LAMMPS Documentation Depending on how you obtained LAMMPS and whether you have built the manual yourself, this directory has a varying number of sub-directories and files. Here is a list with descriptions: README this file src content files for LAMMPS documentation html HTML version of the LAMMPS manual (see html/Manual.html) utils utilities and settings for building the documentation Manual.pdf PDF version of entire manual LAMMPS.epub Manual in ePUB format LAMMPS.mobi Manual in MOBI (Kindle) format lammps.1 man page for the lammps command msi2lmp.1 man page for the msi2lmp command doctree temporary data docenv python virtual environment for generating the manual doxygen Doxygen configuration and output .gitignore list of files and folders to be ignored by git doxygen-warn.log logfile with warnings from running doxygen and: github-development-workflow.md notes on the LAMMPS development workflow documentation_conventions.md notes on writing documentation for LAMMPS If you downloaded a LAMMPS tarball from www.lammps.org, then the html folder and the PDF manual should be included. If you downloaded LAMMPS using GitHub then you either need to build them yourself or read the online version at https://docs.lammps.org/ You can build the HTML and PDF files yourself, by typing "make html" or by "make pdf", respectively. This requires various tools and files. Some of them have to be installed (more on that below). For the rest the build process will attempt to download and install into a python virtual environment and local folders. ---------------- Installing prerequisites for the documentation build To run the HTML documention build toolchain, python 3.8 or later, doxygen 1.8.10 or later, git, and the venv python module have to be installed if not already available. Also internet access is initially required to download external files and tools. Building the PDF format manual requires in addition a compatible LaTeX installation with support for PDFLaTeX and several add-on LaTeX packages installed. This includes: - amsmath - anysize - babel - capt-of - cmap - dvipng - ellipse - fncychap - fontawesom - framed - geometry - gyre - hyperref - hypcap - needspace - pict2e - times - tabulary - titlesec - upquote - wrapfig - xindy Also the latexmk script is required to run PDFLaTeX and related tools. the required number of times to have self-consistent output and include updated bibliography and indices. Building the EPUB format requires LaTeX installation with the same packages as for the PDF format plus the 'dvipng' command to convert the embedded math into images. The MOBI format is generated from the EPUB format file by using the tool 'ebook-convert' from the 'calibre' e-book management software (https://calibre-ebook.com). ---------------- More details this can be found in the manual itself. The online version is at: https://docs.lammps.org/Build_manual.html