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Merge branch 'develop' into feature/snap-packed-idx

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Evan Weinberg
2022-09-29 09:50:33 -07:00
parent 1216188d48 f78c350fa8
commit 60f73b33bf
741 changed files with 67908 additions and 10864 deletions
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30
SECURITY.md
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@ -14,14 +14,14 @@ and tested by the LAMMPS developers, so it is easy to import bad
behavior from calling functions in one of those libraries. behavior from calling functions in one of those libraries.
Thus is is quite easy to crash LAMMPS through malicious input and do all Thus is is quite easy to crash LAMMPS through malicious input and do all
kinds of filesystem manipulations. And because of that LAMMPS should kinds of file system manipulations. And because of that LAMMPS should
**NEVER** be compiled or **run** as superuser, either from a "root" or **NEVER** be compiled or **run** as superuser, either from a "root" or
"administrator" account directly or indirectly via "sudo" or "su". "administrator" account directly or indirectly via "sudo" or "su".
Therefore what could be seen as a security vulnerability is usually Therefore what could be seen as a security vulnerability is usually
either a user mistake or a bug in the code. Bugs can be reported in either a user mistake or a bug in the code. Bugs can be reported in the
the LAMMPS project LAMMPS project [issue tracker on
[issue tracker on GitHub](https://github.com/lammps/lammps/issues). GitHub](https://github.com/lammps/lammps/issues).
To mitigate issues with using homoglyphs or bidirectional reordering in To mitigate issues with using homoglyphs or bidirectional reordering in
unicode, which have been demonstrated as a vector to obfuscate and hide unicode, which have been demonstrated as a vector to obfuscate and hide
@ -30,10 +30,18 @@ for unicode characters and only all-ASCII source code is accepted.
# Version Updates # Version Updates
LAMMPS follows continuous release development model. We aim to keep all LAMMPS follows continuous release development model. We aim to keep to
release versions (stable or patch) fully functional and employ a variety keep the development version (develop branch) always fully functional
of automatic testing procedures to detect failures of existing and employ a variety of automatic testing procedures to detect failures
functionality from adding new features before releases are made. Thus of existing functionality from adding or modifying features. Most of
bugfixes and updates are only integrated into the current development those tests are run on pull requests *before* merging to the development
branch and thus the next (patch) release and users are recommended to branch. The develop branch is protected, so all changes *must* be
update regularly. submitted as a pull request and thus cannot avoid the automated tests.
Additional tests are run *after* merging. Before releases are made
*all* tests must have cleared. Then a release tag is applied and the
release branch fast-forwarded to that tag. Bug fixes and updates are
applied to the current development branch and thus will be available in
the next (patch) release. For stable releases, selected bug fixes are
back-ported and occasionally published as update releases. There are
only updates to the latest stable release.

1
cmake/CMakeLists.txt
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@ -376,6 +376,7 @@ pkg_depends(DIELECTRIC EXTRA-PAIR)
pkg_depends(CG-DNA MOLECULE) pkg_depends(CG-DNA MOLECULE)
pkg_depends(CG-DNA ASPHERE) pkg_depends(CG-DNA ASPHERE)
pkg_depends(ELECTRODE KSPACE) pkg_depends(ELECTRODE KSPACE)
pkg_depends(EXTRA-MOLECULE MOLECULE)
# detect if we may enable OpenMP support by default # detect if we may enable OpenMP support by default
set(BUILD_OMP_DEFAULT OFF) set(BUILD_OMP_DEFAULT OFF)

4
cmake/Modules/Packages/MDI.cmake
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@ -8,8 +8,8 @@ option(DOWNLOAD_MDI "Download and compile the MDI library instead of using an al
if(DOWNLOAD_MDI) if(DOWNLOAD_MDI)
message(STATUS "MDI download requested - we will build our own") message(STATUS "MDI download requested - we will build our own")
set(MDI_URL "https://github.com/MolSSI-MDI/MDI_Library/archive/v1.4.1.tar.gz" CACHE STRING "URL for MDI tarball") set(MDI_URL "https://github.com/MolSSI-MDI/MDI_Library/archive/v1.4.12.tar.gz" CACHE STRING "URL for MDI tarball")
set(MDI_MD5 "f9505fccd4c79301a619f6452dad4ad9" CACHE STRING "MD5 checksum for MDI tarball") set(MDI_MD5 "7a222353ae8e03961d5365e6cd48baee" CACHE STRING "MD5 checksum for MDI tarball")
mark_as_advanced(MDI_URL) mark_as_advanced(MDI_URL)
mark_as_advanced(MDI_MD5) mark_as_advanced(MDI_MD5)
enable_language(C) enable_language(C)

20
cmake/Modules/Packages/ML-IAP.cmake
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@ -25,16 +25,18 @@ if(MLIAP_ENABLE_PYTHON)
endif() endif()
set(MLIAP_BINARY_DIR ${CMAKE_BINARY_DIR}/cython) set(MLIAP_BINARY_DIR ${CMAKE_BINARY_DIR}/cython)
set(MLIAP_CYTHON_SRC ${LAMMPS_SOURCE_DIR}/ML-IAP/mliap_model_python_couple.pyx) file(GLOB MLIAP_CYTHON_SRC ${LAMMPS_SOURCE_DIR}/ML-IAP/*.pyx)
get_filename_component(MLIAP_CYTHON_BASE ${MLIAP_CYTHON_SRC} NAME_WE)
file(MAKE_DIRECTORY ${MLIAP_BINARY_DIR}) file(MAKE_DIRECTORY ${MLIAP_BINARY_DIR})
add_custom_command(OUTPUT ${MLIAP_BINARY_DIR}/${MLIAP_CYTHON_BASE}.cpp ${MLIAP_BINARY_DIR}/${MLIAP_CYTHON_BASE}.h foreach(MLIAP_CYTHON_FILE ${MLIAP_CYTHON_SRC})
COMMAND ${CMAKE_COMMAND} -E copy_if_different ${MLIAP_CYTHON_SRC} ${MLIAP_BINARY_DIR}/${MLIAP_CYTHON_BASE}.pyx get_filename_component(MLIAP_CYTHON_BASE ${MLIAP_CYTHON_FILE} NAME_WE)
COMMAND ${Cythonize_EXECUTABLE} -3 ${MLIAP_BINARY_DIR}/${MLIAP_CYTHON_BASE}.pyx add_custom_command(OUTPUT ${MLIAP_BINARY_DIR}/${MLIAP_CYTHON_BASE}.cpp ${MLIAP_BINARY_DIR}/${MLIAP_CYTHON_BASE}.h
WORKING_DIRECTORY ${MLIAP_BINARY_DIR} COMMAND ${CMAKE_COMMAND} -E copy_if_different ${MLIAP_CYTHON_FILE} ${MLIAP_BINARY_DIR}/${MLIAP_CYTHON_BASE}.pyx
MAIN_DEPENDENCY ${MLIAP_CYTHON_SRC} COMMAND ${Cythonize_EXECUTABLE} -3 ${MLIAP_BINARY_DIR}/${MLIAP_CYTHON_BASE}.pyx
COMMENT "Generating C++ sources with cythonize...") WORKING_DIRECTORY ${MLIAP_BINARY_DIR}
MAIN_DEPENDENCY ${MLIAP_CYTHON_FILE}
COMMENT "Generating C++ sources with cythonize...")
target_sources(lammps PRIVATE ${MLIAP_BINARY_DIR}/${MLIAP_CYTHON_BASE}.cpp)
endforeach()
target_compile_definitions(lammps PRIVATE -DMLIAP_PYTHON) target_compile_definitions(lammps PRIVATE -DMLIAP_PYTHON)
target_sources(lammps PRIVATE ${MLIAP_BINARY_DIR}/${MLIAP_CYTHON_BASE}.cpp)
target_include_directories(lammps PRIVATE ${MLIAP_BINARY_DIR}) target_include_directories(lammps PRIVATE ${MLIAP_BINARY_DIR})
endif() endif()

13
cmake/presets/clang.cmake
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@ -3,6 +3,13 @@
# prefer flang over gfortran, if available # prefer flang over gfortran, if available
find_program(CLANG_FORTRAN NAMES flang gfortran f95) find_program(CLANG_FORTRAN NAMES flang gfortran f95)
set(ENV{OMPI_FC} ${CLANG_FORTRAN}) set(ENV{OMPI_FC} ${CLANG_FORTRAN})
get_filename_component(_tmp_fc ${CLANG_FORTRAN} NAME)
if (_tmp_fc STREQUAL "flang")
set(FC_STD_VERSION "-std=f2018")
set(BUILD_MPI OFF)
else()
set(FC_STD_VERSION "-std=f2003")
endif()
set(CMAKE_CXX_COMPILER "clang++" CACHE STRING "" FORCE) set(CMAKE_CXX_COMPILER "clang++" CACHE STRING "" FORCE)
set(CMAKE_C_COMPILER "clang" CACHE STRING "" FORCE) set(CMAKE_C_COMPILER "clang" CACHE STRING "" FORCE)
@ -10,9 +17,9 @@ set(CMAKE_Fortran_COMPILER ${CLANG_FORTRAN} CACHE STRING "" FORCE)
set(CMAKE_CXX_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE) set(CMAKE_CXX_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE)
set(CMAKE_CXX_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE) set(CMAKE_CXX_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
set(CMAKE_CXX_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE) set(CMAKE_CXX_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
set(CMAKE_Fortran_FLAGS_DEBUG "-Wall -Wextra -g -std=f2003" CACHE STRING "" FORCE) set(CMAKE_Fortran_FLAGS_DEBUG "-Wall -Wextra -g ${FC_STD_VERSION}" CACHE STRING "" FORCE)
set(CMAKE_Fortran_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG -std=f2003" CACHE STRING "" FORCE) set(CMAKE_Fortran_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG ${FC_STD_VERSION}" CACHE STRING "" FORCE)
set(CMAKE_Fortran_FLAGS_RELEASE "-O3 -DNDEBUG -std=f2003" CACHE STRING "" FORCE) set(CMAKE_Fortran_FLAGS_RELEASE "-O3 -DNDEBUG ${FC_STD_VERSION}" CACHE STRING "" FORCE)
set(CMAKE_C_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE) set(CMAKE_C_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE)
set(CMAKE_C_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE) set(CMAKE_C_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
set(CMAKE_C_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE) set(CMAKE_C_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)

4
doc/lammps.1
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@ -1,7 +1,7 @@
.TH LAMMPS "1" "3 August 2022" "2022-8-3" .TH LAMMPS "1" "15 September 2022" "2022-9-15"
.SH NAME .SH NAME
.B LAMMPS .B LAMMPS
\- Molecular Dynamics Simulator. Version 3 August 2022 \- Molecular Dynamics Simulator. Version 15 September 2022
.SH SYNOPSIS .SH SYNOPSIS
.B lmp .B lmp

26
doc/src/Bibliography.rst
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@ -314,7 +314,7 @@ Bibliography
Espanol, Revenga, Physical Review E, 67, 026705 (2003). Espanol, Revenga, Physical Review E, 67, 026705 (2003).
**(Espanol1997)** **(Espanol1997)**
Espanol, Europhys Lett, 40(6): 631-636 (1997). DOI: 10.1209/epl/i1997-00515-8 Espanol, Europhys Lett, 40(6): 631-636 (1997). DOI:10.1209/epl/i1997-00515-8
**(Evans and Morriss)** **(Evans and Morriss)**
Evans and Morriss, Phys Rev A, 30, 1528 (1984). Evans and Morriss, Phys Rev A, 30, 1528 (1984).
@ -368,7 +368,7 @@ Bibliography
Frenkel and Smit, Understanding Molecular Simulation, Academic Press, London, 2002. Frenkel and Smit, Understanding Molecular Simulation, Academic Press, London, 2002.
**(GLE4MD)** **(GLE4MD)**
`http://gle4md.org/ <http://gle4md.org/>`_ `https://gle4md.org/ <https://gle4md.org/>`_
**(Gao)** **(Gao)**
Gao and Weber, Nuclear Instruments and Methods in Physics Research B 191 (2012) 504. Gao and Weber, Nuclear Instruments and Methods in Physics Research B 191 (2012) 504.
@ -401,13 +401,13 @@ Bibliography
Hayre, and Farago, Comp Phys Comm, 185, 524 (2014) Hayre, and Farago, Comp Phys Comm, 185, 524 (2014)
**(Groot)** **(Groot)**
Groot and Warren, J Chem Phys, 107: 4423-4435 (1997). DOI: 10.1063/1.474784 Groot and Warren, J Chem Phys, 107: 4423-4435 (1997). DOI:10.1063/1.474784
**(Guenole)** **(Guenole)**
Guenole, Noehring, Vaid, Houlle, Xie, Prakash, Bitzek, Comput Mater Sci, 175, 109584 (2020). Guenole, Noehring, Vaid, Houlle, Xie, Prakash, Bitzek, Comput Mater Sci, 175, 109584 (2020).
**(Gullet)** **(Gullet)**
Gullet, Wagner, Slepoy, SANDIA Report 2003-8782 (2003). Gullet, Wagner, Slepoy, SANDIA Report 2003-8782 (2003). DOI:10.2172/918395
**(Guo)** **(Guo)**
Guo and Thirumalai, Journal of Molecular Biology, 263, 323-43 (1996). Guo and Thirumalai, Journal of Molecular Biology, 263, 323-43 (1996).
@ -461,7 +461,7 @@ Bibliography
Hunt, Mol Simul, 42, 347 (2016). Hunt, Mol Simul, 42, 347 (2016).
**(IPI)** **(IPI)**
`http://epfl-cosmo.github.io/gle4md/index.html?page=ipi <http://epfl-cosmo.github.io/gle4md/index.html?page=ipi>`_ `https://ipi-code.org/ <https://ipi-code.org/>`
**(IPI-CPC)** **(IPI-CPC)**
Ceriotti, More and Manolopoulos, Comp Phys Comm, 185, 1019-1026 (2014). Ceriotti, More and Manolopoulos, Comp Phys Comm, 185, 1019-1026 (2014).
@ -605,16 +605,16 @@ Bibliography
I.\ Leven et al, J. Chem.Theory Comput. 12, 2896-905 (2016). I.\ Leven et al, J. Chem.Theory Comput. 12, 2896-905 (2016).
**(Li2013_POF)** **(Li2013_POF)**
Li, Hu, Wang, Ma, Zhou, Phys Fluids, 25: 072103 (2013). DOI: 10.1063/1.4812366. Li, Hu, Wang, Ma, Zhou, Phys Fluids, 25: 072103 (2013). DOI:10.1063/1.4812366.
**(Li2014_JCP)** **(Li2014_JCP)**
Li, Tang, Lei, Caswell, Karniadakis, J Comput Phys, 265: 113-127 (2014). DOI: 10.1016/j.jcp.2014.02.003. Li, Tang, Lei, Caswell, Karniadakis, J Comput Phys, 265: 113-127 (2014). DOI:10.1016/j.jcp.2014.02.003.
**(Li2015_CC)** **(Li2015_CC)**
Li, Tang, Li, Karniadakis, Chem Commun, 51: 11038-11040 (2015). DOI: 10.1039/C5CC01684C. Li, Tang, Li, Karniadakis, Chem Commun, 51: 11038-11040 (2015). DOI:10.1039/C5CC01684C.
**(Li2015_JCP)** **(Li2015_JCP)**
Li, Yazdani, Tartakovsky, Karniadakis, J Chem Phys, 143: 014101 (2015). DOI: 10.1063/1.4923254. Li, Yazdani, Tartakovsky, Karniadakis, J Chem Phys, 143: 014101 (2015). DOI:10.1063/1.4923254.
**(Lisal)** **(Lisal)**
M.\ Lisal, J.K. Brennan, J. Bonet Avalos, "Dissipative particle dynamics at isothermal, isobaric, isoenergetic, and isoenthalpic conditions using Shardlow-like splitting algorithms.", M.\ Lisal, J.K. Brennan, J. Bonet Avalos, "Dissipative particle dynamics at isothermal, isobaric, isoenergetic, and isoenthalpic conditions using Shardlow-like splitting algorithms.",
@ -733,8 +733,8 @@ Bibliography
**(Mishin)** **(Mishin)**
Mishin, Mehl, and Papaconstantopoulos, Acta Mater, 53, 4029 (2005). Mishin, Mehl, and Papaconstantopoulos, Acta Mater, 53, 4029 (2005).
**(Mitchell and Finchham)** **(Mitchell and Fincham)**
Mitchell, Finchham, J Phys Condensed Matter, 5, 1031-1038 (1993). Mitchell, Fincham, J Phys Condensed Matter, 5, 1031-1038 (1993).
**(Mitchell2011)** **(Mitchell2011)**
Mitchell. A non-local, ordinary-state-based viscoelasticity model for peridynamics. Sandia National Lab Report, 8064:1-28 (2011). Mitchell. A non-local, ordinary-state-based viscoelasticity model for peridynamics. Sandia National Lab Report, 8064:1-28 (2011).
@ -875,7 +875,7 @@ Bibliography
G.A. Tribello, M. Bonomi, D. Branduardi, C. Camilloni and G. Bussi, Comp. Phys. Comm 185, 604 (2014) G.A. Tribello, M. Bonomi, D. Branduardi, C. Camilloni and G. Bussi, Comp. Phys. Comm 185, 604 (2014)
**(Paquay)** **(Paquay)**
Paquay and Kusters, Biophys. J., 110, 6, (2016). preprint available at `arXiv:1411.3019 <http://arxiv.org/abs/1411.3019/>`_. Paquay and Kusters, Biophys. J., 110, 6, (2016). preprint available at `arXiv:1411.3019 <https://arxiv.org/abs/1411.3019/>`_.
**(Park)** **(Park)**
Park, Schulten, J. Chem. Phys. 120 (13), 5946 (2004) Park, Schulten, J. Chem. Phys. 120 (13), 5946 (2004)
@ -1373,7 +1373,7 @@ Bibliography
Zhu, Tajkhorshid, and Schulten, Biophys. J. 83, 154 (2002). Zhu, Tajkhorshid, and Schulten, Biophys. J. 83, 154 (2002).
**(Ziegler)** **(Ziegler)**
J.F. Ziegler, J. P. Biersack and U. Littmark, "The Stopping and Range of Ions in Matter," Volume 1, Pergamon, 1985. J.F. Ziegler, J. P. Biersack and U. Littmark, "The Stopping and Range of Ions in Matter", Volume 1, Pergamon, 1985.
**(Zimmerman2004)** **(Zimmerman2004)**
Zimmerman, JA; Webb, EB; Hoyt, JJ;. Jones, RE; Klein, PA; Bammann, DJ, "Calculation of stress in atomistic simulation." Special Issue of Modelling and Simulation in Materials Science and Engineering (2004),12:S319. Zimmerman, JA; Webb, EB; Hoyt, JJ;. Jones, RE; Klein, PA; Bammann, DJ, "Calculation of stress in atomistic simulation." Special Issue of Modelling and Simulation in Materials Science and Engineering (2004),12:S319.

