3.3. LAMMPS programming style and requirements for contributions

The following is a summary of the current requirements and recommendations for including contributed source code or documentation into the LAMMPS software distribution.

3.3.1. Motivation

The LAMMPS developers are committed to providing a software package that is versatile, reliable, high-quality, efficient, portable, and easy to maintain and modify. Achieving all of these goals is challenging since a large part of LAMMPS consists of contributed code from many different authors and not many of them are professionally trained programmers and familiar with the idiosyncrasies of maintaining a large software package. In addition, changes that interfere with the parallel efficiency of the core code must be avoided. As LAMMPS continues to grow and more features and functionality are added, it becomes a necessity to be more discriminating with new contributions while also working at the same time to improve the existing code.

The following requirements and recommendations are provided to help maintaining or improving that status. Where possible we utilize available continuous integration tools to search for common programming mistakes, portability limitations, incompatible formatting, and undesired side effects. It is indicated which requirements are strict, and which represent a preference and thus are negotiable or optional.

Please feel free to contact the LAMMPS core developers in case you need additional explanations or clarifications or in case you need assistance in realizing the (strict) requirements for your contributions.

3.3.2. Licensing requirements (strict)

Contributing authors agree when submitting a pull request that their contributions can be distributed under the LAMMPS license conditions. This is the GNU public license in version 2 (not 3 or later) for the publicly distributed versions, e.g. on the LAMMPS homepage or on GitHub. On request we also make a version of LAMMPS available under LGPL 2.1 terms; this will usually be the latest available or a previous stable version with a few LGPL 2.1 incompatible files removed.

Your new source files should have the LAMMPS copyright, GPL notice, and your name and email address at the top, like other user-contributed LAMMPS source files.

Contributions may be under a different license for long as that license does not conflict with the aforementioned terms. Contributions that use code with a conflicting license can be split into two parts:

  1. the core parts (i.e. parts that must be in the src tree) that are licensed under compatible terms and bundled with the LAMMPS sources

  2. an external library that must be downloaded and compiled (either separately or as part of the LAMMPS compilation)

Please note, that this split licensed mode may complicate including the contribution in binary packages.

3.3.3. Using Pull Requests on GitHub (preferred)

All contributions to LAMMPS are processed as pull requests on GitHub (this also applies to the work of the core LAMMPS developers). A tutorial for submitting pull requests on GitHub is provided. If this is still problematic, contributors may contact any of the core LAMMPS developers for help or to create a pull request on their behalf. This latter way of submission may delay the integration as it depends on the amount of time required to prepare the pull request and free time available by the LAMMPS developer in question to spend on this task.

3.3.4. Integration Testing (strict)

Contributed code, like all pull requests, must pass the automated tests on GitHub before it can be merged with the LAMMPS distribution. These tests compile LAMMPS in a variety of environments and settings and run the bundled unit tests. At the discretion of the LAMMPS developer managing the pull request, additional tests may be activated that test for “side effects” on running a collection of input decks and create consistent results. Also, the translation of the documentation to HTML and PDF is tested for.

More specifically, this means that contributed source code must compile with the most current version of LAMMPS with -DLAMMPS_BIGBIG in addition to the default setting of -DLAMMPS_SMALLBIG. The code needs to work correctly in both cases and also in serial and parallel using MPI.

Some “disruptive” changes may break tests and require updates to the testing tools or scripts or tests themselves. This is rare. If in doubt, contact the LAMMPS developer that is assigned to the pull request for further details and explanations and suggestions of what needs to be done.

3.3.5. Documentation (strict)

Contributions that add new styles or commands or augment existing ones must include the corresponding new or modified documentation in ReStructuredText format (.rst files in the doc/src/ folder). The documentation shall be written in American English and the .rst file must use only ASCII characters so it can be cleanly translated to PDF files (via sphinx and PDFLaTeX). Special characters may be included via embedded math expression typeset in a LaTeX subset.

When adding new commands, they need to be integrated into the sphinx documentation system, and the corresponding command tables and lists updated. When translating the documentation into html files there should be no warnings. When adding a new package also some lists describing packages must be updated as well as a package specific description added and, if necessary, some package specific build instructions included.

