14. Building the LAMMPS manual

Depending on how you obtained LAMMPS, the doc directory has 2 or 3 sub-directories and optionally 2 PDF files and 2 e-book format files:

src             # content files for LAMMPS documentation
html            # HTML version of the LAMMPS manual (see html/Manual.html)
tools           # tools and settings for building the documentation
Manual.pdf      # large PDF version of entire manual
Developer.pdf   # small PDF with info about how LAMMPS is structured
LAMMPS.epub     # Manual in ePUB e-book format
LAMMPS.mobi     # Manual in MOBI e-book format

If you downloaded LAMMPS as a tarball from the web site, all these directories and files should be included.

If you downloaded LAMMPS from the public git repository, then the HTML and PDF files are not included. Instead you need to create them, in one of two ways:

You can “fetch” the current HTML and PDF files from the LAMMPS web site. Just type “make fetch”. This should download a html_www directory and Manual_www.pdf/Developer_www.pdf files. Note that if new LAMMPS features have been added more recently than the date of your LAMMPS version, the fetched documentation will include those changes (but your source code will not, unless you update your local repository).
You can build the HTML or PDF files yourself, by typing “make html” or “make pdf”. This requires various tools including Sphinx, git, and the MathJax javascript library, which the build process will attempt to download automatically into a virtual environment in the folder doc/docenv and the folder mathjax, respectively, if not already available. This download is required only once, unless you type “make clean-all”. After that, viewing and processing of the documentation can be done without internet access. To generate the PDF version of the manual, the PDFLaTeX software and several LaTeX packages are required as well. However, those cannot be installed automatically at the moment.

The generation of all documentation is managed by the Makefile in the doc directory.

Documentation Build Options:

make html          # generate HTML in html dir using Sphinx
make pdf           # generate 2 PDF files (Manual.pdf,Developer.pdf)
                   #   in doc dir via htmldoc and pdflatex
make fetch         # fetch HTML doc pages and 2 PDF files from web site
                   #   as a tarball and unpack into html dir and 2 PDFs
make epub          # generate LAMMPS.epub in ePUB format using Sphinx
make mobi          # generate LAMMPS.mobi in MOBI format using ebook-convert
make clean         # remove intermediate RST files created by HTML build
make clean-all     # remove entire build folder and any cached data
make anchor_check  # check for duplicate anchor labels
make style_check   # check for complete and consistent style lists
make package_check # check for complete and consistent package lists
make spelling      # spell-check the manual

14.1. Installing prerequisites for HTML build

To run the HTML documentation build toolchain, Python 3 and virtualenv have to be installed. Here are instructions for common setups:

14.1.1. Ubuntu

sudo apt-get install python-virtualenv

14.1.2. Fedora (up to version 21) and Red Hat Enterprise Linux or CentOS (up to version 7.x)

sudo yum install python3-virtualenv

14.1.3. Fedora (since version 22)

sudo dnf install python3-virtualenv

14.1.4. MacOS X

Python 3

Download the latest Python 3 MacOS X package from https://www.python.org and install it. This will install both Python 3 and pip3.

virtualenv

Once Python 3 is installed, open a Terminal and type

pip3 install virtualenv

This will install virtualenv from the Python Package Index.

14.2. Installing prerequisites for epub build

14.2.1. ePUB

Same as for HTML. This uses mostly the same tools and configuration files as the HTML tree. In addition it uses LaTeX to convert embedded math expressions transparently into embedded images.

For converting the generated ePUB file to a MOBI format file (for e-book readers, like Kindle, that cannot read ePUB), you also need to have the ‘ebook-convert’ tool from the “calibre” software installed. http://calibre-ebook.com/ You first create the ePUB file and then convert it with ‘make mobi’ On the Kindle readers in particular, you also have support for PDF files, so you could download and view the PDF version as an alternative.