Advancements in stratified flows through simulation, experiment and open research software development

About
Date and time of defence	Friday, 27 September 2019 kl 10:00
Location	F3, KTH, Lindstedtsvägen 26, Stockholm
Supervisor	Erik Lindborg, Pierre Augier
PDF	urn:nbn:se:kth:diva-256564
Slides
Errata	Link to document

---

Citation

@phdthesis{Mohanan-advancements-2019,
  author = {Mohanan, Ashwin Vishnu},
  title = {Advancements in Stratified Flows through Simulation, Experiment and Open Research Software Development},
  year = {2019}
}

Requirements

• texlive
• biblatex
• latexmk
• python>=3.6
• git-lfs
• pandoc, pandoc-crossref (included in pandoc-requirements.txt)

I shall also list applications / CLI tools which prove to be handy for several miscalleanous uses. Not mandatory, but good to have:

• zotero, better-bibtex (refrence management, deterministic BibTeX / BibLaTeX export)
• fzf, fzf-bibtex (fuzzy search to cite as you type, note: requires bibtool CLI tool)
• pandoc-citeproc (pandoc filter to process citations)
• zathura (vim-like pdf viewer)
• neovim / vim (needs no introduction)
• vim-pandoc-syntax (conceal and beautify markdown & LaTeX elements)
• ripgrep, sd (rust alternatives to grep and sed)
• inkscape (PDF, EPS editing)
• rubber (LaTeX error log parser)
• vale (natural language style checker)
• textidote (languagetool for LaTeX)
• texlive-localmanager (install missing packages from CTAN in ArchLinux)
• draw.io (create charts online / offline)
• ttf-humor-sans (for xkcd style plots)

Getting started

Clone

git clone --recursive https://github.com/ashwinvis/phd-thesis.git
cd phd-thesis

Note: the --recursive option is important to clone the submodules. If you forget to do that, execute:

git submodule update --init --recursive

For texlive, I use:

# pacman -S texlive-bibtexextra texlive-core texlive-latexextra texlive-science biber
$ yay -S texlive-localmanager-git
$ tllocalmgr install mnsymbol ccicons
$ updmap -user --enable Map=ccicons.map
# texhash

Use appropriate texlive packages suitable for your opertating system.

Setup a python virtual environment.

make python

The requirements are pinned hard with versions specified. These are supposed to work with Python 3.6.x and could be difficult to install with other versions. In that case, use conda:

conda env create --file environment.yml
conda activate phd-thesis

Workflows

This workflow does many things differently:

• Uses biblatex instead of bibtex: less buggy during compilation
• Hand written, easy to modify JFM inspired styles for biblatex (see jfm.bbx and jfm.cbx)
• A glossary, metadata for papers paper.tex autogenerated a .yml file and a template (see templates and scripts subdirectory)
• Chapters written in markdown and compiled to an intermediate LaTeX form during compilation using pandoc (see chapter_%.latex rule in Makefile
• Slides written in markdown and compiled to Beamer form (see slides subdirectory)
• Uses latexmk wherever possible

Always start by activating the virtual environment source pyenv/bin/activate

Compile the whole thesis

make -j

Compile a standalone PDF of a single chapter/section using pandoc

make -j chapter_00_0_intro.pandoc.pdf

Compile a standalone PDF of all chapters in markdwon

make -j chapters.pandoc.pdf

Watch for changes

make watchthesis  # or watchchapter or watchchapters

Clean files

make clean

Clean generated pdfs also

make cleanall

Troubleshooting

• ImageMagick might require extra privileges which are not enabled by default due to security concerns. However this is necessary for texlive package epstopdf. In /etc/ImageMagick-7/policy.xml add the following line:

  <policy domain="delegate" rights="none" pattern="gs" />

• You need to compile the thesis before compiling the slides. This is because the Makefile for the slides assumes the figures are all present.

• If you install a font and matplotlib does not recognize it, run:

  python -c 'from matplotlib import font_manager as fm; fm._rebuild()

License

The chapters in this work Ashwin Vishnu Mohanan are licensed under a Creative Commons Attribution 4.0 International License.

Figures and contents of accompanying papers fall under various licenses, which requires discretion. Feel free to contact me in case of any doubts.