +1,62 @@
Building the LAMMPS manual Building the LAMMPS manual
************************** **************************
Depending on how you obtained LAMMPS, the doc directory has up Depending on how you obtained LAMMPS and whether you have built the
to 6 sub-directories, 2 Nroff files, and optionally 2 PDF files manual yourself, this directory has a number of sub-directories and
plus 2 e-book format files: files. Here is a list with descriptions:
.. code-block:: bash .. code-block:: bash
src # content files for LAMMPS documentation README # brief info about the documentation
html # HTML version of the LAMMPS manual (see html/Manual.html) src # content files for LAMMPS documentation
utils # tools and settings for building the documentation html # HTML version of the LAMMPS manual (see html/Manual.html)
docenv # virtualenv for processing the manual sources utils # tools and settings for building the documentation
doctrees # temporary data from processing the manual lammps.1 # man page for the lammps command
mathjax # code and fonts for rendering math in html msi2lmp.1 # man page for the msi2lmp command
Manual.pdf # large PDF version of entire manual Manual.pdf # large PDF version of entire manual
Developer.pdf # small PDF with info about how LAMMPS is structured Developer.pdf # small PDF with info about how LAMMPS is structured
LAMMPS.epub # Manual in ePUB e-book format LAMMPS.epub # Manual in ePUB e-book format
LAMMPS.mobi # Manual in MOBI e-book format LAMMPS.mobi # Manual in MOBI e-book format
lammps.1 # man page for the lammps command docenv # virtualenv folder for processing the manual sources
msi2lmp.1 # man page for the msi2lmp command doctrees # temporary data from processing the manual
mathjax # code and fonts for rendering math in html
doxygen # doxygen configuration and output
.gitignore # list of files and folders to be ignored by git
doxygen-warn.log # logfile with warnings from running doxygen
github-development-workflow.md # notes on the LAMMPS development workflow
include-file-conventions.md # notes on LAMMPS' include file conventions
If you downloaded LAMMPS as a tarball from the web site, the html folder If you downloaded LAMMPS as a tarball from `the LAMMPS website <lws_>`_,
and the PDF files should be included. the html folder and the PDF files should be included.
If you downloaded LAMMPS from the public git repository, then the HTML If you downloaded LAMMPS from the public git repository, then the HTML
and PDF files are not included. Instead you need to create them, in one and PDF files are not included. Instead you need to create them, in one
of two ways: of two ways:
a. You can "fetch" the current HTML and PDF files from the LAMMPS web a. You can "fetch" the current HTML and PDF files from the LAMMPS web
site. Just type "make fetch". This should download a html_www site. Just type ``make fetch``. This should download a html_www
directory and Manual_www.pdf/Developer_www.pdf files. Note that if directory and Manual_www.pdf/Developer_www.pdf files. Note that if
new LAMMPS features have been added more recently than the date of new LAMMPS features have been added more recently than the date of
your LAMMPS version, the fetched documentation will include those your LAMMPS version, the fetched documentation will include those
changes (but your source code will not, unless you update your local changes (but your source code will not, unless you update your local
repository). repository).
b. You can build the HTML or PDF files yourself, by typing "make html" b. You can build the HTML or PDF files yourself, by typing ``make html``
or "make pdf". This requires various tools including Sphinx, git, or ``make pdf``. This requires various tools and files. Some of them
and the MathJax javascript library, which the build process will attempt have to be installed (more on that below). For the rest the build
to download automatically into a virtual environment in the folder process will attempt to download and install them into a python
doc/docenv and the folder mathjax, respectively, if not already available. virtual environment and local folders. This download is required
This download is required only once, unless you type "make clean-all". only once, unless you type ``make clean-all``. After that, viewing and
After that, viewing and processing of the documentation can be done processing of the documentation can be done without internet access.
without internet access. To generate the PDF version of the manual,
the PDFLaTeX software and several LaTeX packages are required as well.
However, those cannot be installed automatically at the moment.
---------- ----------
The generation of all documentation is managed by the Makefile in The generation of all documentation is managed by the Makefile in the
the doc directory. doc directory. The following documentation related make commands are
available:
.. code-block:: bash .. code-block:: bash
Documentation Build Options:
make html # generate HTML in html dir using Sphinx make html # generate HTML in html dir using Sphinx
make pdf # generate 2 PDF files (Manual.pdf,Developer.pdf) make pdf # generate 2 PDF files (Manual.pdf,Developer.pdf)
# in doc dir via htmldoc and pdflatex # in doc dir via htmldoc and pdflatex
@ -62,8 +64,10 @@ the doc directory.
# as a tarball and unpack into html dir and 2 PDFs # as a tarball and unpack into html dir and 2 PDFs
make epub # generate LAMMPS.epub in ePUB format using Sphinx make epub # generate LAMMPS.epub in ePUB format using Sphinx
make mobi # generate LAMMPS.mobi in MOBI format using ebook-convert make mobi # generate LAMMPS.mobi in MOBI format using ebook-convert
make clean # remove intermediate RST files created by HTML build make clean # remove intermediate RST files created by HTML build
make clean-all # remove entire build folder and any cached data make clean-all # remove entire build folder and any cached data
make anchor_check # check for duplicate anchor labels make anchor_check # check for duplicate anchor labels
make style_check # check for complete and consistent style lists make style_check # check for complete and consistent style lists
make package_check # check for complete and consistent package lists make package_check # check for complete and consistent package lists
@ -74,29 +78,30 @@ the doc directory.
Installing prerequisites for HTML build Installing prerequisites for HTML build
======================================= =======================================
To run the HTML documentation build toolchain, Python 3 and virtualenv To run the HTML documentation build toolchain, python 3, git, doxygen,
have to be installed. Here are instructions for common setups: and virtualenv have to be installed locally. Here are instructions for
common setups:
Ubuntu Ubuntu
------ ------
.. code-block:: bash .. code-block:: bash
sudo apt-get install python-virtualenv sudo apt-get install python-virtualenv git doxygen
Fedora (up to version 21) and Red Hat Enterprise Linux or CentOS (up to version 7.x) Fedora (up to version 21) and Red Hat Enterprise Linux or CentOS (up to version 7.x)
------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------
.. code-block:: bash .. code-block:: bash
sudo yum install python3-virtualenv sudo yum install python3-virtualenv git doxygen
Fedora (since version 22) Fedora (since version 22)
------------------------- -------------------------
.. code-block:: bash .. code-block:: bash
sudo dnf install python3-virtualenv sudo dnf install python3-virtualenv git doxygen
MacOS X MacOS X
------- -------
@ -120,22 +125,92 @@ Once Python 3 is installed, open a Terminal and type
This will install virtualenv from the Python Package Index. This will install virtualenv from the Python Package Index.
---------- Installing prerequisites for PDF build
======================================
Installing prerequisites for epub build In addition to the tools needed for building the HTML format manual,
======================================= a working LaTeX installation with support for PDFLaTeX and a selection
of LaTeX styles/packages are required.
ePUB Installing prerequisites for e-book reader builds
---- =================================================
Same as for HTML. This uses mostly the same tools and configuration In addition to the tools needed for building the HTML format manual,
files as the HTML tree. In addition it uses LaTeX to convert embedded a working LaTeX installation with a few add-on LaTeX packages
as well as the ``dvipng`` tool are required to convert embedded
math expressions transparently into embedded images. math expressions transparently into embedded images.
For converting the generated ePUB file to a MOBI format file For converting the generated ePUB file to a MOBI format file (for e-book
(for e-book readers, like Kindle, that cannot read ePUB), you readers, like Kindle, that cannot read ePUB), you also need to have the
also need to have the 'ebook-convert' tool from the "calibre" ``ebook-convert`` tool from the "calibre" software
software installed. `http://calibre-ebook.com/ <http://calibre-ebook.com/>`_ installed. `http://calibre-ebook.com/ <http://calibre-ebook.com/>`_
You first create the ePUB file and then convert it with 'make mobi' Typing ``make mobi`` will first create the ePUB file and then convert
On the Kindle readers in particular, you also have support for it. On the Kindle readers in particular, you also have support for PDF
PDF files, so you could download and view the PDF version as an alternative. files, so you could download and view the PDF version as an alternative.
Instructions for Developers
===========================
When adding new styles or options to the LAMMPS code, corresponding
documentation is required and either existing files in the ``src``
folder need to be updated or new files added. These files are written
in `reStructuredText <rst_>`_ markup for translation with the Sphinx tool.
Before contributing any documentation, please check that both the HTML
and the PDF format documentation can translate without errors. Please also
check the output to the console for any warnings or problems. There will
be multiple tests run automatically:
- A test for correctness of all anchor labels and their references
- A test that all LAMMPS packages (= folders with sources in
``lammps/src``) are documented and listed. A typical warning shows
the name of the folder with the suspected new package code and the
documentation files where they need to be listed:
.. parsed-literal::
Found 33 standard and 41 user packages
Standard package NEWPACKAGE missing in Packages_standard.rst
Standard package NEWPACKAGE missing in Packages_details.rst
- A test that only standard, printable ASCII text characters are used.
This runs the command ``env LC_ALL=C grep -n '[^ -~]' src/*.rst`` and
thus prints all offending lines with filename and line number
prepended to the screen. Special characters like the Angstrom
:math:`\mathrm{\mathring{A}}` should be typeset with embedded math
(like this ``:math:`\mathrm{\mathring{A}}```\ ).
- A test whether all styles are documented and listed in their
respective overview pages. A typical output with warnings looks like this:
.. parsed-literal::
Parsed style names w/o suffixes from C++ tree in ../src:
Angle styles: 21 Atom styles: 24
Body styles: 3 Bond styles: 17
Command styles: 41 Compute styles: 143
Dihedral styles: 16 Dump styles: 26
Fix styles: 223 Improper styles: 13
Integrate styles: 4 Kspace styles: 15
Minimize styles: 9 Pair styles: 234
Reader styles: 4 Region styles: 8
Compute style entry newcomp is missing or incomplete in Commands_compute.rst
Compute style entry newcomp is missing or incomplete in compute.rst
Fix style entry newfix is missing or incomplete in Commands_fix.rst
Fix style entry newfix is missing or incomplete in fix.rst
Pair style entry new is missing or incomplete in Commands_pair.rst
Pair style entry new is missing or incomplete in pair_style.rst
Found 6 issue(s) with style lists
In addition, there is the option to run a spellcheck on the entire
manual with ``make spelling``. This requires `a library called enchant
<https://github.com/AbiWord/enchant>`_. To avoid printing out *false
positives* (e.g. keywords, names, abbreviations) those can be added to
the file ``lammps/doc/utils/sphinx-config/false_positives.txt``.
.. _rst: https://docutils.readthedocs.io/en/sphinx-docs/user/rst/quickstart.html
.. _lws: https://lammps.sandia.gov

2
doc/src/Modify_fix.rst
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@ -27,7 +27,7 @@ derived class. See fix.h for details.
+---------------------------+--------------------------------------------------------------------------------------------+ +---------------------------+--------------------------------------------------------------------------------------------+
| setup_pre_force | called before force computation in setup (optional) | | setup_pre_force | called before force computation in setup (optional) |
+---------------------------+--------------------------------------------------------------------------------------------+ +---------------------------+--------------------------------------------------------------------------------------------+
| setup | called immediately before the 1st timestep and after forces are computed (optional) | | setup | called immediately before the first timestep and after forces are computed (optional) |
+---------------------------+--------------------------------------------------------------------------------------------+ +---------------------------+--------------------------------------------------------------------------------------------+
| min_setup_pre_force | like setup_pre_force, but for minimizations instead of MD runs (optional) | | min_setup_pre_force | like setup_pre_force, but for minimizations instead of MD runs (optional) |
+---------------------------+--------------------------------------------------------------------------------------------+ +---------------------------+--------------------------------------------------------------------------------------------+

18
doc/src/Modify_kspace.rst
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@ -10,12 +10,12 @@ Ewald.cpp is an example of computing K-space interactions.
Here is a brief description of methods you define in your new derived Here is a brief description of methods you define in your new derived
class. See kspace.h for details. class. See kspace.h for details.
+---------------+----------------------------------------------+ +---------------+------------------------------------------------+
| init | initialize the calculation before a run | | init | initialize the calculation before a run |
+---------------+----------------------------------------------+ +---------------+------------------------------------------------+
| setup | computation before the 1st timestep of a run | | setup | computation before the first timestep of a run |
+---------------+----------------------------------------------+ +---------------+------------------------------------------------+
| compute | every-timestep computation | | compute | every-timestep computation |
+---------------+----------------------------------------------+ +---------------+------------------------------------------------+
| memory_usage | tally of memory usage | | memory_usage | tally of memory usage |
+---------------+----------------------------------------------+ +---------------+------------------------------------------------+

2
doc/src/Packages_details.rst
View File

@ -490,7 +490,7 @@ interactions. These include Ewald, particle-particle particle-mesh
Building with this package requires a 1d FFT library be present on Building with this package requires a 1d FFT library be present on
your system for use by the PPPM solvers. This can be the KISS FFT your system for use by the PPPM solvers. This can be the KISS FFT
library provided with LAMMPS, 3rd party libraries like FFTW, or a library provided with LAMMPS, third party libraries like FFTW, or a
vendor-supplied FFT library. See the :doc:`Build settings <Build_settings>` doc page for details on how to select vendor-supplied FFT library. See the :doc:`Build settings <Build_settings>` doc page for details on how to select
different FFT options for your LAMPMS build. different FFT options for your LAMPMS build.