2
doc/src/Build_development.rst
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@ -140,7 +140,7 @@ of the LAMMPS project on GitHub.
The unit testing facility is integrated into the CMake build process The unit testing facility is integrated into the CMake build process
of the LAMMPS source code distribution itself. It can be enabled by of the LAMMPS source code distribution itself. It can be enabled by
setting ``-D ENABLE_TESTING=on`` during the CMake configuration step. setting ``-D ENABLE_TESTING=on`` during the CMake configuration step.
It requires the `YAML <http://pyyaml.org/>`_ library and development It requires the `YAML <https://pyyaml.org/>`_ library and development
headers (if those are not found locally a recent version will be headers (if those are not found locally a recent version will be
downloaded and compiled along with LAMMPS and the test program) to downloaded and compiled along with LAMMPS and the test program) to
compile and will download and compile a specific recent version of the compile and will download and compile a specific recent version of the

6
doc/src/Build_extras.rst
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@ -314,7 +314,7 @@ detailed information is available at:
In addition to installing the KIM API, it is also necessary to install the In addition to installing the KIM API, it is also necessary to install the
library of KIM models (interatomic potentials). library of KIM models (interatomic potentials).
See `Obtaining KIM Models <http://openkim.org/doc/usage/obtaining-models>`_ to See `Obtaining KIM Models <https://openkim.org/doc/usage/obtaining-models>`_ to
learn how to install a pre-build binary of the OpenKIM Repository of Models. learn how to install a pre-build binary of the OpenKIM Repository of Models.
See the list of all KIM models here: https://openkim.org/browse/models See the list of all KIM models here: https://openkim.org/browse/models
@ -432,7 +432,7 @@ Enabling the extra unit tests have some requirements,
``EAM_Dynamo_MendelevAckland_2007v3_Zr__MO_004835508849_000``, ``EAM_Dynamo_MendelevAckland_2007v3_Zr__MO_004835508849_000``,
``EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005``, and ``EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005``, and
``LennardJones612_UniversalShifted__MO_959249795837_003`` KIM models. ``LennardJones612_UniversalShifted__MO_959249795837_003`` KIM models.
See `Obtaining KIM Models <http://openkim.org/doc/usage/obtaining-models>`_ See `Obtaining KIM Models <https://openkim.org/doc/usage/obtaining-models>`_
to learn how to install a pre-built binary of the OpenKIM Repository of to learn how to install a pre-built binary of the OpenKIM Repository of
Models or see Models or see
`Installing KIM Models <https://openkim.org/doc/usage/obtaining-models/#installing_models>`_ `Installing KIM Models <https://openkim.org/doc/usage/obtaining-models/#installing_models>`_
@ -1053,7 +1053,7 @@ VORONOI package
----------------------------- -----------------------------
To build with this package, you must download and build the To build with this package, you must download and build the
`Voro++ library <http://math.lbl.gov/voro++>`_ or install a `Voro++ library <https://math.lbl.gov/voro++>`_ or install a
binary package provided by your operating system. binary package provided by your operating system.
.. tabs:: .. tabs::

2
doc/src/Build_manual.rst
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@ -176,7 +176,7 @@ math expressions transparently into embedded images.
For converting the generated ePUB file to a MOBI format file (for e-book For converting the generated ePUB file to a MOBI format file (for e-book
readers, like Kindle, that cannot read ePUB), you also need to have the readers, like Kindle, that cannot read ePUB), you also need to have the
``ebook-convert`` tool from the "calibre" software ``ebook-convert`` tool from the "calibre" software
installed. `http://calibre-ebook.com/ <http://calibre-ebook.com/>`_ installed. `https://calibre-ebook.com/ <https://calibre-ebook.com/>`_
Typing ``make mobi`` will first create the ePUB file and then convert Typing ``make mobi`` will first create the ePUB file and then convert
it. On the Kindle readers in particular, you also have support for PDF it. On the Kindle readers in particular, you also have support for 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.

29
doc/src/Build_settings.rst
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@ -111,26 +111,25 @@ LAMMPS can use them if they are available on your system.
files in its default search path. You must specify ``FFT_LIB`` files in its default search path. You must specify ``FFT_LIB``
with the appropriate FFT libraries to include in the link. with the appropriate FFT libraries to include in the link.
The `KISS FFT library <http://kissfft.sf.net>`_ is included in the LAMMPS The `KISS FFT library <https://github.com/mborgerding/kissfft>`_ is
distribution. It is portable across all platforms. Depending on the size included in the LAMMPS distribution. It is portable across all
of the FFTs and the number of processors used, the other libraries listed platforms. Depending on the size of the FFTs and the number of
here can be faster. processors used, the other libraries listed here can be faster.
However, note that long-range Coulombics are only a portion of the However, note that long-range Coulombics are only a portion of the
per-timestep CPU cost, FFTs are only a portion of long-range per-timestep CPU cost, FFTs are only a portion of long-range Coulombics,
Coulombics, and 1d FFTs are only a portion of the FFT cost (parallel and 1d FFTs are only a portion of the FFT cost (parallel communication
communication can be costly). A breakdown of these timings is printed can be costly). A breakdown of these timings is printed to the screen
to the screen at the end of a run when using the at the end of a run when using the :doc:`kspace_style pppm
:doc:`kspace_style pppm <kspace_style>` command. The <kspace_style>` command. The :doc:`Screen and logfile output
:doc:`Screen and logfile output <Run_output>` <Run_output>` page gives more details. A more detailed (and time
page gives more details. A more detailed (and time consuming) consuming) report of the FFT performance is generated with the
report of the FFT performance is generated with the
:doc:`kspace_modify fftbench yes <kspace_modify>` command. :doc:`kspace_modify fftbench yes <kspace_modify>` command.
FFTW is a fast, portable FFT library that should also work on any FFTW is a fast, portable FFT library that should also work on any
platform and can be faster than the KISS FFT library. You can platform and can be faster than the KISS FFT library. You can download
download it from `www.fftw.org <http://www.fftw.org>`_. LAMMPS requires it from `www.fftw.org <https://www.fftw.org>`_. LAMMPS requires version
version 3.X; the legacy version 2.1.X is no longer supported. 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

5
doc/src/Commands_all.rst
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@ -15,7 +15,9 @@
General commands General commands
================ ================
An alphabetic list of general LAMMPS commands. An alphabetic list of general LAMMPS commands. Note that style
commands with many variants, can be more easily accessed via the small
table above.
.. table_from_list:: .. table_from_list::
:columns: 5 :columns: 5
@ -61,6 +63,7 @@ An alphabetic list of general LAMMPS commands.
* :doc:`kspace_modify <kspace_modify>` * :doc:`kspace_modify <kspace_modify>`
* :doc:`kspace_style <kspace_style>` * :doc:`kspace_style <kspace_style>`
* :doc:`label <label>` * :doc:`label <label>`
* :doc:`labelmap <labelmap>`
* :doc:`lattice <lattice>` * :doc:`lattice <lattice>`
* :doc:`log <log>` * :doc:`log <log>`
* :doc:`mass <mass>` * :doc:`mass <mass>`

1
doc/src/Commands_fix.rst
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@ -165,6 +165,7 @@ OPT.
* :doc:`orient/fcc <fix_orient>` * :doc:`orient/fcc <fix_orient>`
* :doc:`orient/eco <fix_orient_eco>` * :doc:`orient/eco <fix_orient_eco>`
* :doc:`pafi <fix_pafi>` * :doc:`pafi <fix_pafi>`
* :doc:`pair <fix_pair>`
* :doc:`phonon <fix_phonon>` * :doc:`phonon <fix_phonon>`
* :doc:`pimd <fix_pimd>` * :doc:`pimd <fix_pimd>`
* :doc:`planeforce <fix_planeforce>` * :doc:`planeforce <fix_planeforce>`

4
doc/src/Developer_updating.rst
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@ -328,7 +328,7 @@ removed so this update is **required** to avoid compilation failure.
Split of fix STORE into fix STORE/GLOBAL and fix STORE/PERATOM Split of fix STORE into fix STORE/GLOBAL and fix STORE/PERATOM
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
.. versionchanged:: TBD .. versionchanged:: 15Sep2022
This change splits the GLOBAL and PERATOM modes of fix STORE into two This change splits the GLOBAL and PERATOM modes of fix STORE into two
separate fixes STORE/GLOBAL and STORE/PERATOM. There was very little separate fixes STORE/GLOBAL and STORE/PERATOM. There was very little
@ -387,7 +387,7 @@ This change is **required** or else the code will not compile.
Use Output::get_dump_by_id() instead of Output::find_dump() Use Output::get_dump_by_id() instead of Output::find_dump()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
.. versionchanged:: TBD .. versionchanged:: 15Sep2022
The accessor function to individual dump style instances has been changed The accessor function to individual dump style instances has been changed
from ``Output::find_dump()`` returning the index of the dump instance in from ``Output::find_dump()`` returning the index of the dump instance in

9
doc/src/Developer_utils.rst
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@ -175,6 +175,12 @@ and parsing files or arguments.
.. doxygenfunction:: is_double .. doxygenfunction:: is_double
:project: progguide :project: progguide
.. doxygenfunction:: is_id
:project: progguide
.. doxygenfunction:: is_type
:project: progguide
Potential file functions Potential file functions
^^^^^^^^^^^^^^^^^^^^^^^^ ^^^^^^^^^^^^^^^^^^^^^^^^
@ -205,6 +211,9 @@ Argument processing
.. doxygenfunction:: expand_args .. doxygenfunction:: expand_args
:project: progguide :project: progguide
.. doxygenfunction:: expand_type
:project: progguide
Convenience functions Convenience functions
^^^^^^^^^^^^^^^^^^^^^ ^^^^^^^^^^^^^^^^^^^^^

2
doc/src/Errors_debug.rst
View File

@ -75,7 +75,7 @@ Using the GDB debugger to get a stack trace
There are two options to use the GDB debugger for identifying the origin There are two options to use the GDB debugger for identifying the origin
of the segmentation fault or similar crash. The GDB debugger has many of the segmentation fault or similar crash. The GDB debugger has many
more features and options, as can be seen for example its `online more features and options, as can be seen for example its `online
documentation <http://sourceware.org/gdb/current/onlinedocs/gdb/>`_. documentation <https://sourceware.org/gdb/current/onlinedocs/gdb/>`_.
Run LAMMPS from within the debugger Run LAMMPS from within the debugger
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

40
doc/src/Errors_messages.rst
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@ -5453,6 +5453,11 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
Mass command must set a type from 1-N where N is the number of atom Mass command must set a type from 1-N where N is the number of atom
types. types.
*Invalid label2type() function syntax in variable formula*
The first argument must be a label map kind (atom, bond, angle,
dihedral, or improper) and the second argument must be a valid type
label that has been assigned to a numeric type.
*Invalid use of library file() function* *Invalid use of library file() function*
This function is called through the library interface. This This function is called through the library interface. This
error should not occur. Contact the developers if it does. error should not occur. Contact the developers if it does.
@ -5585,9 +5590,18 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
*LJ6 off not supported in pair_style buck/long/coul/long* *LJ6 off not supported in pair_style buck/long/coul/long*
Self-explanatory. Self-explanatory.
*Label map is incomplete: all types must be assigned a unique type label*
For a given type-kind (atom types, bond types, etc.) to be written to
the data file, all associated types must be assigned a type label, and
each type label can be assigned to only one numeric type.
*Label wasn't found in input script* *Label wasn't found in input script*
Self-explanatory. Self-explanatory.
*Labelmap command before simulation box is defined*
The labelmap command cannot be used before a read_data,
read_restart, or create_box command.
*Lattice orient vectors are not orthogonal* *Lattice orient vectors are not orthogonal*
The three specified lattice orientation vectors must be mutually The three specified lattice orientation vectors must be mutually
orthogonal. orthogonal.
@ -5863,6 +5877,12 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
*Must not have multiple fixes change box parameter ...* *Must not have multiple fixes change box parameter ...*
Self-explanatory. Self-explanatory.
*Must read Angle Type Labels before Angles*
An Angle Type Labels section of a data file must come before the Angles section.
*Must read Atom Type Labels before Atoms*
An Atom Type Labels section of a data file must come before the Atoms section.
*Must read Atoms before Angles* *Must read Atoms before Angles*
The Atoms section of a data file must come before an Angles section. The Atoms section of a data file must come before an Angles section.
@ -5893,6 +5913,15 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
The Atoms section of a data file must come before a Velocities The Atoms section of a data file must come before a Velocities
section. section.
*Must read Bond Type Labels before Bonds*
A Bond Type Labels section of a data file must come before the Bonds section.
*Must read Dihedral Type Labels before Dihedrals*
An Dihedral Type Labels section of a data file must come before the Dihedrals section.
*Must read Improper Type Labels before Impropers*
An Improper Type Labels section of a data file must come before the Impropers section.
*Must re-specify non-restarted pair style (xxx) after read_restart* *Must re-specify non-restarted pair style (xxx) after read_restart*
For pair styles, that do not store their settings in a restart file, For pair styles, that do not store their settings in a restart file,
it must be defined with a new 'pair_style' command after read_restart. it must be defined with a new 'pair_style' command after read_restart.
@ -7849,6 +7878,10 @@ keyword to allow for additional bonds to be formed
Number of local atoms times number of columns must fit in a 32-bit Number of local atoms times number of columns must fit in a 32-bit
integer for dump. integer for dump.
*Topology type exceeds system topology type*
The number of bond, angle, etc types exceeds the system setting. See
the create_box or read_data command for how to specify these values.
*Tree structure in joint connections* *Tree structure in joint connections*
Fix poems cannot (yet) work with coupled bodies whose joints connect Fix poems cannot (yet) work with coupled bodies whose joints connect
the bodies in a tree structure. the bodies in a tree structure.
@ -7873,6 +7906,13 @@ keyword to allow for additional bonds to be formed
*Two groups cannot be the same in fix spring couple* *Two groups cannot be the same in fix spring couple*
Self-explanatory. Self-explanatory.
*The %s type label %s is already in use for type %s*
For a given type-kind (atom types, bond types, etc.), a given type
label can be assigned to only one numeric type.
*Type label string %s for %s type %s is invalid*
See the labelmap command documentation for valid type labels.
*Unable to initialize accelerator for use* *Unable to initialize accelerator for use*
There was a problem initializing an accelerator for the gpu package There was a problem initializing an accelerator for the gpu package

