3.2. Submitting new features for inclusion in LAMMPS¶
We encourage users to submit new features or modifications for LAMMPS to the core developers so they can be added to the LAMMPS distribution. The preferred way to manage and coordinate this is via the LAMMPS project on GitHub. Please see the GitHub Tutorial for a demonstration on how to do that. An alternative is to contact the LAMMPS developers or the indicated developer of a package or feature directly and send in your contribution via e-mail, but that can add a significant delay on getting your contribution included, depending on how busy the respective developer is, how complex a task it would be to integrate that code, and how many - if any - changes are required before the code can be included.
For any larger modifications or programming project, you are encouraged to contact the LAMMPS developers ahead of time in order to discuss implementation strategies and coding guidelines. That will make it easier to integrate your contribution and results in less work for everybody involved. You are also encouraged to search through the list of open issues on GitHub and submit a new issue for a planned feature, so you would not duplicate the work of others (and possibly get scooped by them) or have your work duplicated by others.
For informal communication with (some of) the LAMMPS developers you may
ask to join the LAMMPS developers on Slack. This slack work space is by invitation
only. Thus for access, please send an e-mail to
explaining what part of LAMMPS you are working on. Only discussions
related to LAMMPS development are tolerated, so this is NOT for
people that look for help with compiling, installing, or using
LAMMPS. Please contact the
lammps-users mailing list or the
LAMMPS forum for those purposes
How quickly your contribution will be integrated depends largely on how much effort it will cause to integrate and test it, how many and what kind of changes it requires to the core codebase, and of how much interest it is to the larger LAMMPS community. Please see below for a checklist of typical requirements. Once you have prepared everything, see the LAMMPS GitHub Tutorial page for instructions on how to submit your changes or new files through a GitHub pull request. If you prefer to submit patches or full files, you should first make certain, that your code works correctly with the latest patch-level version of LAMMPS and contains all bug fixes from it. Then create a gzipped tar file of all changed or added files or a corresponding patch file using ‘diff -u’ or ‘diff -c’ and compress it with gzip. Please only use gzip compression, as this works well and is available on all platforms.
Note that by providing us files to release, you are agreeing to make them open-source, i.e. we can release them under the terms of the GPL (version 2), used as a license for the rest of LAMMPS. And as part of a LGPL (version 2.1) distribution that we make available to developers on request only and with files that are authorized for that kind of distribution removed (e.g. interface to FFTW). See the LAMMPS license page for details.
If you prefer to actively develop and support your add-on feature yourself, then you may wish to make it available for download from your own website, as a user package that LAMMPS users can add to their copy of LAMMPS. See the Offsite LAMMPS packages and tools page of the LAMMPS web site for examples of groups that do this. We are happy to advertise your package and web site from that page. Simply email the developers with info about your package and we will post it there. We recommend to name external packages USER-<name> so they can be easily distinguished from bundled packages that do not have the USER- prefix.
The previous sections of this page describe how to add new “style” files of various kinds to LAMMPS. Packages are simply collections of one or more new class files which are invoked as a new style within a LAMMPS input script. If designed correctly, these additions typically do not require changes to the main core of LAMMPS; they are simply add-on files. If you think your new feature requires non-trivial changes in core LAMMPS files, you should communicate with the developers, since we may or may not want to include those changes for some reason. An example of a trivial change is making a parent-class method “virtual” when you derive a new child class from it.
Here is a checklist of steps you need to follow to submit a single file or package for our consideration. Following these steps will save both you and us time. Please have a look at the existing files in packages in the src directory for examples. If you are uncertain, please ask.
All source files you provide must compile with the most current version of LAMMPS with multiple configurations. In particular you need to test compiling LAMMPS from scratch with -DLAMMPS_BIGBIG set in addition to the default -DLAMMPS_SMALLBIG setting. Your code will need to work correctly in serial and in parallel using MPI.
For consistency with the rest of LAMMPS and especially, if you want your contribution(s) to be added to main LAMMPS code or one of its standard packages, it needs to be written in a style compatible with other LAMMPS source files. This means: 2-character indentation per level, no tabs, no lines over 100 characters. I/O is done via the C-style stdio library (mixing of stdio and iostreams is generally discouraged), class header files should not import any system headers outside of <cstdio>, STL containers should be avoided in headers, system header from the C library should use the C++-style names (<cstdlib>, <cstdio>, or <cstring>) instead of the C-style names <stdlib.h>, <stdio.h>, or <string.h>), and forward declarations used where possible or needed to avoid including headers. All added code should be placed into the LAMMPS_NS namespace or a sub-namespace; global or static variables should be avoided, as they conflict with the modular nature of LAMMPS and the C++ class structure. Header files must not import namespaces with using. This all is so the developers can more easily understand, integrate, and maintain your contribution and reduce conflicts with other parts of LAMMPS. This basically means that the code accesses data structures, performs its operations, and is formatted similar to other LAMMPS source files, including the use of the error class for error and warning messages.