9
doc/src/Python_library.rst
View File

@ -254,12 +254,3 @@ following steps:
* You should now be able to invoke the new interface function from a * You should now be able to invoke the new interface function from a
Python script. Python script.
----------
.. autoclass:: lammps.lammps
:members:
:no-undoc-members:
.. autoclass:: lammps.NeighList
:members:
:no-undoc-members:

2
doc/src/Python_test.rst
View File

@ -10,7 +10,7 @@ and type:
>>> lmp = lammps() >>> lmp = lammps()
If you get no errors, you're ready to use LAMMPS from Python. If the If you get no errors, you're ready to use LAMMPS from Python. If the
2nd command fails, the most common error to see is second command fails, the most common error to see is
.. parsed-literal:: .. parsed-literal::

8
doc/src/Run_options.rst
View File

@ -324,17 +324,17 @@ physical processors is done by MPI before LAMMPS begins. It may be
useful in some cases to alter the rank order. E.g. to insure that useful in some cases to alter the rank order. E.g. to insure that
cores within each node are ranked in a desired order. Or when using cores within each node are ranked in a desired order. Or when using
the :doc:`run_style verlet/split <run_style>` command with 2 partitions the :doc:`run_style verlet/split <run_style>` command with 2 partitions
to insure that a specific Kspace processor (in the 2nd partition) is to insure that a specific Kspace processor (in the second partition) is
matched up with a specific set of processors in the 1st partition. matched up with a specific set of processors in the first partition.
See the :doc:`Speed tips <Speed_tips>` doc page for more details. See the :doc:`Speed tips <Speed_tips>` doc page for more details.
If the keyword *nth* is used with a setting *N*\ , then it means every If the keyword *nth* is used with a setting *N*\ , then it means every
Nth processor will be moved to the end of the ranking. This is useful Nth processor will be moved to the end of the ranking. This is useful
when using the :doc:`run_style verlet/split <run_style>` command with 2 when using the :doc:`run_style verlet/split <run_style>` command with 2
partitions via the -partition command-line switch. The first set of partitions via the -partition command-line switch. The first set of
processors will be in the first partition, the 2nd set in the 2nd processors will be in the first partition, the second set in the second
partition. The -reorder command-line switch can alter this so that partition. The -reorder command-line switch can alter this so that
the 1st N procs in the 1st partition and one proc in the 2nd partition the first N procs in the first partition and one proc in the second partition
will be ordered consecutively, e.g. as the cores on one physical node. will be ordered consecutively, e.g. as the cores on one physical node.
This can boost performance. For example, if you use "-reorder nth 4" This can boost performance. For example, if you use "-reorder nth 4"
and "-partition 9 3" and you are running on 12 processors, the and "-partition 9 3" and you are running on 12 processors, the

2
doc/src/angle_charmm.rst
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@ -37,7 +37,7 @@ The *charmm* angle style uses the potential
E = K (\theta - \theta_0)^2 + K_{ub} (r - r_{ub})^2 E = K (\theta - \theta_0)^2 + K_{ub} (r - r_{ub})^2
with an additional Urey_Bradley term based on the distance :math:`r` between with an additional Urey_Bradley term based on the distance :math:`r` between
the 1st and 3rd atoms in the angle. :math:`K`, :math:`\theta_0`, the first and third atoms in the angle. :math:`K`, :math:`\theta_0`,
:math:`K_{ub}`, and :math:`R_{ub}` are coefficients defined for each angle :math:`K_{ub}`, and :math:`R_{ub}` are coefficients defined for each angle
type. type.

4
doc/src/angle_coeff.rst
View File

@ -31,7 +31,7 @@ Angle coefficients can also be set in the data file read by the
:doc:`read_data <read_data>` command or in a restart file. :doc:`read_data <read_data>` command or in a restart file.
N can be specified in one of two ways. An explicit numeric value can N can be specified in one of two ways. An explicit numeric value can
be used, as in the 1st example above. Or a wild-card asterisk can be be used, as in the first example above. Or a wild-card asterisk can be
used to set the coefficients for multiple angle types. This takes the used to set the coefficients for multiple angle types. This takes the
form "\*" or "\*n" or "n\*" or "m\*n". If N = the number of angle types, form "\*" or "\*n" or "n\*" or "m\*n". If N = the number of angle types,
then an asterisk with no numeric values means all types from 1 to N. A then an asterisk with no numeric values means all types from 1 to N. A
@ -53,7 +53,7 @@ same format as the arguments of the :doc:`angle_coeff <angle_coeff>` command in
script, except that wild-card asterisks should not be used since script, except that wild-card asterisks should not be used since
coefficients for all N types must be listed in the file. For example, coefficients for all N types must be listed in the file. For example,
under the "Angle Coeffs" section of a data file, the line that under the "Angle Coeffs" section of a data file, the line that
corresponds to the 1st example above would be listed as corresponds to the first example above would be listed as
.. parsed-literal:: .. parsed-literal::

10
doc/src/angle_table.rst
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@ -75,7 +75,7 @@ parenthesized comments):
... ...
181 180.0 0.0 0.0 181 180.0 0.0 0.0
A section begins with a non-blank line whose 1st character is not a A section begins with a non-blank line whose first character is not a
"#"; blank lines or lines starting with "#" can be used as comments "#"; blank lines or lines starting with "#" can be used as comments
between sections. The first line begins with a keyword which between sections. The first line begins with a keyword which
identifies the section. The line can contain additional text, but the identifies the section. The line can contain additional text, but the
@ -99,7 +99,7 @@ is in the tabulated file (with effectively no preliminary
interpolation), you should set Ntable = Nfile. interpolation), you should set Ntable = Nfile.
The "FP" parameter is optional. If used, it is followed by two values The "FP" parameter is optional. If used, it is followed by two values
fplo and fphi, which are the 2nd derivatives at the innermost and fplo and fphi, which are the second derivatives at the innermost and
outermost angle settings. These values are needed by the spline outermost angle settings. These values are needed by the spline
construction routines. If not specified by the "FP" parameter, they construction routines. If not specified by the "FP" parameter, they
are estimated (less accurately) by the first two and last two are estimated (less accurately) by the first two and last two
@ -110,9 +110,9 @@ equilibrium angle value, which is used, for example, by the :doc:`fix shake <fix
set to 180.0. set to 180.0.
Following a blank line, the next N lines list the tabulated values. Following a blank line, the next N lines list the tabulated values.
On each line, the 1st value is the index from 1 to N, the 2nd value is On each line, the first value is the index from 1 to N, the second value is
the angle value (in degrees), the 3rd value is the energy (in energy the angle value (in degrees), the third value is the energy (in energy
units), and the 4th is -dE/d(theta) (also in energy units). The 3rd units), and the fourth is -dE/d(theta) (also in energy units). The third
term is the energy of the 3-atom configuration for the specified term is the energy of the 3-atom configuration for the specified
angle. The last term is the derivative of the energy with respect to angle. The last term is the derivative of the energy with respect to
the angle (in degrees, not radians). Thus the units of the last term the angle (in degrees, not radians). Thus the units of the last term

4
doc/src/atc_control_momentum.rst
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@ -15,7 +15,7 @@ Syntax
fix_modify AtC control momentum glc_velocity fix_modify AtC control momentum glc_velocity
fix_modify AtC control momentum hoover fix_modify AtC control momentum hoover
fix_modify AtC control momentum flux [faceset face_set_id, interpolate] fix_modify AtC control momentum flux [faceset face_set_id, interpolate]
* AtC fixID = ID of :doc:`fix atc <fix_atc>` instance * AtC fixID = ID of :doc:`fix atc <fix_atc>` instance
* control = name of the AtC sub-command * control = name of the AtC sub-command
* physics_type = *thermal* or *momentum* * physics_type = *thermal* or *momentum*
@ -52,7 +52,7 @@ the finite element temperature. *flux* is a similar mode, but rather
adds energy to the atoms based on conservation of energy. adds energy to the atoms based on conservation of energy.
*correction_max_iterations* sets the maximum number of iterations to *correction_max_iterations* sets the maximum number of iterations to
compute the 2nd order in time correction term for lambda with the compute the second order in time correction term for lambda with the
fractional step method. The method uses the same tolerance as the fractional step method. The method uses the same tolerance as the
controller's matrix solver. controller's matrix solver.

2
doc/src/atc_control_thermal.rst
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@ -56,7 +56,7 @@ adds energy to the atoms based on conservation of energy. *hoover* and
atoms. atoms.
*correction_max_iterations* sets the maximum number of iterations to *correction_max_iterations* sets the maximum number of iterations to
compute the 2nd order in time correction term for lambda with the compute the second order in time correction term for lambda with the
fractional step method. The method uses the same tolerance as the fractional step method. The method uses the same tolerance as the
controller's matrix solver. controller's matrix solver.

6
doc/src/atc_hardy_fields.rst
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@ -25,8 +25,8 @@ Syntax
- temperature : temperature derived from the relative atomic kinetic energy - temperature : temperature derived from the relative atomic kinetic energy
- kinetic_temperature : temperature derived from the full kinetic energy - kinetic_temperature : temperature derived from the full kinetic energy
- number_density : simple kernel estimation of number of atoms per unit volume - number_density : simple kernel estimation of number of atoms per unit volume
- stress : Cauchy stress tensor for eulerian analysis (atom_element_map), or 1st Piola-Kirchhoff stress tensor for lagrangian analysis - stress : Cauchy stress tensor for eulerian analysis (atom_element_map), or first Piola-Kirchhoff stress tensor for lagrangian analysis
- transformed_stress : 1st Piola-Kirchhoff stress tensor for eulerian analysis (atom_element_map), or Cauchy stress tensor for lagrangian analysis - transformed_stress : first Piola-Kirchhoff stress tensor for eulerian analysis (atom_element_map), or Cauchy stress tensor for lagrangian analysis
- heat_flux : spatial heat flux vector for eulerian, or referential heat flux vector for lagrangian - heat_flux : spatial heat flux vector for eulerian, or referential heat flux vector for lagrangian
- potential_energy : potential energy per unit volume - potential_energy : potential energy per unit volume
- kinetic_energy : kinetic energy per unit volume - kinetic_energy : kinetic energy per unit volume
@ -37,7 +37,7 @@ Syntax
- eshelby_stress : configurational stress (energy-momentum) tensor defined by [Eshelby]_ - eshelby_stress : configurational stress (energy-momentum) tensor defined by [Eshelby]_
- vacancy_concentration : volume fraction of vacancy content - vacancy_concentration : volume fraction of vacancy content
- type_concentration : volume fraction of a specific atom type - type_concentration : volume fraction of a specific atom type
Examples Examples
"""""""" """"""""

4
doc/src/atc_hardy_gradients.rst
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@ -23,8 +23,8 @@ Syntax
- temperature : temperature derived from the relative atomic kinetic energy - temperature : temperature derived from the relative atomic kinetic energy
- kinetic_temperature : temperature derived from the full kinetic energy - kinetic_temperature : temperature derived from the full kinetic energy
- number_density : simple kernel estimation of number of atoms per unit volume - number_density : simple kernel estimation of number of atoms per unit volume
- stress : Cauchy stress tensor for eulerian analysis (atom_element_map), or 1st Piola-Kirchhoff stress tensor for lagrangian analysis - stress : Cauchy stress tensor for eulerian analysis (atom_element_map), or first Piola-Kirchhoff stress tensor for lagrangian analysis
- transformed_stress : 1st Piola-Kirchhoff stress tensor for eulerian analysis (atom_element_map), or Cauchy stress tensor for lagrangian analysis - transformed_stress : first Piola-Kirchhoff stress tensor for eulerian analysis (atom_element_map), or Cauchy stress tensor for lagrangian analysis
- heat_flux : spatial heat flux vector for eulerian, or referential heat flux vector for lagrangian - heat_flux : spatial heat flux vector for eulerian, or referential heat flux vector for lagrangian
- potential_energy : potential energy per unit volume - potential_energy : potential energy per unit volume
- kinetic_energy : kinetic energy per unit volume - kinetic_energy : kinetic energy per unit volume

2
doc/src/atc_hardy_kernel.rst
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@ -25,7 +25,7 @@ Syntax
- *quartic_bar* : <half_width> - *quartic_bar* : <half_width>
- *quartic_cylinder* : <radius> - *quartic_cylinder* : <radius>
- *quartic_sphere* : <radius> - *quartic_sphere* : <radius>
Examples Examples

