Project 4  Update and modernize the LAMMPS manual
Overview and Motivation
History
The LAMMPS manual was originally written in a simple, custom markup
language that would translate plain text files into minimal HTML with a
txt2html
converter program which would mostly deal with structural
elements like headlines, links, lists, tables and similar.
Any mathematical expressions had to be typeset as individual LaTeX pages, translated to JPEG images, cropped and then included as images. This would only work well for larger equations and not for single letters or inline expressions. For larger texts with many equations even this procedure would be cumbersome and hence those were translated from LaTeX to PDF and are included as PDF files.
The PDF version of the manual would then be created from the HTML pages using the HTMLDOC tool.
Modern times
As the LAMMPS software was growing and also its documentation, the minimal approach to processing the manual was showing its limitations and the result HTML and PDF documents were not always very readable.
It was then decided to switch to using the Sphinx documentation
generator software. The documentation is
now written in
reStructuredText and uses
several extensions that allow to import embedded documentation from
Python (directly) and C++ code (via Doxygen), automatic syntax
highlighting, and use much more sophisticated typesetting and
crossreferencing. For example all math equations can now be embedded
directly as LaTeX blocks with the .. math::
directive and will be
rendered in HTML output via the MathJax
JavaScript code while in PDF output, they are included as part of the
LaTeX code that is generated by sphinx. Inline math expressions can now
also easily be typeset with the :math:
role.
Tasks

The current LAMMPS manual still has in places “transcribed” math expressions that could be converted to “:math:
<LaTeX code>
” segments and thus make their respective pages more readable as the correspond better to the equations. 
Add more
.. versionadded::
directives indicating when exactly (recently added) features were included in LAMMPS. That way LAMMPS users with older LAMMPS versions will know more easily that a command is not supported by their LAMMPS version when they read the online version of the manual (representing the latest version). 
There are several PDF files that were created externally and could be converted into reStructuredText and then included into the manual as HowTo documents instead of external PDF files. This specifically allows to add crossreferences to and from the documentation pages of the individual commands.

LAMMPS has many bundled examples but it is not always easy to identify which example could be useful to learn how to use a specific command. GitHub issue #2680 proposes to add information about which examples to look at into the documentation. Examples: pair style e2b, pair style
Example
Old:
where F is the embedding energy which is a function of the atomic
electron density rho, phi is a pair potential interaction, and alpha
and beta are the element types of atoms I and J.
New:
where *F* is the embedding energy which is a function of the atomic
electron density :math:`\rho`, :math:`\phi_{\alpha\beta}()` is a pair
potential interaction, and :math:`\alpha` and :math:`\beta` are the element
types of atoms *i* and *j*.