As appropriate, the text files with the documentation 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

Contributions that add or modify the library interface or “public” APIs from the C++ code or the Fortran module must include suitable doxygen comments in the source and corresponding changes to the documentation sources for the “Programmer Guide” guide section of the LAMMPS manual.

3.3.6. Examples (preferred)

In most cases, it is preferred that example scripts (simple, small, fast to complete on 1 CPU) are included that demonstrate the use of new or extended functionality. These are typically under the examples or examples/PACKAGES directory. A few guidelines for such example input decks.

  • commands that generate output should be commented out (except when the output is the sole purpose or the feature, e.g. for a new compute).

  • commands like log, echo, package, processors, suffix may not be used in the input file (exception: “processors * * 1” or similar is acceptable when used to avoid unwanted domain decomposition of empty volumes).

  • outside of the log files no generated output should be included

  • custom thermo_style settings may not include output measuring CPU or other time as that makes comparing the thermo output between different runs more complicated.

  • input files should be named in.name, data files should be named data.name and log files should be named log.version.name.<compiler>.<ncpu>

  • the total file size of all the inputs and outputs should be small

  • where possible potential files from the “potentials” folder or data file from other folders should be re-used through symbolic links

3.3.7. Howto document (optional)

If your feature requires some more complex steps and explanations to be used correctly or some external or bundled tools or scripts, we recommend that you also contribute a Howto document providing some more background information and some tutorial material. This can also be used to provide more in-depth explanations for bundled examples.

As a general rule-of-thumb, the more clear and self-explanatory you make your documentation, README files and examples, and the easier you make it for people to get started, the more likely it is that users will try out your new feature.

3.3.8. Programming Style Requirements (varied)

The LAMMPS developers aim to employ a consistent programming style and naming conventions across the entire code base, as this helps with maintenance, debugging, and understanding the code, both for developers and users.

The files pair_lj_cut.h, pair_lj_cut.cpp, utils.h, and utils.cpp may serve as representative examples.

Command or Style names, file names, and keywords (mostly strict)

All user-visible command or style names should be all lower case and should only use letters, numbers, or forward slashes. They should be descriptive and initialisms should be avoided unless they are well established (e.g. lj for Lennard-Jones). For a compute style “some/name” the source files must be called compute_some_name.h and compute_some_name.cpp. The “include guard” would then be LMP_COMPUTE_SOME_NAME_H and the class name ComputeSomeName.

Whitespace and permissions (preferred)

Source files should not contain TAB characters unless required by the syntax (e.g. in makefiles) and no trailing whitespace. Text files should be added with Unix-style line endings (LF-only). Git will automatically convert those in both directions when running on Windows; use dos2unix on Linux machines to convert files. Text files should have a line ending on the last line.

All files should have 0644 permissions, i.e writable to the user only and readable by all and no executable permissions. Executable permissions (0755) should only be on shell scripts or python or similar scripts for interpreted script languages.

Indentation and Placement of Braces (strongly preferred)

LAMMPS uses 2 characters per indentation level and lines should be kept within 100 characters wide.

For new files added to the “src” tree, a clang-format configuration file is provided under the name .clang-format. This file is compatible with clang-format version 8 and later. With that file present files can be reformatted according to the configuration with a command like: clang-format -i new-file.cpp. Ideally, this is done while writing the code or before a pull request is submitted. Blocks of code where the reformatting from clang-format yields undesirable output may be protected with placing a pair // clang-format off and // clang-format on comments around that block.

Programming language standards (required)

The core of LAMMPS is written in C++11 in a style that can be mostly described as “C with classes”. Advanced C++ features like operator overloading or excessive use of templates are avoided with the intent to keep the code readable to programmers that have limited C++ programming experience. C++ constructs are acceptable when they help improving the readability and reliability of the code, e.g. when using the std::string class instead of manipulating pointers and calling the string functions of the C library. In addition and number of convenient utility functions and classes for recurring tasks are provided.

Included Fortran code has to be compatible with the Fortran 2003 standard. Python code must be compatible with Python 3.5. Large parts or LAMMPS (including the PYTHON package) are also compatible with Python 2.7. Compatibility with Python 2.7 is desirable, but compatibility with Python 3.5 is required.