389
doc/src/Fortran.rst
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@ -3,7 +3,9 @@ The ``LIBLAMMPS`` Fortran Module
The ``LIBLAMMPS`` module provides an interface to call LAMMPS from a The ``LIBLAMMPS`` module provides an interface to call LAMMPS from a
Fortran code. It is based on the LAMMPS C-library interface and Fortran code. It is based on the LAMMPS C-library interface and
requires a Fortran 2003 compatible compiler to be compiled. requires a Fortran 2003 compatible compiler to be compiled. It is
designed to be self-contained and not require any support functions
written in C, C++, or Fortran.
While C libraries have a defined binary interface (ABI) and can thus be While C libraries have a defined binary interface (ABI) and can thus be
used from multiple compiler versions from different vendors for as long used from multiple compiler versions from different vendors for as long
@ -19,12 +21,20 @@ for a simple program using the Fortran interface would be:
mpifort -o testlib.x lammps.f90 testlib.f90 -L. -llammps mpifort -o testlib.x lammps.f90 testlib.f90 -L. -llammps
Please note, that the MPI compiler wrapper is only required when the Please note, that the MPI compiler wrapper is only required when the
calling the library from an MPI parallel code. Please also note the calling the library from an MPI parallel code. Otherwise, using the
order of the source files: the ``lammps.f90`` file needs to be compiled fortran compiler (gfortran, ifort, flang, etc.) will suffice. It may be
first, since it provides the ``LIBLAMMPS`` module that is imported by necessary to link to additional libraries depending on how LAMMPS was
the Fortran code using the interface. A working example code can be configured and whether the LAMMPS library :doc:`was compiled as a static
found together with equivalent examples in C and C++ in the or shared library <Build_link>`.
``examples/COUPLE/simple`` folder of the LAMMPS distribution.
If the LAMMPS library itself has been compiled with MPI support, the
resulting executable will still be able to run LAMMPS in parallel with
``mpirun`` or equivalent. Please also note that the order of the source
files matters: the ``lammps.f90`` file needs to be compiled first, since
it provides the ``LIBLAMMPS`` module that is imported by the Fortran
code using the interface. A working example code can be found together
with equivalent examples in C and C++ in the ``examples/COUPLE/simple``
folder of the LAMMPS distribution.
.. versionadded:: 9Oct2020 .. versionadded:: 9Oct2020
@ -49,17 +59,18 @@ found together with equivalent examples in C and C++ in the
Creating or deleting a LAMMPS object Creating or deleting a LAMMPS object
************************************ ************************************
With the Fortran interface the creation of a :cpp:class:`LAMMPS With the Fortran interface, the creation of a :cpp:class:`LAMMPS
<LAMMPS_NS::LAMMPS>` instance is included in the constructor for <LAMMPS_NS::LAMMPS>` instance is included in the constructor for
creating the :f:func:`lammps` derived type. To import the definition of creating the :f:func:`lammps` derived type. To import the definition of
that type and its type bound procedures you need to add a ``USE that type and its type bound procedures, you need to add a ``USE
LIBLAMMPS`` statement. Internally it will call either LIBLAMMPS`` statement. Internally it will call either
:cpp:func:`lammps_open_fortran` or :cpp:func:`lammps_open_no_mpi` from :cpp:func:`lammps_open_fortran` or :cpp:func:`lammps_open_no_mpi` from
the C library API to create the class instance. All arguments are the C library API to create the class instance. All arguments are
optional and :cpp:func:`lammps_mpi_init` will be called automatically, optional and :cpp:func:`lammps_mpi_init` will be called automatically,
if it is needed. Similarly, a possible call to :cpp:func:`lammps_finalize` if it is needed. Similarly, a possible call to
is integrated into the :f:func:`close` function and triggered with :cpp:func:`lammps_mpi_finalize` is integrated into the :f:func:`close`
the optional logical argument set to ``.true.``. Here is a simple example: function and triggered with the optional logical argument set to
``.true.``. Here is a simple example:
.. code-block:: fortran .. code-block:: fortran
@ -80,11 +91,11 @@ the optional logical argument set to ``.true.``. Here is a simple example:
END PROGRAM testlib END PROGRAM testlib
It is also possible to pass command line flags from Fortran to C/C++ and It is also possible to pass command line flags from Fortran to C/C++ and
thus make the resulting executable behave similar to the standalone thus make the resulting executable behave similarly to the standalone
executable (it will ignore the `-in/-i` flag, though). This allows to executable (it will ignore the `-in/-i` flag, though). This allows
use the command line to configure accelerator and suffix settings, using the command line to configure accelerator and suffix settings,
configure screen and logfile output, or to set index style variables configure screen and logfile output, or to set index style variables
from the command line and more. Here is a correspondingly adapted from the command line and more. Here is a correspondingly adapted
version of the previous example: version of the previous example:
.. code-block:: fortran .. code-block:: fortran
@ -117,13 +128,13 @@ version of the previous example:
-------------------- --------------------
Executing LAMMPS commands Executing LAMMPS commands
========================= *************************
Once a LAMMPS instance is created, it is possible to "drive" the LAMMPS Once a LAMMPS instance is created, it is possible to "drive" the LAMMPS
simulation by telling LAMMPS to read commands from a file, or pass simulation by telling LAMMPS to read commands from a file or to pass
individual or multiple commands from strings or lists of strings. This individual or multiple commands from strings or lists of strings. This
is done similar to how it is implemented in the `C-library is done similarly to how it is implemented in the :doc:`C-library
<pg_lib_execute>` interface. Before handing off the calls to the interface <Library_execute>`. Before handing off the calls to the
C-library interface, the corresponding Fortran versions of the calls C-library interface, the corresponding Fortran versions of the calls
(:f:func:`file`, :f:func:`command`, :f:func:`commands_list`, and (:f:func:`file`, :f:func:`command`, :f:func:`commands_list`, and
:f:func:`commands_string`) have to make a copy of the strings passed as :f:func:`commands_string`) have to make a copy of the strings passed as
@ -165,6 +176,57 @@ Below is a small demonstration of the uses of the different functions:
--------------- ---------------
Accessing system properties
***************************
The C-library interface allows the :doc:`extraction of different kinds
of information <Library_properties>` about the active simulation
instance and also - in some cases - to apply modifications to it. In
some cases, the C-library interface makes pointers to internal data
structures accessible, thus when accessing them from Fortran, special
care is needed to avoid data corruption and crashes. Thus please see
the documentation of the individual type bound procedures for details.
Below is an example demonstrating some of the possible uses.
.. code-block:: fortran
PROGRAM testprop
USE LIBLAMMPS
USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_double, c_int64_t
TYPE(lammps) :: lmp
INTEGER(kind=8) :: natoms
REAL(c_double), POINTER :: dt
INTEGER(c_int64_t), POINTER :: ntimestep
REAL(kind=8) :: pe, ke
lmp = lammps()
CALL lmp%file('in.sysinit')
natoms = INT(lmp%get_natoms(),8)
WRITE(6,'(A,I8,A)') 'Running a simulation with', natoms, ' atoms'
WRITE(6,'(I8,A,I8,A,I3,A)') lmp%extract_setting('nlocal'), ' local and', &
lmp%extract_setting('nghost'), ' ghost atom. ', &
lmp%extract_setting('ntypes'), ' atom types'
CALL lmp%command('run 2 post no')
dt = lmp%extract_global('dt')
ntimestep = lmp%extract_global('ntimestep')
WRITE(6,'(A,I4,A,F4.1,A)') 'At step:', ntimestep, ' Changing timestep from', dt, ' to 0.5'
dt = 0.5
CALL lmp%command('run 2 post no')
WRITE(6,'(A,I4)') 'At step:', ntimestep
pe = lmp%get_thermo('pe')
ke = lmp%get_thermo('ke')
PRINT*, 'PE = ', pe
PRINT*, 'KE = ', ke
CALL lmp%close(.TRUE.)
END PROGRAM testprop
---------------
The ``LIBLAMMPS`` module API The ``LIBLAMMPS`` module API
**************************** ****************************
@ -178,14 +240,24 @@ of the contents of the ``LIBLAMMPS`` Fortran interface to LAMMPS.
class instance that any of the included calls are forwarded to. class instance that any of the included calls are forwarded to.
:f c_ptr handle: reference to the LAMMPS class :f c_ptr handle: reference to the LAMMPS class
:f close: :f:func:`close` :f subroutine close: :f:func:`close`
:f version: :f:func:`version` :f subroutine error: :f:func:`error`
:f file: :f:func:`file` :f function version: :f:func:`version`
:f command: :f:func:`command` :f subroutine file: :f:func:`file`
:f commands_list: :f:func:`commands_list` :f subroutine command: :f:func:`command`
:f commands_string: :f:func:`commands_string` :f subroutine commands_list: :f:func:`commands_list`
:f subroutine commands_string: :f:func:`commands_string`
:f function get_natoms: :f:func:`get_natoms`
:f function get_thermo: :f:func:`get_thermo`
:f subroutine extract_box: :f:func:`extract_box`
:f subroutine reset_box: :f:func:`reset_box`
:f subroutine memory_usage: :f:func:`memory_usage`
:f function extract_setting: :f:func:`extract_setting`
:f function extract_global: :f:func:`extract_global`
.. f:function:: lammps(args[,comm]) --------
.. f:function:: lammps([args][,comm])
This is the constructor for the Fortran class and will forward This is the constructor for the Fortran class and will forward
the arguments to a call to either :cpp:func:`lammps_open_fortran` the arguments to a call to either :cpp:func:`lammps_open_fortran`
@ -198,10 +270,31 @@ of the contents of the ``LIBLAMMPS`` Fortran interface to LAMMPS.
If *comm* is not provided, ``MPI_COMM_WORLD`` is assumed. For If *comm* is not provided, ``MPI_COMM_WORLD`` is assumed. For
more details please see the documentation of :cpp:func:`lammps_open`. more details please see the documentation of :cpp:func:`lammps_open`.
:p character(len=*) args(*) [optional]: arguments as list of strings :o character(len=\*) args(\*) [optional]: arguments as list of strings
:o integer comm [optional]: MPI communicator :o integer comm [optional]: MPI communicator
:r lammps: an instance of the :f:type:`lammps` derived type :r lammps: an instance of the :f:type:`lammps` derived type
.. note::
The ``MPI_F08`` module, which defines Fortran 2008 bindings for MPI,
is not directly supported by this interface due to the complexities of
supporting both the ``MPI_F08`` and ``MPI`` modules at the same time.
However, you should be able to use the ``MPI_VAL`` member of the
``MPI_comm`` derived type to access the integer value of the
communicator, such as in
.. code-block:: Fortran
PROGRAM testmpi
USE LIBLAMMPS
USE MPI_F08
TYPE(lammps) :: lmp
lmp = lammps(MPI_COMM_SELF%MPI_VAL)
END PROGRAM testmpi
Procedures Bound to the lammps Derived Type
===========================================
.. f:subroutine:: close([finalize]) .. f:subroutine:: close([finalize])
This method will close down the LAMMPS instance through calling This method will close down the LAMMPS instance through calling
@ -211,6 +304,20 @@ of the contents of the ``LIBLAMMPS`` Fortran interface to LAMMPS.
:o logical finalize [optional]: shut down the MPI environment of the LAMMPS library if true. :o logical finalize [optional]: shut down the MPI environment of the LAMMPS library if true.
--------
.. f:subroutine:: error(error_type, error_text)
This method is a wrapper around the :cpp:func:`lammps_error` function and will dispatch
an error through the LAMMPS Error class.
.. versionadded:: TBD
:p integer error_type: constant to select which Error class function to call
:p character(len=\*) error_text: error message
--------
.. f:function:: version() .. f:function:: version()
This method returns the numeric LAMMPS version like :cpp:func:`lammps_version` This method returns the numeric LAMMPS version like :cpp:func:`lammps_version`
@ -224,25 +331,243 @@ of the contents of the ``LIBLAMMPS`` Fortran interface to LAMMPS.
This method will call :cpp:func:`lammps_file` to have LAMMPS read This method will call :cpp:func:`lammps_file` to have LAMMPS read
and process commands from a file. and process commands from a file.
:p character(len=*) filename: name of file with LAMMPS commands :p character(len=\*) filename: name of file with LAMMPS commands
--------
.. f:subroutine:: command(cmd) .. f:subroutine:: command(cmd)
This method will call :cpp:func:`lammps_command` to have LAMMPS This method will call :cpp:func:`lammps_command` to have LAMMPS
execute a single command. execute a single command.
:p character(len=*) cmd: single LAMMPS command :p character(len=\*) cmd: single LAMMPS command
--------
.. f:subroutine:: commands_list(cmds) .. f:subroutine:: commands_list(cmds)
This method will call :cpp:func:`lammps_commands_list` to have LAMMPS This method will call :cpp:func:`lammps_commands_list` to have LAMMPS
execute a list of input lines. execute a list of input lines.
:p character(len=*) cmd(:): list of LAMMPS input lines :p character(len=\*) cmd(:): list of LAMMPS input lines
--------
.. f:subroutine:: commands_string(str) .. f:subroutine:: commands_string(str)
This method will call :cpp:func:`lammps_commands_string` to have LAMMPS This method will call :cpp:func:`lammps_commands_string` to have LAMMPS
execute a block of commands from a string. execute a block of commands from a string.
:p character(len=*) str: LAMMPS input in string :p character(len=\*) str: LAMMPS input in string
--------
.. f:function:: get_natoms()
This function will call :cpp:func:`lammps_get_natoms` and return the number
of atoms in the system.
:r real(c_double): number of atoms
--------
.. f:function:: get_thermo(name)
This function will call :cpp:func:`lammps_get_thermo` and return the value
of the corresponding thermodynamic keyword.
.. versionadded:: TBD
:p character(len=\*) name: string with the name of the thermo keyword
:r real(c_double): value of the requested thermo property or `0.0_c_double`
--------
.. f:subroutine:: extract_box([boxlo][, boxhi][, xy][, yz][, xz][, pflags][, boxflag])
This subroutine will call :cpp:func:`lammps_extract_box`. All
parameters are optional, though obviously at least one should be
present. The parameters *pflags* and *boxflag* are stored in LAMMPS
as integers, but should be declared as ``LOGICAL`` variables when
calling from Fortran.
.. versionadded:: TBD
:o real(c_double) boxlo [dimension(3),optional]: vector in which to store
lower-bounds of simulation box
:o real(c_double) boxhi [dimension(3),optional]: vector in which to store
upper-bounds of simulation box
:o real(c_double) xy [optional]: variable in which to store *xy* tilt factor
:o real(c_double) yz [optional]: variable in which to store *yz* tilt factor
:o real(c_double) xz [optional]: variable in which to store *xz* tilt factor
:o logical pflags [dimension(3),optional]: vector in which to store
periodicity flags (``.TRUE.`` means periodic in that dimension)
:o logical boxflag [optional]: variable in which to store boolean denoting
whether the box will change during a simulation
(``.TRUE.`` means box will change)
.. note::
Note that a frequent use case of this function is to extract only one or
more of the options rather than all seven. For example, assuming "lmp"
represents a properly-initialized LAMMPS instance, the following code will
extract the periodic box settings into the variable "periodic":
.. code-block:: Fortran
! code to start up
logical :: periodic(3)
! code to initialize LAMMPS / run things / etc.
call lmp%extract_box(pflags = periodic)
--------
.. f:subroutine:: reset_box(boxlo, boxhi, xy, yz, xz)
This subroutine will call :cpp:func:`lammps_reset_box`. All parameters
are required.
.. versionadded:: TBD
:p real(c_double) boxlo [dimension(3)]: vector of three doubles containing
the lower box boundary
:p real(c_double) boxhi [dimension(3)]: vector of three doubles containing
the upper box boundary
:p real(c_double) xy: *x--y* tilt factor
:p real(c_double) yz: *y--z* tilt factor
:p real(c_double) xz: *x--z* tilt factor
--------
.. f:subroutine:: memory_usage(meminfo)
This subroutine will call :cpp:func:`lammps_memory_usage` and store the
result in the three-element array *meminfo*.
.. versionadded:: TBD
:p real(c_double) meminfo [dimension(3)]: vector of three doubles in which
to store memory usage data
--------
.. f:function:: get_mpi_comm()
This function returns a Fortran representation of the LAMMPS "world"
communicator.
.. versionadded:: TBD
:r integer: Fortran integer equivalent to the MPI communicator LAMMPS is
using
.. note::
The C library interface currently returns type ``int`` instead of
type ``MPI_Fint``, which is the C type corresponding to Fortran
``INTEGER`` types of the default kind. On most compilers, these
are the same anyway, but this interface exchanges values this way
to avoid warning messages.
.. note::
The `MPI_F08` module, which defines Fortran 2008 bindings for MPI,
is not directly supported by this function. However, you should be
able to convert between the two using the `MPI_VAL` member of the
communicator. For example,
.. code-block:: fortran
USE MPI_F08
USE LIBLAMMPS
TYPE (LAMMPS) :: lmp
TYPE (MPI_Comm) :: comm
! ... [commands to set up LAMMPS/etc.]
comm%MPI_VAL = lmp%get_mpi_comm()
should assign an `MPI_F08` communicator properly.
--------
.. f:function:: extract_setting(keyword)
Query LAMMPS about global settings. See the documentation for the
:cpp:func:`lammps_extract_setting` function from the C library.
.. versionadded:: TBD
:p character(len=\*) keyword: string containing the name of the thermo keyword
:r integer(c_int): value of the queried setting or :math:`-1` if unknown
--------
.. f:function:: extract_global(name)
This function calls :cpp:func:`lammps_extract_global` and returns
either a string or a pointer to internal global LAMMPS data,
depending on the data requested through *name*.
.. versionadded:: TBD
Note that this function actually does not return a value, but rather
associates the pointer on the left side of the assignment to point to
internal LAMMPS data (with the exception of string data, which are
copied and returned as ordinary Fortran strings). Pointers must be of
the correct data type to point to said data (typically
``INTEGER(c_int)``, ``INTEGER(c_int64_t)``, or ``REAL(c_double)``)
and have compatible kind and rank. The pointer being associated with
LAMMPS data is type-, kind-, and rank-checked at run-time via an
overloaded assignment operator. The pointers returned by this
function are generally persistent; therefore it is not necessary to
call the function again, unless a :doc:`clear` command has been
issued, which wipes out and recreates the contents of the
:cpp:class:`LAMMPS <LAMMPS_NS::LAMMPS>` class.
For example,
.. code-block:: fortran
PROGRAM demo
USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_int64_t
USE LIBLAMMPS
TYPE(lammps) :: lmp
INTEGER(c_int), POINTER :: nlocal
INTEGER(c_int64_t), POINTER :: ntimestep
CHARACTER(LEN=10) :: units
REAL(c_double), POINTER :: dt
lmp = lammps()
! other commands
nlocal = lmp%extract_global('nlocal')
ntimestep = lmp%extract_global('ntimestep')
dt = lmp%extract_global('dt')
units = lmp%extract_global('units')
! more commands
lmp.close(.TRUE.)
END PROGRAM demo
would extract the number of atoms on this processor, the current time step,
the size of the current time step, and the units being used into the
variables *nlocal*, *ntimestep*, *dt*, and *units*, respectively.
.. note::
if this function returns a string, the string must have
length greater than or equal to the length of the string (not including the
terminal NULL character) that LAMMPS returns. If the variable's length is
too short, the string will be truncated. As usual in Fortran, strings
are padded with spaces at the end.
:p character(len=\*) name: string with the name of the extracted property
:r polymorphic: pointer to LAMMPS data. The left-hand side of the assignment
should be either a string (if expecting string data) or a C-compatible
pointer (e.g., ``INTEGER (c_int), POINTER :: nlocal``) to the extracted
property. If expecting vector data, the pointer should have dimension ":".
.. warning::
Modifying the data in the location pointed to by the returned pointer
may lead to inconsistent internal data and thus may cause failures or
crashes or bogus simulations. In general it is thus usually better
to use a LAMMPS input command that sets or changes these parameters.
Those will take care of all side effects and necessary updates of
settings derived from such settings.

1
doc/src/Howto.rst
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@ -34,6 +34,7 @@ Settings howto
:maxdepth: 1 :maxdepth: 1
Howto_2d Howto_2d
Howto_type_labels
Howto_triclinic Howto_triclinic
Howto_thermostat Howto_thermostat
Howto_barostat Howto_barostat

2
doc/src/Howto_amoeba.rst
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@ -281,7 +281,7 @@ Here is more information about the extended XYZ format defined and
used by Tinker, and links to programs that convert standard PDB files used by Tinker, and links to programs that convert standard PDB files
to the extended XYZ format: to the extended XYZ format:
* `http://openbabel.org/docs/current/FileFormats/Tinker_XYZ_format.html <http://openbabel.org/docs/current/FileFormats/Tinker_XYZ_format.html>`_ * `https://openbabel.org/docs/current/FileFormats/Tinker_XYZ_format.html <https://openbabel.org/docs/current/FileFormats/Tinker_XYZ_format.html>`_
* `https://github.com/emleddin/pdbxyz-xyzpdb <https://github.com/emleddin/pdbxyz-xyzpdb>`_ * `https://github.com/emleddin/pdbxyz-xyzpdb <https://github.com/emleddin/pdbxyz-xyzpdb>`_
* `https://github.com/TinkerTools/tinker/blob/release/source/pdbxyz.f <https://github.com/TinkerTools/tinker/blob/release/source/pdbxyz.f>`_ * `https://github.com/TinkerTools/tinker/blob/release/source/pdbxyz.f <https://github.com/TinkerTools/tinker/blob/release/source/pdbxyz.f>`_

33
doc/src/Howto_bioFF.rst
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@ -3,24 +3,20 @@ CHARMM, AMBER, COMPASS, and DREIDING force fields
A force field has 2 parts: the formulas that define it and the A force field has 2 parts: the formulas that define it and the
coefficients used for a particular system. Here we only discuss coefficients used for a particular system. Here we only discuss
formulas implemented in LAMMPS that correspond to formulas commonly formulas implemented in LAMMPS that correspond to formulas commonly used
used in the CHARMM, AMBER, COMPASS, and DREIDING force fields. Setting in the CHARMM, AMBER, COMPASS, and DREIDING force fields. Setting
coefficients is done either from special sections in an input data file coefficients is done either from special sections in an input data file
via the :doc:`read_data <read_data>` command or in the input script with via the :doc:`read_data <read_data>` command or in the input script with
commands like :doc:`pair_coeff <pair_coeff>` or commands like :doc:`pair_coeff <pair_coeff>` or :doc:`bond_coeff
:doc:`bond_coeff <bond_coeff>` and so on. See the :doc:`Tools <Tools>` doc <bond_coeff>` and so on. See the :doc:`Tools <Tools>` doc page for
page for additional tools that can use CHARMM, AMBER, or Materials additional tools that can use CHARMM, AMBER, or Materials Studio
Studio generated files to assign force field coefficients and convert generated files to assign force field coefficients and convert their
their output into LAMMPS input. output into LAMMPS input.
See :ref:`(MacKerell) <howto-MacKerell>` for a description of the CHARMM force See :ref:`(MacKerell) <howto-MacKerell>` for a description of the CHARMM
field. See :ref:`(Cornell) <howto-Cornell>` for a description of the AMBER force field. See :ref:`(Cornell) <howto-Cornell>` for a description of
force field. See :ref:`(Sun) <howto-Sun>` for a description of the COMPASS the AMBER force field. See :ref:`(Sun) <howto-Sun>` for a description
force field. of the COMPASS force field.
.. _charmm: http://www.scripps.edu/brooks
.. _amber: http://amber.scripps.edu
The interaction styles listed below compute force field formulas that The interaction styles listed below compute force field formulas that
are consistent with common options in CHARMM or AMBER. See each are consistent with common options in CHARMM or AMBER. See each
@ -41,9 +37,10 @@ command's documentation for the formula it computes.
.. note:: .. note::
For CHARMM, newer *charmmfsw* or *charmmfsh* styles were released For CHARMM, newer *charmmfsw* or *charmmfsh* styles were released in
in March 2017. We recommend they be used instead of the older *charmm* March 2017. We recommend they be used instead of the older *charmm*
styles. See discussion of the differences on the :doc:`pair charmm <pair_charmm>` and :doc:`dihedral charmm <dihedral_charmm>` doc styles. See discussion of the differences on the :doc:`pair charmm
<pair_charmm>` and :doc:`dihedral charmm <dihedral_charmm>` doc
pages. pages.
COMPASS is a general force field for atomistic simulation of common COMPASS is a general force field for atomistic simulation of common