4
doc/src/atc_hardy_rates.rst
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@ -23,8 +23,8 @@ Syntax
- temperature : temperature derived from the relative atomic kinetic energy - temperature : temperature derived from the relative atomic kinetic energy
- kinetic_temperature : temperature derived from the full kinetic energy - kinetic_temperature : temperature derived from the full kinetic energy
- number_density : simple kernel estimation of number of atoms per unit volume - number_density : simple kernel estimation of number of atoms per unit volume
- stress : Cauchy stress tensor for eulerian analysis (atom_element_map), or 1st Piola-Kirchhoff stress tensor for lagrangian analysis - stress : Cauchy stress tensor for eulerian analysis (atom_element_map), or first Piola-Kirchhoff stress tensor for lagrangian analysis
- transformed_stress : 1st Piola-Kirchhoff stress tensor for eulerian analysis (atom_element_map), or Cauchy stress tensor for lagrangian analysis - transformed_stress : first Piola-Kirchhoff stress tensor for eulerian analysis (atom_element_map), or Cauchy stress tensor for lagrangian analysis
- heat_flux : spatial heat flux vector for eulerian, or referential heat flux vector for lagrangian - heat_flux : spatial heat flux vector for eulerian, or referential heat flux vector for lagrangian
- potential_energy : potential energy per unit volume - potential_energy : potential energy per unit volume
- kinetic_energy : kinetic energy per unit volume - kinetic_energy : kinetic energy per unit volume

2
doc/src/atc_remove_species.rst
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@ -38,7 +38,7 @@ Related AtC commands
- :doc:`fix_modify AtC add_species <atc_add_species>` - :doc:`fix_modify AtC add_species <atc_add_species>`
- :doc:`fix_modify AtC add_molecule <atc_add_molecule>` - :doc:`fix_modify AtC add_molecule <atc_add_molecule>`
- :doc:`fix_modify AtC remove_molecule <atc_remove_molecule>` - :doc:`fix_modify AtC remove_molecule <atc_remove_molecule>`
Default Default
""""""" """""""

2
doc/src/atc_set_reference_pe.rst
View File

@ -22,7 +22,7 @@ Examples
fix_modify AtC set reference_potential_energy fix_modify AtC set reference_potential_energy
fix_modify AtC set reference_potential_energy -0.05 fix_modify AtC set reference_potential_energy -0.05
fix_modify AtC set reference_potential_energy myPEvalues fix_modify AtC set reference_potential_energy myPEvalues
Description Description
""""""""""" """""""""""

18
doc/src/atc_time_integration.rst
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@ -33,11 +33,11 @@ Command to select the thermal or momentum time integration.
Options for thermal time integration: Options for thermal time integration:
*gear* *gear*
atomic velocity update with 2nd order Verlet, nodal temperature update atomic velocity update with second order Verlet, nodal temperature update
with 3rd or 4th order Gear, thermostats based on controlling power with third or fourth order Gear, thermostats based on controlling power
*fractional_step* *fractional_step*
atomic velocity update with 2nd order Verlet, mixed nodal temperature atomic velocity update with second order Verlet, mixed nodal temperature
update, 3/4 Gear for continuum and 2 Verlet for atomic contributions, update, 3/4 Gear for continuum and 2 Verlet for atomic contributions,
thermostats based on controlling discrete energy changes thermostats based on controlling discrete energy changes
@ -46,18 +46,18 @@ Options for thermal time integration:
Options for momentum time integration: Options for momentum time integration:
*verlet* *verlet*
atomic velocity update with 2nd order Verlet, nodal temperature update atomic velocity update with second order Verlet, nodal temperature update
with 2nd order Verlet, kinetostats based on controlling force with second order Verlet, kinetostats based on controlling force
*fractional_step* *fractional_step*
atomic velocity update with 2nd order Verlet, mixed nodal momentum atomic velocity update with second order Verlet, mixed nodal momentum
update, 2nd order Verlet for continuum and exact 2nd order Verlet for update, second order Verlet for continuum and exact second order Verlet for
atomic contributions, kinetostats based on controlling discrete atomic contributions, kinetostats based on controlling discrete
momentum changes momentum changes
*gear* *gear*
atomic velocity update with 2nd order Verlet, nodal temperature update atomic velocity update with second order Verlet, nodal temperature update
with 3rd or 4th order Gear, kinetostats based on controlling power. with third or fourth order Gear, kinetostats based on controlling power.
--------- ---------

4
doc/src/bond_coeff.rst
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@ -32,7 +32,7 @@ Bond coefficients can also be set in the data file read by the
:doc:`read_data <read_data>` command or in a restart file. :doc:`read_data <read_data>` command or in a restart file.
N can be specified in one of two ways. An explicit numeric value can N can be specified in one of two ways. An explicit numeric value can
be used, as in the 1st example above. Or a wild-card asterisk can be be used, as in the first example above. Or a wild-card asterisk can be
used to set the coefficients for multiple bond types. This takes the used to set the coefficients for multiple bond types. This takes the
form "\*" or "\*n" or "n\*" or "m\*n". If N = the number of bond types, form "\*" or "\*n" or "n\*" or "m\*n". If N = the number of bond types,
then an asterisk with no numeric values means all types from 1 to N. A then an asterisk with no numeric values means all types from 1 to N. A
@ -54,7 +54,7 @@ same format as the arguments of the bond_coeff command in an input
script, except that wild-card asterisks should not be used since script, except that wild-card asterisks should not be used since
coefficients for all N types must be listed in the file. For example, coefficients for all N types must be listed in the file. For example,
under the "Bond Coeffs" section of a data file, the line that under the "Bond Coeffs" section of a data file, the line that
corresponds to the 1st example above would be listed as corresponds to the first example above would be listed as
.. parsed-literal:: .. parsed-literal::

4
doc/src/bond_fene.rst
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@ -38,8 +38,8 @@ The *fene* bond style uses the potential
to define a finite extensible nonlinear elastic (FENE) potential to define a finite extensible nonlinear elastic (FENE) potential
:ref:`(Kremer) <fene-Kremer>`, used for bead-spring polymer models. The first :ref:`(Kremer) <fene-Kremer>`, used for bead-spring polymer models. The first
term is attractive, the 2nd Lennard-Jones term is repulsive. The term is attractive, the second Lennard-Jones term is repulsive. The
first term extends to :math:`R_0`, the maximum extent of the bond. The 2nd first term extends to :math:`R_0`, the maximum extent of the bond. The second
term is cutoff at :math:`2^\frac{1}{6} \sigma`, the minimum of the LJ potential. term is cutoff at :math:`2^\frac{1}{6} \sigma`, the minimum of the LJ potential.
The following coefficients must be defined for each bond type via the The following coefficients must be defined for each bond type via the

4
doc/src/bond_fene_expand.rst
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@ -32,12 +32,12 @@ The *fene/expand* bond style uses the potential
to define a finite extensible nonlinear elastic (FENE) potential to define a finite extensible nonlinear elastic (FENE) potential
:ref:`(Kremer) <feneexpand-Kremer>`, used for bead-spring polymer models. The first :ref:`(Kremer) <feneexpand-Kremer>`, used for bead-spring polymer models. The first
term is attractive, the 2nd Lennard-Jones term is repulsive. term is attractive, the second Lennard-Jones term is repulsive.
The *fene/expand* bond style is similar to *fene* except that an extra The *fene/expand* bond style is similar to *fene* except that an extra
shift factor of :math:`\Delta` (positive or negative) is added to :math:`r` to shift factor of :math:`\Delta` (positive or negative) is added to :math:`r` to
effectively change the bead size of the bonded atoms. The first term effectively change the bead size of the bonded atoms. The first term
now extends to :math:`R_0 + \Delta` and the 2nd term is cutoff at :math:`2^\frac{1}{6} \sigma + \Delta`. now extends to :math:`R_0 + \Delta` and the second term is cutoff at :math:`2^\frac{1}{6} \sigma + \Delta`.
The following coefficients must be defined for each bond type via the The following coefficients must be defined for each bond type via the
:doc:`bond_coeff <bond_coeff>` command as in the example above, or in :doc:`bond_coeff <bond_coeff>` command as in the example above, or in

8
doc/src/bond_table.rst
View File

@ -74,7 +74,7 @@ parenthesized comments):
... ...
101 1.00 338.0000 -1352.0000 101 1.00 338.0000 -1352.0000
A section begins with a non-blank line whose 1st character is not a A section begins with a non-blank line whose first character is not a
"#"; blank lines or lines starting with "#" can be used as comments "#"; blank lines or lines starting with "#" can be used as comments
between sections. The first line begins with a keyword which between sections. The first line begins with a keyword which
identifies the section. The line can contain additional text, but the identifies the section. The line can contain additional text, but the
@ -109,9 +109,9 @@ equilibrium bond length, which is used, for example, by the :doc:`fix shake <fix
length is to the distance in the table with the lowest potential energy. length is to the distance in the table with the lowest potential energy.
Following a blank line, the next N lines list the tabulated values. Following a blank line, the next N lines list the tabulated values.
On each line, the 1st value is the index from 1 to N, the 2nd value is On each line, the first value is the index from 1 to N, the second value is
the bond length r (in distance units), the 3rd value is the energy (in the bond length r (in distance units), the third value is the energy (in
energy units), and the 4th is the force (in force units). The bond energy units), and the fourth is the force (in force units). The bond
lengths must range from a LO value to a HI value, and increase from lengths must range from a LO value to a HI value, and increase from
one line to the next. If the actual bond length is ever smaller than one line to the next. If the actual bond length is ever smaller than
the LO value or larger than the HI value, then the calculation is the LO value or larger than the HI value, then the calculation is

4
doc/src/boundary.rst
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@ -76,9 +76,9 @@ atoms becomes less than 50.0. This can be useful if you start a
simulation with an empty box or if you wish to leave room on one side simulation with an empty box or if you wish to leave room on one side
of the box, e.g. for atoms to evaporate from a surface. of the box, e.g. for atoms to evaporate from a surface.
For triclinic (non-orthogonal) simulation boxes, if the 2nd dimension For triclinic (non-orthogonal) simulation boxes, if the second dimension
of a tilt factor (e.g. y for xy) is periodic, then the periodicity is of a tilt factor (e.g. y for xy) is periodic, then the periodicity is
enforced with the tilt factor offset. If the 1st dimension is enforced with the tilt factor offset. If the first dimension is
shrink-wrapped, then the shrink wrapping is applied to the tilted box shrink-wrapped, then the shrink wrapping is applied to the tilted box
face, to encompass the atoms. E.g. for a positive xy tilt, the xlo face, to encompass the atoms. E.g. for a positive xy tilt, the xlo
and xhi faces of the box are planes tilting in the +y direction as y and xhi faces of the box are planes tilting in the +y direction as y

2
doc/src/box.rst
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@ -38,7 +38,7 @@ skewed the triclinic box is; see the :doc:`Howto triclinic <Howto_triclinic>` do
boxes in LAMMPS. boxes in LAMMPS.
LAMMPS normally requires that no tilt factor can skew the box more LAMMPS normally requires that no tilt factor can skew the box more
than half the distance of the parallel box length, which is the 1st than half the distance of the parallel box length, which is the first
dimension in the tilt factor (x for xz). If *tilt* is set to dimension in the tilt factor (x for xz). If *tilt* is set to
*small*\ , which is the default, then an error will be *small*\ , which is the default, then an error will be
generated if a box is created which exceeds this limit. If *tilt* generated if a box is created which exceeds this limit. If *tilt*

8
doc/src/compute_adf.rst
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@ -82,9 +82,9 @@ neighbor atom in each requested ADF.
is what is specified with the :doc:`neighbor <neighbor>` command. is what is specified with the :doc:`neighbor <neighbor>` command.
The *itypeN*\ ,\ *jtypeN*\ ,\ *ktypeN* settings can be specified in one of two The *itypeN*\ ,\ *jtypeN*\ ,\ *ktypeN* settings can be specified in one of two
ways. An explicit numeric value can be used, as in the 1st example ways. An explicit numeric value can be used, as in the first example
above. Or a wild-card asterisk can be used to specify a range of atom above. Or a wild-card asterisk can be used to specify a range of atom
types as in the 2nd example above. types as in the second example above.
This takes the form "\*" or "\*n" or "n\*" or "m\*n". If N = the This takes the form "\*" or "\*n" or "n\*" or "m\*n". If N = the
number of atom types, then an asterisk with no numeric values means number of atom types, then an asterisk with no numeric values means
all types from 1 to N. A leading asterisk means all types from 1 to n all types from 1 to N. A leading asterisk means all types from 1 to n
@ -92,12 +92,12 @@ all types from 1 to N. A leading asterisk means all types from 1 to n
(inclusive). A middle asterisk means all types from m to n (inclusive). A middle asterisk means all types from m to n
(inclusive). (inclusive).
If *itypeN*\ , *jtypeN*\ , and *ktypeN* are single values, as in the 1st example If *itypeN*\ , *jtypeN*\ , and *ktypeN* are single values, as in the first example
above, this means that the ADF is computed where atoms of type *itypeN* above, this means that the ADF is computed where atoms of type *itypeN*
are the central atom, and neighbor atoms of type *jtypeN* and *ktypeN* are the central atom, and neighbor atoms of type *jtypeN* and *ktypeN*
are forming the angle. If any of *itypeN*\ , *jtypeN*\ , or *ktypeN* are forming the angle. If any of *itypeN*\ , *jtypeN*\ , or *ktypeN*
represent a range of values via represent a range of values via
the wild-card asterisk, as in the 2nd example above, this means that the the wild-card asterisk, as in the second example above, this means that the
ADF is computed where atoms of any of the range of types represented ADF is computed where atoms of any of the range of types represented
by *itypeN* are the central atom, and the angle is formed by two neighbors, by *itypeN* are the central atom, and the angle is formed by two neighbors,
one neighbor in the range of types represented by *jtypeN* and another neighbor one neighbor in the range of types represented by *jtypeN* and another neighbor

