init: Thesis repository.

.editorconfig

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+[*]
+end_of_line = lf
+insert_final_newline = true
+charset = utf-8
+
+indent_style = tab
+indent_size = 4
+trim_trailing_whitespace = false
+
+[*.yml]
+indent_style = space

.gitattributes

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+# Binary
+*.pdf filter=lfs diff=lfs merge=lfs -text
+*.odt filter=lfs diff=lfs merge=lfs -text
+*.doc filter=lfs diff=lfs merge=lfs -text
+
+# Image
+*.jpg filter=lfs diff=lfs merge=lfs -text
+*.jpeg filter=lfs diff=lfs merge=lfs -text
+*.png filter=lfs diff=lfs merge=lfs -text
+*.gif filter=lfs diff=lfs merge=lfs -text
+*.psd filter=lfs diff=lfs merge=lfs -text
+*.ai filter=lfs diff=lfs merge=lfs -text
+
+*.exr filter=lfs diff=lfs merge=lfs -text
+*.tga filter=lfs diff=lfs merge=lfs -text
+*.aif filter=lfs diff=lfs merge=lfs -text
+*.ttf filter=lfs diff=lfs merge=lfs -text
+
+# Audio
+*.mp3 filter=lfs diff=lfs merge=lfs -text
+*.wav filter=lfs diff=lfs merge=lfs -text
+*.ogg filter=lfs diff=lfs merge=lfs -text
+
+# Video
+*.mp4 filter=lfs diff=lfs merge=lfs -text
+*.mov filter=lfs diff=lfs merge=lfs -text
+
+# 3D Object
+*.fbx filter=lfs diff=lfs merge=lfs -text
+*.blend filter=lfs diff=lfs merge=lfs -text
+*.obj filter=lfs diff=lfs merge=lfs -text
+
+# Library
+*.dll filter=lfs diff=lfs merge=lfs -text
+
+# Archive
+*.a filter=lfs diff=lfs merge=lfs -text
+*.zip filter=lfs diff=lfs merge=lfs -text
+*.mat filter=lfs diff=lfs merge=lfs -text