113
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@ -33,46 +33,6 @@ reference state of a bond. Bonds that are created midway into a run,
such as those created by pouring grains using :doc:`fix pour such as those created by pouring grains using :doc:`fix pour
<fix_pour>`, are initialized on that timestep. <fix_pour>`, are initialized on that timestep.
As bonds can be broken between neighbor list builds, the
:doc:`special_bonds <special_bonds>` command works differently for BPM
bond styles. There are two possible settings which determine how pair
interactions work between bonded particles. First, one can turn off
all pair interactions between bonded particles. Unlike :doc:`bond
quartic <bond_quartic>`, this is not done by subtracting pair forces
during the bond computation but rather by dynamically updating the
special bond list. This is the default behavior of BPM bond styles and
is done by updating the 1-2 special bond list as bonds break. To do
this, LAMMPS requires :doc:`newton <newton>` bond off such that all
processors containing an atom know when a bond breaks. Additionally,
one must do either (A) or (B).
A) Use the following special bond settings
.. code-block:: LAMMPS
special_bonds lj 0 1 1 coul 1 1 1
These settings accomplish two goals. First, they turn off 1-3 and 1-4
special bond lists, which are not currently supported for BPMs. As
BPMs often have dense bond networks, generating 1-3 and 1-4 special
bond lists is expensive. By setting the lj weight for 1-2 bonds to
zero, this turns off pairwise interactions. Even though there are no
charges in BPM models, setting a nonzero coul weight for 1-2 bonds
ensures all bonded neighbors are still included in the neighbor list
in case bonds break between neighbor list builds.
B) Alternatively, one can simply overlay pair interactions such that all
bonded particles also feel pair interactions. This can be
accomplished by using the *overlay/pair* keyword present in all bpm
bond styles and by using the following special bond settings
.. code-block:: LAMMPS
special_bonds lj/coul 1 1 1
See the :doc:`Howto <Howto_broken_bonds>` page on broken bonds for
more information.
---------- ----------
Currently there are two types of bonds included in the BPM Currently there are two types of bonds included in the BPM
@ -91,12 +51,6 @@ This also requires a unique integrator :doc:`fix nve/bpm/sphere
<fix_nve_bpm_sphere>` which numerically integrates orientation similar <fix_nve_bpm_sphere>` which numerically integrates orientation similar
to :doc:`fix nve/asphere <fix_nve_asphere>`. to :doc:`fix nve/asphere <fix_nve_asphere>`.
To monitor the fracture of bonds in the system, all BPM bond styles
have the ability to record instances of bond breakage to output using
the :doc:`dump local <dump>` command. Additionally, one can use
:doc:`compute nbond/atom <compute_nbond_atom>` to tally the current
number of bonds per atom.
In addition to bond styles, a new pair style :doc:`pair bpm/spring In addition to bond styles, a new pair style :doc:`pair bpm/spring
<pair_bpm_spring>` was added to accompany the bpm/spring bond <pair_bpm_spring>` was added to accompany the bpm/spring bond
style. This pair style is simply a hookean repulsion with similar style. This pair style is simply a hookean repulsion with similar
@ -104,6 +58,73 @@ velocity damping as its sister bond style.
---------- ----------
Bond data can be output using a combination of standard LAMMPS commands.
A list of IDs for bonded atoms can be generated using the
:doc:`compute property/local <compute_property_local>` command.
Various properties of bonds can be computed using the
:doc:`compute bond/local <compute_bond_local>` command. This
command allows one to access data saved to the bond's history
such as the reference length of the bond. More information on
bond history data can be found on the documentation pages for the specific
BPM bond styles. Finally, this data can be output using a :doc:`dump local <dump>`
command. As one may output many columns from the same compute, the
:doc:`dump modify <dump_modify>` *colname* option may be used to provide
more helpful column names. An example of this procedure is found in
/examples/bpm/pour/. External software, such as OVITO, can read these dump
files to render bond data.
----------
As bonds can be broken between neighbor list builds, the
:doc:`special_bonds <special_bonds>` command works differently for BPM
bond styles. There are two possible settings which determine how pair
interactions work between bonded particles. First, one can overlay
pair forces with bond forces such that all bonded particles also
feel pair interactions. This can be accomplished by using the *overlay/pair*
keyword present in all bpm bond styles and by using the following special
bond settings
.. code-block:: LAMMPS
special_bonds lj/coul 1 1 1
Alternatively, one can turn off all pair interactions between bonded
particles. Unlike :doc:`bond quartic <bond_quartic>`, this is not done
by subtracting pair forces during the bond computation but rather by
dynamically updating the special bond list. This is the default behavior
of BPM bond styles and is done by updating the 1-2 special bond list as
bonds break. To do this, LAMMPS requires :doc:`newton <newton>` bond off
such that all processors containing an atom know when a bond breaks.
Additionally, one must use the following special bond settings
.. code-block:: LAMMPS
special_bonds lj 0 1 1 coul 1 1 1
These settings accomplish two goals. First, they turn off 1-3 and 1-4
special bond lists, which are not currently supported for BPMs. As
BPMs often have dense bond networks, generating 1-3 and 1-4 special
bond lists is expensive. By setting the lj weight for 1-2 bonds to
zero, this turns off pairwise interactions. Even though there are no
charges in BPM models, setting a nonzero coul weight for 1-2 bonds
ensures all bonded neighbors are still included in the neighbor list
in case bonds break between neighbor list builds.
To monitor the fracture of bonds in the system, all BPM bond styles
have the ability to record instances of bond breakage to output using
the :doc:`dump local <dump>` command. Since one may frequently output
a list of broken bonds and the time they broke, the
:doc:`dump modify <dump_modify>` option *header no* may be useful to
avoid repeatedly printing the header of the dump file. An example of
this procedure is found in /examples/bpm/impact/. Additionally,
one can use :doc:`compute nbond/atom <compute_nbond_atom>` to tally the
current number of bonds per atom.
See the :doc:`Howto <Howto_broken_bonds>` page on broken bonds for
more information.
----------
While LAMMPS has many utilities to create and delete bonds, *only* While LAMMPS has many utilities to create and delete bonds, *only*
the following are currently compatible with BPM bond styles: the following are currently compatible with BPM bond styles:

2
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@ -10,7 +10,7 @@ changes or additions you have made to LAMMPS into the official LAMMPS
distribution. It uses the process of updating this very tutorial as an distribution. It uses the process of updating this very tutorial as an
example to describe the individual steps and options. You need to be example to describe the individual steps and options. You need to be
familiar with git and you may want to have a look at the `git book familiar with git and you may want to have a look at the `git book
<http://git-scm.com/book/>`_ to familiarize yourself with some of the <https://git-scm.com/book/>`_ to familiarize yourself with some of the
more advanced git features used below. more advanced git features used below.
As of fall 2016, submitting contributions to LAMMPS via pull requests As of fall 2016, submitting contributions to LAMMPS via pull requests

2
doc/src/Howto_manifold.rst
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@ -47,4 +47,4 @@ to the relevant fixes.
.. _Paquay1: .. _Paquay1:
**(Paquay)** Paquay and Kusters, Biophys. J., 110, 6, (2016). **(Paquay)** Paquay and Kusters, Biophys. J., 110, 6, (2016).
preprint available at `arXiv:1411.3019 <http://arxiv.org/abs/1411.3019/>`_. preprint available at `arXiv:1411.3019 <https://arxiv.org/abs/1411.3019/>`_.

2
doc/src/Howto_spc.rst
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@ -38,7 +38,7 @@ the partial charge assignments change:
See the :ref:`(Berendsen) <howto-Berendsen>` reference for more details on both See the :ref:`(Berendsen) <howto-Berendsen>` reference for more details on both
the SPC and SPC/E models. the SPC and SPC/E models.
Wikipedia also has a nice article on `water models <http://en.wikipedia.org/wiki/Water_model>`_. Wikipedia also has a nice article on `water models <https://en.wikipedia.org/wiki/Water_model>`_.
---------- ----------

16
doc/src/Howto_spins.rst
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@ -30,9 +30,11 @@ can be coupled to another Langevin thermostat applied to the atoms
using :doc:`fix langevin <fix_langevin>` in order to simulate using :doc:`fix langevin <fix_langevin>` in order to simulate
thermostatted spin-lattice systems. thermostatted spin-lattice systems.
The magnetic Gilbert damping can also be applied using :doc:`fix langevin/spin <fix_langevin_spin>`. It allows to either dissipate The magnetic damping can also be applied
the thermal energy of the Langevin thermostat, or to perform a using :doc:`fix langevin/spin <fix_langevin_spin>`.
relaxation of the magnetic configuration toward an equilibrium state. It allows to either dissipate the thermal energy of the Langevin
thermostat, or to perform a relaxation of the magnetic configuration
toward an equilibrium state.
The command :doc:`fix setforce/spin <fix_setforce>` allows to set the The command :doc:`fix setforce/spin <fix_setforce>` allows to set the
components of the magnetic precession vectors (while erasing and components of the magnetic precession vectors (while erasing and
@ -52,9 +54,11 @@ All the computed magnetic properties can be output by two main
commands. The first one is :doc:`compute spin <compute_spin>`, that commands. The first one is :doc:`compute spin <compute_spin>`, that
enables to evaluate magnetic averaged quantities, such as the total enables to evaluate magnetic averaged quantities, such as the total
magnetization of the system along x, y, or z, the spin temperature, or magnetization of the system along x, y, or z, the spin temperature, or
the magnetic energy. The second command is :doc:`compute property/atom <compute_property_atom>`. It enables to output all the the magnetic energy. The second command
per atom magnetic quantities. Typically, the orientation of a given is :doc:`compute property/atom <compute_property_atom>`.
magnetic spin, or the magnetic force acting on this spin. It enables to output all the per atom magnetic quantities. Typically,
the orientation of a given magnetic spin, or the magnetic force
acting on this spin.
---------- ----------

2
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@ -49,7 +49,7 @@ details:
| :math:`\theta` of HOH angle = 104.52\ :math:`^{\circ}` | :math:`\theta` of HOH angle = 104.52\ :math:`^{\circ}`
| |
Wikipedia also has a nice article on `water models <http://en.wikipedia.org/wiki/Water_model>`_. Wikipedia also has a nice article on `water models <https://en.wikipedia.org/wiki/Water_model>`_.
---------- ----------

2
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@ -97,7 +97,7 @@ This leads to slightly larger cost for the long-range calculation, so
you can test the trade-off for your model. The OM distance and the LJ you can test the trade-off for your model. The OM distance and the LJ
and Coulombic cutoffs are set in the :doc:`pair_style lj/cut/tip4p/long <pair_lj_cut_tip4p>` command. and Coulombic cutoffs are set in the :doc:`pair_style lj/cut/tip4p/long <pair_lj_cut_tip4p>` command.
Wikipedia also has a nice article on `water models <http://en.wikipedia.org/wiki/Water_model>`_. Wikipedia also has a nice article on `water models <https://en.wikipedia.org/wiki/Water_model>`_.
---------- ----------

126
doc/src/Howto_type_labels.rst Normal file
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@ -0,0 +1,126 @@
Type labels
===========
.. versionadded:: 15Sep2022
Each atom in LAMMPS has an associated numeric atom type. Similarly,
each bond, angle, dihedral, and improper is assigned a bond type,
angle type, and so on. The primary use of these types is to map
potential (force field) parameters to the interactions of the atom,
bond, angle, dihedral, and improper.
By default, type values are entered as integers from 1 to Ntypes
wherever they appear in LAMMPS input or output files. The total number
Ntypes for each interaction is "locked in" when the simulation box
is created.
A recent addition to LAMMPS is the option to use strings - referred
to as type labels - as an alternative. Using type labels instead of
numeric types can be advantageous in various scenarios. For example,
type labels can make inputs more readable and generic (i.e. usable through
the :doc:`include command <include>` for different systems with different
numerical values assigned to types. This generality also applies to
other inputs like data files read by :doc:`read_data <read_data>` or
molecule template files read by the :doc:`molecule <molecule>`
command. See below for a list of other commands that can use
type labels in different ways.
LAMMPS will *internally* continue to use numeric types, which means
that many previous restrictions still apply. For example, the total
number of types is locked in when creating the simulation box, and
potential parameters for each type must be provided even if not used
by any interactions.
A collection of type labels for all type-kinds (atom types, bond types,
etc.) is stored as a "label map" which is simply a list of numeric types
and their associated type labels. Within a type-kind, each type label
must be unique. It can be assigned to only one numeric type. To read
and write type labels to data files for a given type-kind, *all*
associated numeric types need have a type label assigned. Partial
maps can be saved with the :doc:`labelmap write <labelmap>` command
and read back with the :doc:`include <include>` command.
Valid type labels can contain most ASCII characters, but cannot start
with a number, a '#', or a '*'. Also, labels must not contain whitespace
characters. When using the :doc:`labelmap command <labelmap>` in the
LAMMPS input, if certain characters appear in the type label, such as
the single (') or double (") quote or the '#' character, the label
must be put in either double, single, or triple (""") quotes. Triple
quotes allow for the most generic type label strings, but they require
to have a leading and trailing blank space. When defining type labels
the blanks will be ignored. Example:
.. code-block:: LAMMPS
labelmap angle 1 """ C1'-C2"-C3# """
This command will map the string ```C1'-C2"-C3#``` to the angle type 1.
There are two ways to define label maps. One is via the :doc:`labelmap
<labelmap>` command. The other is via the :doc:`read_data <read_data>`
command. A data file can have sections such as *Atom Type Labels*, *Bond
Type Labels*, etc., which assign type labels to numeric types. The
label map can be written out to data files by the :doc:`write_data
<write_data>` command. This map is also written to and read from
restart files, by the :doc:`write_restart <write_restart>` and
:doc:`read_restart <read_restart>` commands.
----------
Use of type labels in LAMMPS input or output
""""""""""""""""""""""""""""""""""""""""""""
Many LAMMPS input script commands that take a numeric type as an
argument can use the associated type label instead. If a type label
is not defined for a particular numeric type, only its numeric type
can be used.
This example assigns labels to the atom types, and then uses the type
labels to redefine the pair coefficients.
.. code-block:: LAMMPS
pair_coeff 1 2 1.0 1.0 # numeric types
labelmap atom 1 C 2 H
pair_coeff C H 1.0 1.0 # type labels
Adding support for type labels to various commands is an ongoing
project. If an input script command (or a section in a file read by a
command) allows substituting a type label for a numeric type argument,
it will be explicitly mentioned in that command's documentation page.
As a temporary measure, input script commands can take advantage of
variables and how they can be expanded during processing of the input.
The variables can use functions that will translate type label strings
to their respective number as defined in the current label map. See the
:doc:`variable <variable>` command for details.
For example, here is how the pair_coeff command could be used with
type labels if it did not yet support them, either with an explicit
variable command or an implicit variable used in the pair_coeff
command.
.. code-block:: LAMMPS
labelmap atom 1 C 2 H
variable atom1 equal label2type(atom,C)
variable atom2 equal label2type(atom,H)
pair_coeff ${atom1} ${atom2} 1.0 1.0
.. code-block:: LAMMPS
labelmap atom 1 C 2 H
pair_coeff $(label2type(atom,C)) $(label2type(atom,H)) 80.0 1.2
----------
Commands that can use label types
"""""""""""""""""""""""""""""""""
Any workflow that involves reading multiple data files, molecule
templates or a combination of the two can be streamlined by using type
labels instead of numeric types, because types are automatically synced
between the files. The creation of simulation-ready reaction templates
for :doc:`fix bond/react <fix_bond_react>` is much simpler when using
type labels, and results in templates that can be used without
modification in multiple simulations or different systems.

7
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@ -17,9 +17,10 @@ formats. See the :doc:`Tools <Tools>` page for details.
A Python-based toolkit distributed by our group can read native LAMMPS A Python-based toolkit distributed by our group can read native LAMMPS
dump files, including custom dump files with additional columns of dump files, including custom dump files with additional columns of
user-specified atom information, and convert them to various formats user-specified atom information, and convert them to various formats or
or pipe them into visualization software directly. See the `Pizza.py WWW site <pizza_>`_ for details. Specifically, Pizza.py can convert pipe them into visualization software directly. See the `Pizza.py WWW
LAMMPS dump files into PDB, XYZ, `EnSight <ensight_>`_, and VTK formats. site <pizza_>`_ for details. Specifically, Pizza.py can convert LAMMPS
dump files into PDB, XYZ, `EnSight <ensight_>`_, and VTK formats.
Pizza.py can pipe LAMMPS dump files directly into the Raster3d and Pizza.py can pipe LAMMPS dump files directly into the Raster3d and
RasMol visualization programs. Pizza.py has tools that do interactive RasMol visualization programs. Pizza.py has tools that do interactive
3d OpenGL visualization and one that creates SVG images of dump file 3d OpenGL visualization and one that creates SVG images of dump file

4
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@ -5,7 +5,7 @@ Binaries are available for MacOS or Linux via `Conda <conda_>`_.
First, one must setup the Conda package manager on your system. Follow the First, one must setup the Conda package manager on your system. Follow the
instructions to install `Miniconda <mini_conda_install_>`_, then create a conda instructions to install `Miniconda <mini_conda_install_>`_, then create a conda
environment (named `my-lammps-env` or whatever you prefer) for your lammps environment (named `my-lammps-env` or whatever you prefer) for your LAMMPS
install: install:
.. code-block:: bash .. code-block:: bash
@ -13,7 +13,7 @@ install:
% conda config --add channels conda-forge % conda config --add channels conda-forge
% conda create -n my-lammps-env % conda create -n my-lammps-env
Then, you can install lammps on your system with the following command: Then, you can install LAMMPS on your system with the following command:
.. code-block:: bash .. code-block:: bash

2
doc/src/Install_windows.rst
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@ -6,7 +6,7 @@ Windows system can be downloaded from this site:
.. parsed-literal:: .. parsed-literal::
`http://packages.lammps.org/windows.html <http://packages.lammps.org/windows.html>`_ `https://packages.lammps.org/windows.html <https://packages.lammps.org/windows.html>`_
Note that each installer package has a date in its name, which Note that each installer package has a date in its name, which
corresponds to the LAMMPS version of the same date. Installers for corresponds to the LAMMPS version of the same date. Installers for

4
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@ -4,13 +4,13 @@ Authors of LAMMPS
The primary LAMMPS developers are at Sandia National Labs and Temple The primary LAMMPS developers are at Sandia National Labs and Temple
University: University:
* `Steve Plimpton <sjp_>`_, sjplimp at sandia.gov * `Steve Plimpton <sjp_>`_, sjplimp at gmail.com
* Aidan Thompson, athomps at sandia.gov * Aidan Thompson, athomps at sandia.gov
* Stan Moore, stamoor at sandia.gov * Stan Moore, stamoor at sandia.gov
* Axel Kohlmeyer, akohlmey at gmail.com * Axel Kohlmeyer, akohlmey at gmail.com
* Richard Berger, richard.berger at outlook.com * Richard Berger, richard.berger at outlook.com
.. _sjp: http://www.cs.sandia.gov/~sjplimp .. _sjp: https://sjplimp.github.io
.. _lws: https://www.lammps.org .. _lws: https://www.lammps.org
Past developers include Paul Crozier and Mark Stevens, both at Sandia, Past developers include Paul Crozier and Mark Stevens, both at Sandia,

2
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@ -27,7 +27,7 @@ namely https://www.lammps.org.
The original publication describing the parallel algorithms used in the The original publication describing the parallel algorithms used in the
initial versions of LAMMPS is: initial versions of LAMMPS is:
`S. Plimpton, Fast Parallel Algorithms for Short-Range Molecular Dynamics, J Comp Phys, 117, 1-19 (1995). <http://www.sandia.gov/~sjplimp/papers/jcompphys95.pdf>`_ `S. Plimpton, Fast Parallel Algorithms for Short-Range Molecular Dynamics, J Comp Phys, 117, 1-19 (1995). <https://doi.org/10.1006/jcph.1995.1039>`_
DOI for the LAMMPS source code DOI for the LAMMPS source code

4
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@ -95,7 +95,7 @@ commands)
* metal-organic framework potentials (QuickFF, MO-FF) * metal-organic framework potentials (QuickFF, MO-FF)
* implicit solvent potentials: hydrodynamic lubrication, Debye * implicit solvent potentials: hydrodynamic lubrication, Debye
* force-field compatibility with common CHARMM, AMBER, DREIDING, OPLS, GROMACS, COMPASS options * force-field compatibility with common CHARMM, AMBER, DREIDING, OPLS, GROMACS, COMPASS options
* access to the `OpenKIM Repository <http://openkim.org>`_ of potentials via :doc:`kim command <kim_commands>` * access to the `OpenKIM Repository <https://openkim.org>`_ of potentials via the :doc:`kim command <kim_commands>`
* hybrid potentials: multiple pair, bond, angle, dihedral, improper potentials can be used in one simulation * hybrid potentials: multiple pair, bond, angle, dihedral, improper potentials can be used in one simulation
* overlaid potentials: superposition of multiple pair potentials (including many-body) with optional scale factor * overlaid potentials: superposition of multiple pair potentials (including many-body) with optional scale factor
@ -205,7 +205,7 @@ Pre- and post-processing
.. _pizza: https://lammps.github.io/pizza .. _pizza: https://lammps.github.io/pizza
.. _python: http://www.python.org .. _python: https://www.python.org
.. _special: .. _special:

6
doc/src/Intro_nonfeatures.rst
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@ -33,7 +33,7 @@ Here are suggestions on how to perform these tasks:
linear bead-spring polymer chains. The moltemplate program is a true linear bead-spring polymer chains. The moltemplate program is a true
molecular builder that will generate complex molecular models. See molecular builder that will generate complex molecular models. See
the :doc:`Tools <Tools>` page for details on tools packaged with the :doc:`Tools <Tools>` page for details on tools packaged with
LAMMPS. The `Pre/post processing page <http:/www.lammps.org/prepost.html>`_ of the LAMMPS website LAMMPS. The `Pre/post processing page <https:/www.lammps.org/prepost.html>`_ of the LAMMPS website
describes a variety of third 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
@ -80,5 +80,5 @@ Here are suggestions on how to perform these tasks:
`Pizza.py <https://lammps.github.io/pizza>`_ which can do certain kinds of `Pizza.py <https://lammps.github.io/pizza>`_ which can do certain kinds of
setup, analysis, plotting, and visualization (via OpenGL) for LAMMPS setup, analysis, plotting, and visualization (via OpenGL) for LAMMPS
simulations. It thus provides some functionality for several of the simulations. It thus provides some functionality for several of the
above bullets. Pizza.py is written in `Python <http://www.python.org>`_ above bullets. Pizza.py is written in `Python <https://www.python.org>`_
and is available for download from `this page <http://www.cs.sandia.gov/~sjplimp/download.html>`_. and is available for download from `this page <https://sjplimp.github.io/download.html>`_.