6
doc/src/compute_chunk_atom.rst
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@ -218,8 +218,8 @@ into ellipses.
The created bins (and hence the chunk IDs) are numbered consecutively The created bins (and hence the chunk IDs) are numbered consecutively
from 1 to the number of bins = *Nchunk*\ . For *bin2d* and *bin3d*\ , the from 1 to the number of bins = *Nchunk*\ . For *bin2d* and *bin3d*\ , the
numbering varies most rapidly in the first dimension (which could be numbering varies most rapidly in the first dimension (which could be
x, y, or z), next rapidly in the 2nd dimension, and most slowly in the x, y, or z), next rapidly in the second dimension, and most slowly in the
3rd dimension. For *bin/sphere*\ , the bin with smallest radii is chunk third dimension. For *bin/sphere*\ , the bin with smallest radii is chunk
1 and the bni with largest radii is chunk Nchunk = *ncbin*\ . For 1 and the bni with largest radii is chunk Nchunk = *ncbin*\ . For
*bin/cylinder*\ , the numbering varies most rapidly in the dimension *bin/cylinder*\ , the numbering varies most rapidly in the dimension
along the cylinder axis and most slowly in the radial direction. along the cylinder axis and most slowly in the radial direction.
@ -614,7 +614,7 @@ Note that for the *bin/sphere* style, the radii *srmin* and *srmax* are
scaled by the lattice spacing or reduced value of the *x* dimension. scaled by the lattice spacing or reduced value of the *x* dimension.
Note that for the *bin/cylinder* style, the radii *crmin* and *crmax* Note that for the *bin/cylinder* style, the radii *crmin* and *crmax*
are scaled by the lattice spacing or reduced value of the 1st are scaled by the lattice spacing or reduced value of the first
dimension perpendicular to the cylinder axis. E.g. y for an x-axis dimension perpendicular to the cylinder axis. E.g. y for an x-axis
cylinder, x for a y-axis cylinder, and x for a z-axis cylinder. cylinder, x for a y-axis cylinder, and x for a z-axis cylinder.

2
doc/src/compute_coord_atom.rst
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@ -63,7 +63,7 @@ keywords are listed, a single coordination number is calculated, which
includes atoms of all types (same as the "\*" format, see below). includes atoms of all types (same as the "\*" format, see below).
The *typeN* keywords can be specified in one of two ways. An explicit The *typeN* keywords can be specified in one of two ways. An explicit
numeric value can be used, as in the 2nd example above. Or a numeric value can be used, as in the second example above. Or a
wild-card asterisk can be used to specify a range of atom types. This wild-card asterisk can be used to specify a range of atom types. This
takes the form "\*" or "\*n" or "n\*" or "m\*n". If N = the number of takes the form "\*" or "\*n" or "n\*" or "m\*n". If N = the number of
atom types, then an asterisk with no numeric values means all types atom types, then an asterisk with no numeric values means all types

2
doc/src/compute_displace_atom.rst
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@ -36,7 +36,7 @@ all effects due to atoms passing through periodic boundaries.
A vector of four quantities per atom is calculated by this compute. A vector of four quantities per atom is calculated by this compute.
The first 3 elements of the vector are the dx,dy,dz displacements. The first 3 elements of the vector are the dx,dy,dz displacements.
The 4th component is the total displacement, i.e. sqrt(dx\*dx + dy\*dy + The fourth component is the total displacement, i.e. sqrt(dx\*dx + dy\*dy +
dz\*dz). dz\*dz).
The displacement of an atom is from its original position at the time The displacement of an atom is from its original position at the time

2
doc/src/compute_fep.rst
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@ -224,7 +224,7 @@ the pair\_\*.cpp file associated with the potential.
Similar to the :doc:`pair_coeff <pair_coeff>` command, I and J can be Similar to the :doc:`pair_coeff <pair_coeff>` command, I and J can be
specified in one of two ways. Explicit numeric values can be used for specified in one of two ways. Explicit numeric values can be used for
each, as in the 1st example above. I <= J is required. LAMMPS sets each, as in the first example above. I <= J is required. LAMMPS sets
the coefficients for the symmetric J,I interaction to the same the coefficients for the symmetric J,I interaction to the same
values. A wild-card asterisk can be used in place of or in conjunction values. A wild-card asterisk can be used in place of or in conjunction
with the I,J arguments to set the coefficients for multiple pairs of with the I,J arguments to set the coefficients for multiple pairs of

2
doc/src/compute_group_group.rst
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@ -64,7 +64,7 @@ If the *kspace* keyword is set to *yes*\ , which is not the default, and
if a :doc:`kspace_style <kspace_style>` is defined, then the interaction if a :doc:`kspace_style <kspace_style>` is defined, then the interaction
energy will include a Kspace component which is the long-range energy will include a Kspace component which is the long-range
Coulombic energy between all the atoms in the first group and all the Coulombic energy between all the atoms in the first group and all the
atoms in the 2nd group. Likewise, the interaction force calculated by atoms in the second group. Likewise, the interaction force calculated by
this compute will include the force on the compute group atoms due to this compute will include the force on the compute group atoms due to
long-range Coulombic interactions with atoms in the specified group2. long-range Coulombic interactions with atoms in the specified group2.

2
doc/src/compute_msd.rst
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@ -38,7 +38,7 @@ parameter of mean-squared displacement, see the :doc:`compute msd/nongauss <comp
A vector of four quantities is calculated by this compute. The first 3 A vector of four quantities is calculated by this compute. The first 3
elements of the vector are the squared dx,dy,dz displacements, summed elements of the vector are the squared dx,dy,dz displacements, summed
and averaged over atoms in the group. The 4th element is the total and averaged over atoms in the group. The fourth element is the total
squared displacement, i.e. (dx\*dx + dy\*dy + dz\*dz), summed and squared displacement, i.e. (dx\*dx + dy\*dy + dz\*dz), summed and
averaged over atoms in the group. averaged over atoms in the group.

2
doc/src/compute_msd_chunk.rst
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@ -36,7 +36,7 @@ they can be used to measure properties of a system.
Four quantities are calculated by this compute for each chunk. The Four quantities are calculated by this compute for each chunk. The
first 3 quantities are the squared dx,dy,dz displacements of the first 3 quantities are the squared dx,dy,dz displacements of the
center-of-mass. The 4th component is the total squared displacement, center-of-mass. The fourth component is the total squared displacement,
i.e. (dx\*dx + dy\*dy + dz\*dz) of the center-of-mass. These i.e. (dx\*dx + dy\*dy + dz\*dz) of the center-of-mass. These
calculations include all effects due to atoms passing through periodic calculations include all effects due to atoms passing through periodic
boundaries. boundaries.

4
doc/src/compute_msd_nongauss.rst
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@ -39,7 +39,7 @@ element of the vector is the total squared dx,dy,dz displacements
drsquared = (dx\*dx + dy\*dy + dz\*dz) of atoms, and the second is the drsquared = (dx\*dx + dy\*dy + dz\*dz) of atoms, and the second is the
fourth power of these displacements drfourth = (dx\*dx + dy\*dy + fourth power of these displacements drfourth = (dx\*dx + dy\*dy +
dz\*dz)\*(dx\*dx + dy\*dy + dz\*dz), summed and averaged over atoms in the dz\*dz)\*(dx\*dx + dy\*dy + dz\*dz), summed and averaged over atoms in the
group. The 3rd component is the nonGaussian diffusion parameter NGP = group. The third component is the nonGaussian diffusion parameter NGP =
3\*drfourth/(5\*drsquared\*drsquared), i.e. 3\*drfourth/(5\*drsquared\*drsquared), i.e.
.. math:: .. math::
@ -68,7 +68,7 @@ page for an overview of LAMMPS output options.
The vector values are "intensive". The first vector value will be in The vector values are "intensive". The first vector value will be in
distance\^2 :doc:`units <units>`, the second is in distance\^4 units, and distance\^2 :doc:`units <units>`, the second is in distance\^4 units, and
the 3rd is dimensionless. the third is dimensionless.
Restrictions Restrictions
"""""""""""" """"""""""""

2
doc/src/compute_property_chunk.rst
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@ -63,7 +63,7 @@ chunkID. This means that the original chunk IDs (e.g. molecule IDs)
will have been compressed to remove chunk IDs with no atoms assigned will have been compressed to remove chunk IDs with no atoms assigned
to them. Thus a compressed chunk ID of 3 may correspond to an original to them. Thus a compressed chunk ID of 3 may correspond to an original
chunk ID (molecule ID in this case) of 415. The *id* attribute will chunk ID (molecule ID in this case) of 415. The *id* attribute will
then be 415 for the 3rd chunk. then be 415 for the third chunk.
The *coordN* attributes can only be used if a *binning* style was used The *coordN* attributes can only be used if a *binning* style was used
in the :doc:`compute chunk/atom <compute_chunk_atom>` command referenced in the :doc:`compute chunk/atom <compute_chunk_atom>` command referenced

6
doc/src/compute_rdf.rst
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@ -97,7 +97,7 @@ listed, then a separate histogram is generated for each
*itype*\ ,\ *jtype* pair. *itype*\ ,\ *jtype* pair.
The *itypeN* and *jtypeN* settings can be specified in one of two The *itypeN* and *jtypeN* settings can be specified in one of two
ways. An explicit numeric value can be used, as in the 4th example ways. An explicit numeric value can be used, as in the fourth example
above. Or a wild-card asterisk can be used to specify a range of atom above. Or a wild-card asterisk can be used to specify a range of atom
types. This takes the form "\*" or "\*n" or "n\*" or "m\*n". If N = the types. This takes the form "\*" or "\*n" or "n\*" or "m\*n". If N = the
number of atom types, then an asterisk with no numeric values means number of atom types, then an asterisk with no numeric values means
@ -106,11 +106,11 @@ all types from 1 to N. A leading asterisk means all types from 1 to n
(inclusive). A middle asterisk means all types from m to n (inclusive). A middle asterisk means all types from m to n
(inclusive). (inclusive).
If both *itypeN* and *jtypeN* are single values, as in the 4th example If both *itypeN* and *jtypeN* are single values, as in the fourth example
above, this means that a g(r) is computed where atoms of type *itypeN* above, this means that a g(r) is computed where atoms of type *itypeN*
are the central atom, and atoms of type *jtypeN* are the distribution are the central atom, and atoms of type *jtypeN* are the distribution
atom. If either *itypeN* and *jtypeN* represent a range of values via atom. If either *itypeN* and *jtypeN* represent a range of values via
the wild-card asterisk, as in the 5th example above, this means that a the wild-card asterisk, as in the fifth example above, this means that a
g(r) is computed where atoms of any of the range of types represented g(r) is computed where atoms of any of the range of types represented
by *itypeN* are the central atom, and atoms of any of the range of by *itypeN* are the central atom, and atoms of any of the range of
types represented by *jtypeN* are the distribution atom. types represented by *jtypeN* are the distribution atom.

