lammps/doc

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
Developer.pdf     PDF with info about how LAMMPS is structured
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
mathjax           code and fonts for rendering math in html
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
include-file-conventions.md      notes on LAMMPS' include file conventions
documentation_conventions.md     notes on writing documentation for LAMMPS

If you downloaded a LAMMPS tarball from lammps.sandia.gov, then the html
folder and the PDF manual should be included. If you downloaded LAMMPS
from GitHub then you either need to download them or build them.

(a) You can "fetch" the current HTML and PDF files from the LAMMPS web
site.  Just type "make fetch".  This should create a html_www dir and
Manual_www.pdf/Developer_www.pdf files.  These files will always
represent the latest published patch/development version of LAMMPS.

(b) 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.

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Installing prerequisites for the documentation build

To run the HTML documention build toolchain, python 3.x, doxygen, git,
and virtualenv have to be installed.  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
- fncychap
- framed
- geometry
- hyperref
- hypcap
- needspace
- times
- tabulary
- upquote
- wrapfig

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).
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More details this can be found in the manual itself. The online
version is at: https://lammps.sandia.gov/doc/Manual_build.html