This purpose of this document is to provide a point of reference for LAMMPS developers and contributors as to what conventions should be used to structure and format files in the LAMMPS manual.

Last change: 2022-12-30

In fall 2019, the LAMMPS documentation file format has changed from a home grown markup designed to generate HTML format files only, to reStructuredText. For a transition period all files in the old .txt format were transparently converted to .rst and then processed. The txt2rst tool is still included in the distribution to obtain an initial .rst file for legacy integration into the manual. Since that transition to reStructured text, many of the artifacts of the translation have been removed though, and parts of the documentation refactored and expanded to take advantage of the capabilities reStructuredText and associated tools. The conversion from the source to the final formats (HTML, PDF, and optionally e-book reader formats ePUB and MOBI) is mostly automated and controlled by a Makefile in the doc folder. This makefile assumes that the processing is done on a Unix-like machine and Python 3.5 or later and a matching venv module are available. Additional Python packages (like the Sphinx tool and several extensions) are transparently installed into a virtual environment over the internet using the pip package manager. Further requirements and details are discussed in the manual.

The refactoring and improving of the documentation is an ongoing process, so statements in this document may not always be fully up-to-date. When in doubt, contact the LAMMPS developers.

The layout and formatting of added files should follow the example of the existing files. Since many of those were initially derived from their former .txt format versions and the manual has been maintained in that format for many years, there is a large degree of consistency already, so comparison with similar files should give you a good idea what kind of information and sections are needed.

For headlines we try to follow the conventions posted here. It seems to be sufficient to have this consistent only within any single file and it is not (yet) enforced strictly, but making this globally consistent makes it easier to move sections around.

File names, folders, paths, (shell) commands, definitions, makefile settings and similar should be formatted as "literals" with double backward quotes bracketing the item: ``path/to/some/file``

Keywords and options are formatted in italics: *option*

Mathematical expressions, equations, symbols are typeset using either a .. math: block or the :math: role.

Groups of shell commands or LAMMPS input script or C/C++/Python source code should be typeset into a .. code-block:: section. A syntax highlighting extension for LAMMPS input scripts is provided, so LAMMPS can be used to indicate the language in the code block in addition to bash, c, c++, console, csh, diff, fortran, json, make, perl, powershell, python, sh, or tcl, text, or yaml. When no syntax style is indicated, no syntax highlighting is performed. When typesetting commands executed on the shell, please do not prefix commands with a shell prompt and use bash highlighting, except when the block also shows the output from that command. In the latter case, please use a dollar sign as the shell prompt and console for syntax highlighting.

As an alternative, e.g. to typeset the syntax of file formats a .. parsed-literal:: block can be used, which allows some formatting directives, which means that related characters need to be escaped with a preceding backslash: \*.

For more compact display of alternatives (e.g. compilation or configuration directions for CMake versus GNU make) a .. tabs:: block can be used, followed by multiple .. tab:: blocks, one for each alternative. This is only used for HTML output. For other outputs, the .. tabs:: directive is transparently removed and the individual .. tab:: blocks will be replaced with an .. admonition:: block. Thus in PDF and ePUB output those will be realized as sequential and plain notes.

Special remarks can be highlighted with a .. note:: block and strong warnings can be put into a .. warning:: block. For notes with a title, use .. admonition:: title text followed by :class: note.

When adding a new style (e.g. pair style or a compute or a fix) or a new command, it is required to include the corresponding documentation in reStructuredText format. Those are often new files that need to be added. In order to be included in the documentation, those new files need to be referenced in a .. toctree:: block. Most of those use patterns with wild cards, so the addition will be automatic. However, those additions also need to be added to some lists of styles or commands. The make style\_check command when executed in the doc folder will perform a test and report any missing entries and list the affected files. Any references defined with .. \_refname: have to be unique across all documentation files and this can be checked for with make anchor\_check. Finally, a spell-check should be done, which is triggered via make spelling. Any offenses need to be corrected and false positives should be added to the file utils/sphinx-config/false\_positives.txt.

When adding a new package, the package must be added to the list of packages in the Packages_list.rst file. If additional build instructions need to be followed, a corresponding section should be added to the Build_extras.rst file and linked from the list at the top of the file as well as the equivalent list in the Build_packages.rst file.

A detailed description of the package and pointers to configuration, included commands and examples, external pages, author information and more should be added to the Packages_details.rst file.