2
doc/src/compute_temp_cs.rst
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@ -49,7 +49,7 @@ respective group IDs, which can be defined using the
must be the same and there should be one bond defined between a pair must be the same and there should be one bond defined between a pair
of atoms in the two groups. Non-polarized ions which might also be of atoms in the two groups. Non-polarized ions which might also be
included in the treated system should not be included into either of included in the treated system should not be included into either of
these groups, they are taken into account by the *group-ID* (2nd these groups, they are taken into account by the *group-ID* (second
argument) of the compute. argument) of the compute.
The temperature is calculated by the formula KE = dim/2 N k T, where The temperature is calculated by the formula KE = dim/2 N k T, where

2
doc/src/compute_ti.rst
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@ -76,7 +76,7 @@ with respect to *lambda*\ .
To perform this calculation, you provide one or more atom types as To perform this calculation, you provide one or more atom types as
*atype*\ . *Atype* can be specified in one of two ways. An explicit *atype*\ . *Atype* can be specified in one of two ways. An explicit
numeric values can be used, as in the 1st example above. Or a numeric values can be used, as in the first example above. Or a
wildcard asterisk can be used in place of or in conjunction with the wildcard asterisk can be used in place of or in conjunction with the
*atype* argument to select multiple atom types. This takes the form *atype* argument to select multiple atom types. This takes the form
"\*" or "\*n" or "n\*" or "m\*n". If N = the number of atom types, then "\*" or "\*n" or "n\*" or "m\*n". If N = the number of atom types, then

2
doc/src/compute_vacf.rst
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@ -33,7 +33,7 @@ A vector of four quantities is calculated by this compute. The first 3
elements of the vector are vx \* vx0 (and similarly for the y and z elements of the vector are vx \* vx0 (and similarly for the y and z
components), summed and averaged over atoms in the group. Vx is the components), summed and averaged over atoms in the group. Vx is the
current x-component of velocity for the atom, vx0 is the initial current x-component of velocity for the atom, vx0 is the initial
x-component of velocity for the atom. The 4th element of the vector x-component of velocity for the atom. The fourth element of the vector
is the total VACF, i.e. (vx\*vx0 + vy\*vy0 + vz\*vz0), summed and is the total VACF, i.e. (vx\*vx0 + vy\*vy0 + vz\*vz0), summed and
averaged over atoms in the group. averaged over atoms in the group.

6
doc/src/dihedral_charmm.rst
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@ -73,7 +73,7 @@ or :doc:`read_restart <read_restart>` commands:
The weighting factor is required to correct for double counting The weighting factor is required to correct for double counting
pairwise non-bonded Lennard-Jones interactions in cyclic systems or pairwise non-bonded Lennard-Jones interactions in cyclic systems or
when using the CHARMM dihedral style with non-CHARMM force fields. when using the CHARMM dihedral style with non-CHARMM force fields.
With the CHARMM dihedral style, interactions between the 1st and 4th With the CHARMM dihedral style, interactions between the first and fourth
atoms in a dihedral are skipped during the normal non-bonded force atoms in a dihedral are skipped during the normal non-bonded force
computation and instead evaluated as part of the dihedral using computation and instead evaluated as part of the dihedral using
special epsilon and sigma values specified with the special epsilon and sigma values specified with the
@ -93,7 +93,7 @@ which applies to all 1-4 interactions in the system. For CHARMM force
fields, the special_bonds 1-4 interaction scaling factor should be set fields, the special_bonds 1-4 interaction scaling factor should be set
to 0.0. Since the corresponding 1-4 non-bonded interactions are to 0.0. Since the corresponding 1-4 non-bonded interactions are
computed with the dihedral. This means that if any of the weighting computed with the dihedral. This means that if any of the weighting
factors defined as dihedral coefficients (4th coeff above) are factors defined as dihedral coefficients (fourth coeff above) are
non-zero, then you must use a pair style with "lj/charmm" and set the non-zero, then you must use a pair style with "lj/charmm" and set the
special_bonds 1-4 scaling factor to 0.0 (which is the special_bonds 1-4 scaling factor to 0.0 (which is the
default). Otherwise 1-4 non-bonded interactions in dihedrals will be default). Otherwise 1-4 non-bonded interactions in dihedrals will be
@ -115,7 +115,7 @@ details.
Note that for AMBER force fields, which use pair styles with "lj/cut", Note that for AMBER force fields, which use pair styles with "lj/cut",
the special_bonds 1-4 scaling factor should be set to the AMBER the special_bonds 1-4 scaling factor should be set to the AMBER
defaults (1/2 and 5/6) and all the dihedral weighting factors (4th defaults (1/2 and 5/6) and all the dihedral weighting factors (fourth
coeff above) must be set to 0.0. In this case, you can use any pair coeff above) must be set to 0.0. In this case, you can use any pair
style you wish, since the dihedral does not need any Lennard-Jones style you wish, since the dihedral does not need any Lennard-Jones
parameter information and will not compute any 1-4 non-bonded parameter information and will not compute any 1-4 non-bonded

4
doc/src/dihedral_coeff.rst
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@ -31,7 +31,7 @@ Dihedral coefficients can also be set in the data file read by the
:doc:`read_data <read_data>` command or in a restart file. :doc:`read_data <read_data>` command or in a restart file.
N can be specified in one of two ways. An explicit numeric value can N can be specified in one of two ways. An explicit numeric value can
be used, as in the 1st example above. Or a wild-card asterisk can be be used, as in the first example above. Or a wild-card asterisk can be
used to set the coefficients for multiple dihedral types. This takes the used to set the coefficients for multiple dihedral types. This takes the
form "\*" or "\*n" or "n\*" or "m\*n". If N = the number of dihedral types, form "\*" or "\*n" or "n\*" or "m\*n". If N = the number of dihedral types,
then an asterisk with no numeric values means all types from 1 to N. A then an asterisk with no numeric values means all types from 1 to N. A
@ -53,7 +53,7 @@ same format as the arguments of the dihedral_coeff command in an input
script, except that wild-card asterisks should not be used since script, except that wild-card asterisks should not be used since
coefficients for all N types must be listed in the file. For example, coefficients for all N types must be listed in the file. For example,
under the "Dihedral Coeffs" section of a data file, the line that under the "Dihedral Coeffs" section of a data file, the line that
corresponds to the 1st example above would be listed as corresponds to the first example above would be listed as
.. parsed-literal:: .. parsed-literal::

16
doc/src/dihedral_table.rst
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@ -92,7 +92,7 @@ or blank lines.
... ...
30 180.0 -0.707106781187 30 180.0 -0.707106781187
A section begins with a non-blank line whose 1st character is not a A section begins with a non-blank line whose first character is not a
"#"; blank lines or lines starting with "#" can be used as comments "#"; blank lines or lines starting with "#" can be used as comments
between sections. The first line begins with a keyword which between sections. The first line begins with a keyword which
identifies the section. The line can contain additional text, but the identifies the section. The line can contain additional text, but the
@ -102,10 +102,10 @@ any order) one or more parameters for the table. Each parameter is a
keyword followed by one or more numeric values. keyword followed by one or more numeric values.
Following a blank line, the next N lines list the tabulated values. On Following a blank line, the next N lines list the tabulated values. On
each line, the 1st value is the index from 1 to N, the 2nd value is each line, the first value is the index from 1 to N, the second value is
the angle value, the 3rd value is the energy (in energy units), and the angle value, the third value is the energy (in energy units), and
the 4th is -dE/d(phi) also in energy units). The 3rd term is the the fourth is -dE/d(phi) also in energy units). The third term is the
energy of the 4-atom configuration for the specified angle. The 4th energy of the 4-atom configuration for the specified angle. The fourth
term (when present) is the negative derivative of the energy with term (when present) is the negative derivative of the energy with
respect to the angle (in degrees, or radians depending on whether the respect to the angle (in degrees, or radians depending on whether the
user selected DEGREES or RADIANS). Thus the units of the last term user selected DEGREES or RADIANS). Thus the units of the last term
@ -147,9 +147,9 @@ choice of angle units).
The optional "NOF" keyword allows the user to omit the forces The optional "NOF" keyword allows the user to omit the forces
(negative energy derivatives) from the table file (normally located in (negative energy derivatives) from the table file (normally located in
the 4th column). In their place, forces will be calculated the fourth column). In their place, forces will be calculated
automatically by differentiating the potential energy function automatically by differentiating the potential energy function
indicated by the 3rd column of the table (using either linear or indicated by the third column of the table (using either linear or
spline interpolation). spline interpolation).
The optional "DEGREES" keyword allows the user to specify angles in The optional "DEGREES" keyword allows the user to specify angles in
@ -157,7 +157,7 @@ degrees instead of radians (default).
The optional "RADIANS" keyword allows the user to specify angles in The optional "RADIANS" keyword allows the user to specify angles in
radians instead of degrees. (Note: This changes the way the forces radians instead of degrees. (Note: This changes the way the forces
are scaled in the 4th column of the data file.) are scaled in the fourth column of the data file.)
The optional "CHECKU" keyword is followed by a filename. This allows The optional "CHECKU" keyword is followed by a filename. This allows
the user to save all of the *Ntable* different entries in the the user to save all of the *Ntable* different entries in the

16
doc/src/dihedral_table_cut.rst
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@ -113,7 +113,7 @@ or blank lines.
... ...
30 180.0 -0.707106781187 30 180.0 -0.707106781187
A section begins with a non-blank line whose 1st character is not a A section begins with a non-blank line whose first character is not a
"#"; blank lines or lines starting with "#" can be used as comments "#"; blank lines or lines starting with "#" can be used as comments
between sections. The first line begins with a keyword which between sections. The first line begins with a keyword which
identifies the section. The line can contain additional text, but the identifies the section. The line can contain additional text, but the
@ -123,10 +123,10 @@ any order) one or more parameters for the table. Each parameter is a
keyword followed by one or more numeric values. keyword followed by one or more numeric values.
Following a blank line, the next N lines list the tabulated values. On Following a blank line, the next N lines list the tabulated values. On
each line, the 1st value is the index from 1 to N, the 2nd value is each line, the first value is the index from 1 to N, the second value is
the angle value, the 3rd value is the energy (in energy units), and the angle value, the third value is the energy (in energy units), and
the 4th is -dE/d(phi) also in energy units). The 3rd term is the the fourth is -dE/d(phi) also in energy units). The third term is the
energy of the 4-atom configuration for the specified angle. The 4th energy of the 4-atom configuration for the specified angle. The fourth
term (when present) is the negative derivative of the energy with term (when present) is the negative derivative of the energy with
respect to the angle (in degrees, or radians depending on whether the respect to the angle (in degrees, or radians depending on whether the
user selected DEGREES or RADIANS). Thus the units of the last term user selected DEGREES or RADIANS). Thus the units of the last term
@ -168,9 +168,9 @@ choice of angle units).
The optional "NOF" keyword allows the user to omit the forces The optional "NOF" keyword allows the user to omit the forces
(negative energy derivatives) from the table file (normally located in (negative energy derivatives) from the table file (normally located in
the 4th column). In their place, forces will be calculated the fourth column). In their place, forces will be calculated
automatically by differentiating the potential energy function automatically by differentiating the potential energy function
indicated by the 3rd column of the table (using either linear or indicated by the third column of the table (using either linear or
spline interpolation). spline interpolation).
The optional "DEGREES" keyword allows the user to specify angles in The optional "DEGREES" keyword allows the user to specify angles in
@ -178,7 +178,7 @@ degrees instead of radians (default).
The optional "RADIANS" keyword allows the user to specify angles in The optional "RADIANS" keyword allows the user to specify angles in
radians instead of degrees. (Note: This changes the way the forces radians instead of degrees. (Note: This changes the way the forces
are scaled in the 4th column of the data file.) are scaled in the fourth column of the data file.)
The optional "CHECKU" keyword is followed by a filename. This allows The optional "CHECKU" keyword is followed by a filename. This allows
the user to save all of the *Ntable* different entries in the the user to save all of the *Ntable* different entries in the

22
doc/src/dump_image.rst
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@ -134,17 +134,23 @@ Only atoms in the specified group are rendered in the image. The
alter what atoms are included in the image. alter what atoms are included in the image.
The filename suffix determines whether a JPEG, PNG, or PPM file is The filename suffix determines whether a JPEG, PNG, or PPM file is
created with the *image* dump style. If the suffix is ".jpg" or created with the *image* dump style. If the suffix is ".jpg" or
".jpeg", then a JPEG format file is created, if the suffix is ".png", ".jpeg", then a `JPEG format <jpeg_format_>`_ file is created, if the
then a PNG format is created, else a PPM (aka NETPBM) format file is suffix is ".png", then a `PNG format <png_format_>`_ is created, else
created. The JPEG and PNG files are binary; PPM has a text mode a `PPM (aka NETPBM) format <ppm_format_>`_ file is created.
header followed by binary data. JPEG images have lossy compression; The JPEG and PNG files are binary; PPM has a text mode header followed
PNG has lossless compression; and PPM files are uncompressed but can by binary data. JPEG images have lossy compression, PNG has lossless
be compressed with gzip, if LAMMPS has been compiled with compression, and PPM files are uncompressed but can be compressed with
-DLAMMPS_GZIP and a ".gz" suffix is used. gzip, if LAMMPS has been compiled with -DLAMMPS_GZIP and a ".gz" suffix
is used.
.. _jpeg_format: https://jpeg.org/jpeg/
.. _png_format: https://en.wikipedia.org/wiki/Portable_Network_Graphics
.. _ppm_format: https://en.wikipedia.org/wiki/Netpbm
Similarly, the format of the resulting movie is chosen with the Similarly, the format of the resulting movie is chosen with the
*movie* dump style. This is handled by the underlying FFmpeg converter *movie* dump style. This is handled by the underlying FFmpeg converter
and thus details have to be looked up in the FFmpeg documentation. and thus details have to be looked up in the `FFmpeg documentation
<http://ffmpeg.org/ffmpeg.html>`_.
Typical examples are: .avi, .mpg, .m4v, .mp4, .mkv, .flv, .mov, .gif Typical examples are: .avi, .mpg, .m4v, .mp4, .mkv, .flv, .mov, .gif
Additional settings of the movie compression like bitrate and Additional settings of the movie compression like bitrate and
framerate can be set using the :doc:`dump_modify <dump_modify>` command. framerate can be set using the :doc:`dump_modify <dump_modify>` command.