.gitignore

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+####################
+# - Standard Ignores
+####################
+dev
+
+
+####################
+# - LaTeX Ignores (https://github.com/github/gitignore/blob/master/TeX.gitignore)
+####################
+
+## Output Ignores
+notes_[1-9].pdf
+proj_[1-9].pdf
+hw_[1-9].pdf
+
+notes_[1-9][1-9].pdf
+proj_[1-9][1-9].pdf
+hw_[1-9][1-9].pdf
+
+## Core latex/pdflatex auxiliary files:
+*.aux
+*.lof
+*.log
+*.lot
+*.fls
+*.out
+*.toc
+*.fmt
+*.fot
+*.cb
+*.cb2
+.*.lb
+
+## Intermediate documents:
+*.dvi
+*.xdv
+*-converted-to.*
+
+## Generated if empty string is given at "Please type another file name for output:"
+.pdf
+
+## Bibliography auxiliary files (bibtex/biblatex/biber):
+*.bbl
+*.bcf
+*.blg
+*-blx.aux
+*-blx.bib
+*.run.xml
+
+## Build tool auxiliary files:
+*.fdb_latexmk
+*.synctex
+*.synctex(busy)
+*.synctex.gz
+*.synctex.gz(busy)
+*.pdfsync
+
+## Build tool directories for auxiliary files
+# latexrun
+latex.out/
+
+## Auxiliary and intermediate files from other packages:
+# algorithms
+*.alg
+*.loa
+
+# achemso
+acs-*.bib
+
+# amsthm
+*.thm
+
+# beamer
+*.nav
+*.pre
+*.snm
+*.vrb
+
+# changes
+*.soc
+
+# comment
+*.cut
+
+# cprotect
+*.cpt
+
+# elsarticle (documentclass of Elsevier journals)
+*.spl
+
+# endnotes
+*.ent
+
+# fixme
+*.lox
+
+# feynmf/feynmp
+*.mf
+*.mp
+*.t[1-9]
+*.t[1-9][0-9]
+*.tfm
+
+#(r)(e)ledmac/(r)(e)ledpar
+*.end
+*.?end
+*.[1-9]
+*.[1-9][0-9]
+*.[1-9][0-9][0-9]
+*.[1-9]R
+*.[1-9][0-9]R
+*.[1-9][0-9][0-9]R
+*.eledsec[1-9]
+*.eledsec[1-9]R
+*.eledsec[1-9][0-9]
+*.eledsec[1-9][0-9]R
+*.eledsec[1-9][0-9][0-9]
+*.eledsec[1-9][0-9][0-9]R
+
+# glossaries
+*.acn
+*.acr
+*.glg
+*.glo
+*.gls
+*.glsdefs
+*.lzo
+*.lzs
+
+# uncomment this for glossaries-extra (will ignore makeindex's style files!)
+# *.ist
+
+# gnuplottex
+*-gnuplottex-*
+
+# gregoriotex
+*.gaux
+*.gtex
+
+# htlatex
+*.4ct
+*.4tc
+*.idv
+*.lg
+*.trc
+*.xref
+
+# hyperref
+*.brf
+
+# knitr
+*-concordance.tex
+# TODO Uncomment the next line if you use knitr and want to ignore its generated tikz files
+# *.tikz
+*-tikzDictionary
+
+# listings
+*.lol
+
+# luatexja-ruby
+*.ltjruby
+
+# makeidx
+*.idx
+*.ilg
+*.ind
+
+# minitoc
+*.maf
+*.mlf
+*.mlt
+*.mtc
+*.mtc[0-9]*
+*.slf[0-9]*
+*.slt[0-9]*
+*.stc[0-9]*
+
+# minted
+_minted*
+*.pyg
+
+# morewrites
+*.mw
+
+# nomencl
+*.nlg
+*.nlo
+*.nls
+
+# pax
+*.pax
+
+# pdfpcnotes
+*.pdfpc
+
+# sagetex
+*.sagetex.sage
+*.sagetex.py
+*.sagetex.scmd
+
+# scrwfile
+*.wrt
+
+# sympy
+*.sout
+*.sympy
+sympy-plots-for-*.tex/
+
+# pdfcomment
+*.upa
+*.upb
+
+# pythontex
+*.pytxcode
+pythontex-files-*/
+
+# tcolorbox
+*.listing
+
+# thmtools
+*.loe
+
+# TikZ & PGF
+*.dpth
+*.md5
+*.auxlock
+
+# todonotes
+*.tdo
+
+# vhistory
+*.hst
+*.ver
+
+# easy-todo
+*.lod
+
+# xcolor
+*.xcp
+
+# xmpincl
+*.xmpi
+
+# xindy
+*.xdy
+
+# xypic precompiled matrices and outlines
+*.xyc
+*.xyd
+
+# endfloat
+*.ttt
+*.fff
+
+# Latexian
+TSWLatexianTemp*
+
+## Editors:
+# WinEdt
+*.bak
+*.sav
+
+# Texpad
+.texpadtmp
+
+# LyX
+*.lyx~
+
+# Kile
+*.backup
+
+# gummi
+.*.swp
+
+# KBibTeX
+*~[0-9]*
+
+# TeXnicCenter
+*.tps
+
+# auto folder when using emacs and auctex
+./auto/*
+*.el
+
+# expex forward references with \gathertags
+*-tags.tex
+
+# standalone packages
+*.sta
+
+# Makeindex log files
+*.lpz
+
+# xwatermark package
+*.xwm
+
+# REVTeX puts footnotes in the bibliography by default, unless the nofootinbib
+# option is specified. Footnotes are the stored in a file with suffix Notes.bib.
+# Uncomment the next line to have this generated file ignored.
+#*Notes.bib

