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 developer is you contact, how complex a task it would be to integrate that code, and how many - if any - changes are required before the code can be included.

For any larger modifications or programming project, you are encouraged to contact the LAMMPS developers ahead of time, in order to discuss implementation strategies and coding guidelines, that will make it easier to integrate your contribution and result in less work for everybody involved. You are also encouraged to search through the list 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 slack@lammps.org 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 for those purposes instead.

How quickly your contribution will be integrated depends largely on how much effort it will cause to integrate and test it, how much it requires changes to the core codebase, and of how much interest it is to the larger LAMMPS community. Please see below for a checklist of typical requirements. Once you have prepared everything, see the 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 on all platforms.

If the new features/files are broadly useful we may add them as core files to LAMMPS or as part of a standard package. Else we will add them as a user-contributed file or user package. Examples of user packages are in src sub-directories that start with USER. The USER-MISC package is simply a collection of (mostly) unrelated single files, which is the simplest way to have your contribution quickly added to the LAMMPS distribution. All the standard and user packages are listed and described on the Packages details doc page.

Note that by providing us files to release, you are agreeing to make them open-source, i.e. we can release them under the terms of the GPL, used as a license for the rest of LAMMPS. See the LAMMPS license doc page for details.

With user packages and files, all we are really providing (aside from the fame and fortune that accompanies having your name in the source code and on the Authors page of the LAMMPS WWW site), is a means for you to distribute your work to the LAMMPS user community, and a mechanism for others to easily try out your new feature. This may help you find bugs or make contact with new collaborators. Note that you’re also implicitly agreeing to support your code which means answer questions, fix bugs, and maintain it if LAMMPS changes in some way that breaks it (an unusual event).

Note

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.

The previous sections of this doc 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 user 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 80 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.

  • If you want your contribution to be added as a user-contributed feature, and it’s a single file (actually a *.cpp and *.h file) it can rapidly be added to the USER-MISC directory. Send us the one-line entry to add to the USER-MISC/README file in that dir, along with the 2 source files. You can do this multiple times if you wish to contribute several individual features.

  • If you want your contribution to be added as a user-contribution and it is several related features, it is probably best to make it a user package directory with a name like USER-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. See other README and Install.sh files in other USER directories as examples. Send us a tarball of this USER-FOO directory.

  • Your new source files need to have the LAMMPS copyright, GPL notice, and your name and email address at the top, like other user-contributed LAMMPS source files. They need to create a class that is inside the LAMMPS namespace. If the file is for one of the USER packages, including USER-MISC, then we are not as picky about the coding style (see above). I.e. the files do not need to be in the same stylistic format and syntax as other LAMMPS files, though that would be nice for developers as well as users who try to read your code.

  • You must also create 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 doc page should also include literature citations as appropriate; see the bottom of doc/fix_nh.rst for examples and the earlier part of the same file for how to format the cite itself. Citation labels must be unique across all .rst files. The “Restrictions” section of the doc page should indicate if your command is only available if LAMMPS is built with the appropriate USER-MISC or USER-FOO package. See other user package doc files for examples of how to do this. 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/USER for examples of input scripts other users provided for their packages. These example inputs are also required for validating memory accesses and testing for memory leaks with valgrind

  • If there is a paper of yours describing your feature (either the algorithm/science behind the feature itself, or its initial usage, or its implementation in LAMMPS), you can add the citation to the *.cpp source file. See src/USER-EFF/atom_vec_electron.cpp for an example. A LaTeX citation is stored in a variable at the top of the file and a single line of code that references the variable is added to the constructor of the class. Whenever a user invokes your feature from their input script, this will cause LAMMPS to output the citation to a log.cite file and prompt the user to examine the file. Note that you should only use this for a paper you or your group authored. E.g. adding a cite in the code for a paper by Nose and Hoover if you write a fix that implements their integrator is not the intended usage. That kind of citation should just be in the doc page you provide.

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.