6
doc/src/dump_modify.rst
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@ -306,7 +306,7 @@ must enclose in quotes if it is more than one field. The *int* and
*float* keywords take a single format argument and are applied to all *float* keywords take a single format argument and are applied to all
integer or floating-point quantities output. The setting for *M integer or floating-point quantities output. The setting for *M
string* also takes a single format argument which is used for the Mth string* also takes a single format argument which is used for the Mth
value output in each line, e.g. the 5th column is output in high value output in each line, e.g. the fifth column is output in high
precision for "format 5 %20.15g". precision for "format 5 %20.15g".
.. note:: .. note::
@ -419,7 +419,7 @@ be written, by processors 0,25,50,75. Each will collect information
from itself and the next 24 processors and write it to a dump file. from itself and the next 24 processors and write it to a dump file.
For the *fileper* keyword, the specified value of Np means write one For the *fileper* keyword, the specified value of Np means write one
file for every Np processors. For example, if Np = 4, every 4th file for every Np processors. For example, if Np = 4, every fourth
processor (0,4,8,12,etc) will collect information from itself and the processor (0,4,8,12,etc) will collect information from itself and the
next 3 processors and write it to a dump file. next 3 processors and write it to a dump file.
@ -790,7 +790,7 @@ for the sequential style; otherwise the value is ignored. It
specifies the bin size to use within the range for assigning specifies the bin size to use within the range for assigning
consecutive colors to. For example, if the range is from -10.0 to consecutive colors to. For example, if the range is from -10.0 to
10.0 and a *delta* of 1.0 is used, then 20 colors will be assigned to 10.0 and a *delta* of 1.0 is used, then 20 colors will be assigned to
the range. The first will be from -10.0 <= color1 < -9.0, then 2nd the range. The first will be from -10.0 <= color1 < -9.0, then second
from -9.0 <= color2 < -8.0, etc. from -9.0 <= color2 < -8.0, etc.
The *N* setting is how many entries follow. The format of the entries The *N* setting is how many entries follow. The format of the entries

2
doc/src/dynamical_matrix.rst
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@ -70,7 +70,7 @@ See the :doc:`Build package <Build_package>` doc page for more info.
Related commands Related commands
"""""""""""""""" """"""""""""""""
:doc:`fix phonon <fix_phonon>`, :doc:`fix numdiff <fix_numdiff>`, :doc:`fix phonon <fix_phonon>`, :doc:`fix numdiff <fix_numdiff>`,
:doc:`compute hma <compute_hma>` uses an analytic formulation of the :doc:`compute hma <compute_hma>` uses an analytic formulation of the
Hessian provided by a pair_style's Pair::single_hessian() function, Hessian provided by a pair_style's Pair::single_hessian() function,

2
doc/src/fix_adapt.rst
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@ -229,7 +229,7 @@ specified, but are ignored.
Similar to the :doc:`pair_coeff command <pair_coeff>`, I and J can be Similar to the :doc:`pair_coeff command <pair_coeff>`, I and J can be
specified in one of two ways. Explicit numeric values can be used for specified in one of two ways. Explicit numeric values can be used for
each, as in the 1st example above. I <= J is required. LAMMPS sets each, as in the first example above. I <= J is required. LAMMPS sets
the coefficients for the symmetric J,I interaction to the same values. the coefficients for the symmetric J,I interaction to the same values.
A wild-card asterisk can be used in place of or in conjunction with A wild-card asterisk can be used in place of or in conjunction with

2
doc/src/fix_adapt_fep.rst
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@ -199,7 +199,7 @@ specified, but are ignored.
Similar to the :doc:`pair_coeff command <pair_coeff>`, I and J can be Similar to the :doc:`pair_coeff command <pair_coeff>`, I and J can be
specified in one of two ways. Explicit numeric values can be used for specified in one of two ways. Explicit numeric values can be used for
each, as in the 1st example above. I <= J is required. LAMMPS sets each, as in the first example above. I <= J is required. LAMMPS sets
the coefficients for the symmetric J,I interaction to the same values. the coefficients for the symmetric J,I interaction to the same values.
A wild-card asterisk can be used in place of or in conjunction with A wild-card asterisk can be used in place of or in conjunction with

2
doc/src/fix_ave_chunk.rst
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@ -435,7 +435,7 @@ column is only used if the *compress* keyword was set to *yes* for the
the original chunk IDs (e.g. molecule IDs) will have been compressed the original chunk IDs (e.g. molecule IDs) will have been compressed
to remove chunk IDs with no atoms assigned to them. Thus a compressed to remove chunk IDs with no atoms assigned to them. Thus a compressed
chunk ID of 3 may correspond to an original chunk ID or molecule ID of chunk ID of 3 may correspond to an original chunk ID or molecule ID of
415. The OrigID column will list 415 for the 3rd chunk. 415. The OrigID column will list 415 for the third chunk.
The CoordN columns only appear if a *binning* style was used in the The CoordN columns only appear if a *binning* style was used in the
:doc:`compute chunk/atom <compute_chunk_atom>` command. For *bin/1d*\ , :doc:`compute chunk/atom <compute_chunk_atom>` command. For *bin/1d*\ ,

2
doc/src/fix_ave_correlate.rst
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@ -321,7 +321,7 @@ accessed on timesteps that are multiples of *Nfreq* since that is when
averaging is performed. The global array has # of rows = *Nrepeat* averaging is performed. The global array has # of rows = *Nrepeat*
and # of columns = Npair+2. The first column has the time delta (in and # of columns = Npair+2. The first column has the time delta (in
timesteps) between the pairs of input values used to calculate the timesteps) between the pairs of input values used to calculate the
correlation, as described above. The 2nd column has the number of correlation, as described above. The second column has the number of
samples contributing to the correlation average, as described above. samples contributing to the correlation average, as described above.
The remaining Npair columns are for I,J pairs of the N input values, The remaining Npair columns are for I,J pairs of the N input values,
as determined by the *type* keyword, as described above. as determined by the *type* keyword, as described above.

6
doc/src/fix_ave_histo.rst
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@ -346,10 +346,10 @@ values:
* 4 = max value of all input values, including ones not histogrammed * 4 = max value of all input values, including ones not histogrammed
The global array has # of rows = Nbins and # of columns = 3. The The global array has # of rows = Nbins and # of columns = 3. The
first column has the bin coordinate, the 2nd column has the count of first column has the bin coordinate, the second column has the count of
values in that histogram bin, and the 3rd column has the bin count values in that histogram bin, and the third column has the bin count
divided by the total count (not including missing counts), so that the divided by the total count (not including missing counts), so that the
values in the 3rd column sum to 1.0. values in the third column sum to 1.0.
The vector and array values calculated by this fix are all treated as The vector and array values calculated by this fix are all treated as
intensive. If this is not the case, e.g. due to histogramming intensive. If this is not the case, e.g. due to histogramming

12
doc/src/fix_bond_create.rst
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@ -154,13 +154,13 @@ of type *angletype*\ , with parameters assigned by the corresponding
.. note:: .. note::
LAMMPS stores and maintains a data structure with a list of the LAMMPS stores and maintains a data structure with a list of the
1st, 2nd, and 3rd neighbors of each atom (within the bond topology of first, second, and third neighbors of each atom (within the bond topology of
the system) for use in weighting pairwise interactions for bonded the system) for use in weighting pairwise interactions for bonded
atoms. Note that adding a single bond always adds a new 1st neighbor atoms. Note that adding a single bond always adds a new first neighbor
but may also induce \*many\* new 2nd and 3rd neighbors, depending on the but may also induce \*many\* new second and third neighbors, depending on the
molecular topology of your system. The "extra special per atom" molecular topology of your system. The "extra special per atom"
parameter must typically be set to allow for the new maximum total parameter must typically be set to allow for the new maximum total
size (1st + 2nd + 3rd neighbors) of this per-atom list. There are 2 size (first + second + third neighbors) of this per-atom list. There are 2
ways to do this. See the :doc:`read_data <read_data>` or ways to do this. See the :doc:`read_data <read_data>` or
:doc:`create_box <create_box>` commands for details. :doc:`create_box <create_box>` commands for details.
@ -172,12 +172,12 @@ of type *angletype*\ , with parameters assigned by the corresponding
considered for pairwise interactions, using the weighting rules set by considered for pairwise interactions, using the weighting rules set by
the :doc:`special_bonds <special_bonds>` command. Consider a new bond the :doc:`special_bonds <special_bonds>` command. Consider a new bond
created between atoms I,J. If J has a bonded neighbor K, then K created between atoms I,J. If J has a bonded neighbor K, then K
becomes a 2nd neighbor of I. Even if the *atype* keyword is not used becomes a second neighbor of I. Even if the *atype* keyword is not used
to create angle I-J-K, the pairwise interaction between I and K will to create angle I-J-K, the pairwise interaction between I and K will
be potentially turned off or weighted by the 1-3 weighting specified be potentially turned off or weighted by the 1-3 weighting specified
by the :doc:`special_bonds <special_bonds>` command. This is the case by the :doc:`special_bonds <special_bonds>` command. This is the case
even if the "angle yes" option was used with that command. The same even if the "angle yes" option was used with that command. The same
is true for 3rd neighbors (1-4 interactions), the *dtype* keyword, and is true for third neighbors (1-4 interactions), the *dtype* keyword, and
the "dihedral yes" option used with the the "dihedral yes" option used with the
:doc:`special_bonds <special_bonds>` command. :doc:`special_bonds <special_bonds>` command.

2
doc/src/fix_box_relax.rst
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@ -371,7 +371,7 @@ the meaning of the xy,xz,yz tilt factors.
The *scaleyz yes* and *scalexz yes* keyword/value pairs can not be used The *scaleyz yes* and *scalexz yes* keyword/value pairs can not be used
for 2D simulations. *scaleyz yes*\ , *scalexz yes*\ , and *scalexy yes* options for 2D simulations. *scaleyz yes*\ , *scalexz yes*\ , and *scalexy yes* options
can only be used if the 2nd dimension in the keyword is periodic, can only be used if the second dimension in the keyword is periodic,
and if the tilt factor is not coupled to the barostat via keywords and if the tilt factor is not coupled to the barostat via keywords
*tri*\ , *yz*\ , *xz*\ , and *xy*\ . *tri*\ , *yz*\ , *xz*\ , and *xy*\ .

2
doc/src/fix_cmap.rst
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@ -66,7 +66,7 @@ in the body of the data file like this with N lines:
N 3 314 315 317 318 330 N 3 314 315 317 318 330
The first column is an index from 1 to N to enumerate the CMAP terms; The first column is an index from 1 to N to enumerate the CMAP terms;
it is ignored by LAMMPS. The 2nd column is the "type" of the it is ignored by LAMMPS. The second column is the "type" of the
interaction; it is an index into the CMAP force field file. The interaction; it is an index into the CMAP force field file. The
remaining 5 columns are the atom IDs of the atoms in the two 4-atom remaining 5 columns are the atom IDs of the atoms in the two 4-atom
dihedrals that overlap to create the CMAP 5-body interaction. Note dihedrals that overlap to create the CMAP 5-body interaction. Note

6
doc/src/fix_deform.rst
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@ -104,7 +104,7 @@ can be modeled using the :ref:`USER-UEF package <PKG-USER-UEF>` and its :doc:`fi
For the *x*\ , *y*\ , *z* parameters, the associated dimension cannot be For the *x*\ , *y*\ , *z* parameters, the associated dimension cannot be
shrink-wrapped. For the *xy*\ , *yz*\ , *xz* parameters, the associated shrink-wrapped. For the *xy*\ , *yz*\ , *xz* parameters, the associated
2nd dimension cannot be shrink-wrapped. Dimensions not varied by this second dimension cannot be shrink-wrapped. Dimensions not varied by this
command can be periodic or non-periodic. Dimensions corresponding to command can be periodic or non-periodic. Dimensions corresponding to
unspecified parameters can also be controlled by a :doc:`fix npt <fix_nh>` or :doc:`fix nph <fix_nh>` command. unspecified parameters can also be controlled by a :doc:`fix npt <fix_nh>` or :doc:`fix nph <fix_nh>` command.
@ -463,7 +463,7 @@ and the final tilt factor at the end of the simulation would be 0.0.
During each flip event, atoms are remapped into the new box in the During each flip event, atoms are remapped into the new box in the
appropriate manner. appropriate manner.
The one exception to this rule is if the 1st dimension in the tilt The one exception to this rule is if the first dimension in the tilt
factor (x for xy) is non-periodic. In that case, the limits on the factor (x for xy) is non-periodic. In that case, the limits on the
tilt factor are not enforced, since flipping the box in that dimension tilt factor are not enforced, since flipping the box in that dimension
does not change the atom positions due to non-periodicity. In this does not change the atom positions due to non-periodicity. In this
@ -601,7 +601,7 @@ Restrictions
You cannot apply x, y, or z deformations to a dimension that is You cannot apply x, y, or z deformations to a dimension that is
shrink-wrapped via the :doc:`boundary <boundary>` command. shrink-wrapped via the :doc:`boundary <boundary>` command.
You cannot apply xy, yz, or xz deformations to a 2nd dimension (y in You cannot apply xy, yz, or xz deformations to a second dimension (y in
xy) that is shrink-wrapped via the :doc:`boundary <boundary>` command. xy) that is shrink-wrapped via the :doc:`boundary <boundary>` command.
Related commands Related commands

