June 2018 beautification

Organisation of the ABINIT June 2018 beautification, Monday 4 June - Wednesday 14 June 2018.

I expect your contributions to be in a branch named “user_name”/beauty. So, please start from your develop branch (v8.9.3 of ABINIT), branch your own “beauty” branch, upgrade it to the latest trunk/develop, work in it, then issue a merge request (using Gitlab) from “user_name”/beauty to trunk/develop.

Explicitly, issue

1. git checkout develop
2. git branch beauty
3. git checkout beauty
4. git merge remotes/trunk/develop (or your method to sync with the trunk)

then beautify the code, then issue the proper merge request to trunk/develop, then mention in the task list that you have done the job !

This beautification will be focused on the documentation. Indeed, as a response to the recommendations made at the last developer workshop, in Frejus May 2017, “topics” have been introduced and lead to completion, a centralized bibliography database has been set up, and a new global infrastructure based on mkdocs (and markdown) has been established. However:

• A. There are still MANY isolated bibliographical references in the descriptions of input variables or lessons of the tutorial (or other files), to be ported inside the bibliography database.
• B. Many line breaks have disappeared in the input variable descriptions (so, one big paragraph appears instead of several paragraphs)
• C. Equations might still be in “text” style, while they should be now in "LaTex" style (interpreted using MathJax)
• D. Specific improvements of lessons of the tutorials and other files could be made, thanks to the new mkdocs infrastructure.
• E. It remains to be checked that no inadvertent deterioration of the documentation has occurred.
• F. One might also check the correctness of links and other information (like the coherence between the sections of output files pasted in the text, and the output files themselves, available from the links)

As an indication, each contributor might have to dedicate about three hours to this work (including, if not yet done, reading the mkdocs documentation and possibly training a bit with the mksite script). By the way, suggestions for improvements of the mkdocs infrastructure is also welcome, see the dedicated page.

Check first whether it exists already in the bibliographical database (file doc/abiref.bib), and if so, simply refer to it using a “cite” wikilink. Otherwise, introduce the adequate bibtex information

All the needed documentation is available at :

• https://docs.abinit.org/developers/abimkdocs
• https://docs.abinit.org/developers/markdown

Going through it for the first time might be 15-20 minutes. Training might be another 15 minutes (e.g. starting the server with ./mksite.py serve –dirtyreload, then trying to make some fake modifications).

Most of the following files have been assigned to contributors :

1. Input variables contained in abimkdocs, see the files variables_abinit.py, variables_aim.py, variables_anaddb.py, variables_optic.py. Of course, the file variables_abinit.py is too big to be taken by one developer. In this respect, the input variables of ABINIT will be distributed according to their “varset” (“Basic”, “Bethe-Salpeter”, Developers“, “DMFT”, … see the list e.g. in the leftmost column of the input variables Web pages, as an example, see https://docs.abinit.org/variables/basic/#accuracy). There are 17 such “varsets”. Counting 17 varsets for ABINIT + ANADDB + AIM + OPTIC make for 20 sets of input variables.
2. Lessons of the Tutorial : 38 *.md files contained in doc/tutorial ;
3. Theory : 8 *.md files contained in doc/theory ;

So, the work will consists in the beautification of 46 *.md files, 17 varsets and 3 remaining variables*.py files. To summarize, 66 tasks to be distributed.

Moreover, as the addition of new tutorial and documentation is facilitated with respect to the previous procedure, adding new tutorials or documentation for new executables might also be done by volunteers, or any filling of holes in the documentation. For example, multibinit and tdep documentation is missing (but is underway for multibinit !), the tutorial on spin/spin-orbit could be extended, the tutorial on source_code should be rewritten from scratch…