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Merge branch 'develop' into fix-cmake-python-install

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Axel Kohlmeyer 2022-10-07 17:04:29 -04:00
parent ea8f08c295 967c84cb69
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30
SECURITY.md
View File

@ -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.
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
"administrator" account directly or indirectly via "sudo" or "su".
Therefore what could be seen as a security vulnerability is usually
either a user mistake or a bug in the code. Bugs can be reported in
the LAMMPS project
[issue tracker on GitHub](https://github.com/lammps/lammps/issues).
either a user mistake or a bug in the code. Bugs can be reported in the
LAMMPS project [issue tracker on
GitHub](https://github.com/lammps/lammps/issues).
To mitigate issues with using homoglyphs or bidirectional reordering in
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
LAMMPS follows continuous release development model. We aim to keep all
release versions (stable or patch) fully functional and employ a variety
of automatic testing procedures to detect failures of existing
functionality from adding new features before releases are made. Thus
bugfixes and updates are only integrated into the current development
branch and thus the next (patch) release and users are recommended to
update regularly.
LAMMPS follows continuous release development model. We aim to keep to
keep the development version (develop branch) always fully functional
and employ a variety of automatic testing procedures to detect failures
of existing functionality from adding or modifying features. Most of
those tests are run on pull requests *before* merging to the development
branch. The develop branch is protected, so all changes *must* be
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.

5
cmake/CMakeLists.txt
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@ -12,6 +12,11 @@ endif()
if(POLICY CMP0109)
cmake_policy(SET CMP0109 OLD)
endif()
# set policy to silence warnings about timestamps of downloaded files. review occasionally if it may be set to NEW
if(POLICY CMP0135)
cmake_policy(SET CMP0135 OLD)
endif()
########################################
project(lammps CXX)

27
cmake/Modules/Packages/MDI.cmake
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@ -49,6 +49,14 @@ if(DOWNLOAD_MDI)
set(MDI_USE_PYTHON_PLUGINS ON)
endif()
endif()
# python plugins are not supported and thus must be always off on Windows
if(CMAKE_SYSTEM_NAME STREQUAL "Windows")
unset(Python_Development_FOUND)
set(MDI_USE_PYTHON_PLUGINS OFF)
if(CMAKE_CROSSCOMPILING)
set(CMAKE_INSTALL_LIBDIR lib)
endif()
endif()
# download/ build MDI library
# always build static library with -fpic
@ -57,8 +65,9 @@ if(DOWNLOAD_MDI)
ExternalProject_Add(mdi_build
URL ${MDI_URL}
URL_MD5 ${MDI_MD5}
PREFIX ${CMAKE_CURRENT_BINARY_DIR}/mdi_build_ext
CMAKE_ARGS
-DCMAKE_INSTALL_PREFIX=<INSTALL_DIR>
-DCMAKE_INSTALL_PREFIX=${CMAKE_CURRENT_BINARY_DIR}/mdi_build_ext
-DCMAKE_C_COMPILER=${CMAKE_C_COMPILER}
-DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
-DCMAKE_MAKE_PROGRAM=${CMAKE_MAKE_PROGRAM}
@ -70,23 +79,23 @@ if(DOWNLOAD_MDI)
-Dplugins=ON
-Dpython_plugins=${MDI_USE_PYTHON_PLUGINS}
UPDATE_COMMAND ""
INSTALL_COMMAND ""
BUILD_BYPRODUCTS "<BINARY_DIR>/MDI_Library/libmdi.a"
INSTALL_COMMAND ${CMAKE_COMMAND} --build ${CMAKE_CURRENT_BINARY_DIR}/mdi_build_ext/src/mdi_build-build --target install
BUILD_BYPRODUCTS "${CMAKE_CURRENT_BINARY_DIR}/mdi_build_ext/${CMAKE_INSTALL_LIBDIR}/mdi/${CMAKE_STATIC_LIBRARY_PREFIX}mdi${CMAKE_STATIC_LIBRARY_SUFFIX}"
)
# where is the compiled library?
ExternalProject_get_property(mdi_build BINARY_DIR)
set(MDI_BINARY_DIR "${BINARY_DIR}/MDI_Library")
ExternalProject_get_property(mdi_build PREFIX)
# workaround for older CMake versions
file(MAKE_DIRECTORY ${MDI_BINARY_DIR})
file(MAKE_DIRECTORY ${PREFIX}/${CMAKE_INSTALL_LIBDIR}/mdi)
file(MAKE_DIRECTORY ${PREFIX}/include/mdi)
# create imported target for the MDI library
add_library(LAMMPS::MDI UNKNOWN IMPORTED)
add_dependencies(LAMMPS::MDI mdi_build)
set_target_properties(LAMMPS::MDI PROPERTIES
IMPORTED_LOCATION "${MDI_BINARY_DIR}/libmdi.a"
INTERFACE_INCLUDE_DIRECTORIES ${MDI_BINARY_DIR}
)
IMPORTED_LOCATION "${PREFIX}/${CMAKE_INSTALL_LIBDIR}/mdi/${CMAKE_STATIC_LIBRARY_PREFIX}mdi${CMAKE_STATIC_LIBRARY_SUFFIX}"
INTERFACE_INCLUDE_DIRECTORIES ${PREFIX}/include/mdi
)
set(MDI_DEP_LIBS "")
# if compiling with python plugins we need

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

20
cmake/Modules/Packages/ML-PACE.cmake
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@ -1,6 +1,6 @@
set(PACELIB_URL "https://github.com/ICAMS/lammps-user-pace/archive/refs/tags/v.2021.10.25.fix2.tar.gz" CACHE STRING "URL for PACE evaluator library sources")
set(PACELIB_URL "https://github.com/ICAMS/lammps-user-pace/archive/refs/tags/v.2022.09.27.tar.gz" CACHE STRING "URL for PACE evaluator library sources")
set(PACELIB_MD5 "32394d799bc282bb57696c78c456e64f" CACHE STRING "MD5 checksum of PACE evaluator library tarball")
set(PACELIB_MD5 "ad6c8597076479bd55059f5947d51acc" CACHE STRING "MD5 checksum of PACE evaluator library tarball")
mark_as_advanced(PACELIB_URL)
mark_as_advanced(PACELIB_MD5)
@ -15,23 +15,9 @@ execute_process(
)
get_newest_file(${CMAKE_BINARY_DIR}/lammps-user-pace-* lib-pace)
# enforce building libyaml-cpp as static library and turn off optional features
set(YAML_BUILD_SHARED_LIBS OFF)
set(YAML_CPP_BUILD_CONTRIB OFF)
set(YAML_CPP_BUILD_TOOLS OFF)
add_subdirectory(${lib-pace}/yaml-cpp build-yaml-cpp)
set(YAML_CPP_INCLUDE_DIR ${lib-pace}/yaml-cpp/include)
file(GLOB PACE_EVALUATOR_INCLUDE_DIR ${lib-pace}/ML-PACE)
file(GLOB PACE_EVALUATOR_SOURCES ${lib-pace}/ML-PACE/*.cpp)
list(FILTER PACE_EVALUATOR_SOURCES EXCLUDE REGEX pair_pace.cpp)
add_library(pace STATIC ${PACE_EVALUATOR_SOURCES})
add_subdirectory(${lib-pace} build-pace)
set_target_properties(pace PROPERTIES CXX_EXTENSIONS ON OUTPUT_NAME lammps_pace${LAMMPS_MACHINE})
target_include_directories(pace PUBLIC ${PACE_EVALUATOR_INCLUDE_DIR} ${YAML_CPP_INCLUDE_DIR})
target_link_libraries(pace PRIVATE yaml-cpp-pace)
if(CMAKE_PROJECT_NAME STREQUAL "lammps")
target_link_libraries(lammps PRIVATE pace)
endif()

24
doc/src/Bibliography.rst
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@ -314,7 +314,7 @@ Bibliography
Espanol, Revenga, Physical Review E, 67, 026705 (2003).
**(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, Phys Rev A, 30, 1528 (1984).
@ -368,7 +368,7 @@ Bibliography
Frenkel and Smit, Understanding Molecular Simulation, Academic Press, London, 2002.
**(GLE4MD)**
`http://gle4md.org/ <http://gle4md.org/>`_
`https://gle4md.org/ <https://gle4md.org/>`_
**(Gao)**
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)
**(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, Noehring, Vaid, Houlle, Xie, Prakash, Bitzek, Comput Mater Sci, 175, 109584 (2020).
**(Gullet)**
Gullet, Wagner, Slepoy, SANDIA Report 2003-8782 (2003).
Gullet, Wagner, Slepoy, SANDIA Report 2003-8782 (2003). DOI:10.2172/918395
**(Guo)**
Guo and Thirumalai, Journal of Molecular Biology, 263, 323-43 (1996).
@ -461,7 +461,7 @@ Bibliography
Hunt, Mol Simul, 42, 347 (2016).
**(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)**
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).
**(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)**
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)**
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)**
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)**
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, Mehl, and Papaconstantopoulos, Acta Mater, 53, 4029 (2005).
**(Mitchell and Finchham)**
Mitchell, Finchham, J Phys Condensed Matter, 5, 1031-1038 (1993).
**(Mitchell and Fincham)**
Mitchell, Fincham, J Phys Condensed Matter, 5, 1031-1038 (1993).
**(Mitchell2011)**
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)
**(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, Schulten, J. Chem. Phys. 120 (13), 5946 (2004)

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
of the LAMMPS source code distribution itself. It can be enabled by
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
downloaded and compiled along with LAMMPS and the test program) to
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
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.
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_ErcolessiAdams_1994_Al__MO_123629422045_005``, and
``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
Models or see
`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
`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.
.. tabs::