4
doc/src/Intro_opensource.rst
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@ -23,9 +23,9 @@ applies to LAMMPS is in the LICENSE file included in the LAMMPS distribution.
.. _lgpl: https://www.gnu.org/licenses/old-licenses/lgpl-2.1.html .. _lgpl: https://www.gnu.org/licenses/old-licenses/lgpl-2.1.html
.. _gnuorg: http://www.gnu.org .. _gnuorg: https://www.gnu.org
.. _opensource: http://www.opensource.org .. _opensource: https://www.opensource.org
Here is a more specific summary of what the GPL means for LAMMPS users: Here is a more specific summary of what the GPL means for LAMMPS users:

6
doc/src/Library_create.rst
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@ -11,6 +11,7 @@ This section documents the following functions:
- :cpp:func:`lammps_mpi_finalize` - :cpp:func:`lammps_mpi_finalize`
- :cpp:func:`lammps_kokkos_finalize` - :cpp:func:`lammps_kokkos_finalize`
- :cpp:func:`lammps_python_finalize` - :cpp:func:`lammps_python_finalize`
- :cpp:func:`lammps_error`
-------------------- --------------------
@ -115,3 +116,8 @@ calling program.
.. doxygenfunction:: lammps_python_finalize .. doxygenfunction:: lammps_python_finalize
:project: progguide :project: progguide
-----------------------
.. doxygenfunction:: lammps_error
:project: progguide

30
doc/src/Library_properties.rst
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@ -15,21 +15,21 @@ This section documents the following functions:
-------------------- --------------------
The library interface allows extraction of different kinds of The library interface allows the extraction of different kinds of
information about the active simulation instance and also information about the active simulation instance and also - in some
modifications to it. This enables combining of a LAMMPS simulation cases - to apply modifications to it. This enables combining of a
with other processing and simulation methods computed by the calling LAMMPS simulation with other processing and simulation methods computed
code, or by another code that is coupled to LAMMPS via the library by the calling code, or by another code that is coupled to LAMMPS via
interface. In some cases the data returned is direct reference to the the library interface. In some cases the data returned is direct
original data inside LAMMPS, cast to a void pointer. In that case the reference to the original data inside LAMMPS, cast to a void pointer.
data needs to be cast to a suitable pointer for the calling program to In that case the data needs to be cast to a suitable pointer for the
access it, and you may need to know the correct dimensions and calling program to access it, and you may need to know the correct
lengths. This also means you can directly change those value(s) from dimensions and lengths. This also means you can directly change those
the calling program, e.g. to modify atom positions. Of course, this value(s) from the calling program, e.g. to modify atom positions. Of
should be done with care. When accessing per-atom data, please note course, this should be done with care. When accessing per-atom data,
that this data is the per-processor **local** data and is indexed please note that this data is the per-processor **local** data and is
accordingly. Per-atom data can change sizes and ordering at every indexed accordingly. Per-atom data can change sizes and ordering at
neighbor list rebuild or atom sort event as atoms migrate between every neighbor list rebuild or atom sort event as atoms migrate between
sub-domains and processors. sub-domains and processors.
.. code-block:: C .. code-block:: C

7
doc/src/Library_utility.rst
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@ -19,6 +19,7 @@ functions. They do not directly call the LAMMPS library.
- :cpp:func:`lammps_force_timeout` - :cpp:func:`lammps_force_timeout`
- :cpp:func:`lammps_has_error` - :cpp:func:`lammps_has_error`
- :cpp:func:`lammps_get_last_error_message` - :cpp:func:`lammps_get_last_error_message`
- :cpp:func:`lammps_python_api_version`
The :cpp:func:`lammps_free` function is a clean-up function to free The :cpp:func:`lammps_free` function is a clean-up function to free
memory that the library had allocated previously via other function memory that the library had allocated previously via other function
@ -100,3 +101,9 @@ where such memory buffers were allocated that require the use of
.. doxygenfunction:: lammps_get_last_error_message .. doxygenfunction:: lammps_get_last_error_message
:project: progguide :project: progguide
-----------------------
.. doxygenfunction:: lammps_python_api_version
:project: progguide

48
doc/src/Packages_details.rst
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@ -134,6 +134,8 @@ commands to write and read data using the ADIOS library.
**Authors:** Norbert Podhorszki (ORNL) from the ADIOS developer team. **Authors:** Norbert Podhorszki (ORNL) from the ADIOS developer team.
.. versionadded:: 28Feb2019
**Install:** **Install:**
This package has :ref:`specific installation instructions <adios>` on the :doc:`Build extras <Build_extras>` page. This package has :ref:`specific installation instructions <adios>` on the :doc:`Build extras <Build_extras>` page.
@ -276,7 +278,7 @@ the barostat as outlined in:
N. J. H. Dunn and W. G. Noid, "Bottom-up coarse-grained models that N. J. H. Dunn and W. G. Noid, "Bottom-up coarse-grained models that
accurately describe the structure, pressure, and compressibility of accurately describe the structure, pressure, and compressibility of
molecular liquids," J. Chem. Phys. 143, 243148 (2015). molecular liquids", J. Chem. Phys. 143, 243148 (2015).
**Authors:** Nicholas J. H. Dunn and Michael R. DeLyser (The **Authors:** Nicholas J. H. Dunn and Michael R. DeLyser (The
Pennsylvania State University) Pennsylvania State University)
@ -364,6 +366,8 @@ and also support self-propelled particles.
**Authors:** Sam Cameron (University of Bristol), **Authors:** Sam Cameron (University of Bristol),
Stefan Paquay (while at Brandeis University) (initial version of fix propel/self) Stefan Paquay (while at Brandeis University) (initial version of fix propel/self)
.. versionadded:: 14May2021
Example inputs are in the examples/PACKAGES/brownian folder. Example inputs are in the examples/PACKAGES/brownian folder.
---------- ----------
@ -592,6 +596,8 @@ To use this package, also the :ref:`KSPACE <PKG-KSPACE>` and
**Author:** Trung Nguyen and Monica Olvera de la Cruz (Northwestern U) **Author:** Trung Nguyen and Monica Olvera de la Cruz (Northwestern U)
.. versionadded:: 2Jul2021
**Supporting info:** **Supporting info:**
* src/DIELECTRIC: filenames -> commands * src/DIELECTRIC: filenames -> commands
@ -932,6 +938,10 @@ EXTRA-MOLECULE package
Additional bond, angle, dihedral, and improper styles that are less commonly used. Additional bond, angle, dihedral, and improper styles that are less commonly used.
**Install:**
To use this package, also the :ref:`MOLECULE <PKG-MOLECULE>` package needs to be installed.
**Supporting info:** **Supporting info:**
* src/EXTRA-MOLECULE: filenames -> commands * src/EXTRA-MOLECULE: filenames -> commands
@ -1067,7 +1077,7 @@ H5MD is a format for molecular simulations, built on top of HDF5.
This package implements a :doc:`dump h5md <dump_h5md>` command to output This package implements a :doc:`dump h5md <dump_h5md>` command to output
LAMMPS snapshots in this format. LAMMPS snapshots in this format.
.. _HDF5: http://www.hdfgroup.org/HDF5 .. _HDF5: https://www.hdfgroup.org/solutions/hdf5
To use this package you must have the HDF5 library available on your To use this package you must have the HDF5 library available on your
system. system.
@ -1508,6 +1518,8 @@ workflows via the `MolSSI Driver Interface
**Author:** Taylor Barnes - MolSSI, taylor.a.barnes at gmail.com **Author:** Taylor Barnes - MolSSI, taylor.a.barnes at gmail.com
.. versionadded:: 14May2021
**Install:** **Install:**
This package has :ref:`specific installation instructions <mdi>` on This package has :ref:`specific installation instructions <mdi>` on
@ -1592,6 +1604,8 @@ of Alabama), Leonid V. Zhigilei (University of Virginia)
**Author of the *mesocnt* styles:** **Author of the *mesocnt* styles:**
Philipp Kloza (U Cambridge) Philipp Kloza (U Cambridge)
.. versionadded:: 15Jun2020
**Supporting info:** **Supporting info:**
* src/MESONT: filenames -> commands * src/MESONT: filenames -> commands
@ -1684,6 +1698,8 @@ compiled on your system.
**Author:** Andreas Singraber **Author:** Andreas Singraber
.. versionadded:: 27May2021
**Install:** **Install:**
This package has :ref:`specific installation instructions <ml-hdnnp>` on the This package has :ref:`specific installation instructions <ml-hdnnp>` on the
@ -1718,6 +1734,10 @@ must be installed.
**Author:** Aidan Thompson (Sandia), Nicholas Lubbers (LANL). **Author:** Aidan Thompson (Sandia), Nicholas Lubbers (LANL).
.. versionadded:: 30Jun2020
.. versionadded:: 30Jun2020
**Supporting info:** **Supporting info:**
* src/ML-IAP: filenames -> commands * src/ML-IAP: filenames -> commands
@ -1762,6 +1782,8 @@ Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1.
^4: University of British Columbia, Vancouver, BC, Canada ^4: University of British Columbia, Vancouver, BC, Canada
.. versionadded:: 14May2021
**Install:** **Install:**
This package has :ref:`specific installation instructions <ml-pace>` on the This package has :ref:`specific installation instructions <ml-pace>` on the
@ -1825,6 +1847,8 @@ of a neural network.
This package was written by Christopher Barrett This package was written by Christopher Barrett
with contributions by Doyl Dickel, Mississippi State University. with contributions by Doyl Dickel, Mississippi State University.
.. versionadded:: 27May2021
**Supporting info:** **Supporting info:**
* src/ML-RANN: filenames -> commands * src/ML-RANN: filenames -> commands
@ -1950,7 +1974,7 @@ support for new file formats can be added to LAMMPS (or VMD or other
programs that use them) without having to re-compile the application programs that use them) without having to re-compile the application
itself. More information about the VMD molfile plugins can be found itself. More information about the VMD molfile plugins can be found
at at
`http://www.ks.uiuc.edu/Research/vmd/plugins/molfile <http://www.ks.uiuc.edu/Research/vmd/plugins/molfile>`_. `https://www.ks.uiuc.edu/Research/vmd/plugins/molfile <https://www.ks.uiuc.edu/Research/vmd/plugins/molfile>`_.
**Author:** Axel Kohlmeyer (Temple U). **Author:** Axel Kohlmeyer (Temple U).
@ -2041,7 +2065,7 @@ NETCDF package
Dump styles for writing NetCDF formatted dump files. NetCDF is a Dump styles for writing NetCDF formatted dump files. NetCDF is a
portable, binary, self-describing file format developed on top of portable, binary, self-describing file format developed on top of
HDF5. The file contents follow the AMBER NetCDF trajectory conventions HDF5. The file contents follow the AMBER NetCDF trajectory conventions
(http://ambermd.org/netcdf/nctraj.xhtml), but include extensions. (https://ambermd.org/netcdf/nctraj.xhtml), but include extensions.
To use this package you must have the NetCDF library available on your To use this package you must have the NetCDF library available on your
system. system.
@ -2052,7 +2076,7 @@ tools:
* `Ovito <ovito_>`_ (Ovito supports the AMBER convention and the extensions mentioned above) * `Ovito <ovito_>`_ (Ovito supports the AMBER convention and the extensions mentioned above)
* `VMD <vmd-home_>`_ * `VMD <vmd-home_>`_
.. _ovito: http://www.ovito.org .. _ovito: https://www.ovito.org
.. _vmd-home: https://www.ks.uiuc.edu/Research/vmd/ .. _vmd-home: https://www.ks.uiuc.edu/Research/vmd/
@ -2260,6 +2284,8 @@ try to load the contained plugins automatically at start-up.
**Authors:** Axel Kohlmeyer (Temple U) **Authors:** Axel Kohlmeyer (Temple U)
.. versionadded:: 8Apr2021
**Supporting info:** **Supporting info:**
* src/PLUGIN: filenames -> commands * src/PLUGIN: filenames -> commands
@ -2413,7 +2439,7 @@ A :doc:`fix qmmm <fix_qmmm>` command which allows LAMMPS to be used as
the MM code in a QM/MM simulation. This is currently only available the MM code in a QM/MM simulation. This is currently only available
in combination with the `Quantum ESPRESSO <espresso_>`_ package. in combination with the `Quantum ESPRESSO <espresso_>`_ package.
.. _espresso: http://www.quantum-espresso.org .. _espresso: https://www.quantum-espresso.org
To use this package you must have Quantum ESPRESSO (QE) available on To use this package you must have Quantum ESPRESSO (QE) available on
your system and include its coupling library in the compilation and your system and include its coupling library in the compilation and
@ -2825,7 +2851,7 @@ collection of atoms by wrapping the `Voro++ library <voro-home_>`_. This
can be used to calculate the local volume or each atoms or its near can be used to calculate the local volume or each atoms or its near
neighbors. neighbors.
.. _voro-home: http://math.lbl.gov/voro++ .. _voro-home: https://math.lbl.gov/voro++
To use this package you must have the Voro++ library available on your To use this package you must have the Voro++ library available on your
system. system.
@ -2859,9 +2885,9 @@ A :doc:`dump vtk <dump_vtk>` command which outputs snapshot info in the
`VTK format <vtk_>`_, enabling visualization by `Paraview <paraview_>`_ or `VTK format <vtk_>`_, enabling visualization by `Paraview <paraview_>`_ or
other visualization packages. other visualization packages.
.. _vtk: http://www.vtk.org .. _vtk: https://www.vtk.org
.. _paraview: http://www.paraview.org .. _paraview: https://www.paraview.org
To use this package you must have VTK library available on your To use this package you must have VTK library available on your
system. system.
@ -2898,11 +2924,13 @@ which discuss the `QuickFF <quickff_>`_ methodology.
.. _vanduyfhuys2015: https://doi.org/10.1002/jcc.23877 .. _vanduyfhuys2015: https://doi.org/10.1002/jcc.23877
.. _vanduyfhuys2018: https://doi.org/10.1002/jcc.25173 .. _vanduyfhuys2018: https://doi.org/10.1002/jcc.25173
.. _quickff: http://molmod.github.io/QuickFF .. _quickff: https://molmod.github.io/QuickFF
.. _yaff: https://github.com/molmod/yaff .. _yaff: https://github.com/molmod/yaff
**Author:** Steven Vandenbrande. **Author:** Steven Vandenbrande.
.. versionadded:: 1Feb2019
**Supporting info:** **Supporting info:**
* src/YAFF/README * src/YAFF/README

20
doc/src/Python_examples.rst
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@ -43,26 +43,18 @@ Note that for AtomEye, you need version 3, and there is a line in the
scripts that specifies the path and name of the executable. See the scripts that specifies the path and name of the executable. See the
AtomEye web pages for more details: AtomEye web pages for more details:
* `http://li.mit.edu/Archive/Graphics/A/ <atomeye_>`_ * `http://li.mit.edu/Archive/Graphics/A/ <http://li.mit.edu/Archive/Graphics/A/>`_
* `http://li.mit.edu/Archive/Graphics/A3/A3.html <atomeye3_>`_ * `http://li.mit.edu/Archive/Graphics/A3/A3.html <http://li.mit.edu/Archive/Graphics/A3/A3.html>`_
.. _atomeye: http://li.mit.edu/Archive/Graphics/A/ The latter link is to AtomEye 3 which has the scripting capability
needed by these Python scripts.
.. _atomeye3: http://li.mit.edu/Archive/Graphics/A3/A3.html
The latter link is to AtomEye 3 which has the scripting
capability needed by these Python scripts.
Note that for PyMol, you need to have built and installed the Note that for PyMol, you need to have built and installed the
open-source version of PyMol in your Python, so that you can import it open-source version of PyMol in your Python, so that you can import it
from a Python script. See the PyMol web pages for more details: from a Python script. See the PyMol web pages for more details:
* `https://www.pymol.org <pymolhome_>`_ * `https://www.pymol.org <https://www.pymol.org>`_
* `https://github.com/schrodinger/pymol-open-source <pymolopen_>`_ * `https://github.com/schrodinger/pymol-open-source <https://github.com/schrodinger/pymol-open-source>`_
.. _pymolhome: https://www.pymol.org
.. _pymolopen: https://github.com/schrodinger/pymol-open-source
The latter link is to the open-source version. The latter link is to the open-source version.

10
doc/src/Python_head.rst
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@ -18,17 +18,17 @@ together.
Python_error Python_error
Python_trouble Python_trouble
If you are not familiar with `Python <http://www.python.org>`_, it is a If you are not familiar with `Python <https://www.python.org>`_, it is a
powerful scripting and programming language which can do almost powerful scripting and programming language which can do almost
everything that compiled languages like C, C++, or Fortran can do in everything that compiled languages like C, C++, or Fortran can do in
fewer lines of code. It also comes with a large collection of add-on fewer lines of code. It also comes with a large collection of add-on
modules for many purposes (either bundled or easily installed from modules for many purposes (either bundled or easily installed from
Python code repositories). The major drawback is slower execution speed Python code repositories). The major drawback is slower execution speed
of the script code compared to compiled programming languages. But when of the script code compared to compiled programming languages. But when
the script code is interfaced to optimized compiled code, performance can the script code is interfaced to optimized compiled code, performance
be on par with a standalone executable, for as long as the scripting is can be on par with a standalone executable, for as long as the scripting
restricted to high-level operations. Thus Python is also convenient to is restricted to high-level operations. Thus Python is also convenient
use as a "glue" language to "drive" a program through its library to use as a "glue" language to "drive" a program through its library
interface, or to hook multiple pieces of software together, such as a interface, or to hook multiple pieces of software together, such as a
simulation code and a visualization tool, or to run a coupled simulation code and a visualization tool, or to run a coupled
multi-scale or multi-physics model. multi-scale or multi-physics model.