Compatibility with these older programming language standards is very important to maintain portability, especially with HPC cluster environments, which tend to be running older software stacks and LAMMPS users may be required to use those older tools or not have the option to install newer compilers.

Programming conventions (varied)

The following is a collection of conventions that should be applied when writing code for LAMMPS. Following these steps will make it much easier to integrate your contribution. Please have a look at the existing files in packages in the src directory for examples. As a demonstration for how can be adapted to these conventions you may compare the REAXFF package with the what it looked like when it was called USER-REAXC. If you are uncertain, please ask.

  • system headers or from installed libraries are include with angular brackets (example: #include <vector>), while local include file use double quotes (example: #include "atom.h").

  • when including system header files from the C library use the

    C++-style names (<cstdlib> or <cstring>) instead of the C-style names (<stdlib.h> or <string.h>)

  • the order of #include statements in a file some_name.cpp that implements a class SomeName defined in a header file some_name.h should be as follows:

    • #include "some_name.h" followed by an empty line

    • LAMMPS include files e.g. #include "comm.h" or #include "modify.h" in alphabetical order followed by an empty line

    • system header files from the C++ or C standard library followed by an empty line

    • using namespace LAMMPS_NS or other namespace imports.

  • I/O is done via the C-style stdio library and not iostreams.

  • Output to the screen and the logfile should be using the corresponding FILE pointers and only be done on MPI rank 0. Use the utils::logmesg() convenience function where possible.

  • Header files, especially those defining a “style”, should only use the absolute minimum number of include files and must not contain any using statements. Typically that would be only the header for the base class. Instead any include statements should be put into the corresponding implementation files and forward declarations be used. For implementation files, the “include what you use” principle should be employed. However, there is the notable exception that when the pointers.h header is included (or one of the base classes derived from it) certain headers will always be included and thus do not need to be explicitly specified. These are: mpi.h, cstddef, cstdio, cstdlib, string, utils.h, vector, fmt/format.h, climits, cinttypes. This also means any such file can assume that FILE, NULL, and INT_MAX are defined.

  • Header files that define a new LAMMPS style (i.e. that have a SomeStyle(some/name,SomeName); macro in them) should only use the include file for the base class and otherwise use forward declarations and pointers; when interfacing to a library use the PIMPL (pointer to implementation) approach where you have a pointer to a struct that contains all library specific data (and thus requires the library header) but use a forward declaration and define the struct only in the implementation file. This is a strict requirement since this is where type clashes between packages and hard to find bugs have regularly manifested in the past.

  • Please use clang-format only to 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 on commends 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/off throughout your files to protect individual sections from being reformatted.

  • We rarely accept new styles in the core src folder. Thus 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 may be added to one of the EXTRA- packages or the MISC package.

3.3.9. Contributing a 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.

3.3.10. Build system (strongly preferred)

LAMMPS currently supports two build systems: one that is based on traditional Makefiles and one that is based on CMake. Thus your contribution must be compatible with and support both.

For a single pair of header and implementation files that are an independent feature, it is usually only required to add them to src/.gitignore`.

For traditional make, if your contributed files or package depend on other LAMMPS style files or packages 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 may need to be made to cmake/CMakeLists.txt, some of the files in cmake/presets, and possibly a file with specific instructions needs to be added to cmake/Modules/Packages/. Please check out how this is handled for existing packages and ask the LAMMPS developers if you need assistance.

3.3.11. Citation reminder (suggested)

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/DIFFRACTION/compute_saed.cpp for an example. A BibTeX format citation is stored in a string variable at the top of the file and a single line of code registering this variable is added to the constructor of the class. When your feature is used, by default, LAMMPS will print the brief info and the DOI in the first line to the screen and the full citation to the log file.

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. Please 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 latter 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.

3.3.12. Testing (optional)

If your contribution contains new utility functions or a supporting class (i.e. anything that does not depend on a LAMMPS object), new unit tests should be added to a suitable folder in the unittest tree. When adding a new LAMMPS style computing forces or selected fixes, a .yaml file with a test configuration and reference data should be added for the styles where a suitable tester program already exists (e.g. pair styles, bond styles, etc.). Please see this section in the manual for more information on how to enable, run, and expand testing.