19
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
readers, like Kindle, that cannot read ePUB), you also need to have the
``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
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.
@ -216,9 +216,20 @@ be multiple tests run automatically:
- A test that only standard, printable ASCII text characters are used.
This runs the command ``env LC_ALL=C grep -n '[^ -~]' src/*.rst`` and
thus prints all offending lines with filename and line number
prepended to the screen. Special characters like the Angstrom
:math:`\mathrm{\mathring{A}}` should be typeset with embedded math
(like this ``:math:`\mathrm{\mathring{A}}```\ ).
prepended to the screen. Special characters like Greek letters
(:math:`\alpha~~\sigma~~\epsilon`), super- or subscripts
(:math:`x^2~~\mathrm{U}_{LJ}`), mathematical expressions
(:math:`\frac{1}{2}\mathrm{N}~~x\to\infty`), or the Angstrom symbol
(:math:`\AA`) should be typeset with embedded LaTeX (like this
``:math:`\alpha \sigma \epsilon```, ``:math:`x^2 \mathrm{E}_{LJ}```,
``:math:`\frac{1}{2}\mathrm{N} x\to\infty```, or ``:math:`\AA```\ ).
- Embedded LaTeX is rendered in HTML output with `MathJax
<https://www.mathjax.org/>`_ and in PDF output by passing the embedded
text to LaTeX. Some care has to be taken, though, since there are
limitations which macros and features can be used in either mode, so
it is recommended to always check whether any new or changed
documentation does translate and render correctly with either output.
- A test whether all styles are documented and listed in their
respective overview pages. A typical output with warnings looks like this:

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``
with the appropriate FFT libraries to include in the link.
The `KISS FFT library <http://kissfft.sf.net>`_ is included in the LAMMPS
distribution. It is portable across all platforms. Depending on the size
of the FFTs and the number of processors used, the other libraries listed
here can be faster.
The `KISS FFT library <https://github.com/mborgerding/kissfft>`_ is
included in the LAMMPS distribution. It is portable across all
platforms. Depending on the size of the FFTs and the number of
processors used, the other libraries listed here can be faster.
However, note that long-range Coulombics are only a portion of the
per-timestep CPU cost, FFTs are only a portion of long-range
Coulombics, and 1d FFTs are only a portion of the FFT cost (parallel
communication can be costly). A breakdown of these timings is printed
to the screen at the end of a run when using the
:doc:`kspace_style pppm <kspace_style>` command. The
:doc:`Screen and logfile output <Run_output>`
page gives more details. A more detailed (and time consuming)
report of the FFT performance is generated with the
per-timestep CPU cost, FFTs are only a portion of long-range Coulombics,
and 1d FFTs are only a portion of the FFT cost (parallel communication
can be costly). A breakdown of these timings is printed to the screen
at the end of a run when using the :doc:`kspace_style pppm
<kspace_style>` command. The :doc:`Screen and logfile output
<Run_output>` page gives more details. A more detailed (and time
consuming) report of the FFT performance is generated with the
:doc:`kspace_modify fftbench yes <kspace_modify>` command.
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
download it from `www.fftw.org <http://www.fftw.org>`_. LAMMPS requires
version 3.X; the legacy version 2.1.X is no longer supported.
platform and can be faster than the KISS FFT library. You can download
it from `www.fftw.org <https://www.fftw.org>`_. LAMMPS requires version
3.X; the legacy version 2.1.X is no longer supported.
Building FFTW for your box should be as simple as ``./configure; make;
make install``. The install command typically requires root privileges

1
doc/src/Commands_pair.rst
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@ -236,6 +236,7 @@ OPT.
* :doc:`oxrna2/xstk <pair_oxrna2>`
* :doc:`oxrna2/coaxstk <pair_oxrna2>`
* :doc:`pace (k) <pair_pace>`
* :doc:`pace/extrapolation <pair_pace>`
* :doc:`peri/eps <pair_peri>`
* :doc:`peri/lps (o) <pair_peri>`
* :doc:`peri/pmb (o) <pair_peri>`

2
doc/src/Errors_debug.rst
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@ -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
of the segmentation fault or similar crash. The GDB debugger has many
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
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

1410
doc/src/Fortran.rst
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1
doc/src/Howto.rst
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@ -85,6 +85,7 @@ Packages howto
Howto_coreshell
Howto_drude
Howto_drude2
Howto_peri
Howto_manifold
Howto_spins

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
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/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
coefficients used for a particular system. Here we only discuss
formulas implemented in LAMMPS that correspond to formulas commonly
used in the CHARMM, AMBER, COMPASS, and DREIDING force fields. Setting
formulas implemented in LAMMPS that correspond to formulas commonly used
in the CHARMM, AMBER, COMPASS, and DREIDING force fields. Setting
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
commands like :doc:`pair_coeff <pair_coeff>` or
:doc:`bond_coeff <bond_coeff>` and so on. See the :doc:`Tools <Tools>` doc
page for additional tools that can use CHARMM, AMBER, or Materials
Studio generated files to assign force field coefficients and convert
their output into LAMMPS input.
commands like :doc:`pair_coeff <pair_coeff>` or :doc:`bond_coeff
<bond_coeff>` and so on. See the :doc:`Tools <Tools>` doc page for
additional tools that can use CHARMM, AMBER, or Materials Studio
generated files to assign force field coefficients and convert their
output into LAMMPS input.
See :ref:`(MacKerell) <howto-MacKerell>` for a description of the CHARMM force
field. See :ref:`(Cornell) <howto-Cornell>` for a description of the AMBER
force field. See :ref:`(Sun) <howto-Sun>` for a description of the COMPASS
force field.
.. _charmm: http://www.scripps.edu/brooks
.. _amber: http://amber.scripps.edu
See :ref:`(MacKerell) <howto-MacKerell>` for a description of the CHARMM
force field. See :ref:`(Cornell) <howto-Cornell>` for a description of
the AMBER force field. See :ref:`(Sun) <howto-Sun>` for a description
of the COMPASS force field.
The interaction styles listed below compute force field formulas that
are consistent with common options in CHARMM or AMBER. See each
@ -41,9 +37,10 @@ command's documentation for the formula it computes.
.. note::
For CHARMM, newer *charmmfsw* or *charmmfsh* styles were released
in 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
For CHARMM, newer *charmmfsw* or *charmmfsh* styles were released in
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
pages.
COMPASS is a general force field for atomistic simulation of common

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
example to describe the individual steps and options. You need to be
familiar with git and you may want to have a look at the `git book
<http://git-scm.com/book/>`_ to familiarize yourself with some of the
<https://git-scm.com/book/>`_ to familiarize yourself with some of the
more advanced git features used below.
As of fall 2016, submitting contributions to LAMMPS via pull requests

2
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@ -47,4 +47,4 @@ to the relevant fixes.
.. _Paquay1:
**(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/>`_.

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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
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
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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
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 thermal energy of the Langevin thermostat, or to perform a
relaxation of the magnetic configuration toward an equilibrium state.
The magnetic damping can also be applied
using :doc:`fix langevin/spin <fix_langevin_spin>`.
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
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
enables to evaluate magnetic averaged quantities, such as the total
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
per atom magnetic quantities. Typically, the orientation of a given
magnetic spin, or the magnetic force acting on this spin.
the magnetic energy. The second command
is :doc:`compute property/atom <compute_property_atom>`.
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}`
|
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
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>`_.
----------

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
dump files, including custom dump files with additional columns of
user-specified atom information, and convert them to various formats
or pipe them into visualization software directly. See the `Pizza.py WWW site <pizza_>`_ for details. Specifically, Pizza.py can convert
LAMMPS dump files into PDB, XYZ, `EnSight <ensight_>`_, and VTK formats.
user-specified atom information, and convert them to various formats or
pipe them into visualization software directly. See the `Pizza.py WWW
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
RasMol visualization programs. Pizza.py has tools that do interactive
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
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:
.. code-block:: bash
@ -13,7 +13,7 @@ install:
% conda config --add channels conda-forge
% 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

2
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@ -6,7 +6,7 @@ Windows system can be downloaded from this site:
.. 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
corresponds to the LAMMPS version of the same date. Installers for

4
doc/src/Intro_authors.rst
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@ -4,13 +4,13 @@ Authors of LAMMPS
The primary LAMMPS developers are at Sandia National Labs and Temple
University:
* `Steve Plimpton <sjp_>`_, sjplimp at sandia.gov
* `Steve Plimpton <sjp_>`_, sjplimp at gmail.com
* Aidan Thompson, athomps at sandia.gov
* Stan Moore, stamoor at sandia.gov
* Axel Kohlmeyer, akohlmey at gmail.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
Past developers include Paul Crozier and Mark Stevens, both at Sandia,

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

4
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@ -95,7 +95,7 @@ commands)
* metal-organic framework potentials (QuickFF, MO-FF)
* implicit solvent potentials: hydrodynamic lubrication, Debye
* 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
* 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
.. _python: http://www.python.org
.. _python: https://www.python.org
.. _special:

6
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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
molecular builder that will generate complex molecular models. See
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,
some LAMMPS internal commands allow to reconstruct, or selectively add
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
setup, analysis, plotting, and visualization (via OpenGL) for LAMMPS
simulations. It thus provides some functionality for several of the
above bullets. Pizza.py is written in `Python <http://www.python.org>`_
and is available for download from `this page <http://www.cs.sandia.gov/~sjplimp/download.html>`_.
above bullets. Pizza.py is written in `Python <https://www.python.org>`_
and is available for download from `this page <https://sjplimp.github.io/download.html>`_.