6
doc/src/fix_eos_table.rst
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@ -66,7 +66,7 @@ parenthesized comments):
... ...
500 10.0 0.500 500 10.0 0.500
A section begins with a non-blank line whose 1st character is not a A section begins with a non-blank line whose first character is not a
"#"; blank lines or lines starting with "#" can be used as comments "#"; blank lines or lines starting with "#" can be used as comments
between sections. The first line begins with a keyword which between sections. The first line begins with a keyword which
identifies the section. The line can contain additional text, but the identifies the section. The line can contain additional text, but the
@ -86,8 +86,8 @@ to match exactly what is in the tabulated file (with effectively no
preliminary interpolation), you should set Ntable = Nfile. preliminary interpolation), you should set Ntable = Nfile.
Following a blank line, the next N lines list the tabulated values. Following a blank line, the next N lines list the tabulated values.
On each line, the 1st value is the index from 1 to N, the 2nd value is On each line, the first value is the index from 1 to N, the second value is
the internal temperature (in temperature units), the 3rd value is the the internal temperature (in temperature units), the third value is the
internal energy (in energy units). internal energy (in energy units).
Note that the internal temperature and internal energy values must Note that the internal temperature and internal energy values must

6
doc/src/fix_eos_table_rx.rst
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@ -106,7 +106,7 @@ parenthesized comments):
... ...
500 10.0 0.500 ... 1.0000 500 10.0 0.500 ... 1.0000
A section begins with a non-blank line whose 1st character is not a A section begins with a non-blank line whose first character is not a
"#"; blank lines or lines starting with "#" can be used as comments "#"; blank lines or lines starting with "#" can be used as comments
between sections. The first line begins with a keyword which between sections. The first line begins with a keyword which
identifies the section. The line can contain additional text, but the identifies the section. The line can contain additional text, but the
@ -121,8 +121,8 @@ What LAMMPS does is a preliminary interpolation by creating splines
using the Nfile tabulated values as nodal points. using the Nfile tabulated values as nodal points.
Following a blank line, the next N lines list the tabulated values. Following a blank line, the next N lines list the tabulated values.
On each line, the 1st value is the index from 1 to N, the 2nd value is On each line, the first value is the index from 1 to N, the second value is
the internal temperature (in temperature units), the 3rd value until the internal temperature (in temperature units), the third value until
the *m+3* value are the internal energies of the m species (in energy units). the *m+3* value are the internal energies of the m species (in energy units).
Note that all internal temperature and internal energy values must Note that all internal temperature and internal energy values must

30
doc/src/fix_external.rst
View File

@ -109,20 +109,42 @@ etc.
To use this fix during energy minimization, the energy corresponding To use this fix during energy minimization, the energy corresponding
to the added forces must also be set so as to be consistent with the to the added forces must also be set so as to be consistent with the
added forces. Otherwise the minimization will not converge correctly. added forces. Otherwise the minimization will not converge correctly.
Correspondingly, the global virial needs to be updated to be use this
fix with variable cell calculations (e.g. :doc:`fix box/relax <fix_box_relax>`
or :doc:`fix npt <fix_nh>`).
This can be done from the external driver by calling this public This can be done from the external driver by calling these public
method of the FixExternal class: methods of the FixExternal class:
.. code-block:: c++ .. code-block:: c++
void set_energy(double eng); void set_energy_global(double eng);
void set_virial_global(double *virial);
where eng is the potential energy. Eng is an extensive quantity, where *eng* is the potential energy, and *virial* an array of the 6
stress tensor components. Eng is an extensive quantity,
meaning it should be the sum over per-atom energies of all affected meaning it should be the sum over per-atom energies of all affected
atoms. It should also be provided in :doc:`energy units <units>` atoms. It should also be provided in :doc:`energy units <units>`
consistent with the simulation. See the details below for how to consistent with the simulation. See the details below for how to
insure this energy setting is used appropriately in a minimization. insure this energy setting is used appropriately in a minimization.
Additional public methods that the caller can use to update system
properties are:
.. code-block:: c++
void set_energy_peratom(double *eng);
void set_virial_peratom(double **virial);
void set_vector_length(int n);
void set_vector(int idx, double val);
These allow to set per-atom energy contributions, per-atom stress
contributions, the length and individual values of a global vector
of properties that the caller code may want to communicate to LAMMPS
(e.g. for use in :doc:`fix ave/time <fix_ave_time>` or in
:doc:`equal-style variables <variable>` or for
:doc:`custom thermo output <thermo_style>`.
---------- ----------
**Restart, fix_modify, output, run start/stop, minimize info:** **Restart, fix_modify, output, run start/stop, minimize info:**

8
doc/src/fix_nh.rst
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@ -432,7 +432,7 @@ equilibrium liquids can not support a shear stress and that
equilibrium solids can not support shear stresses that exceed the equilibrium solids can not support shear stresses that exceed the
yield stress. yield stress.
One exception to this rule is if the 1st dimension in the tilt factor One exception to this rule is if the first dimension in the tilt factor
(x for xy) is non-periodic. In that case, the limits on the tilt (x for xy) is non-periodic. In that case, the limits on the tilt
factor are not enforced, since flipping the box in that dimension does factor are not enforced, since flipping the box in that dimension does
not change the atom positions due to non-periodicity. In this mode, not change the atom positions due to non-periodicity. In this mode,
@ -673,7 +673,7 @@ Restrictions
*X*\ , *y*\ , *z* cannot be barostatted if the associated dimension is not *X*\ , *y*\ , *z* cannot be barostatted if the associated dimension is not
periodic. *Xy*\ , *xz*\ , and *yz* can only be barostatted if the periodic. *Xy*\ , *xz*\ , and *yz* can only be barostatted if the
simulation domain is triclinic and the 2nd dimension in the keyword simulation domain is triclinic and the second dimension in the keyword
(\ *y* dimension in *xy*\ ) is periodic. *Z*\ , *xz*\ , and *yz*\ , cannot be (\ *y* dimension in *xy*\ ) is periodic. *Z*\ , *xz*\ , and *yz*\ , cannot be
barostatted for 2D simulations. The :doc:`create_box <create_box>`, barostatted for 2D simulations. The :doc:`create_box <create_box>`,
:doc:`read data <read_data>`, and :doc:`read_restart <read_restart>` :doc:`read data <read_data>`, and :doc:`read_restart <read_restart>`
@ -687,7 +687,7 @@ is not allowed in the Nose/Hoover formulation.
The *scaleyz yes* and *scalexz yes* keyword/value pairs can not be used The *scaleyz yes* and *scalexz yes* keyword/value pairs can not be used
for 2D simulations. *scaleyz yes*\ , *scalexz yes*\ , and *scalexy yes* options for 2D simulations. *scaleyz yes*\ , *scalexz yes*\ , and *scalexy yes* options
can only be used if the 2nd dimension in the keyword is periodic, can only be used if the second dimension in the keyword is periodic,
and if the tilt factor is not coupled to the barostat via keywords and if the tilt factor is not coupled to the barostat via keywords
*tri*\ , *yz*\ , *xz*\ , and *xy*\ . *tri*\ , *yz*\ , *xz*\ , and *xy*\ .
@ -710,7 +710,7 @@ Default
The keyword defaults are tchain = 3, pchain = 3, mtk = yes, tloop = 1, The keyword defaults are tchain = 3, pchain = 3, mtk = yes, tloop = 1,
ploop = 1, nreset = 0, drag = 0.0, dilate = all, couple = none, ploop = 1, nreset = 0, drag = 0.0, dilate = all, couple = none,
flip = yes, scaleyz = scalexz = scalexy = yes if periodic in 2nd flip = yes, scaleyz = scalexz = scalexy = yes if periodic in second
dimension and not coupled to barostat, otherwise no. dimension and not coupled to barostat, otherwise no.
---------- ----------

8
doc/src/fix_npt_cauchy.rst
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@ -354,7 +354,7 @@ equilibrium liquids can not support a shear stress and that
equilibrium solids can not support shear stresses that exceed the equilibrium solids can not support shear stresses that exceed the
yield stress. yield stress.
One exception to this rule is if the 1st dimension in the tilt factor One exception to this rule is if the first dimension in the tilt factor
(x for xy) is non-periodic. In that case, the limits on the tilt (x for xy) is non-periodic. In that case, the limits on the tilt
factor are not enforced, since flipping the box in that dimension does factor are not enforced, since flipping the box in that dimension does
not change the atom positions due to non-periodicity. In this mode, not change the atom positions due to non-periodicity. In this mode,
@ -555,7 +555,7 @@ LAMMPS was built with that package. See the :doc:`Build package <Build_package>
*X*\ , *y*\ , *z* cannot be barostatted if the associated dimension is not *X*\ , *y*\ , *z* cannot be barostatted if the associated dimension is not
periodic. *Xy*\ , *xz*\ , and *yz* can only be barostatted if the periodic. *Xy*\ , *xz*\ , and *yz* can only be barostatted if the
simulation domain is triclinic and the 2nd dimension in the keyword simulation domain is triclinic and the second dimension in the keyword
(\ *y* dimension in *xy*\ ) is periodic. *Z*\ , *xz*\ , and *yz*\ , cannot be (\ *y* dimension in *xy*\ ) is periodic. *Z*\ , *xz*\ , and *yz*\ , cannot be
barostatted for 2D simulations. The :doc:`create_box <create_box>`, barostatted for 2D simulations. The :doc:`create_box <create_box>`,
:doc:`read data <read_data>`, and :doc:`read_restart <read_restart>` :doc:`read data <read_data>`, and :doc:`read_restart <read_restart>`
@ -569,7 +569,7 @@ is not allowed in the Nose/Hoover formulation.
The *scaleyz yes* and *scalexz yes* keyword/value pairs can not be used The *scaleyz yes* and *scalexz yes* keyword/value pairs can not be used
for 2D simulations. *scaleyz yes*\ , *scalexz yes*\ , and *scalexy yes* options for 2D simulations. *scaleyz yes*\ , *scalexz yes*\ , and *scalexy yes* options
can only be used if the 2nd dimension in the keyword is periodic, can only be used if the second dimension in the keyword is periodic,
and if the tilt factor is not coupled to the barostat via keywords and if the tilt factor is not coupled to the barostat via keywords
*tri*\ , *yz*\ , *xz*\ , and *xy*\ . *tri*\ , *yz*\ , *xz*\ , and *xy*\ .
@ -626,7 +626,7 @@ Default
The keyword defaults are tchain = 3, pchain = 3, mtk = yes, tloop = The keyword defaults are tchain = 3, pchain = 3, mtk = yes, tloop =
ploop = 1, nreset = 0, drag = 0.0, dilate = all, couple = none, ploop = 1, nreset = 0, drag = 0.0, dilate = all, couple = none,
cauchystat = no, cauchystat = no,
scaleyz = scalexz = scalexy = yes if periodic in 2nd dimension and scaleyz = scalexz = scalexy = yes if periodic in second dimension and
not coupled to barostat, otherwise no. not coupled to barostat, otherwise no.
---------- ----------

6
doc/src/fix_poems.rst
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@ -39,7 +39,7 @@ useful for treating a large biomolecule as a collection of connected,
coarse-grained particles. coarse-grained particles.
The coupling, associated motion constraints, and time integration is The coupling, associated motion constraints, and time integration is
performed by the software package `Parallelizable Open source Efficient Multibody Software (POEMS) <poems_>`_ which computes the performed by the software package `Parallelizable Open source Efficient Multibody Software (POEMS)` which computes the
constrained rigid-body motion of articulated (jointed) multibody constrained rigid-body motion of articulated (jointed) multibody
systems :ref:`(Anderson) <Anderson>`. POEMS was written and is distributed systems :ref:`(Anderson) <Anderson>`. POEMS was written and is distributed
by Prof Kurt Anderson, his graduate student Rudranarayan Mukherjee, by Prof Kurt Anderson, his graduate student Rudranarayan Mukherjee,
@ -48,8 +48,6 @@ and other members of his group at Rensselaer Polytechnic Institute
copyright information on POEMS and other details, please refer to the copyright information on POEMS and other details, please refer to the
documents in the poems directory distributed with LAMMPS. documents in the poems directory distributed with LAMMPS.
.. _poems: http://www.rpi.edu/~anderk5/lab
This fix updates the positions and velocities of the rigid atoms with This fix updates the positions and velocities of the rigid atoms with
a constant-energy time integration, so you should not update the same a constant-energy time integration, so you should not update the same
atoms via other fixes (e.g. nve, nvt, npt, temp/rescale, langevin). atoms via other fixes (e.g. nve, nvt, npt, temp/rescale, langevin).
@ -123,7 +121,7 @@ command. This fix is not invoked during :doc:`energy minimization <minimize>`.
Restrictions Restrictions
"""""""""""" """"""""""""
This fix is part of the POEMS package. It is only enabled if LAMMPS This fix is part of the :ref:`POEMS <PKG-POEMS>` package. It is only enabled if LAMMPS
was built with that package, which also requires the POEMS library be was built with that package, which also requires the POEMS library be
built and linked with LAMMPS. See the :doc:`Build package <Build_package>` doc page for more info. built and linked with LAMMPS. See the :doc:`Build package <Build_package>` doc page for more info.