2
doc/src/Run_options.rst
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@ -495,7 +495,7 @@ run:
write_dump group-ID dumpstyle dumpfile arg1 arg2 ... write_dump group-ID dumpstyle dumpfile arg1 arg2 ...
Note that the specified restartfile and dumpfile names may contain Note that the specified restartfile and dumpfile names may contain
wild-card characters ("\*","%") as explained on the wild-card characters ("\*" or "%") as explained on the
:doc:`read_restart <read_restart>` and :doc:`write_dump <write_dump>` doc :doc:`read_restart <read_restart>` and :doc:`write_dump <write_dump>` doc
pages. The use of "%" means that a parallel restart file and/or pages. The use of "%" means that a parallel restart file and/or
parallel dump file can be read and/or written. Note that a filename parallel dump file can be read and/or written. Note that a filename

4
doc/src/Run_windows.rst
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@ -25,8 +25,8 @@ in parallel, follow these steps.
Download and install a compatible MPI library binary package: Download and install a compatible MPI library binary package:
* for 32-bit Windows: `mpich2-1.4.1p1-win-ia32.msi <http://download.lammps.org/thirdparty/mpich2-1.4.1p1-win-ia32.msi>`_ * for 32-bit Windows: `mpich2-1.4.1p1-win-ia32.msi <https://download.lammps.org/thirdparty/mpich2-1.4.1p1-win-ia32.msi>`_
* for 64-bit Windows: `mpich2-1.4.1p1-win-x86-64.msi <http://download.lammps.org/thirdparty/mpich2-1.4.1p1-win-x86-64.msi>`_ * for 64-bit Windows: `mpich2-1.4.1p1-win-x86-64.msi <https://download.lammps.org/thirdparty/mpich2-1.4.1p1-win-x86-64.msi>`_
The LAMMPS Windows installer packages will automatically adjust your The LAMMPS Windows installer packages will automatically adjust your
path for the default location of this MPI package. After the path for the default location of this MPI package. After the

2
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@ -39,7 +39,7 @@ toolkit software on your system (this is only tested on Linux
and unsupported on Windows): and unsupported on Windows):
* Check if you have an NVIDIA GPU: cat /proc/driver/nvidia/gpus/\*/information * Check if you have an NVIDIA GPU: cat /proc/driver/nvidia/gpus/\*/information
* Go to http://www.nvidia.com/object/cuda_get.html * Go to https://developer.nvidia.com/cuda-downloads
* Install a driver and toolkit appropriate for your system (SDK is not necessary) * Install a driver and toolkit appropriate for your system (SDK is not necessary)
* Run lammps/lib/gpu/nvc_get_devices (after building the GPU library, see below) to * Run lammps/lib/gpu/nvc_get_devices (after building the GPU library, see below) to
list supported devices and properties list supported devices and properties

4
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@ -536,6 +536,6 @@ supported.
References References
"""""""""" """"""""""
* Brown, W.M., Carrillo, J.-M.Y., Mishra, B., Gavhane, N., Thakkar, F.M., De Kraker, A.R., Yamada, M., Ang, J.A., Plimpton, S.J., "Optimizing Classical Molecular Dynamics in LAMMPS," in Intel Xeon Phi Processor High Performance Programming: Knights Landing Edition, J. Jeffers, J. Reinders, A. Sodani, Eds. Morgan Kaufmann. * Brown, W.M., Carrillo, J.-M.Y., Mishra, B., Gavhane, N., Thakkar, F.M., De Kraker, A.R., Yamada, M., Ang, J.A., Plimpton, S.J., "Optimizing Classical Molecular Dynamics in LAMMPS", in Intel Xeon Phi Processor High Performance Programming: Knights Landing Edition, J. Jeffers, J. Reinders, A. Sodani, Eds. Morgan Kaufmann.
* Brown, W. M., Semin, A., Hebenstreit, M., Khvostov, S., Raman, K., Plimpton, S.J. `Increasing Molecular Dynamics Simulation Rates with an 8-Fold Increase in Electrical Power Efficiency. <http://dl.acm.org/citation.cfm?id=3014915>`_ 2016 High Performance Computing, Networking, Storage and Analysis, SC16: International Conference (pp. 82-95). * Brown, W. M., Semin, A., Hebenstreit, M., Khvostov, S., Raman, K., Plimpton, S.J. `Increasing Molecular Dynamics Simulation Rates with an 8-Fold Increase in Electrical Power Efficiency. <https://dl.acm.org/citation.cfm?id=3014915>`_ 2016 High Performance Computing, Networking, Storage and Analysis, SC16: International Conference (pp. 82-95).
* Brown, W.M., Carrillo, J.-M.Y., Gavhane, N., Thakkar, F.M., Plimpton, S.J. Optimizing Legacy Molecular Dynamics Software with Directive-Based Offload. Computer Physics Communications. 2015. 195: p. 95-101. * Brown, W.M., Carrillo, J.-M.Y., Gavhane, N., Thakkar, F.M., Plimpton, S.J. Optimizing Legacy Molecular Dynamics Software with Directive-Based Offload. Computer Physics Communications. 2015. 195: p. 95-101.

2
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@ -97,7 +97,7 @@ sub-section.
A description of the multi-threading strategy used in the OPENMP A description of the multi-threading strategy used in the OPENMP
package and some performance examples are package and some performance examples are
`presented here <http://sites.google.com/site/akohlmey/software/lammps-icms/lammps-icms-tms2011-talk.pdf?attredirects=0&d=1>`_. `presented here <https://drive.google.com/file/d/1d1gLK6Ru6aPYB50Ld2tO10Li8zgPVNB8/view?usp=sharing>`_.
Guidelines for best performance Guidelines for best performance
""""""""""""""""""""""""""""""" """""""""""""""""""""""""""""""

13
doc/src/Tools.rst
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@ -205,6 +205,7 @@ scripts are available:
whitespace.py # detects TAB characters and trailing whitespace whitespace.py # detects TAB characters and trailing whitespace
homepage.py # detects outdated LAMMPS homepage URLs (pointing to sandia.gov instead of lammps.org) homepage.py # detects outdated LAMMPS homepage URLs (pointing to sandia.gov instead of lammps.org)
errordocs.py # detects deprecated error docs in header files errordocs.py # detects deprecated error docs in header files
versiontags.py # detects .. versionadded:: or .. versionchanged:: with pending version date
The tools need to be given the main folder of the LAMMPS distribution The tools need to be given the main folder of the LAMMPS distribution
or individual file names as argument and will by default check them or individual file names as argument and will by default check them
@ -397,7 +398,7 @@ ipp tool
------------------ ------------------
The tools/ipp directory contains a Perl script ipp which can be used The tools/ipp directory contains a Perl script ipp which can be used
to facilitate the creation of a complicated file (say, a lammps input to facilitate the creation of a complicated file (say, a LAMMPS input
script or tools/createatoms input file) using a template file. script or tools/createatoms input file) using a template file.
ipp was created and is maintained by Reese Jones (Sandia), rjones at ipp was created and is maintained by Reese Jones (Sandia), rjones at
@ -512,8 +513,8 @@ with an ``.inputrc`` file in the home directory. For application
specific customization, the LAMMPS shell uses the name "lammps-shell". specific customization, the LAMMPS shell uses the name "lammps-shell".
For more information about using and customizing an application using For more information about using and customizing an application using
readline, please see the available documentation at: readline, please see the available documentation at:
`http://www.gnu.org/s/readline/#Documentation https://www.gnu.org/software/readline/
<http://www.gnu.org/s/readline/#Documentation>`_
Additional commands Additional commands
^^^^^^^^^^^^^^^^^^^ ^^^^^^^^^^^^^^^^^^^
@ -715,7 +716,7 @@ See the README.pdf file for more information.
These scripts were written by Arun Subramaniyan at Purdue Univ These scripts were written by Arun Subramaniyan at Purdue Univ
(asubrama at purdue.edu). (asubrama at purdue.edu).
.. _matlabhome: http://www.mathworks.com .. _matlabhome: https://www.mathworks.com
---------- ----------
@ -1046,7 +1047,7 @@ the binary file. This usually is a so-called little endian hardware
SWIG interface SWIG interface
-------------- --------------
The `SWIG tool <http://swig.org>`_ offers a mostly automated way to The `SWIG tool <https://swig.org>`_ offers a mostly automated way to
incorporate compiled code modules into scripting languages. It incorporate compiled code modules into scripting languages. It
processes the function prototypes in C and generates wrappers for a wide processes the function prototypes in C and generates wrappers for a wide
variety of scripting languages from it. Thus it can also be applied to variety of scripting languages from it. Thus it can also be applied to
@ -1126,7 +1127,7 @@ data passed or returned as pointers are included in the ``lammps.i``
file. So most of the functionality of the library interface should be file. So most of the functionality of the library interface should be
accessible. What works and what does not depends a bit on the accessible. What works and what does not depends a bit on the
individual language for which the wrappers are built and how well SWIG individual language for which the wrappers are built and how well SWIG
supports those. The `SWIG documentation <http://swig.org/doc.html>`_ supports those. The `SWIG documentation <https://swig.org/doc.html>`_
has very detailed instructions and recommendations. has very detailed instructions and recommendations.
Usage examples Usage examples

50
doc/src/angle_coeff.rst
View File

@ -10,7 +10,7 @@ Syntax
angle_coeff N args angle_coeff N args
* N = angle type (see asterisk form below) * N = numeric angle type (see asterisk form below), or type label
* args = coefficients for one or more angle types * args = coefficients for one or more angle types
Examples Examples
@ -22,6 +22,9 @@ Examples
angle_coeff * 5.0 angle_coeff * 5.0
angle_coeff 2*10 5.0 angle_coeff 2*10 5.0
labelmap angle 1 hydroxyl
angle_coeff hydroxyl 300.0 107.0
Description Description
""""""""""" """""""""""
@ -30,18 +33,24 @@ The number and meaning of the coefficients depends on the angle style.
Angle coefficients can also be set in the data file read by the 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 :math:`N` can be specified in one of two ways. An explicit numeric
be used, as in the first example above. Or a wild-card asterisk can be value can be used, as in the first example above. Or :math:`N` can be a
used to set the coefficients for multiple angle types. This takes the type label, which is an alphanumeric string defined by the
form "\*" or "\*n" or "n\*" or "m\*n". If N = the number of angle types, :doc:`labelmap <labelmap>` command or in a section of a data file read
then an asterisk with no numeric values means all types from 1 to N. A by the :doc:`read_data <read_data>` command.
leading asterisk means all types from 1 to n (inclusive). A trailing
asterisk means all types from n to N (inclusive). A middle asterisk
means all types from m to n (inclusive).
Note that using an :doc:`angle_coeff <angle_coeff>` command can override a previous setting For numeric values only, a wild-card asterisk can be used to set the
for the same angle type. For example, these commands set the coeffs coefficients for multiple angle types. This takes the form "\*" or
for all angle types, then overwrite the coeffs for just angle type 2: "\*n" or "n\*" or "m\*n". If :math:`N` is the number of angle types,
then an asterisk with no numeric values means all types from 1 to
:math:`N`. A leading asterisk means all types from 1 to n (inclusive).
A trailing asterisk means all types from n to :math:`N` (inclusive). A
middle asterisk means all types from m to n (inclusive).
Note that using an :doc:`angle_coeff <angle_coeff>` command can
override a previous setting for the same angle type. For example,
these commands set the coeffs for all angle types, then overwrite the
coeffs for just angle type 2:
.. code-block:: LAMMPS .. code-block:: LAMMPS
@ -49,11 +58,11 @@ for all angle types, then overwrite the coeffs for just angle type 2:
angle_coeff 2 50.0 107.0 angle_coeff 2 50.0 107.0
A line in a data file that specifies angle coefficients uses the exact A line in a data file that specifies angle coefficients uses the exact
same format as the arguments of the :doc:`angle_coeff <angle_coeff>` command in an input same format as the arguments of the :doc:`angle_coeff <angle_coeff>`
script, except that wild-card asterisks should not be used since command in an input script, except that wild-card asterisks should not
coefficients for all N types must be listed in the file. For example, be used since coefficients for all :math:`N` types must be listed in the
under the "Angle Coeffs" section of a data file, the line that file. For example, under the "Angle Coeffs" section of a data file, the
corresponds to the first example above would be listed as line that corresponds to the first example above would be listed as
.. parsed-literal:: .. parsed-literal::
@ -61,15 +70,14 @@ corresponds to the first example above would be listed as
The :doc:`angle_style class2 <angle_class2>` is an exception to this The :doc:`angle_style class2 <angle_class2>` is an exception to this
rule, in that an additional argument is used in the input script to rule, in that an additional argument is used in the input script to
allow specification of the cross-term coefficients. See its allow specification of the cross-term coefficients. See its doc page
doc page for details. for details.
---------- ----------
The list of all angle styles defined in LAMMPS is given on the The list of all angle styles defined in LAMMPS is given on the
:doc:`angle_style <angle_style>` doc page. They are also listed in more :doc:`angle_style <angle_style>` doc page. They are also listed in more
compact form on the :ref:`Commands angle <angle>` doc compact form on the :ref:`Commands angle <angle>` doc page.
page.
On either of those pages, click on the style to display the formula it On either of those pages, click on the style to display the formula it
computes and its coefficients as specified by the associated computes and its coefficients as specified by the associated

2
doc/src/angle_mesocnt.rst
View File

@ -24,7 +24,7 @@ Examples
Description Description
""""""""""" """""""""""
.. versionadded:: TBD .. versionadded:: 15Sep2022
The *mesocnt* angle style uses the potential The *mesocnt* angle style uses the potential

58
doc/src/bond_bpm_rotational.rst
View File

@ -138,15 +138,14 @@ the *overlay/pair* keyword. These settings require specific
restrictions. Further details can be found in the `:doc: how to restrictions. Further details can be found in the `:doc: how to
<Howto_BPM>` page on BPMs. <Howto_BPM>` page on BPMs.
If the *store/local* keyword is used, this fix will track bonds that If the *store/local* keyword is used, an internal fix will track bonds that
break during the simulation. Whenever a bond breaks, data is processed break during the simulation. Whenever a bond breaks, data is processed
and transferred to an internal fix labeled *fix_ID*. This allows the and transferred to an internal fix labeled *fix_ID*. This allows the
local data to be accessed by other LAMMPS commands. local data to be accessed by other LAMMPS commands. Following this optional
Following any optional keyword/value arguments, a list of one or more keyword, a list of one or more attributes is specified. These include the
attributes is specified. These include the IDs of the two atoms in IDs of the two atoms in the bond. The other attributes for the two atoms
the bond. The other attributes for the two atoms include the timestep include the timestep during which the bond broke and the current/initial
during which the bond broke and the current/initial center of mass center of mass position of the two atoms.
position of the two atoms.
Data is continuously accumulated over intervals of *N* Data is continuously accumulated over intervals of *N*
timesteps. At the end of each interval, all of the saved accumulated timesteps. At the end of each interval, all of the saved accumulated
@ -177,29 +176,38 @@ Restart and other info
This bond style writes the reference state of each bond to This bond style writes the reference state of each bond to
:doc:`binary restart files <restart>`. Loading a restart file will :doc:`binary restart files <restart>`. Loading a restart file will
properly resume bonds. properly resume bonds. However, the reference state is NOT
written to data files. Therefore reading a data file will not
restore bonds and will cause their reference states to be redefined.
The single() function of these pair styles returns 0.0 for the energy If the *store/local* option is used, an internal fix will calculate
of a pairwise interaction, since energy is not conserved in these a local vector or local array depending on the number of input values.
dissipative potentials. It also returns only the normal component of The length of the vector or number of rows in the array is the number
the pairwise interaction force. of recorded, broken bonds. If a single input is specified, a local
vector is produced. If two or more inputs are specified, a local array
The accumulated data is not written to restart files and should be is produced where the number of columns = the number of inputs. The
output before a restart file is written to avoid missing data. vector or array can be accessed by any command that uses local values
from a compute as input. See the :doc:`Howto output <Howto_output>` page
The internal fix calculates a local vector or local array depending on the for an overview of LAMMPS output options.
number of input values. The length of the vector or number of rows in
the array is the number of recorded, lost interactions. If a single
input is specified, a local vector is produced. If two or more inputs
are specified, a local array is produced where the number of columns =
the number of inputs. The vector or array can be accessed by any
command that uses local values from a compute as input. See the
:doc:`Howto output <Howto_output>` page for an overview of LAMMPS
output options.
The vector or array will be floating point values that correspond to The vector or array will be floating point values that correspond to
the specified attribute. the specified attribute.
The single() function of this bond style returns 0.0 for the energy
of a bonded interaction, since energy is not conserved in these
dissipative potentials. It also returns only the normal component of
the bonded interaction force. However, the single() function also
calculates 7 extra bond quantities. The first 4 are data from the
reference state of the bond including the initial distance between particles
:math:`r_0` followed by the :math:`x`, :math:`y`, and :math:`z` components
of the initial unit vector pointing to particle I from particle J. The next 3
quantities (5-7) are the :math:`x`, :math:`y`, and :math:`z` components
of the total force, including normal and tangential contributions, acting
on particle I.
These extra quantities can be accessed by the :doc:`compute bond/local <compute_bond_local>`
command, as *b1*, *b2*, ..., *b7*\ .
Restrictions Restrictions
"""""""""""" """"""""""""

49
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@ -103,15 +103,14 @@ the *overlay/pair* keyword. These settings require specific
restrictions. Further details can be found in the `:doc: how to restrictions. Further details can be found in the `:doc: how to
<Howto_BPM>` page on BPMs. <Howto_BPM>` page on BPMs.
If the *store/local* keyword is used, this fix will track bonds that If the *store/local* keyword is used, an internal fix will track bonds that
break during the simulation. Whenever a bond breaks, data is processed break during the simulation. Whenever a bond breaks, data is processed
and transferred to an internal fix labeled *fix_ID*. This allows the and transferred to an internal fix labeled *fix_ID*. This allows the
local data to be accessed by other LAMMPS commands. local data to be accessed by other LAMMPS commands. Following this optional
Following any optional keyword/value arguments, a list of one or more keyword, a list of one or more attributes is specified. These include the
attributes is specified. These include the IDs of the two atoms in IDs of the two atoms in the bond. The other attributes for the two atoms
the bond. The other attributes for the two atoms include the timestep include the timestep during which the bond broke and the current/initial
during which the bond broke and the current/initial center of mass center of mass position of the two atoms.
position of the two atoms.
Data is continuously accumulated over intervals of *N* Data is continuously accumulated over intervals of *N*
timesteps. At the end of each interval, all of the saved accumulated timesteps. At the end of each interval, all of the saved accumulated
@ -141,28 +140,30 @@ Restart and other info
This bond style writes the reference state of each bond to This bond style writes the reference state of each bond to
:doc:`binary restart files <restart>`. Loading a restart :doc:`binary restart files <restart>`. Loading a restart
file will properly resume bonds. file will properly restore bonds. However, the reference state is NOT
written to data files. Therefore reading a data file will not
restore bonds and will cause their reference states to be redefined.
The single() function of these pair styles returns 0.0 for the energy If the *store/local* option is used, an internal fix will calculate
of a pairwise interaction, since energy is not conserved in these a local vector or local array depending on the number of input values.
dissipative potentials. The length of the vector or number of rows in the array is the number
of recorded, broken bonds. If a single input is specified, a local
The accumulated data is not written to restart files and should be vector is produced. If two or more inputs are specified, a local array
output before a restart file is written to avoid missing data. is produced where the number of columns = the number of inputs. The
vector or array can be accessed by any command that uses local values
The internal fix calculates a local vector or local array depending on the from a compute as input. See the :doc:`Howto output <Howto_output>` page
number of input values. The length of the vector or number of rows in for an overview of LAMMPS output options.
the array is the number of recorded, lost interactions. If a single
input is specified, a local vector is produced. If two or more inputs
are specified, a local array is produced where the number of columns =
the number of inputs. The vector or array can be accessed by any
command that uses local values from a compute as input. See the
:doc:`Howto output <Howto_output>` page for an overview of LAMMPS
output options.
The vector or array will be floating point values that correspond to The vector or array will be floating point values that correspond to
the specified attribute. the specified attribute.
The single() function of this bond style returns 0.0 for the energy
of a bonded interaction, since energy is not conserved in these
dissipative potentials. The single() function also calculates an
extra bond quantity, the initial distance :math:`r_0`. This
extra quantity can be accessed by the
:doc:`compute bond/local <compute_bond_local>` command as *b1*\ .
Restrictions Restrictions
"""""""""""" """"""""""""