4
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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
.. _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:

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

8
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@ -6,6 +6,7 @@ fixes, or variables in LAMMPS using the following functions:
- :cpp:func:`lammps_extract_compute`
- :cpp:func:`lammps_extract_fix`
- :cpp:func:`lammps_extract_variable_datatype`
- :cpp:func:`lammps_extract_variable`
- :cpp:func:`lammps_set_variable`
@ -21,6 +22,11 @@ fixes, or variables in LAMMPS using the following functions:
-----------------------
.. doxygenfunction:: lammps_extract_variable_datatype
:project: progguide
-----------------------
.. doxygenfunction:: lammps_extract_variable
:project: progguide
@ -36,3 +42,5 @@ fixes, or variables in LAMMPS using the following functions:
.. doxygenenum:: _LMP_STYLE_CONST
.. doxygenenum:: _LMP_TYPE_CONST
.. doxygenenum:: _LMP_VAR_CONST

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

7
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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_has_error`
- :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
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
:project: progguide
-----------------------
.. doxygenfunction:: lammps_python_api_version
:project: progguide

43
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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.
.. versionadded:: 28Feb2019
**Install:**
This package has :ref:`specific installation instructions <adios>` on the :doc:`Build extras <Build_extras>` page.
@ -364,6 +366,8 @@ and also support self-propelled particles.
**Authors:** Sam Cameron (University of Bristol),
Stefan Paquay (while at Brandeis University) (initial version of fix propel/self)
.. versionadded:: 14May2021
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)
.. versionadded:: 2Jul2021
**Supporting info:**
* src/DIELECTRIC: filenames -> commands
@ -1071,7 +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
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
system.
@ -1512,6 +1518,8 @@ workflows via the `MolSSI Driver Interface
**Author:** Taylor Barnes - MolSSI, taylor.a.barnes at gmail.com
.. versionadded:: 14May2021
**Install:**
This package has :ref:`specific installation instructions <mdi>` on
@ -1596,6 +1604,8 @@ of Alabama), Leonid V. Zhigilei (University of Virginia)
**Author of the *mesocnt* styles:**
Philipp Kloza (U Cambridge)
.. versionadded:: 15Jun2020
**Supporting info:**
* src/MESONT: filenames -> commands
@ -1688,6 +1698,8 @@ compiled on your system.
**Author:** Andreas Singraber
.. versionadded:: 27May2021
**Install:**
This package has :ref:`specific installation instructions <ml-hdnnp>` on the
@ -1722,6 +1734,10 @@ must be installed.
**Author:** Aidan Thompson (Sandia), Nicholas Lubbers (LANL).
.. versionadded:: 30Jun2020
.. versionadded:: 30Jun2020
**Supporting info:**
* src/ML-IAP: filenames -> commands
@ -1766,6 +1782,8 @@ Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1.
^4: University of British Columbia, Vancouver, BC, Canada
.. versionadded:: 14May2021
**Install:**
This package has :ref:`specific installation instructions <ml-pace>` on the
@ -1829,6 +1847,8 @@ of a neural network.
This package was written by Christopher Barrett
with contributions by Doyl Dickel, Mississippi State University.
.. versionadded:: 27May2021
**Supporting info:**
* src/ML-RANN: filenames -> commands
@ -1954,7 +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
itself. More information about the VMD molfile plugins can be found
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).
@ -2045,7 +2065,7 @@ NETCDF package
Dump styles for writing NetCDF formatted dump files. NetCDF is a
portable, binary, self-describing file format developed on top of
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
system.
@ -2056,7 +2076,7 @@ tools:
* `Ovito <ovito_>`_ (Ovito supports the AMBER convention and the extensions mentioned above)
* `VMD <vmd-home_>`_
.. _ovito: http://www.ovito.org
.. _ovito: https://www.ovito.org
.. _vmd-home: https://www.ks.uiuc.edu/Research/vmd/
@ -2200,6 +2220,7 @@ Foster (UTSA).
**Supporting info:**
* src/PERI: filenames -> commands
* :doc:`Peridynamics Howto <Howto_peri>`
* `doc/PDF/PDLammps_overview.pdf <PDF/PDLammps_overview.pdf>`_
* `doc/PDF/PDLammps_EPS.pdf <PDF/PDLammps_EPS.pdf>`_
* `doc/PDF/PDLammps_VES.pdf <PDF/PDLammps_VES.pdf>`_
@ -2264,6 +2285,8 @@ try to load the contained plugins automatically at start-up.
**Authors:** Axel Kohlmeyer (Temple U)
.. versionadded:: 8Apr2021
**Supporting info:**
* src/PLUGIN: filenames -> commands
@ -2417,7 +2440,7 @@ 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
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
your system and include its coupling library in the compilation and
@ -2829,7 +2852,7 @@ 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
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
system.
@ -2863,9 +2886,9 @@ A :doc:`dump vtk <dump_vtk>` command which outputs snapshot info in the
`VTK format <vtk_>`_, enabling visualization by `Paraview <paraview_>`_ or
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
system.
@ -2902,11 +2925,13 @@ which discuss the `QuickFF <quickff_>`_ methodology.
.. _vanduyfhuys2015: https://doi.org/10.1002/jcc.23877
.. _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
**Author:** Steven Vandenbrande.
.. versionadded:: 1Feb2019
**Supporting info:**
* src/YAFF/README

20
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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
AtomEye web pages for more details:
* `http://li.mit.edu/Archive/Graphics/A/ <atomeye_>`_
* `http://li.mit.edu/Archive/Graphics/A3/A3.html <atomeye3_>`_
* `http://li.mit.edu/Archive/Graphics/A/ <http://li.mit.edu/Archive/Graphics/A/>`_
* `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/
.. _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.
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
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:
* `https://www.pymol.org <pymolhome_>`_
* `https://github.com/schrodinger/pymol-open-source <pymolopen_>`_
.. _pymolhome: https://www.pymol.org
.. _pymolopen: https://github.com/schrodinger/pymol-open-source
* `https://www.pymol.org <https://www.pymol.org>`_
* `https://github.com/schrodinger/pymol-open-source <https://github.com/schrodinger/pymol-open-source>`_
The latter link is to the open-source version.

10
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@ -18,17 +18,17 @@ together.
Python_error
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
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
modules for many purposes (either bundled or easily installed from
Python code repositories). The major drawback is slower execution speed
of the script code compared to compiled programming languages. But when
the script code is interfaced to optimized compiled code, performance can
be on par with a standalone executable, for as long as the scripting is
restricted to high-level operations. Thus Python is also convenient to
use as a "glue" language to "drive" a program through its library
the script code is interfaced to optimized compiled code, performance
can be on par with a standalone executable, for as long as the scripting
is restricted to high-level operations. Thus Python is also convenient
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
simulation code and a visualization tool, or to run a coupled
multi-scale or multi-physics model.

34
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@ -38,6 +38,40 @@ using the NumPy access method.
for n in np.nditer(nlist):
print(" atom {} with ID {}".format(n,tags[n]))
Another example for extracting a full neighbor list without evaluating a
potential is shown below.
.. code-block:: python
from lammps import lammps
import numpy as np
lmp = lammps()
lmp.commands_string("""
newton off
region box block -2 2 -2 2 -2 2
lattice fcc 1.0
create_box 1 box
create_atoms 1 box
mass 1 1.0
pair_style zero 1.0 full
pair_coeff * *
run 0 post no""")
# look up the neighbor list
nlidx = lmp.find_pair_neighlist('zero')
nl = lmp.numpy.get_neighlist(nlidx)
tags = lmp.extract_atom('id')
print("full neighbor list with {} entries".format(nl.size))
# print neighbor list contents
for i in range(0,nl.size):
idx, nlist = nl.get(i)
print("\natom {} with ID {} has {} neighbors:".format(idx,tags[idx],nlist.size))
if nlist.size > 0:
for n in np.nditer(nlist):
pass
print(" atom {} with ID {}".format(n,tags[n]))
**Methods:**
* :py:meth:`lammps.get_neighlist() <lammps.lammps.get_neighlist()>`: Get neighbor list for given index

9
doc/src/Run_basics.rst
View File

@ -30,12 +30,13 @@ executable itself can be placed elsewhere.
.. note::
The redirection operator "<" will not always work when running
in parallel with mpirun or mpiexec; for those systems the -in form is required.
The redirection operator "<" will not always work when running in
parallel with ``mpirun`` or ``mpiexec``; for those systems the -in
form is required.
As LAMMPS runs it prints info to the screen and a logfile named
*log.lammps*\ . More info about output is given on the
:doc:`screen and logfile output <Run_output>` page.
*log.lammps*\ . More info about output is given on the :doc:`screen and
logfile output <Run_output>` page.
If LAMMPS encounters errors in the input script or while running a
simulation it will print an ERROR message and stop or a WARNING

20
doc/src/Run_options.rst
View File

@ -93,13 +93,13 @@ switch is not set (the default), LAMMPS will operate as if the KOKKOS
package were not installed; i.e. you can run standard LAMMPS or with
the GPU or OPENMP packages, for testing or benchmarking purposes.
Additional optional keyword/value pairs can be specified which
determine how Kokkos will use the underlying hardware on your
platform. These settings apply to each MPI task you launch via the
"mpirun" or "mpiexec" command. You may choose to run one or more MPI
tasks per physical node. Note that if you are running on a desktop
machine, you typically have one physical node. On a cluster or
supercomputer there may be dozens or 1000s of physical nodes.
Additional optional keyword/value pairs can be specified which determine
how Kokkos will use the underlying hardware on your platform. These
settings apply to each MPI task you launch via the ``mpirun`` or
``mpiexec`` command. You may choose to run one or more MPI tasks per
physical node. Note that if you are running on a desktop machine, you
typically have one physical node. On a cluster or supercomputer there
may be dozens or 1000s of physical nodes.
Either the full word or an abbreviation can be used for the keywords.
Note that the keywords do not use a leading minus sign. I.e. the
@ -148,9 +148,9 @@ one of these 4 environment variables
MV2_COMM_WORLD_LOCAL_RANK (Mvapich)
OMPI_COMM_WORLD_LOCAL_RANK (OpenMPI)
which are initialized by the "srun", "mpirun" or "mpiexec" commands.
The environment variable setting for each MPI rank is used to assign a
unique GPU ID to the MPI task.
which are initialized by the ``srun``, ``mpirun``, or ``mpiexec``
commands. The environment variable setting for each MPI rank is used to
assign a unique GPU ID to the MPI task.
.. parsed-literal::