2
doc/src/fix_precession_spin.rst
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@ -158,7 +158,7 @@ atom_style "spin" was declared. See the :doc:`Build package <Build_package>` do
The *precession/spin* style can only be declared once. If more The *precession/spin* style can only be declared once. If more
than one precession type (for example combining an anisotropy and a Zeeman interactions) than one precession type (for example combining an anisotropy and a Zeeman interactions)
has to be declared, they have to be chained in the same command has to be declared, they have to be chained in the same command
line (as shown in the examples above). line (as shown in the examples above).
Related commands Related commands
"""""""""""""""" """"""""""""""""

2
doc/src/fix_recenter.rst
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@ -116,7 +116,7 @@ Restrictions
"""""""""""" """"""""""""
This fix should not be used with an x,y,z setting that causes a large This fix should not be used with an x,y,z setting that causes a large
shift in the system on the 1st timestep, due to the requested COM shift in the system on the first timestep, due to the requested COM
being very different from the initial COM. This could cause atoms to being very different from the initial COM. This could cause atoms to
be lost, especially in parallel. Instead, use the be lost, especially in parallel. Instead, use the
:doc:`displace_atoms <displace_atoms>` command, which can be used to :doc:`displace_atoms <displace_atoms>` command, which can be used to

2
doc/src/fix_restrain.rst
View File

@ -162,7 +162,7 @@ the restraint is
.. math:: .. math::
E = 0 \qquad\quad\quad ,if\;r \ge r_0 E = 0 \qquad\quad\quad ,if\;r \ge r_0
with the following coefficients: with the following coefficients:
* :math:`K` (energy/distance\^2) * :math:`K` (energy/distance\^2)

4
doc/src/fix_rigid.rst
View File

@ -248,7 +248,7 @@ differences may accumulate to produce divergent trajectories.
will be built only at the very first *run* command and maintained for will be built only at the very first *run* command and maintained for
as long as the rigid fix is defined. For example, you might think you as long as the rigid fix is defined. For example, you might think you
could displace the atoms in a body or add a large velocity to each atom could displace the atoms in a body or add a large velocity to each atom
in a body to make it move in a desired direction before a 2nd run is in a body to make it move in a desired direction before a second run is
performed, using the :doc:`set <set>` or performed, using the :doc:`set <set>` or
:doc:`displace_atoms <displace_atoms>` or :doc:`velocity <velocity>` :doc:`displace_atoms <displace_atoms>` or :doc:`velocity <velocity>`
commands. But these commands will not affect the internal attributes commands. But these commands will not affect the internal attributes
@ -727,7 +727,7 @@ In all case, the rigid bodies and non-rigid particles both contribute
to the global pressure and the box is scaled the same by any of the to the global pressure and the box is scaled the same by any of the
barostatting fixes. barostatting fixes.
You could even use the 2nd and 3rd options for a non-hybrid simulation You could even use the second and third options for a non-hybrid simulation
consisting of only rigid bodies, assuming you give :doc:`fix npt <fix_nh>` an empty group, though it's an odd thing to do. The consisting of only rigid bodies, assuming you give :doc:`fix npt <fix_nh>` an empty group, though it's an odd thing to do. The
barostatting fixes (:doc:`fix npt <fix_nh>` and :doc:`fix press/berensen <fix_press_berendsen>`) will monitor the pressure barostatting fixes (:doc:`fix npt <fix_nh>` and :doc:`fix press/berensen <fix_press_berendsen>`) will monitor the pressure
and change the box dimensions, but not time integrate any particles. and change the box dimensions, but not time integrate any particles.

2
doc/src/fix_rigid_meso.rst
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@ -108,7 +108,7 @@ internal energy and extrapolated velocity are also updated.
will be built only at the very first *run* command and maintained for will be built only at the very first *run* command and maintained for
as long as the rigid fix is defined. For example, you might think you as long as the rigid fix is defined. For example, you might think you
could displace the particles in a body or add a large velocity to each particle could displace the particles in a body or add a large velocity to each particle
in a body to make it move in a desired direction before a 2nd run is in a body to make it move in a desired direction before a second run is
performed, using the :doc:`set <set>` or performed, using the :doc:`set <set>` or
:doc:`displace_atoms <displace_atoms>` or :doc:`velocity <velocity>` :doc:`displace_atoms <displace_atoms>` or :doc:`velocity <velocity>`
commands. But these commands will not affect the internal attributes commands. But these commands will not affect the internal attributes

10
doc/src/fix_rx.rst
View File

@ -18,7 +18,7 @@ Syntax
* file = filename containing the reaction kinetic equations and Arrhenius parameters * file = filename containing the reaction kinetic equations and Arrhenius parameters
* localTemp = *none,lucy* = no local temperature averaging or local temperature defined through Lucy weighting function * localTemp = *none,lucy* = no local temperature averaging or local temperature defined through Lucy weighting function
* matrix = *sparse, dense* format for the stoichiometric matrix * matrix = *sparse, dense* format for the stoichiometric matrix
* solver = *lammps_rk4,rkf45* = rk4 is an explicit 4th order Runge-Kutta method; rkf45 is an adaptive 4th-order Runge-Kutta-Fehlberg method * solver = *lammps_rk4,rkf45* = rk4 is an explicit fourth order Runge-Kutta method; rkf45 is an adaptive fourth-order Runge-Kutta-Fehlberg method
* minSteps = # of steps for rk4 solver or minimum # of steps for rkf45 (rk4 or rkf45) * minSteps = # of steps for rk4 solver or minimum # of steps for rkf45 (rk4 or rkf45)
* maxSteps = maximum number of steps for the rkf45 solver (rkf45 only) * maxSteps = maximum number of steps for the rkf45 solver (rkf45 only)
* relTol = relative tolerance for the rkf45 solver (rkf45 only) * relTol = relative tolerance for the rkf45 solver (rkf45 only)
@ -61,9 +61,9 @@ of *m* ordinary differential equations (ODEs) that describe the change
in concentration of a given species as a function of time are then in concentration of a given species as a function of time are then
constructed based on the *n* reaction rate equations. constructed based on the *n* reaction rate equations.
The ODE systems are solved over the full DPD timestep *dt* using either a 4th The ODE systems are solved over the full DPD timestep *dt* using either a fourth
order Runge-Kutta *rk4* method with a fixed step-size *h*\ , specified order Runge-Kutta *rk4* method with a fixed step-size *h*\ , specified
by the *lammps_rk4* keyword, or a 4th order Runge-Kutta-Fehlberg (rkf45) method by the *lammps_rk4* keyword, or a fourth order Runge-Kutta-Fehlberg (rkf45) method
with an adaptive step-size for *h*\ . The number of ODE steps per DPD timestep with an adaptive step-size for *h*\ . The number of ODE steps per DPD timestep
for the rk4 method is optionally specified immediately after the rk4 for the rk4 method is optionally specified immediately after the rk4
keyword. The ODE step-size is set as *dt/num_steps*. Smaller keyword. The ODE step-size is set as *dt/num_steps*. Smaller
@ -76,7 +76,7 @@ can be specified by the user or estimated internally. It is recommended that the
specify *h0* since this will generally reduced the number of ODE integration steps specify *h0* since this will generally reduced the number of ODE integration steps
required. *h0* is defined as *dt / min_steps* if min_steps >= 1. If min_steps == 0, required. *h0* is defined as *dt / min_steps* if min_steps >= 1. If min_steps == 0,
*h0* is estimated such that an explicit Euler method would likely produce *h0* is estimated such that an explicit Euler method would likely produce
an acceptable solution. This is generally overly conservative for the 4th-order an acceptable solution. This is generally overly conservative for the fourth-order
method and users are advised to specify *h0* as some fraction of the DPD timestep. method and users are advised to specify *h0* as some fraction of the DPD timestep.
For small DPD timesteps, only one step may be necessary depending upon the tolerances. For small DPD timesteps, only one step may be necessary depending upon the tolerances.
Note that more than min_steps ODE steps may be taken depending upon the ODE stiffness Note that more than min_steps ODE steps may be taken depending upon the ODE stiffness
@ -172,7 +172,7 @@ parenthesized comments):
... ...
1.0 no + 1.0 co = 0.5 n2 + 1.0 co2 1.66E+06 0.0 0.69 1.0 no + 1.0 co = 0.5 n2 + 1.0 co2 1.66E+06 0.0 0.69
A section begins with a non-blank line whose 1st character is not a A section begins with a non-blank line whose first character is not a
"#"; blank lines or lines starting with "#" can be used as comments "#"; blank lines or lines starting with "#" can be used as comments
between sections. between sections.

6
doc/src/fix_saed_vtk.rst
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@ -45,7 +45,7 @@ Description
""""""""""" """""""""""
Time average computed intensities from :doc:`compute saed <compute_saed>` and Time average computed intensities from :doc:`compute saed <compute_saed>` and
write output to a file in the 3rd generation vtk image data format for write output to a file in the third generation vtk image data format for
visualization directly in parallelized visualization software packages visualization directly in parallelized visualization software packages
like ParaView and VisIt. Note that if no time averaging is done, this like ParaView and VisIt. Note that if no time averaging is done, this
command can be used as a convenient way to simply output diffraction command can be used as a convenient way to simply output diffraction
@ -92,7 +92,7 @@ averaging is done; values are simply generated on timesteps
---------- ----------
The output for fix ave/time/saed is a file written with the 3rd generation The output for fix ave/time/saed is a file written with the third generation
vtk image data formatting. The filename assigned by the *file* keyword is vtk image data formatting. The filename assigned by the *file* keyword is
appended with _N.vtk where N is an index (0,1,2...) to account for multiple appended with _N.vtk where N is an index (0,1,2...) to account for multiple
diffraction intensity outputs. diffraction intensity outputs.
@ -156,7 +156,7 @@ running or windowed average.
The *file* keyword allows a filename to be specified. Every *Nfreq* The *file* keyword allows a filename to be specified. Every *Nfreq*
steps, the vector of saed intensity data is written to a new file using steps, the vector of saed intensity data is written to a new file using
the 3rd generation vtk format. The base of each file is assigned by the third generation vtk format. The base of each file is assigned by
the *file* keyword and this string is appended with _N.vtk where N is the *file* keyword and this string is appended with _N.vtk where N is
an index (0,1,2...) to account for situations with multiple diffraction an index (0,1,2...) to account for situations with multiple diffraction
intensity outputs. intensity outputs.

2
doc/src/fix_smd.rst
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@ -126,7 +126,7 @@ displacement).
The force is the total force on the group of atoms by the spring. In The force is the total force on the group of atoms by the spring. In
the case of the *couple* style, it is the force on the fix group the case of the *couple* style, it is the force on the fix group
(group-ID) or the negative of the force on the 2nd group (group-ID2). (group-ID) or the negative of the force on the second group (group-ID2).
The vector values calculated by this fix are "extensive". The vector values calculated by this fix are "extensive".
No parameter of this fix can be used with the *start/stop* keywords of No parameter of this fix can be used with the *start/stop* keywords of

2
doc/src/fix_spring.rst
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@ -118,7 +118,7 @@ various :doc:`output commands <Howto_output>`. The first 3 quantities
in the vector are xyz components of the total force added to the group in the vector are xyz components of the total force added to the group
of atoms by the spring. In the case of the *couple* style, it is the of atoms by the spring. In the case of the *couple* style, it is the
force on the fix group (group-ID) or the negative of the force on the force on the fix group (group-ID) or the negative of the force on the
2nd group (group-ID2). The 4th quantity in the vector is the second group (group-ID2). The fourth quantity in the vector is the
magnitude of the force added by the spring, as a positive value if magnitude of the force added by the spring, as a positive value if
(r-R0) > 0 and a negative value if (r-R0) < 0. This sign convention (r-R0) > 0 and a negative value if (r-R0) < 0. This sign convention
can be useful when using the spring force to compute a potential of can be useful when using the spring force to compute a potential of

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