30
doc/src/bond_coeff.rst
View File

@ -10,7 +10,7 @@ Syntax
bond_coeff N args bond_coeff N args
* N = bond type (see asterisk form below) * N = numeric bond type (see asterisk form below), or type label
* args = coefficients for one or more bond types * args = coefficients for one or more bond types
Examples Examples
@ -21,7 +21,10 @@ Examples
bond_coeff 5 80.0 1.2 bond_coeff 5 80.0 1.2
bond_coeff * 30.0 1.5 1.0 1.0 bond_coeff * 30.0 1.5 1.0 1.0
bond_coeff 1*4 30.0 1.5 1.0 1.0 bond_coeff 1*4 30.0 1.5 1.0 1.0
bond_coeff 1 harmonic 200.0 1.0 bond_coeff 1 harmonic 200.0 1.0 (for bond_style hybrid)
labelmap bond 5 carbonyl
bond_coeff carbonyl 80.0 1.2
Description Description
""""""""""" """""""""""
@ -31,14 +34,19 @@ The number and meaning of the coefficients depends on the bond style.
Bond coefficients can also be set in the data file read by the 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 :math:`N` can be specified in one of several ways. An explicit numeric
be used, as in the first example above. Or a wild-card asterisk can be value can be used, as in the first example above. Or :math:`N` can be a
used to set the coefficients for multiple bond types. This takes the type label, which is an alphanumeric string defined by the
form "\*" or "\*n" or "n\*" or "m\*n". If N = the number of bond types, :doc:`labelmap <labelmap>` command or in a section of a data file read
then an asterisk with no numeric values means all types from 1 to N. A by the :doc:`read_data <read_data>` command.
For numeric values only, a wild-card asterisk can be used to set the
coefficients for multiple bond types. This takes the form "\*" or "\*n"
or "n\*" or "m\*n". If :math:`N` is the number of bond types, then an
asterisk with no numeric values means all types from 1 to :math:`N`. A
leading asterisk means all types from 1 to n (inclusive). A trailing leading asterisk means all types from 1 to n (inclusive). A trailing
asterisk means all types from n to N (inclusive). A middle asterisk asterisk means all types from n to :math:`N` (inclusive). A middle
means all types from m to n (inclusive). asterisk means all types from m to n (inclusive).
Note that using a bond_coeff command can override a previous setting Note that using a bond_coeff command can override a previous setting
for the same bond type. For example, these commands set the coeffs for the same bond type. For example, these commands set the coeffs
@ -52,8 +60,8 @@ for all bond types, then overwrite the coeffs for just bond type 2:
A line in a data file that specifies bond coefficients uses the exact A line in a data file that specifies bond coefficients uses the exact
same format as the arguments of the bond_coeff command in an input 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 :math:`N` types must be listed in the file. For
under the "Bond Coeffs" section of a data file, the line that example, under the "Bond Coeffs" section of a data file, the line that
corresponds to the first example above would be listed as corresponds to the first example above would be listed as
.. parsed-literal:: .. parsed-literal::

2
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@ -22,7 +22,7 @@ Examples
Description Description
""""""""""" """""""""""
.. versionadded:: TBD .. versionadded:: 15Sep2022
The *mesocnt* bond style is a wrapper for the :doc:`harmonic The *mesocnt* bond style is a wrapper for the :doc:`harmonic
<bond_harmonic>` style, and uses the potential <bond_harmonic>` style, and uses the potential

1
doc/src/commands_list.rst
View File

@ -56,6 +56,7 @@ Commands
kspace_modify kspace_modify
kspace_style kspace_style
label label
labelmap
lattice lattice
log log
mass mass

2
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View File

@ -78,7 +78,7 @@ These values can be accessed by any command that uses global array
values from a compute as input. See the :doc:`Howto output <Howto_output>` page for an overview of LAMMPS output values from a compute as input. See the :doc:`Howto output <Howto_output>` page for an overview of LAMMPS output
options. options.
The array values are "intensive." The array values will be in The array values are "intensive". The array values will be in
mass-velocity-distance :doc:`units <units>`. mass-velocity-distance :doc:`units <units>`.
Restrictions Restrictions

2
doc/src/compute_ave_sphere_atom.rst
View File

@ -35,6 +35,8 @@ Examples
Description Description
""""""""""" """""""""""
.. versionadded:: 7Jan2022
Define a computation that calculates the local mass density and Define a computation that calculates the local mass density and
temperature for each atom based on its neighbors inside a spherical temperature for each atom based on its neighbors inside a spherical
cutoff. If an atom has :math:`M` neighbors, then its local mass density is cutoff. If an atom has :math:`M` neighbors, then its local mass density is

18
doc/src/compute_bond_local.rst
View File

@ -13,7 +13,7 @@ Syntax
* ID, group-ID are documented in :doc:`compute <compute>` command * ID, group-ID are documented in :doc:`compute <compute>` command
* bond/local = style name of this compute command * bond/local = style name of this compute command
* one or more values may be appended * one or more values may be appended
* value = *dist* or *dx* or *dy* or *dz* or *engpot* or *force* or *fx* or *fy* or *fz* or *engvib* or *engrot* or *engtrans* or *omega* or *velvib* or *v_name* * value = *dist* or *dx* or *dy* or *dz* or *engpot* or *force* or *fx* or *fy* or *fz* or *engvib* or *engrot* or *engtrans* or *omega* or *velvib* or *v_name* or *bN*
.. parsed-literal:: .. parsed-literal::
@ -29,6 +29,7 @@ Syntax
*omega* = magnitude of bond angular velocity *omega* = magnitude of bond angular velocity
*velvib* = vibrational velocity along the bond length *velvib* = vibrational velocity along the bond length
*v_name* = equal-style variable with name (see below) *v_name* = equal-style variable with name (see below)
*bN* = bond style specific quantities for allowed N values
* zero or more keyword/args pairs may be appended * zero or more keyword/args pairs may be appended
* keyword = *set* * keyword = *set*
@ -47,7 +48,7 @@ Examples
compute 1 all bond/local engpot compute 1 all bond/local engpot
compute 1 all bond/local dist engpot force compute 1 all bond/local dist engpot force
compute 1 all bond/local dist fx fy fz compute 1 all bond/local dist fx fy fz b1 b2
compute 1 all bond/local dist v_distsq set dist d compute 1 all bond/local dist v_distsq set dist d
@ -147,6 +148,19 @@ those quantities via the :doc:`compute reduce <compute_reduce>` command
with thermo output, and the :doc:`fix ave/histo <fix_ave_histo>` with thermo output, and the :doc:`fix ave/histo <fix_ave_histo>`
command will histogram the length\ :math:`^2` values and write them to a file. command will histogram the length\ :math:`^2` values and write them to a file.
A bond style may define additional bond quantities which can be
accessed as *b1* to *bN*, where N is defined by the bond style. Most
bond styles do not define any additional quantities, so N = 0. An
example of ones that do are the :doc:`BPM bond styles <Howto_bpm>`
which store the reference state between two particles. See
individual bond styles for details.
When using *bN* with bond style *hybrid*, the output will be the Nth
quantity from the sub-style that computes the bonded interaction
(based on bond type). If that sub-style does not define a *bN*,
the output will be 0.0. The maximum allowed N is the maximum number
of quantities provided by any sub-style.
---------- ----------
The local data stored by this command is generated by looping over all The local data stored by this command is generated by looping over all

2
doc/src/compute_born_matrix.rst
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@ -182,7 +182,7 @@ by any command that uses global values from a compute as input. See
the :doc:`Howto output <Howto_output>` doc page for an overview of the :doc:`Howto output <Howto_output>` doc page for an overview of
LAMMPS output options. LAMMPS output options.
The array values calculated by this compute are all "extensive." The array values calculated by this compute are all "extensive".
Restrictions Restrictions
"""""""""""" """"""""""""

2
doc/src/compute_com.rst
View File

@ -49,7 +49,7 @@ accessed by indices 1--3 by any command that uses global vector values
from a compute as input. See the :doc:`Howto output <Howto_output>` doc from a compute as input. See the :doc:`Howto output <Howto_output>` doc
page for an overview of LAMMPS output options. page for an overview of LAMMPS output options.
The vector values are "intensive." The vector values will be in The vector values are "intensive". The vector values will be in
distance :doc:`units <units>`. distance :doc:`units <units>`.
Restrictions Restrictions

2
doc/src/compute_com_chunk.rst
View File

@ -77,7 +77,7 @@ values can be accessed by any command that uses global array values
from a compute as input. See the :doc:`Howto output <Howto_output>` doc from a compute as input. See the :doc:`Howto output <Howto_output>` doc
page for an overview of LAMMPS output options. page for an overview of LAMMPS output options.
The array values are "intensive." The array values will be in The array values are "intensive". The array values will be in
distance :doc:`units <units>`. distance :doc:`units <units>`.
Restrictions Restrictions

17
doc/src/compute_damage_atom.rst
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@ -24,16 +24,18 @@ Description
""""""""""" """""""""""
Define a computation that calculates the per-atom damage for each atom Define a computation that calculates the per-atom damage for each atom
in a group. This is a quantity relevant for :doc:`Peridynamics models <pair_peri>`. See `this document <PDF/PDLammps_overview.pdf>`_ in a group. This is a quantity relevant for :doc:`Peridynamics models
for an overview of LAMMPS commands for Peridynamics modeling. <pair_peri>`. See `this document <PDF/PDLammps_overview.pdf>`_ for an
overview of LAMMPS commands for Peridynamics modeling.
The "damage" of a Peridynamics particles is based on the bond breakage The "damage" of a Peridynamics particles is based on the bond breakage
between the particle and its neighbors. If all the bonds are broken between the particle and its neighbors. If all the bonds are broken
the particle is considered to be fully damaged. the particle is considered to be fully damaged.
See the `PDLAMMPS user guide <http://www.sandia.gov/~mlparks/papers/PDLAMMPS.pdf>`_ for a formal See the `PDLAMMPS user guide
definition of "damage" and more details about Peridynamics as it is <https://download.lammps.org/pdfs/PDLAMMPS_user_guide.pdf>`_ for a
implemented in LAMMPS. formal definition of "damage" and more details about Peridynamics as it
is implemented in LAMMPS.
This command can be used with all the Peridynamic pair styles. This command can be used with all the Peridynamic pair styles.
@ -53,8 +55,9 @@ The per-atom vector values are unitless numbers (damage) :math:`\ge 0.0`.
Restrictions Restrictions
"""""""""""" """"""""""""
This compute is part of the PERI package. It is only enabled if This compute is part of the PERI package. It is only enabled if LAMMPS
LAMMPS was built with that package. See the :doc:`Build package <Build_package>` page for more info. was built with that package. See the :doc:`Build package
<Build_package>` page for more info.
Related commands Related commands
"""""""""""""""" """"""""""""""""

22
doc/src/compute_dilatation_atom.rst
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@ -24,7 +24,8 @@ Description
""""""""""" """""""""""
Define a computation that calculates the per-atom dilatation for each Define a computation that calculates the per-atom dilatation for each
atom in a group. This is a quantity relevant for :doc:`Peridynamics models <pair_peri>`. See `this document <PDF/PDLammps_overview.pdf>`_ atom in a group. This is a quantity relevant for :doc:`Peridynamics
models <pair_peri>`. See `this document <PDF/PDLammps_overview.pdf>`_
for an overview of LAMMPS commands for Peridynamics modeling. for an overview of LAMMPS commands for Peridynamics modeling.
For small deformation, dilatation of is the measure of the volumetric For small deformation, dilatation of is the measure of the volumetric
@ -32,13 +33,14 @@ strain.
The dilatation :math:`\theta` for each peridynamic particle :math:`i` is The dilatation :math:`\theta` for each peridynamic particle :math:`i` is
calculated as a sum over its neighbors with unbroken bonds, where the calculated as a sum over its neighbors with unbroken bonds, where the
contribution of the :math:`ij` pair is a function of the change in bond length contribution of the :math:`ij` pair is a function of the change in bond
(versus the initial length in the reference state), the volume length (versus the initial length in the reference state), the volume
fraction of the particles and an influence function. See the fraction of the particles and an influence function. See the `PDLAMMPS
`PDLAMMPS user guide <http://www.sandia.gov/~mlparks/papers/PDLAMMPS.pdf>`_ for user guide <https://download.lammps.org/pdfs/PDLAMMPS_user_guide.pdf>`_
a formal definition of dilatation. for a formal definition of dilatation.
This command can only be used with a subset of the Peridynamic :doc:`pair styles <pair_peri>`: peri/lps, peri/ves and peri/eps. This command can only be used with a subset of the Peridynamic
:doc:`pair styles <pair_peri>`: peri/lps, peri/ves and peri/eps.
The dilatation value will be 0.0 for atoms not in the specified The dilatation value will be 0.0 for atoms not in the specified
compute group. compute group.
@ -56,9 +58,9 @@ The per-atom vector values are unitless numbers :math:`(\theta \ge 0.0)`.
Restrictions Restrictions
"""""""""""" """"""""""""
This compute is part of the PERI package. It is only enabled if This compute is part of the PERI package. It is only enabled if LAMMPS
LAMMPS was built with that package. See the was built with that package. See the :doc:`Build package
:doc:`Build package <Build_package>` page for more info. <Build_package>` page for more info.
Related commands Related commands
"""""""""""""""" """"""""""""""""

2
doc/src/compute_dipole.rst
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@ -54,7 +54,7 @@ the computed dipole moment and a global vector of length 3 with the
dipole vector. See the :doc:`Howto output <Howto_output>` page for dipole vector. See the :doc:`Howto output <Howto_output>` page for
an overview of LAMMPS output options. an overview of LAMMPS output options.
The computed values are "intensive." The array values will be in The computed values are "intensive". The array values will be in
dipole units (i.e., charge :doc:`units <units>` times distance dipole units (i.e., charge :doc:`units <units>` times distance
:doc:`units <units>`). :doc:`units <units>`).

2
doc/src/compute_dipole_chunk.rst
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@ -86,7 +86,7 @@ chunk. These values can be accessed by any command that uses global
array values from a compute as input. See the :doc:`Howto output array values from a compute as input. See the :doc:`Howto output
<Howto_output>` page for an overview of LAMMPS output options. <Howto_output>` page for an overview of LAMMPS output options.
The array values are "intensive." The array values will be in The array values are "intensive". The array values will be in
dipole units (i.e., charge :doc:`units <units>` times distance dipole units (i.e., charge :doc:`units <units>` times distance
:doc:`units <units>`). :doc:`units <units>`).

2
doc/src/compute_erotate_asphere.rst
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@ -48,7 +48,7 @@ used by any command that uses a global scalar value from a compute as
input. See the :doc:`Howto output <Howto_output>` page for an input. See the :doc:`Howto output <Howto_output>` page for an
overview of LAMMPS output options. overview of LAMMPS output options.
The scalar value calculated by this compute is "extensive." The The scalar value calculated by this compute is "extensive". The
scalar value will be in energy :doc:`units <units>`. scalar value will be in energy :doc:`units <units>`.
Restrictions Restrictions

2
doc/src/compute_erotate_rigid.rst
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@ -48,7 +48,7 @@ of all the rigid bodies). This value can be used by any command that
uses a global scalar value from a compute as input. See the :doc:`Howto output <Howto_output>` page for an overview of LAMMPS output uses a global scalar value from a compute as input. See the :doc:`Howto output <Howto_output>` page for an overview of LAMMPS output
options. options.
The scalar value calculated by this compute is "extensive." The The scalar value calculated by this compute is "extensive". The
scalar value will be in energy :doc:`units <units>`. scalar value will be in energy :doc:`units <units>`.
Restrictions Restrictions

2
doc/src/compute_erotate_sphere.rst
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@ -44,7 +44,7 @@ used by any command that uses a global scalar value from a compute as
input. See the :doc:`Howto output <Howto_output>` page for an input. See the :doc:`Howto output <Howto_output>` page for an
overview of LAMMPS output options. overview of LAMMPS output options.
The scalar value calculated by this compute is "extensive." The The scalar value calculated by this compute is "extensive". The
scalar value will be in energy :doc:`units <units>`. scalar value will be in energy :doc:`units <units>`.
Restrictions Restrictions

4
doc/src/compute_event_displace.rst
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@ -40,7 +40,7 @@ further than the threshold distance.
If the system is undergoing significant center-of-mass motion, If the system is undergoing significant center-of-mass motion,
due to thermal motion, an external force, or an initial net momentum, due to thermal motion, an external force, or an initial net momentum,
then this compute will not be able to distinguish that motion from then this compute will not be able to distinguish that motion from
local atom displacements and may generate "false positives." local atom displacements and may generate "false positives".
Output info Output info
""""""""""" """""""""""
@ -50,7 +50,7 @@ used by any command that uses a global scalar value from a compute as
input. See the :doc:`Howto output <Howto_output>` page for an input. See the :doc:`Howto output <Howto_output>` page for an
overview of LAMMPS output options. overview of LAMMPS output options.
The scalar value calculated by this compute is "intensive." The The scalar value calculated by this compute is "intensive". The
scalar value will be a 0 or 1 as explained above. scalar value will be a 0 or 1 as explained above.
Restrictions Restrictions

2
doc/src/compute_fep.rst
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@ -299,7 +299,7 @@ These output results can be used by any command that uses a global
scalar or vector from a compute as input. See the :doc:`Howto output <Howto_output>` page for an overview of LAMMPS output scalar or vector from a compute as input. See the :doc:`Howto output <Howto_output>` page for an overview of LAMMPS output
options. For example, the computed values can be averaged using :doc:`fix ave/time <fix_ave_time>`. options. For example, the computed values can be averaged using :doc:`fix ave/time <fix_ave_time>`.
The values calculated by this compute are "extensive." The values calculated by this compute are "extensive".
Restrictions Restrictions
"""""""""""" """"""""""""

2
doc/src/compute_fep_ta.rst
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@ -34,6 +34,8 @@ Examples
Description Description
""""""""""" """""""""""
.. versionadded:: 4May2022
Define a computation that calculates the change in the free energy due Define a computation that calculates the change in the free energy due
to a test-area (TA) perturbation :ref:`(Gloor) <Gloor>`. The test-area to a test-area (TA) perturbation :ref:`(Gloor) <Gloor>`. The test-area
approach can be used to determine the interfacial tension of the system approach can be used to determine the interfacial tension of the system

2
doc/src/compute_group_group.rst
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@ -140,7 +140,7 @@ vector values from a compute as input. See the
options. options.
Both the scalar and vector values calculated by this compute are Both the scalar and vector values calculated by this compute are
"extensive." The scalar value will be in energy :doc:`units <units>`. "extensive". The scalar value will be in energy :doc:`units <units>`.
The vector values will be in force :doc:`units <units>`. The vector values will be in force :doc:`units <units>`.
Restrictions Restrictions

2
doc/src/compute_gyration.rst
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@ -69,7 +69,7 @@ vector values from a compute as input. See the :doc:`Howto output <Howto_output
options. options.
The scalar and vector values calculated by this compute are The scalar and vector values calculated by this compute are
"intensive." The scalar and vector values will be in distance and "intensive". The scalar and vector values will be in distance and
distance\ :math:`^2` :doc:`units <units>`, respectively. distance\ :math:`^2` :doc:`units <units>`, respectively.
Restrictions Restrictions

2
doc/src/compute_gyration_shape.rst
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@ -78,7 +78,7 @@ vector values from a compute as input. See the
options. options.
The vector values calculated by this compute are The vector values calculated by this compute are
"intensive." The first five vector values will be in "intensive". The first five vector values will be in
distance\ :math:`2` :doc:`units <units>` while the sixth one is dimensionless. distance\ :math:`2` :doc:`units <units>` while the sixth one is dimensionless.
Restrictions Restrictions