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:
* for 32-bit Windows: `mpich2-1.4.1p1-win-ia32.msi <http://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 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 <https://download.lammps.org/thirdparty/mpich2-1.4.1p1-win-x86-64.msi>`_
The LAMMPS Windows installer packages will automatically adjust your
path for the default location of this MPI package. After the

15
doc/src/Speed_gpu.rst
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@ -39,7 +39,7 @@ toolkit software on your system (this is only tested on Linux
and unsupported on Windows):
* 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)
* Run lammps/lib/gpu/nvc_get_devices (after building the GPU library, see below) to
list supported devices and properties
@ -76,10 +76,11 @@ instructions.
**Run with the GPU package from the command line:**
The mpirun or mpiexec command sets the total number of MPI tasks used
by LAMMPS (one or multiple per compute node) and the number of MPI
tasks used per node. E.g. the mpirun command in MPICH does this via
its -np and -ppn switches. Ditto for OpenMPI via -np and -npernode.
The ``mpirun`` or ``mpiexec`` command sets the total number of MPI tasks
used by LAMMPS (one or multiple per compute node) and the number of MPI
tasks used per node. E.g. the ``mpirun`` command in MPICH does this via
its ``-np`` and ``-ppn`` switches. Ditto for OpenMPI via ``-np`` and
``-npernode``.
When using the GPU package, you cannot assign more than one GPU to a
single MPI task. However multiple MPI tasks can share the same GPU,
@ -129,8 +130,8 @@ GPU package pair styles.
**Or run with the GPU package by editing an input script:**
The discussion above for the mpirun/mpiexec command, MPI tasks/node,
and use of multiple MPI tasks/GPU is the same.
The discussion above for the ``mpirun`` or ``mpiexec`` command, MPI
tasks/node, and use of multiple MPI tasks/GPU is the same.
Use the :doc:`suffix gpu <suffix>` command, or you can explicitly add an
"gpu" suffix to individual styles in your input script, e.g.

2
doc/src/Speed_intel.rst
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@ -537,5 +537,5 @@ 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., 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.

17
doc/src/Speed_kokkos.rst
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@ -72,12 +72,12 @@ See the :ref:`Build extras <kokkos>` page for instructions.
Running LAMMPS with the KOKKOS package
""""""""""""""""""""""""""""""""""""""
All Kokkos operations occur within the context of an individual MPI
task running on a single node of the machine. The total number of MPI
tasks used by LAMMPS (one or multiple per compute node) is set in the
usual manner via the mpirun or mpiexec commands, and is independent of
Kokkos. E.g. the mpirun command in OpenMPI does this via its -np and
-npernode switches. Ditto for MPICH via -np and -ppn.
All Kokkos operations occur within the context of an individual MPI task
running on a single node of the machine. The total number of MPI tasks
used by LAMMPS (one or multiple per compute node) is set in the usual
manner via the ``mpirun`` or ``mpiexec`` commands, and is independent of
Kokkos. E.g. the mpirun command in OpenMPI does this via its ``-np`` and
``-npernode`` switches. Ditto for MPICH via ``-np`` and ``-ppn``.
Running on a multi-core CPU
^^^^^^^^^^^^^^^^^^^^^^^^^^^
@ -168,7 +168,7 @@ for your MPI installation), binding can be forced with these flags:
.. parsed-literal::
OpenMPI 1.8: mpirun -np 2 --bind-to socket --map-by socket ./lmp_openmpi ...
OpenMPI 1.8: mpirun -np 2 --bind-to socket --map-by socket ./lmp_openmpi ...
Mvapich2 2.0: mpiexec -np 2 --bind-to socket --map-by socket ./lmp_mvapich ...
For binding threads with KOKKOS OpenMP, use thread affinity environment
@ -310,7 +310,8 @@ Alternatively the effect of the "-sf" or "-pk" switches can be
duplicated by adding the :doc:`package kokkos <package>` or :doc:`suffix kk <suffix>` commands to your input script.
The discussion above for building LAMMPS with the KOKKOS package, the
mpirun/mpiexec command, and setting appropriate thread are the same.
``mpirun`` or ``mpiexec`` command, and setting appropriate thread
properties are the same.
You must still use the "-k on" :doc:`command-line switch <Run_options>`
to enable the KOKKOS package, and specify its additional arguments for

10
doc/src/Speed_omp.rst
View File

@ -33,8 +33,8 @@ These examples assume one or more 16-core nodes.
mpirun -np 4 lmp_omp -sf omp -pk omp 4 -in in.script # 4 MPI tasks, 4 threads/task
mpirun -np 32 -ppn 4 lmp_omp -sf omp -pk omp 4 -in in.script # 8 nodes, 4 MPI tasks/node, 4 threads/task
The mpirun or mpiexec command sets the total number of MPI tasks used
by LAMMPS (one or multiple per compute node) and the number of MPI
The ``mpirun`` or ``mpiexec`` command sets the total number of MPI tasks
used by LAMMPS (one or multiple per compute node) and the number of MPI
tasks used per node. E.g. the mpirun command in MPICH does this via
its -np and -ppn switches. Ditto for OpenMPI via -np and -npernode.
@ -58,8 +58,8 @@ OMP_NUM_THREADS environment variable.
Or run with the OPENMP package by editing an input script
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
The discussion above for the mpirun/mpiexec command, MPI tasks/node,
and threads/MPI task is the same.
The discussion above for the ``mpirun`` or ``mpiexec`` command, MPI
tasks/node, and threads/MPI task is the same.
Use the :doc:`suffix omp <suffix>` command, or you can explicitly add an
"omp" suffix to individual styles in your input script, e.g.
@ -97,7 +97,7 @@ sub-section.
A description of the multi-threading strategy used in the OPENMP
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
"""""""""""""""""""""""""""""""

24
doc/src/Speed_packages.rst
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@ -117,33 +117,15 @@ script.
with all its accelerator packages installed. Note however that the
INTEL and KOKKOS packages require you to choose one of their
hardware options when building for a specific platform. I.e. CPU or
Phi option for the INTEL package. Or the OpenMP, Cuda, or Phi
option for the KOKKOS package.
Phi option for the INTEL package. Or the OpenMP, CUDA, HIP, SYCL,
or Phi option for the KOKKOS package. Or the OpenCL, HIP, or CUDA
option for the GPU package.
These are the exceptions. You cannot build a single executable with:
* both the INTEL Phi and KOKKOS Phi options
* the INTEL Phi or Kokkos Phi option, and the GPU package
See the examples/accelerate/README and make.list files for sample
Make.py commands that build LAMMPS with any or all of the accelerator
packages. As an example, here is a command that builds with all the
GPU related packages installed (GPU, KOKKOS with Cuda), including
settings to build the needed auxiliary GPU libraries for Kepler GPUs:
.. code-block:: bash
Make.py -j 16 -p omp gpu kokkos -cc nvcc wrap=mpi -gpu mode=double arch=35 -kokkos cuda arch=35 lib-all file mpi
The examples/accelerate directory also has input scripts that can be
used with all of the accelerator packages. See its README file for
details.
Likewise, the bench directory has FERMI and KEPLER and PHI
sub-directories with Make.py commands and input scripts for using all
the accelerator packages on various machines. See the README files in
those directories.
As mentioned above, the `Benchmark page <https://www.lammps.org/bench.html>`_ of the LAMMPS website gives
performance results for the various accelerator packages for several
of the standard LAMMPS benchmark problems, as a function of problem

13
doc/src/Tools.rst
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@ -205,6 +205,7 @@ scripts are available:
whitespace.py # detects TAB characters and trailing whitespace
homepage.py # detects outdated LAMMPS homepage URLs (pointing to sandia.gov instead of lammps.org)
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
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
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.
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".
For more information about using and customizing an application using
readline, please see the available documentation at:
`http://www.gnu.org/s/readline/#Documentation
<http://www.gnu.org/s/readline/#Documentation>`_
https://www.gnu.org/software/readline/
Additional commands
^^^^^^^^^^^^^^^^^^^
@ -715,7 +716,7 @@ See the README.pdf file for more information.
These scripts were written by Arun Subramaniyan at Purdue Univ
(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
--------------
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
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
@ -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
accessible. What works and what does not depends a bit on the
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.
Usage examples

10
doc/src/bond_mm3.rst
View File

@ -26,14 +26,14 @@ as defined in :ref:`(Allinger) <mm3-allinger1989>`
.. math::
E = K (r - r_0)^2 \left[ 1 - 2.55(r-r_0) + (7/12) 2.55^2(r-r_0)^2 \right]
E = K (r - r_0)^2 \left[ 1 - 2.55(r-r_0) + \frac{7}{12} 2.55^2(r-r_0)^2 \right]
where :math:`r_0` is the equilibrium value of the bond, and :math:`K` is a
prefactor. The anharmonic prefactors have units angstrom\^(-n):
-2.55 angstrom\^(-1) and (7/12)2.55\^2 angstrom\^(-2). The code takes
prefactor. The anharmonic prefactors have units :math:`\AA^{-n}`:
:math:`-2.55 \AA^{-1}` and :math:`\frac{7}{12} 2.55^2 \AA^{-2}`. The code takes
care of the necessary unit conversion for these factors internally.
Note that the MM3 papers contains an error in Eq (1):
(7/12)2.55 should be replaced with (7/12)2.55\^2
Note that the MM3 papers contain an error in Eq (1):
:math:`\frac{7}{12} 2.55` should be replaced with :math:`\frac{7}{12} 2.55^2`
The following coefficients must be defined for each bond type via the
:doc:`bond_coeff <bond_coeff>` command as in the example above, or in