To simplify reformatting contributed code in a way that is compatible with the LAMMPS formatting styles, you can use clang-format (version 8 or later). The LAMMPS distribution includes a suitable
.clang-formatfile which will be applied if you run
clang-format -i some_file.cppon your files inside the LAMMPS src tree. Please only reformat files that you have contributed. For header files containing a
SomeStyle(keyword, ClassName)macros it is required to have this macro embedded with a pair of
// clang-format off,
// clang-format oncommends and the line must be terminated with a semi-colon (;). Example:
#ifdef COMMAND_CLASS // clang-format off CommandStyle(run,Run); // clang-format on #else #ifndef LMP_RUN_H [...]
You may also use
// clang-format on/offthroughout your file to protect sections of the file from being reformatted.
Please review the list of available Packages to see if your contribution could be added to be added to one of them. It should fit into the general purposed of that package. If it does not fit well, it can be added to one of the EXTRA- packages or the MISC package.
If your contribution has several related features that are not covered by one of the existing packages or is dependent on a library (bundled or external), it is best to make it a package directory with a name like FOO. In addition to your new files, the directory should contain a README text file. The README should contain your name and contact information and a brief description of what your new package does. If your files depend on other LAMMPS style files also being installed (e.g. because your file is a derived class from the other LAMMPS class), then an Install.sh file is also needed to check for those dependencies and modifications to src/Depend.sh to trigger the checks. See other README and Install.sh files in other directories as examples. Similarly for CMake support changes need to be made to cmake/CMakeLists.txt, the files in cmake/presets, and possibly a file to cmake/Modules/Packages/ added. Please check out how this is handled for existing packages and ask the LAMMPS developers if you need assistance. Please submit a pull request on GitHub or send us a tarball of this FOO directory and all modified files. Pull requests are strongly encouraged since they greatly reduce the effort required to integrate a contribution and simplify the process of adjusting the contributed code to cleanly fit into the LAMMPS distribution.
Your new source files need to have the LAMMPS copyright, GPL notice, and your name and email address at the top, like other user-contributed LAMMPS source files. They need to create a class that is inside the LAMMPS namespace. To simplify maintenance, we may ask to adjust the programming style and formatting style to closer match the rest of LAMMPS. We bundle a clang-format configuration file that can help with adjusting the formatting, although this is not a strict requirement.
You must also create a documentation file for each new command or style you are adding to LAMMPS. For simplicity and convenience, the documentation of groups of closely related commands or styles may be combined into a single file. This will be one file for a single-file feature. For a package, it might be several files. These are text files with a .rst extension using the reStructuredText markup language, that are then converted to HTML and PDF using the Sphinx documentation generator tool. Running Sphinx with the included configuration requires Python 3.x. Configuration settings and custom extensions for this conversion are included in the source distribution, and missing python packages will be transparently downloaded into a virtual environment via pip. Thus, if your local system is missing required packages, you need access to the internet. The translation can be as simple as doing “make html pdf” in the doc folder. As appropriate, the text files can include inline mathematical expression or figures (see doc/JPG for examples). Additional PDF files with further details (see doc/PDF for examples) may also be included. The page should also include literature citations as appropriate; see the bottom of doc/fix_nh.rst for examples and the earlier part of the same file for how to format the cite itself. Citation labels must be unique across all .rst files. The “Restrictions” section of the page should indicate if your command is only available if LAMMPS is built with the appropriate FOO package. See other package doc files for examples of how to do this. Please run at least “make html” and “make spelling” and carefully inspect and proofread the resulting HTML format doc page before submitting your code. Upon submission of a pull request, checks for error free completion of the HTML and PDF build will be performed and also a spell check, a check for correct anchors and labels, and a check for completeness of references all styles in their corresponding tables and lists is run. In case the spell check reports false positives they can be added to the file doc/utils/sphinx-config/false_positives.txt
For a new package (or even a single command) you should include one or more example scripts demonstrating its use. These should run in no more than a couple minutes, even on a single processor, and not require large data files as input. See directories under examples/PACKAGES for examples of input scripts other users provided for their packages. These example inputs are also required for validating memory accesses and testing for memory leaks with valgrind
If there is a paper of yours describing your feature (either the algorithm/science behind the feature itself, or its initial usage, or its implementation in LAMMPS), you can add the citation to the *.cpp source file. See src/EFF/atom_vec_electron.cpp for an example. A LaTeX citation is stored in a variable at the top of the file and a single line of code registering this variable is added to the constructor of the class. If there is additional functionality (which may have been added later) described in a different publication, additional citation descriptions may be added for as long as they are only registered when the corresponding keyword activating this functionality is used. With these options it is possible to have LAMMPS output a specific citation reminder whenever a user invokes your feature from their input script. Note that you should only use this for the most relevant paper for a feature and a publication that you or your group authored. E.g. adding a citation in the code for a paper by Nose and Hoover if you write a fix that implements their integrator is not the intended usage. That kind of citation should just be included in the documentation page you provide describing your contribution. If you are not sure what the best option would be, please contact the LAMMPS developers for advice.
Finally, as a general rule-of-thumb, the more clear and self-explanatory you make your documentation and README files, and the easier you make it for people to get started, e.g. by providing example scripts, the more likely it is that users will try out your new feature.