2
doc/src/compute_gyration_shape_chunk.rst
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@ -80,7 +80,7 @@ See the :doc:`Howto output <Howto_output>` page for an overview of LAMMPS
output options. output options.
The array calculated by this compute is The array calculated by this compute is
"intensive." The first five columns will be in "intensive". The first five columns will be in
distance\ :math:`^2` :doc:`units <units>` while the sixth one is dimensionless. distance\ :math:`^2` :doc:`units <units>` while the sixth one is dimensionless.
Restrictions Restrictions

14
doc/src/compute_heat_flux.rst
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@ -142,14 +142,14 @@ command that uses global vector values from a compute as input.
See the :doc:`Howto output <Howto_output>` documentation for an overview of See the :doc:`Howto output <Howto_output>` documentation for an overview of
LAMMPS output options. LAMMPS output options.
The vector values calculated by this compute are "extensive," meaning The vector values calculated by this compute are "extensive", meaning
they scale with the number of atoms in the simulation. They can be they scale with the number of atoms in the simulation. They can be
divided by the appropriate volume to get a flux, which would then be divided by the appropriate volume to get a flux, which would then be an
an "intensive" value, meaning independent of the number of atoms in "intensive" value, meaning independent of the number of atoms in the
the simulation. Note that if the compute is "all," then the simulation. Note that if the compute group is "all", then the
appropriate volume to divide by is the simulation box volume. appropriate volume to divide by is the simulation box volume. However,
However, if a sub-group is used, it should be the volume containing if a group with a subset of atoms is used, it should be the volume
those atoms. containing those atoms.
The vector values will be in energy\*velocity :doc:`units <units>`. Once The vector values will be in energy\*velocity :doc:`units <units>`. Once
divided by a volume the units will be that of flux, namely divided by a volume the units will be that of flux, namely

2
doc/src/compute_hma.rst
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@ -172,7 +172,7 @@ requested as arguments to the command (the potential energy, pressure and/or hea
capacity). The elements of the vector can be accessed by indices 1--n by any capacity). The elements of the vector can be accessed by indices 1--n by any
command that uses global vector values as input. See the :doc:`Howto output <Howto_output>` page for an overview of LAMMPS output options. command that uses global vector values as input. See the :doc:`Howto output <Howto_output>` page for an overview of LAMMPS output options.
The vector values calculated by this compute are "extensive." The The vector values calculated by this compute are "extensive". The
scalar value will be in energy :doc:`units <units>`. scalar value will be in energy :doc:`units <units>`.
Restrictions Restrictions

2
doc/src/compute_inertia_chunk.rst
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@ -84,7 +84,7 @@ by any command that uses global array values from a compute as input. See the
:doc:`Howto output <Howto_output>` page for an overview of LAMMPS output :doc:`Howto output <Howto_output>` page for an overview of LAMMPS output
options. options.
The array values are "intensive." The array values will be in The array values are "intensive". The array values will be in
mass\*distance\ :math:`^2` :doc:`units <units>`. mass\*distance\ :math:`^2` :doc:`units <units>`.
Restrictions Restrictions

2
doc/src/compute_ke.rst
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@ -52,7 +52,7 @@ can be used by any command that uses a global scalar value from a
compute as input. See the :doc:`Howto output <Howto_output>` doc page compute as input. See the :doc:`Howto output <Howto_output>` doc page
for an overview of LAMMPS output options. for an overview of LAMMPS output options.
The scalar value calculated by this compute is "extensive." The The scalar value calculated by this compute is "extensive". The
scalar value will be in energy :doc:`units <units>`. scalar value will be in energy :doc:`units <units>`.
Restrictions Restrictions

2
doc/src/compute_ke_rigid.rst
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@ -48,7 +48,7 @@ global scalar value from a compute as input. See the
:doc:`Howto output <Howto_output>` page for an overview of LAMMPS output :doc:`Howto output <Howto_output>` page for an overview of LAMMPS output
options. options.
The scalar value calculated by this compute is "extensive." The The scalar value calculated by this compute is "extensive". The
scalar value will be in energy :doc:`units <units>`. scalar value will be in energy :doc:`units <units>`.
Restrictions Restrictions

2
doc/src/compute_momentum.rst
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@ -37,7 +37,7 @@ length 3. This value can be used by any command that uses a global
vector value from a compute as input. See the :doc:`Howto output <Howto_output>` page for an overview of LAMMPS output vector value from a compute as input. See the :doc:`Howto output <Howto_output>` page for an overview of LAMMPS output
options. options.
The vector value calculated by this compute is "extensive." The vector The vector value calculated by this compute is "extensive". The vector
value will be in mass\*velocity :doc:`units <units>`. value will be in mass\*velocity :doc:`units <units>`.
Restrictions Restrictions

2
doc/src/compute_msd.rst
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@ -105,7 +105,7 @@ accessed by indices 1--4 by any command that uses global vector values
from a compute as input. See the :doc:`Howto output <Howto_output>` doc from a compute as input. See the :doc:`Howto output <Howto_output>` doc
page for an overview of LAMMPS output options. page for an overview of LAMMPS output options.
The vector values are "intensive." The vector values will be in The vector values are "intensive". The vector values will be in
distance\ :math:`^2` :doc:`units <units>`. distance\ :math:`^2` :doc:`units <units>`.
Restrictions Restrictions

2
doc/src/compute_msd_chunk.rst
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@ -121,7 +121,7 @@ These values can be accessed by any command that uses global array values from
a compute as input. See the :doc:`Howto output <Howto_output>` page for an a compute as input. See the :doc:`Howto output <Howto_output>` page for an
overview of LAMMPS output options. overview of LAMMPS output options.
The array values are "intensive." The array values will be in The array values are "intensive". The array values will be in
distance\ :math:`^2` :doc:`units <units>`. distance\ :math:`^2` :doc:`units <units>`.
Restrictions Restrictions

2
doc/src/compute_msd_nongauss.rst
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@ -67,7 +67,7 @@ accessed by indices 1--3 by any command that uses global vector values
from a compute as input. See the :doc:`Howto output <Howto_output>` doc from a compute as input. See the :doc:`Howto output <Howto_output>` doc
page for an overview of LAMMPS output options. 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\ :math:`^2` :doc:`units <units>`, the second is in distance\ :math:`^2` :doc:`units <units>`, the second is in
distance\ :math:`^4` units, and the third is dimensionless. distance\ :math:`^4` units, and the third is dimensionless.

2
doc/src/compute_omega_chunk.rst
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@ -84,7 +84,7 @@ These values can be accessed by any command that uses global array
values from a compute as input. See the :doc:`Howto output <Howto_output>` values from a compute as input. See the :doc:`Howto output <Howto_output>`
page for an overview of LAMMPS output options. page for an overview of LAMMPS output options.
The array values are "intensive." The array values will be in The array values are "intensive". The array values will be in
velocity/distance :doc:`units <units>`. velocity/distance :doc:`units <units>`.
Restrictions Restrictions

4
doc/src/compute_pair.rst
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@ -93,7 +93,9 @@ Restrictions
Related commands Related commands
"""""""""""""""" """"""""""""""""
:doc:`compute pe <compute_pe>`, :doc:`compute bond <compute_bond>` :doc:`compute pe <compute_pe>`, :doc:`compute bond <compute_bond>`,
:doc:`fix pair <fix_pair>`
Default Default
""""""" """""""

4
doc/src/compute_pe.rst
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@ -27,7 +27,7 @@ Description
""""""""""" """""""""""
Define a computation that calculates the potential energy of the Define a computation that calculates the potential energy of the
entire system of atoms. The specified group must be "all." See the entire system of atoms. The specified group must be "all". See the
:doc:`compute pe/atom <compute_pe_atom>` command if you want per-atom :doc:`compute pe/atom <compute_pe_atom>` command if you want per-atom
energies. These per-atom values could be summed for a group of atoms energies. These per-atom values could be summed for a group of atoms
via the :doc:`compute reduce <compute_reduce>` command. via the :doc:`compute reduce <compute_reduce>` command.
@ -73,7 +73,7 @@ value can be used by any command that uses a global scalar value from
a compute as input. See the :doc:`Howto output <Howto_output>` doc page a compute as input. See the :doc:`Howto output <Howto_output>` doc page
for an overview of LAMMPS output options. for an overview of LAMMPS output options.
The scalar value calculated by this compute is "extensive." The The scalar value calculated by this compute is "extensive". The
scalar value will be in energy :doc:`units <units>`. scalar value will be in energy :doc:`units <units>`.
Restrictions Restrictions

2
doc/src/compute_plasticity_atom.rst
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@ -73,5 +73,5 @@ none
.. _Mitchell: .. _Mitchell:
**(Mitchell)** Mitchell, "A non-local, ordinary-state-based **(Mitchell)** Mitchell, "A non-local, ordinary-state-based
viscoelasticity model for peridynamics," Sandia National Lab Report, viscoelasticity model for peridynamics", Sandia National Lab Report,
8064:1-28 (2011). 8064:1-28 (2011).

6
doc/src/compute_pressure.rst
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@ -29,7 +29,7 @@ Description
""""""""""" """""""""""
Define a computation that calculates the pressure of the entire system Define a computation that calculates the pressure of the entire system
of atoms. The specified group must be "all." See the of atoms. The specified group must be "all". See the
:doc:`compute stress/atom <compute_stress_atom>` command if you want per-atom :doc:`compute stress/atom <compute_stress_atom>` command if you want per-atom
pressure (stress). These per-atom values could be summed for a group pressure (stress). These per-atom values could be summed for a group
of atoms via the :doc:`compute reduce <compute_reduce>` command. of atoms via the :doc:`compute reduce <compute_reduce>` command.
@ -115,7 +115,7 @@ LAMMPS starts up, as if this command were in the input script:
compute thermo_press all pressure thermo_temp compute thermo_press all pressure thermo_temp
where thermo_temp is the ID of a similarly defined compute of style where thermo_temp is the ID of a similarly defined compute of style
"temp." See the :doc:`thermo_style <thermo_style>` command for more details. "temp". See the :doc:`thermo_style <thermo_style>` command for more details.
---------- ----------
@ -137,7 +137,7 @@ The ordering of values in the symmetric pressure tensor is as follows:
:math:`p_{xz},` :math:`p_{yz}.` :math:`p_{xz},` :math:`p_{yz}.`
The scalar and vector values calculated by this compute are The scalar and vector values calculated by this compute are
"intensive." The scalar and vector values will be in pressure "intensive". The scalar and vector values will be in pressure
:doc:`units <units>`. :doc:`units <units>`.
Restrictions Restrictions

2
doc/src/compute_property_atom.rst
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@ -167,7 +167,7 @@ triangular particles and define the corner points of each triangle.
In addition, the various per-atom quantities listed above for specific In addition, the various per-atom quantities listed above for specific
packages are only accessible by this command. packages are only accessible by this command.
.. versionchanged:: TBD .. versionchanged:: 15Sep2022
The *espin* property was previously called *spin*. The *espin* property was previously called *spin*.

2
doc/src/compute_property_chunk.rst
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@ -110,7 +110,7 @@ accessed by any command that uses global values from a compute as
input. See the :doc:`Howto output <Howto_output>` page for an input. See the :doc:`Howto output <Howto_output>` page for an
overview of LAMMPS output options. overview of LAMMPS output options.
The vector or array values are "intensive." The values will be The vector or array values are "intensive". The values will be
unitless or in the units discussed above. unitless or in the units discussed above.
Restrictions Restrictions

2
doc/src/compute_property_local.rst
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@ -164,7 +164,7 @@ the type of the bond, from 1 to Nbtypes = # of bond types. The number
of bond types is defined in the data file read by the of bond types is defined in the data file read by the
:doc:`read_data <read_data>` command. :doc:`read_data <read_data>` command.
The attributes that start with "a," "d," and "i" refer to similar values The attributes that start with "a", "d", and "i" refer to similar values
for :doc:`angles <angle_style>`, :doc:`dihedrals <dihedral_style>`, and for :doc:`angles <angle_style>`, :doc:`dihedrals <dihedral_style>`, and
:doc:`impropers <improper_style>`. :doc:`impropers <improper_style>`.

2
doc/src/compute_rdf.rst
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@ -166,7 +166,7 @@ by any command that uses a global values from a compute as input. See
the :doc:`Howto output <Howto_output>` page for an overview of the :doc:`Howto output <Howto_output>` page for an overview of
LAMMPS output options. LAMMPS output options.
The array values calculated by this compute are all "intensive." The array values calculated by this compute are all "intensive".
The first column of array values will be in distance The first column of array values will be in distance
:doc:`units <units>`. The :math:`g(r)` columns of array values are normalized :doc:`units <units>`. The :math:`g(r)` columns of array values are normalized

12
doc/src/compute_reduce.rst
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@ -128,7 +128,7 @@ inputs to this fix by using the
:doc:`compute property/atom <compute_property_atom>` command and then specifying :doc:`compute property/atom <compute_property_atom>` command and then specifying
an input value from that compute. an input value from that compute.
If a value begins with "c\_," a compute ID must follow which has been If a value begins with "c\_", a compute ID must follow which has been
previously defined in the input script. Computes can generate previously defined in the input script. Computes can generate
per-atom or local quantities. See the individual per-atom or local quantities. See the individual
:doc:`compute <compute>` page for details. If no bracketed integer :doc:`compute <compute>` page for details. If no bracketed integer
@ -139,7 +139,7 @@ compute styles and :doc:`add them to LAMMPS <Modify>`. See the
discussion above for how :math:`I` can be specified with a wildcard asterisk discussion above for how :math:`I` can be specified with a wildcard asterisk
to effectively specify multiple values. to effectively specify multiple values.
If a value begins with "f\_," a fix ID must follow which has been If a value begins with "f\_", a fix ID must follow which has been
previously defined in the input script. Fixes can generate per-atom previously defined in the input script. Fixes can generate per-atom
or local quantities. See the individual :doc:`fix <fix>` page for or local quantities. See the individual :doc:`fix <fix>` page for
details. Note that some fixes only produce their values on certain details. Note that some fixes only produce their values on certain
@ -152,7 +152,7 @@ is used. Users can also write code for their own fix style and
:math:`I` can be specified with a wildcard asterisk to effectively specify :math:`I` can be specified with a wildcard asterisk to effectively specify
multiple values. multiple values.
If a value begins with "v\_," a variable name must follow which has If a value begins with "v\_", a variable name must follow which has
been previously defined in the input script. It must be an been previously defined in the input script. It must be an
:doc:`atom-style variable <variable>`. Atom-style variables can :doc:`atom-style variable <variable>`. Atom-style variables can
reference thermodynamic keywords and various per-atom attributes, or reference thermodynamic keywords and various per-atom attributes, or
@ -197,7 +197,7 @@ global vector of values, the length of which is equal to the number of
inputs specified. inputs specified.
As discussed below, for the *sum*, *sumabs*, and *sumsq* modes, the value(s) As discussed below, for the *sum*, *sumabs*, and *sumsq* modes, the value(s)
produced by this compute are all "extensive," meaning their value produced by this compute are all "extensive", meaning their value
scales linearly with the number of atoms involved. If normalized scales linearly with the number of atoms involved. If normalized
values are desired, this compute can be accessed by the values are desired, this compute can be accessed by the
:doc:`thermo_style custom <thermo_style>` command with :doc:`thermo_style custom <thermo_style>` command with
@ -218,9 +218,9 @@ compute as input. See the :doc:`Howto output <Howto_output>` doc page
for an overview of LAMMPS output options. for an overview of LAMMPS output options.
All the scalar or vector values calculated by this compute are All the scalar or vector values calculated by this compute are
"intensive," except when the *sum*, *sumabs*, or *sumsq* modes are used on "intensive", except when the *sum*, *sumabs*, or *sumsq* modes are used on
per-atom or local vectors, in which case the calculated values are per-atom or local vectors, in which case the calculated values are
"extensive." "extensive".
The scalar or vector values will be in whatever :doc:`units <units>` the The scalar or vector values will be in whatever :doc:`units <units>` the
quantities being reduced are in. quantities being reduced are in.

2
doc/src/compute_reduce_chunk.rst
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@ -102,7 +102,7 @@ The commands below can be added to the examples/in.micelle script.
Imagine a collection of polymer chains or small molecules with Imagine a collection of polymer chains or small molecules with
hydrophobic end groups. All the hydrophobic (HP) atoms are assigned hydrophobic end groups. All the hydrophobic (HP) atoms are assigned
to a group called "phobic." to a group called "phobic".
These commands will assign a unique cluster ID to all HP atoms within These commands will assign a unique cluster ID to all HP atoms within
a specified distance of each other. A cluster will contain all HP a specified distance of each other. A cluster will contain all HP

24
doc/src/compute_sna_atom.rst
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@ -228,18 +228,20 @@ command:
See section below on output for a detailed explanation of the data See section below on output for a detailed explanation of the data
layout in the global array. layout in the global array.
.. versionadded:: 3Aug2022
The compute *sna/grid* and *sna/grid/local* commands calculate The compute *sna/grid* and *sna/grid/local* commands calculate
bispectrum components for a regular grid of points. bispectrum components for a regular grid of points. These are
These are calculated from the local density of nearby atoms *i'* calculated from the local density of nearby atoms *i'* around each grid
around each grid point, as if there was a central atom *i* point, as if there was a central atom *i* at the grid point. This is
at the grid point. This is useful for characterizing fine-scale useful for characterizing fine-scale structure in a configuration of
structure in a configuration of atoms, and it is used atoms, and it is used in the `MALA package
in the `MALA package <https://github.com/casus/mala>`_ <https://github.com/casus/mala>`_ to build machine-learning surrogates
to build machine-learning surrogates for finite-temperature Kohn-Sham for finite-temperature Kohn-Sham density functional theory (:ref:`Ellis
density functional theory (:ref:`Ellis et al. <Ellis2021>`) et al. <Ellis2021>`) Neighbor atoms not in the group do not contribute
Neighbor atoms not in the group do not contribute to the to the bispectrum components of the grid points. The distance cutoff
bispectrum components of the grid points. The distance cutoff :math:`R_{ii'}` :math:`R_{ii'}` assumes that *i* has the same type as the neighbor atom
assumes that *i* has the same type as the neighbor atom *i'*. *i'*.
Compute *sna/grid* calculates a global array containing bispectrum Compute *sna/grid* calculates a global array containing bispectrum
components for a regular grid of points. components for a regular grid of points.

2
doc/src/compute_stress_profile.rst
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@ -114,7 +114,7 @@ This array can be output with :doc:`fix ave/time <fix_ave_time>`,
compute p all stress/cartesian x 0.1 compute p all stress/cartesian x 0.1
fix 2 all ave/time 100 1 100 c_p[*] file dump_p.out mode vector fix 2 all ave/time 100 1 100 c_p[*] file dump_p.out mode vector
The values calculated by this compute are "intensive." The stress The values calculated by this compute are "intensive". The stress
values will be in pressure :doc:`units <units>`. The number density values will be in pressure :doc:`units <units>`. The number density
values are in inverse volume :doc:`units <units>`. values are in inverse volume :doc:`units <units>`.

2
doc/src/compute_tally.rst
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@ -182,7 +182,7 @@ Output info
from individual atoms in both groups). from individual atoms in both groups).
Both the scalar and vector values calculated by this compute are Both the scalar and vector values calculated by this compute are
"extensive." "extensive".
Restrictions Restrictions
"""""""""""" """"""""""""

2
doc/src/compute_temp.rst
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@ -91,7 +91,7 @@ vector values from a compute as input. See the
:doc:`Howto output <Howto_output>` page for an overview of LAMMPS output :doc:`Howto output <Howto_output>` page for an overview of LAMMPS output
options. options.
The scalar value calculated by this compute is "intensive." The The scalar value calculated by this compute is "intensive". The
vector values are "extensive". vector values are "extensive".
The scalar value will be in temperature :doc:`units <units>`. The The scalar value will be in temperature :doc:`units <units>`. The

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