19
doc/src/bond_quartic.rst
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@ -28,11 +28,18 @@ The *quartic* bond style uses the potential
.. math::
E = K (r - R_c)^ 2 (r - R_c - B_1) (r - R_c - B_2) + U_0 + 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} - \left(\frac{\sigma}{r}\right)^6 \right] + \epsilon
E & = E_q + E_{LJ} \\
E_q & = K (r - R_c)^ 2 (r - R_c - B_1) (r - R_c - B_2) + U_0 \\
E_{LJ} & = \left\{ \begin{array} {l@{\quad:\quad}l}
4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} - \left(\frac{\sigma}{r}\right)^6 \right] + \epsilon & r < 2^{\frac{1}{6}}, \epsilon = 1, \sigma = 1 \\
0 & r >= 2^{\frac{1}{6}}
\end{array} \right.
to define a bond that can be broken as the simulation proceeds (e.g.
due to a polymer being stretched). The :math:`\sigma` and :math:`\epsilon` used in the
LJ portion of the formula are both set equal to 1.0 by LAMMPS.
due to a polymer being stretched). The :math:`\sigma` and
:math:`\epsilon` used in the LJ portion of the formula are both set
equal to 1.0 by LAMMPS and the LJ portion is cut off at its minimum,
i.e. at :math:`r_c = 2^{\frac{1}{6}}`.
The following coefficients must be defined for each bond type via the
:doc:`bond_coeff <bond_coeff>` command as in the example above, or in
@ -46,9 +53,9 @@ or :doc:`read_restart <read_restart>` commands:
* :math:`U_0` (energy)
This potential was constructed to mimic the FENE bond potential for
coarse-grained polymer chains. When monomers with :math:`\sigma = \epsilon = 1.0`
are used, the following choice of parameters gives a quartic potential that
looks nearly like the FENE potential:
coarse-grained polymer chains. When monomers with :math:`\sigma =
\epsilon = 1.0` are used, the following choice of parameters gives a
quartic potential that looks nearly like the FENE potential:
.. math::

2
doc/src/compute_ave_sphere_atom.rst
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@ -35,6 +35,8 @@ Examples
Description
"""""""""""
.. versionadded:: 7Jan2022
Define a computation that calculates the local mass density and
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

3
doc/src/compute_chunk_atom.rst
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@ -602,8 +602,7 @@ be used. For non-orthogonal (triclinic) simulation boxes, only the
*reduced* option may be used.
A *box* value selects standard distance units as defined by the
:doc:`units <units>` command (e.g., :math:`\mathrm{\mathring A}`
for units = *real* or *metal*).
:doc:`units <units>` command (e.g., :math:`\AA` for units = *real* or *metal*).
A *lattice* value means the distance units are in lattice spacings.
The :doc:`lattice <lattice>` command must have been previously used to
define the lattice spacing. A *reduced* value means normalized

16
doc/src/compute_damage_atom.rst
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@ -24,16 +24,17 @@ Description
"""""""""""
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>`_
for an overview of LAMMPS commands for Peridynamics modeling.
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.
The "damage" of a Peridynamics particles is based on the bond breakage
between the particle and its neighbors. If all the bonds are broken
the particle is considered to be fully damaged.
See the `PDLAMMPS user guide <http://www.sandia.gov/~mlparks/papers/PDLAMMPS.pdf>`_ for a formal
definition of "damage" and more details about Peridynamics as it is
implemented in LAMMPS.
See the :doc:`Peridynamics Howto <Howto_peri>` for a 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.
@ -53,8 +54,9 @@ The per-atom vector values are unitless numbers (damage) :math:`\ge 0.0`.
Restrictions
""""""""""""
This compute is part of the PERI package. It is only enabled if
LAMMPS was built with that package. See the :doc:`Build package <Build_package>` page for more info.
This compute is part of the PERI package. It is only enabled if LAMMPS
was built with that package. See the :doc:`Build package
<Build_package>` page for more info.
Related commands
""""""""""""""""

20
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
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 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
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
(versus the initial length in the reference state), the volume
contribution of the :math:`ij` pair is a function of the change in bond
length (versus the initial length in the reference state), the volume
fraction of the particles and an influence function. See the
`PDLAMMPS user guide <http://www.sandia.gov/~mlparks/papers/PDLAMMPS.pdf>`_ for
a formal definition of dilatation.
:doc:`Peridynamics Howto <Howto_peri>` 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
compute group.
@ -56,9 +58,9 @@ The per-atom vector values are unitless numbers :math:`(\theta \ge 0.0)`.
Restrictions
""""""""""""
This compute is part of the PERI package. It is only enabled if
LAMMPS was built with that package. See the
:doc:`Build package <Build_package>` page for more info.
This compute is part of the PERI package. It is only enabled if LAMMPS
was built with that package. See the :doc:`Build package
<Build_package>` page for more info.
Related commands
""""""""""""""""

2
doc/src/compute_displace_atom.rst
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@ -95,7 +95,7 @@ something like the following commands:
refresh c_dsp delay 100
The :doc:`dump_modify thresh <dump_modify>` command will only output
atoms that have displaced more than :math:`0.6~\mathrm{\mathring A}` on each
atoms that have displaced more than :math:`0.6~\AA` on each
snapshot (assuming metal units). The dump_modify *refresh* option triggers a
call to this compute at the end of every dump.

4
doc/src/compute_entropy_atom.rst
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@ -97,13 +97,13 @@ by the corresponding volume. This option can be useful when dealing with
inhomogeneous systems such as those that have surfaces.
Here are typical input parameters for fcc aluminum (lattice
constant :math:`4.05~\mathrm{\mathring A}`),
constant :math:`4.05~\AA`),
.. parsed-literal::
compute 1 all entropy/atom 0.25 5.7 avg yes 3.7
and for bcc sodium (lattice constant 4.23 Angstroms),
and for bcc sodium (lattice constant :math:`4.23~\AA`),
.. parsed-literal::

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

3
doc/src/compute_rigid_local.rst
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@ -109,8 +109,7 @@ The *mass* attribute is the total mass of the rigid body.
There are two options for outputting the coordinates of the center of
mass (COM) of the body. The *x*, *y*, *z* attributes write the COM
"unscaled", in the appropriate distance :doc:`units <units>`
(:math:`\mathrm{\mathring A}`,
sigma, etc). Use *xu*, *yu*, *zu* if you want the COM "unwrapped" by
(:math:`\AA`, :math:`\sigma`, etc). Use *xu*, *yu*, *zu* if you want the COM "unwrapped" by
the image flags for each body. Unwrapped means that if the body
COM has passed through a periodic boundary one or more times, the value
is generated what the COM coordinate would be if it had not been

2
doc/src/compute_saed.rst
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@ -86,7 +86,7 @@ will defined using the *c* values for the spacing along each reciprocal
lattice axis. Note that manual mapping of the reciprocal space mesh is
good for comparing diffraction results from multiple simulations; however
it can reduce the likelihood that Bragg reflections will be satisfied
unless small spacing parameters (:math:`<0.05~\mathrm{\mathring A}^-1`)
unless small spacing parameters (:math:`<0.05~\AA^-1`)
are implemented. Meshes with manual spacing do not require a periodic
boundary.

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

6
doc/src/compute_temp_cs.rst
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@ -29,7 +29,7 @@ Description
Define a computation that calculates the temperature of a system based
on the center-of-mass velocity of atom pairs that are bonded to each
other. This compute is designed to be used with the adiabatic
core/shell model of :ref:`(Mitchell and Finchham) <MitchellFinchham1>`.
core/shell model of :ref:`(Mitchell and Fincham) <MitchellFincham1>`.
See the :doc:`Howto coreshell <Howto_coreshell>` page for an overview of
the model as implemented in LAMMPS. Specifically, this compute
enables correct temperature calculation and thermostatting of
@ -127,7 +127,7 @@ none
----------
.. _MitchellFinchham1:
.. _MitchellFincham1:
**(Mitchell and Finchham)** Mitchell, Finchham, J Phys Condensed Matter,
**(Mitchell and Fincham)** Mitchell, Fincham, J Phys Condensed Matter,
5, 1031-1038 (1993).

2
doc/src/compute_temp_ramp.rst
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@ -58,7 +58,7 @@ constant, and :math:`T` is the absolute temperature.
The *units* keyword determines the meaning of the distance units used
for coordinates (*clo*, *chi*) and velocities (*vlo*, *vhi*). A *box* value
selects standard distance units as defined by the :doc:`units <units>`
command (e.g., :math:`\mathrm{\mathring{A}}` for units = real or metal). A
command (e.g., :math:`\AA` for units = real or metal). A
*lattice* value means the distance units are in lattice spacings (i.e.,
velocity in lattice spacings per unit time). The :doc:`lattice <lattice>`
command must have been previously used to define the lattice spacing.

32
doc/src/compute_voronoi_atom.rst
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@ -154,25 +154,25 @@ which must be installed on your system when building LAMMPS for use
with this compute. See instructions on obtaining and installing the
Voro++ software in the src/VORONOI/README file.
.. _voronoi: http://math.lbl.gov/voro++/
.. _voronoi: https://math.lbl.gov/voro++/
.. note::
The calculation of Voronoi volumes is performed by each
processor for the atoms it owns, and includes the effect of ghost
atoms stored by the processor. This assumes that the Voronoi cells of
owned atoms are not affected by atoms beyond the ghost atom cut-off
distance. This is usually a good assumption for liquid and solid
systems, but may lead to underestimation of Voronoi volumes in low
density systems. By default, the set of ghost atoms stored by each
processor is determined by the cutoff used for
:doc:`pair_style <pair_style>` interactions. The cutoff can be set
explicitly via the :doc:`comm_modify cutoff <comm_modify>` command. The
Voronoi cells for atoms adjacent to empty regions will extend into
those regions up to the communication cutoff in :math:`x`, :math:`y`, or
:math:`z`. In that situation, an exterior face is created at the cutoff
distance normal to the :math:`x`, :math:`y`, or :math:`z` direction.
For triclinic systems, the exterior face is parallel to the corresponding
The calculation of Voronoi volumes is performed by each processor for
the atoms it owns, and includes the effect of ghost atoms stored by
the processor. This assumes that the Voronoi cells of owned atoms
are not affected by atoms beyond the ghost atom cut-off distance.
This is usually a good assumption for liquid and solid systems, but
may lead to underestimation of Voronoi volumes in low density
systems. By default, the set of ghost atoms stored by each processor
is determined by the cutoff used for :doc:`pair_style <pair_style>`
interactions. The cutoff can be set explicitly via the
:doc:`comm_modify cutoff <comm_modify>` command. The Voronoi cells
for atoms adjacent to empty regions will extend into those regions up
to the communication cutoff in :math:`x`, :math:`y`, or :math:`z`.
In that situation, an exterior face is created at the cutoff distance
normal to the :math:`x`, :math:`y`, or :math:`z` direction. For
triclinic systems, the exterior face is parallel to the corresponding
reciprocal lattice vector.
.. note::

2
doc/src/compute_xrd.rst
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@ -91,7 +91,7 @@ reciprocal lattice axis. Note that manual mapping of the reciprocal
space mesh is good for comparing diffraction results from multiple
simulations; however, it can reduce the likelihood that Bragg
reflections will be satisfied unless small spacing parameters
(:math:`< 0.05~\mathrm{\mathring{A}}^{-1}`) are implemented.
(:math:`< 0.05~\AA^{-1}`) are implemented.
Meshes with manual spacing do not require a periodic boundary.
The limits of the reciprocal lattice mesh are determined by range of

6
doc/src/create_atoms.rst
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@ -189,6 +189,10 @@ to the area of that triangle.
beneficial to exclude computing interactions between the created
particles using :doc:`neigh_modify exclude <neigh_modify>`.
.. versionchanged:: 2Jun2022
The *porosity* style has been renamed to *random* with added functionality.
For the *random* style, *N* particles are added to the system at
randomly generated coordinates, which can be useful for generating an
amorphous system. The particles are created one by one using the
@ -460,7 +464,7 @@ The *units* keyword determines the meaning of the distance units used
to specify the coordinates of the one particle created by the *single*
style, or the overlap distance *Doverlap* by the *overlap* keyword. A
*box* value selects standard distance units as defined by the
:doc:`units <units>` command (e.g., :math:`\mathrm{\mathring{A}}` for
:doc:`units <units>` command (e.g., :math:`\AA` for
units = *real* or *metal*\ . A *lattice* value means the distance units are in
lattice spacings.

2
doc/src/delete_atoms.rst
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@ -116,6 +116,8 @@ must be in both the specified group and region. If *group-ID* = all,
there is effectively no group criterion. If *region-ID* is specified
as NULL, no region criterion is imposed.
.. versionadded:: 4May2022
For style *variable*, all atoms for which the atom-style variable with
the given name evaluates to non-zero will be deleted. Additional atoms
can be deleted if they are in a molecule for which one or more atoms

2
doc/src/displace_atoms.rst
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@ -104,7 +104,7 @@ atom's rotation.
Distance units for displacements and the origin point of the *rotate*
style are determined by the setting of *box* or *lattice* for the
*units* keyword. *Box* means distance units as defined by the
:doc:`units <units>` command (e.g., :math:`\mathrm{\mathring A}` for
:doc:`units <units>` command (e.g., :math:`\AA` for
*real* or *metal* units). *Lattice* means distance units are in lattice
spacings. The :doc:`lattice <lattice>` command must have been previously used
to define the lattice spacing.

4
doc/src/dump.rst
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@ -480,7 +480,7 @@ style.
----------
Note that *atom*, *custom*, *dcd*, *xtc*, and *xyz* style dump files
can be read directly by `VMD <http://www.ks.uiuc.edu/Research/vmd>`_, a
can be read directly by `VMD <https://www.ks.uiuc.edu/Research/vmd>`_, a
popular molecular viewing program.
----------
@ -693,7 +693,7 @@ charge.
There are several options for outputting atom coordinates. The *x*,
*y*, and *z* attributes write atom coordinates "unscaled", in the
appropriate distance :doc:`units <units>` (:math:`\mathrm{\mathring A}`,
appropriate distance :doc:`units <units>` (:math:`\AA`,
:math:`\sigma`, etc.). Use *xs*, *ys*, and *zs* if you want the
coordinates "scaled" to the box size so that each value is 0.0 to 1.0.
If the simulation box is triclinic (tilted), then all atom coords will

6
doc/src/dump_h5md.rst
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@ -64,7 +64,7 @@ stored within the same file by defining several dumps. A dump that
refers (via *file_from*) to an already open dump ID and that concerns
another particle group must specify *create_group yes*.
.. _h5md: http://nongnu.org/h5md/
.. _h5md: https://nongnu.org/h5md/
Each data element is written every N\*N_element steps. For *image*, no
sub-interval is needed as it must be present at the same interval as
@ -113,7 +113,7 @@ the `HDF5 <HDF5-ws_>`_ library installed (C bindings are sufficient) on
your system. The library ch5md is compiled with the h5cc wrapper
provided by the HDF5 library.
.. _HDF5-ws: http://www.hdfgroup.org/HDF5/
.. _HDF5-ws: https://www.hdfgroup.org/solutions/hdf5/
----------
@ -129,4 +129,4 @@ Related commands
**(de Buyl)** de Buyl, Colberg and Hofling, H5MD: A structured,
efficient, and portable file format for molecular data,
Comp. Phys. Comm. 185(6), 1546-1553 (2014) -
`[arXiv:1308.6382] <http://arxiv.org/abs/1308.6382/>`_.
`[arXiv:1308.6382] <https://arxiv.org/abs/1308.6382/>`_.

4
doc/src/dump_image.rst
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@ -212,7 +212,7 @@ is used.
Similarly, the format of the resulting movie is chosen with the
*movie* dump style. This is handled by the underlying FFmpeg converter
and thus details have to be looked up in the `FFmpeg documentation
<http://ffmpeg.org/ffmpeg.html>`_. Typical examples are: .avi, .mpg,
<https://ffmpeg.org/ffmpeg.html>`_. Typical examples are: .avi, .mpg,
.m4v, .mp4, .mkv, .flv, .mov, .gif Additional settings of the movie
compression like bitrate and framerate can be set using the
dump_modify command as described below.
@ -642,7 +642,7 @@ MPEG or other movie file you can use:
cat snap.*.ppm | ffmpeg -y -f image2pipe -c:v ppm -i - -b:v 2400k movie.avi
Front ends for FFmpeg exist for multiple platforms. For more
information see the `FFmpeg homepage <http://www.ffmpeg.org/>`_
information see the `FFmpeg homepage <https://www.ffmpeg.org/>`_
----------

8
doc/src/dump_modify.rst
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@ -632,7 +632,7 @@ calculates the displacement of each atom from its reference position.
The "4" index is the scalar displacement; 1, 2, and 3 are the :math:`xyz`
components of the displacement. The :doc:`dump_modify thresh <dump_modify>`
command will cause only atoms that have displaced more than
:math:`0.6~\mathrm{\mathring A}` to be output on a given snapshot (assuming
:math:`0.6~\AA` to be output on a given snapshot (assuming
metal units). However, note that when an atom is output, we also need to
update the reference position for that atom to its new coordinates. So that it
will not be output in every snapshot thereafter. That reference position is
@ -675,7 +675,7 @@ value of *yes* means atom coords are written in normalized units from
0.0 to 1.0 in each box dimension. If the simulation box is triclinic
(tilted), then all atom coords will still be between 0.0 and 1.0. A
value of *no* means they are written in absolute distance units
(e.g., :math:`\mathrm{\mathring A}` or :math:`\sigma`).
(e.g., :math:`\AA` or :math:`\sigma`).
Using this keyword will reset all custom header names set with
*dump_modify colname* to their respective default values.
@ -687,7 +687,7 @@ when writing to XTC files. By default, they are initialized for
whatever :doc:`units <units>` style is being used, to write out
coordinates in nanometers and time in picoseconds. For example, for *real*
units, LAMMPS defines *sfactor* = 0.1 and *tfactor* = 0.001, since the
:math:`\mathrm{\mathring A}` and fs used by *real* units are 0.1 nm and
:math:`\AA` and fs used by *real* units are 0.1 nm and
0.001 ps, respectively. If you are using a units system with distance and time
units far from nm and ps, you may wish to write XTC files with
different units, since the compression algorithm used in XTC files is
@ -881,7 +881,7 @@ levels that sacrifice compression for performance. 0 is the default,
positive levels are 1 to 22, with 22 being the most expensive
compression. Zstd promises higher compression/decompression speeds for
similar compression ratios. For more details see
`http://facebook.github.io/zstd/`.
`https://facebook.github.io/zstd/`.
In addition, Zstd compressed files can include a checksum of the
entire contents. The Zstd enabled dump styles enable this feature by

2
doc/src/dump_molfile.rst
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@ -34,7 +34,7 @@ Dump a snapshot of atom coordinates and selected additional quantities
to one or more files every N timesteps in one of several formats.
Only information for atoms in the specified group is dumped. This
specific dump style uses molfile plugins that are bundled with the
`VMD <http://www.ks.uiuc.edu/Research/vmd>`_ molecular visualization and
`VMD <https://www.ks.uiuc.edu/Research/vmd>`_ molecular visualization and
analysis program.
Unless the filename contains a \* character, the output will be written

14
doc/src/dump_netcdf.rst
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@ -48,21 +48,17 @@ rank.
NetCDF files can be directly visualized via the following tools:
Ovito (http://www.ovito.org/). Ovito supports the AMBER convention and
all extensions of this dump style.
* VMD (http://www.ks.uiuc.edu/Research/vmd/).
* AtomEye (http://www.libatoms.org/). The libAtoms version of AtomEye
contains a NetCDF reader that is not present in the standard
distribution of AtomEye.
* Ovito (https://www.ovito.org/). Ovito supports the AMBER convention and
all extensions of this dump style.
* VMD (https://www.ks.uiuc.edu/Research/vmd/).
In addition to per-atom data, :doc:`thermo <thermo>` data can be included in the
dump file. The data included in the dump file is identical to the data specified
by :doc:`thermo_style <thermo_style>`.
.. _netcdf-home: http://www.unidata.ucar.edu/software/netcdf/
.. _netcdf-home: https://www.unidata.ucar.edu/software/netcdf/
.. _pnetcdf-home: http://trac.mcs.anl.gov/projects/parallel-netcdf/
.. _pnetcdf-home: https://trac.mcs.anl.gov/projects/parallel-netcdf/
----------

26
doc/src/dump_vtk.rst
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@ -29,8 +29,9 @@ Description
"""""""""""
Dump a snapshot of atom quantities to one or more files every :math:`N`
timesteps in a format readable by the `VTK visualization toolkit <http://www.vtk.org>`_ or other visualization tools that use it,
such as `ParaView <http://www.paraview.org>`_. The time steps on which dump
timesteps in a format readable by the `VTK visualization toolkit
<https://www.vtk.org>`_ or other visualization tools that use it, such
as `ParaView <https://www.paraview.org>`_. The time steps on which dump
output is written can also be controlled by a variable; see the
:doc:`dump_modify every <dump_modify>` command for details.
@ -38,8 +39,8 @@ This dump style is similar to :doc:`dump_style custom <dump>` but uses
the VTK library to write data to VTK simple legacy or XML format,
depending on the filename extension specified for the dump file. This
can be either *\*.vtk* for the legacy format or *\*.vtp* and *\*.vtu*,
respectively, for XML format; see the
`VTK homepage <http://www.vtk.org/VTK/img/file-formats.pdf>`_ for a detailed
respectively, for XML format; see the `VTK homepage
<https://www.vtk.org/VTK/img/file-formats.pdf>`_ for a detailed
description of these formats. Since this naming convention conflicts
with the way binary output is usually specified (see below), the
:doc:`dump_modify binary <dump_modify>` command allows setting of a
@ -61,14 +62,15 @@ determine the kind of output.
.. warning::
Unless the :doc:`dump_modify sort <dump_modify>` option
is invoked, the lines of atom information written to dump files will
be in an indeterminate order for each snapshot. This is even true
when running on a single processor, if the :doc:`atom_modify sort <atom_modify>` option is on, which it is by default. In this
case atoms are re-ordered periodically during a simulation, due to
spatial sorting. It is also true when running in parallel, because
data for a single snapshot is collected from multiple processors, each
of which owns a subset of the atoms.
Unless the :doc:`dump_modify sort <dump_modify>` option is invoked,
the lines of atom information written to dump files will be in an
indeterminate order for each snapshot. This is even true when
running on a single processor, if the :doc:`atom_modify sort
<atom_modify>` option is on, which it is by default. In this case
atoms are re-ordered periodically during a simulation, due to spatial
sorting. It is also true when running in parallel, because data for
a single snapshot is collected from multiple processors, each of
which owns a subset of the atoms.
For the *vtk* style, sorting is off by default. See the
:doc:`dump_modify <dump_modify>` page for details.

4
doc/src/fix_acks2_reaxff.rst
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@ -71,7 +71,7 @@ potential in eV, *gamma*, the valence orbital exponent, and *bcut*, the
bond cutoff distance. Note that these 4 quantities are also in the
ReaxFF potential file, except that eta is defined here as twice the eta
value in the ReaxFF file. Note that unlike the rest of LAMMPS, the units
of this fix are hard-coded to be :math:`\mathrm{\mathring{A}}`, eV, and
of this fix are hard-coded to be :math:`\AA`, eV, and
electronic charge.
The optional *maxiter* keyword allows changing the max number
@ -111,7 +111,7 @@ LAMMPS was built with that package. See the :doc:`Build package
This fix does not correctly handle interactions involving multiple
periodic images of the same atom. Hence, it should not be used for
periodic cell dimensions less than :math:`10~\mathrm{\mathring{A}}`.
periodic cell dimensions less than :math:`10~\AA`.
This fix may be used in combination with :doc:`fix efield <fix_efield>`
and will apply the external electric field during charge equilibration,

2
doc/src/fix_adapt.rst
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@ -319,6 +319,8 @@ with fix_adapt are
----------
.. versionadded:: 4May2022
The *angle* keyword uses the specified variable to change the value of
an angle coefficient over time, very similar to how the *pair* keyword
operates. The only difference is that now an angle coefficient for a

2
doc/src/fix_append_atoms.rst
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@ -79,7 +79,7 @@ measured from zhi and is set with the *extent* argument.
The *units* keyword determines the meaning of the distance units used
to define a wall position, but only when a numeric constant is used.
A *box* value selects standard distance units as defined by the
:doc:`units <units>` command (e.g., :math:`\mathrm{\mathring A}`
:doc:`units <units>` command (e.g., :math:`\AA`
for units = real or metal.
A *lattice* value means the distance units are in lattice spacings.
The :doc:`lattice <lattice>` command must have been previously used to

6
doc/src/fix_bocs.rst
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@ -59,7 +59,7 @@ Note both the COMMA and the SPACE separating the volume's
value and its corresponding pressure correction. The volumes in the file
must be uniformly spaced. Both the volumes and the pressure corrections
should be provided in the proper units, e.g. if you are using *units real*,
the volumes should all be in cubic angstroms, and the pressure corrections
the volumes should all be in cubic Angstroms, and the pressure corrections
should all be in atmospheres. Furthermore, the table should start/end at a
volume considerably smaller/larger than you expect your system to sample
during the simulation. If the system ever reaches a volume outside of the
@ -72,8 +72,8 @@ With the *analytic* option, the arguments are as follows:
... analytic V_avg N_particles N_coeff Coeff_1 Coeff_2 ... Coeff_N
Note that *V_avg* and *Coeff_i* should all be in the proper units, e.g. if you
are using *units real*, *V_avg* should be in cubic angstroms, and the
coefficients should all be in atmospheres \* cubic angstroms.
are using *units real*, *V_avg* should be in cubic Angstroms, and the
coefficients should all be in atmospheres \* cubic Angstroms.
----------

2
doc/src/fix_external.rst
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@ -78,7 +78,7 @@ example of how this is done. This sample application performs
classical MD using quantum forces computed by a density functional
code `Quest <quest_>`_.
.. _quest: http://dft.sandia.gov/Quest
.. _quest: https://dft.sandia.gov/Quest
----------

2
doc/src/fix_gle.rst
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@ -159,7 +159,7 @@ Related commands
.. _GLE4MD:
**(GLE4MD)** `http://gle4md.org/ <http://gle4md.org/>`_
**(GLE4MD)** `https://gle4md.org/ <https://gle4md.org/>`_
.. _Ceriotti2:

59
doc/src/fix_imd.rst
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@ -51,16 +51,11 @@ from the main execution thread and potentially lower the inferred
latencies for slow communication links. This feature has only been
tested under linux.
There are example scripts for using this package with LAMMPS in
examples/PACKAGES/imd. Additional examples and a driver for use with the
Novint Falcon game controller as haptic device can be found at:
http://sites.google.com/site/akohlmey/software/vrpn-icms.
The source code for this fix includes code developed by the
Theoretical and Computational Biophysics Group in the Beckman
Institute for Advanced Science and Technology at the University of
Illinois at Urbana-Champaign. We thank them for providing a software
interface that allows codes like LAMMPS to hook to `VMD <VMD_>`_.
The source code for this fix includes code developed by the Theoretical
and Computational Biophysics Group in the Beckman Institute for Advanced
Science and Technology at the University of Illinois at
Urbana-Champaign. We thank them for providing a software interface that
allows codes like LAMMPS to hook to `VMD <VMD_>`_.
Upon initialization of the fix, it will open a communication port on
the node with MPI task 0 and wait for an incoming connection. As soon
@ -93,8 +88,8 @@ to send "unwrapped" coordinates to the IMD client that undo the
wrapping back of coordinates into the principle unit cell, as done by
default in LAMMPS. The *fscale* keyword allows to apply a scaling
factor to forces transmitted by the IMD client. The IMD protocols
stipulates that forces are transferred in kcal/mol/angstrom under the
assumption that coordinates are given in angstrom. For LAMMPS runs
stipulates that forces are transferred in kcal/mol/Angstrom under the
assumption that coordinates are given in Angstrom. For LAMMPS runs
with different units or as a measure to tweak the forces generated by
the manipulation of the IMD client, this option allows to make
adjustments.
@ -117,40 +112,40 @@ VMD are the following:
In the Mouse menu of the VMD Main window, select "Mouse -> Force ->
Atom". You may alternately select "Residue", or "Fragment" to apply
forces to whole residues or fragments. Your mouse can now be used to
apply forces to your simulation. Click on an atom, residue, or
fragment and drag to apply a force. Click quickly without moving the
mouse to turn the force off. You can also use a variety of 3D position
trackers to apply forces to your simulation. Game controllers or haptic
devices with force-feedback such as the Novint Falcon or Sensable
PHANTOM allow you to feel the resistance due to inertia or interactions
with neighbors that the atoms experience you are trying to move, as if
they were real objects. See the `VMD IMD Homepage <imdvmd_>`_ and the
`VRPN-ICMS Homepage <vrpnicms_>`_ for more details.
apply forces to your simulation. Click on an atom, residue, or fragment
and drag to apply a force. Click quickly without moving the mouse to
turn the force off. You can also use a variety of 3D position trackers
to apply forces to your simulation. Game controllers or haptic devices
with force-feedback such as the Novint Falcon or Sensable PHANTOM allow
you to feel the resistance due to inertia or interactions with neighbors
that the atoms experience you are trying to move, as if they were real
objects. See the `VMD IMD Homepage <imdvmd_>`_ for more details.
If IMD control messages are received, a line of text describing the
message and its effect will be printed to the LAMMPS output screen, if
screen output is active.
.. _VMD: http://www.ks.uiuc.edu/Research/vmd
.. _VMD: https://www.ks.uiuc.edu/Research/vmd
.. _imdvmd: http://www.ks.uiuc.edu/Research/vmd/imd/
.. _vrpnicms: http://sites.google.com/site/akohlmey/software/vrpn-icms
.. _imdvmd: https://www.ks.uiuc.edu/Research/vmd/imd/
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
No information about this fix is written to :doc:`binary restart files <restart>`. None of the :doc:`fix_modify <fix_modify>` options
are relevant to this fix. No global scalar or vector or per-atom
quantities are stored by this fix for access by various :doc:`output commands <Howto_output>`. No parameter of this fix can be used
with the *start/stop* keywords of the :doc:`run <run>` command. This
fix is not invoked during :doc:`energy minimization <minimize>`.
No information about this fix is written to :doc:`binary restart files
<restart>`. None of the :doc:`fix_modify <fix_modify>` options are
relevant to this fix. No global scalar or vector or per-atom quantities
are stored by this fix for access by various :doc:`output commands
<Howto_output>`. No parameter of this fix can be used with the
*start/stop* keywords of the :doc:`run <run>` command. This fix is not
invoked during :doc:`energy minimization <minimize>`.
Restrictions
""""""""""""
This fix is part of the MISC package. It is only enabled if
LAMMPS was built with that package. See the :doc:`Build package <Build_package>` page for more info.
This fix is part of the MISC package. It is only enabled if LAMMPS was
built with that package. See the :doc:`Build package <Build_package>`
page for more info.
When used in combination with VMD, a topology or coordinate file has
to be loaded, which matches (in number and ordering of atoms) the

2
doc/src/fix_ipi.rst
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@ -111,4 +111,4 @@ Related commands
.. _ipihome:
**(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>`_

4
doc/src/fix_langevin_spin.rst
View File

@ -40,7 +40,7 @@ the following stochastic differential equation:
\times\left( \vec{\omega}_{i} \times\vec{s}_{i} \right) \right)
with :math:`\lambda` the transverse damping, and :math:`\eta` a random vector.
This equation is referred to as the stochastic Landau-Lifshitz-Gilbert (sLLG)
This equation is referred to as the stochastic Landau-Lifshitz (sLL)
equation.
The components of :math:`\eta` are drawn from a Gaussian probability
@ -49,7 +49,7 @@ the external thermostat T (in K in metal units).
More details about this implementation are reported in :ref:`(Tranchida) <Tranchida2>`.
Note: due to the form of the sLLG equation, this fix has to be defined just
Note: due to the form of the sLL equation, this fix has to be defined just
before the nve/spin fix (and after all other magnetic fixes).
As an example:

2
doc/src/fix_latte.rst
View File

@ -81,6 +81,8 @@ The *coulomb* argument is not yet supported by fix latte (as of Sept
Coulomb potential as an alternative to LATTE performing the
calculation.
.. versionadded:: 15Sep2022
The *exclude* argument allows this fix to work in tandem with another
fix which may decide to delete one or more atoms of molecules. The
specified fixID is the ID of the other fix.

2
doc/src/fix_mdi_qm.rst
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@ -43,6 +43,8 @@ Examples
Description
"""""""""""
.. versionadded:: 3Aug2022
This command enables LAMMPS to act as a client with another server
code that will compute the total energy, per-atom forces, and total
virial for atom conformations and simulation box size/shapes that

3
doc/src/fix_nh_uef.rst
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@ -210,7 +210,8 @@ use :doc:`change_box <change_box>` before invoking the fix.
.. note::
When resuming from restart files, you may need to use :doc:`box tilt large <box>` since lammps has internal criteria from lattice
When resuming from restart files, you may need to use :doc:`box tilt
large <box>` since LAMMPS has internal criteria from lattice
reduction that are not the same as the criteria in the numerical
lattice reduction algorithm.

2
doc/src/fix_numdiff_virial.rst
View File

@ -25,6 +25,8 @@ Examples
Description
"""""""""""
.. versionadded:: 17Feb2022
Calculate the virial stress tensor through a finite difference calculation of
energy versus strain. These values can be compared to the analytic virial
tensor computed by pair styles, bond styles, etc. This can be useful for

2
doc/src/fix_nve_manifold_rattle.rst
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@ -108,4 +108,4 @@ every = 0, tchain = 3
.. _Paquay2:
**(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/fix_nvt_manifold_rattle.rst
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@ -82,4 +82,4 @@ Related commands
.. _Paquay3:
**(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/>`_.

4
doc/src/fix_phonon.rst
View File

@ -134,7 +134,7 @@ for other systems, *nasr* = 10 is typically sufficient.
The *map_file* contains the mapping information between the lattice
indices and the atom IDs, which tells the code which atom sits at
which lattice point; the lattice indices start from 0. An auxiliary
code, `latgen <http://code.google.com/p/latgen>`_, can be employed to
code, `latgen <https://code.google.com/p/latgen>`_, can be employed to
generate the compatible map file for various crystals.
In case one simulates a non-periodic system, where the whole simulation
@ -143,7 +143,7 @@ that the mapping info will be generated internally and a file is not
needed. In this case, the dynamical matrix at only the gamma-point
will/can be evaluated. Please keep in mind that fix-phonon is designed
for cyrstals, it will be inefficient and even degrade the performance
of lammps in case the unit cell is too large.
of LAMMPS in case the unit cell is too large.
The calculated dynamical matrix elements are written out in
:doc:`energy/distance\^2/mass <units>` units. The coordinates for *q*

2
doc/src/fix_qeq_reaxff.rst
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@ -124,7 +124,7 @@ LAMMPS was built with that package. See the :doc:`Build package
This fix does not correctly handle interactions involving multiple
periodic images of the same atom. Hence, it should not be used for
periodic cell dimensions less than 10 angstroms.
periodic cell dimensions less than 10 Angstroms.
This fix may be used in combination with :doc:`fix efield <fix_efield>`
and will apply the external electric field during charge equilibration,

2
doc/src/fix_qmmm.rst
View File

@ -31,7 +31,7 @@ wave DFT package. Electrostatic coupling is in preparation and the
interface has been written in a manner that coupling to other QM codes
should be possible without changes to LAMMPS itself.
.. _espresso: http://www.quantum-espresso.org
.. _espresso: https://www.quantum-espresso.org
The interface code for this is in the lib/qmmm directory of the LAMMPS
distribution and is being made available at this early stage of

11
doc/src/fix_shake.rst
View File

@ -58,10 +58,13 @@ Description
Apply bond and angle constraints to specified bonds and angles in the
simulation by either the SHAKE or RATTLE algorithms. This typically
enables a longer timestep. The SHAKE or RATTLE algorithms, however, can
*only* be applied during molecular dynamics runs. When this fix is used
during a minimization, the constraints are *approximated* by strong
harmonic restraints.
enables a longer timestep. The SHAKE or RATTLE constraint algorithms,
however, can *only* be applied during molecular dynamics runs.
.. versionchanged:: 15Sep2022
These fixes may still be used during minimization. In that case the
constraints are *approximated* by strong harmonic restraints.
**SHAKE vs RATTLE:**

9
doc/src/kspace_style.rst
View File

@ -301,7 +301,7 @@ and for mixed periodic and non-periodic boundaries.
MSM is most competitive versus Ewald and PPPM when only relatively
low accuracy forces, about 1e-4 relative error or less accurate,
are needed. Note that use of a larger Coulombic cutoff (i.e. 15
angstroms instead of 10 angstroms) provides better MSM accuracy for
Angstroms instead of 10 Angstroms) provides better MSM accuracy for
both the real space and grid computed forces.
Currently calculation of the full pressure tensor in MSM is expensive.
@ -314,9 +314,10 @@ pressure simulation with MSM will cause the code to run slower.
----------
The *scafacos* style is a wrapper on the `ScaFaCoS Coulomb solver library <http://www.scafacos.de>`_ which provides a variety of solver
methods which can be used with LAMMPS. The paper by :ref:`(Sutman) <Sutmann2014>`
gives an overview of ScaFaCoS.
The *scafacos* style is a wrapper on the `ScaFaCoS Coulomb solver
library <http://www.scafacos.de>`_ which provides a variety of solver
methods which can be used with LAMMPS. The paper by :ref:`(Sutman)
<Sutmann2014>` gives an overview of ScaFaCoS.
ScaFaCoS was developed by a consortium of German research facilities
with a BMBF (German Ministry of Science and Education) funded project

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