ref/.gitignore

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+fem
+chiroptics

ref/bookmarks.md

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+# Articles
+## Wave Optics
+Fourier Modal Method:
+- <https://github.com/facebookresearch/fmmax>
+
+
+
+## FDTD
+<https://github.com/flaport/fdtd>
+
+
+
+## Maxwell-Bloch
+<https://maxwellbloch.readthedocs.io/en/stable/>
+
+
+
+## Diffraction
+<https://rafael-fuente.github.io/simulating-diffraction-patterns-with-the-angular-spectrum-method-and-python.html>
+
+
+
+## Chiroptical Properties
+**Chiroptical Properties Overview**
+- <https://www.nature.com/articles/s41377-020-00367-8>
+- *Also PDF*.
+
+Circular Dichroism Spectroscopy
+- <https://chem.libretexts.org/Bookshelves/Analytical_Chemistry/Physical_Methods_in_Chemistry_and_Nano_Science_(Barron)/07%3A_Molecular_and_Solid_State_Structure/7.07%3A_Circular_Dichroism_Spectroscopy_and_its_Application_for_Determination_of_Secondary_Structure_of_Optically_Active_Species>
+
+Absolute Configuration
+- Spatial arrangement of atoms within a chiral molecular entity
+- <https://en.wikipedia.org/wiki/Absolute_configuration>
+
+Optical Rotary Dispersion
+- Variation in the optical rotation of a substance with a change in the wavelength of light.
+- <https://en.wikipedia.org/wiki/Optical_rotatory_dispersion>
+
+
+
+## Molecular Dynamics related to Varying Chiral Responses to EM Fields
+Perspectives on external electric fields in molecular simulation: progress, prospects and challenges
+- General overview of molecular simulation type stuff.
+- Brings me to *English et al.* article.
+- <https://pubs.rsc.org/en/content/articlehtml/2015/cp/c5cp00629e#cit62>
+
+Coupling of translational and rotational motion in chiral liquids in electromagnetic and circularly polarised electric fields 
+- <https://pubmed.ncbi.nlm.nih.gov/22401453/>
+
+
+
+## General PDE Learning
+Intro to Maxwell PDE Solutions
+- Slides: <https://cmpp.readthedocs.io/en/latest/_static/lec3-2021.pdf>
+
+## FEM Tool Aggregators
+Resume of This Guy:
+- <https://mbarzegary.github.io/whatiuse/>
+
+Blog Post of This Guy:
+- <https://www.matecdev.com/posts/differences-fdtd-fem-mom.html>
+
+Differentiable Solvers (fluid-focused):
+- <https://danmackinlay.name/notebook/pde_solvers_diff.html#phiflow>
+
+Survey of Julia-Based PDE Solvers:
+- <https://github.com/JuliaPDE/SurveyofPDEPackages>
+
+## Geometry Tools
+pygmsh
+- Nice abstraction on top of `gmsh`.
+- PyPi: <https://pypi.org/project/pygmsh/>
+
+## FEM Learning
+Wikipedia: <https://en.wikipedia.org/wiki/Finite_element_method>
+
+Finite Element Encyclopedia
+- Home: <https://defelement.com/>
+- Nedelec: <https://defelement.com/elements/nedelec1.html>
+
+Introduction to FEM for Maxwell
+- <https://www.math.uci.edu/~chenlong/226/FEMMaxwell.pdf>
+
+## FEM Solvers
+COMSOL
+- **NOT Open Source**. Pedatory license.
+- General-purpose PDE solver.
+- Limited Python Interface: <https://mph.readthedocs.io/en/stable/installation.html>
+
+FEniCS
+- **NO GPU**
+- Extremely advanced Python muliphysics solver.
+- Project: <https://fenicsproject.org/>
+- Sphere EM Scattering: <https://docs.fenicsproject.org/dolfinx/v0.7.2/python/demos/demo_axis.html>
+- Finite Elements for Maxwell Solvers: <https://fenicsproject.org/olddocs/dolfin/2018.1.0/python/demos/maxwell-eigenvalues/demo_maxwell-eigenvalues.py.html>
+- Maxwell Eigenvalue FEM Solver: <https://github.com/gamstc/fenics_maxwell/blob/master/maxwell_eigs_simple.py>
+- JAX Integration for Autograd: <https://github.com/IvanYashchuk/jax-fenics>
+- Tutorial: <https://jsdokken.com/dolfinx-tutorial/chapter3/em.html>
+- Multiphysics Models in FEniCS: <https://www.sciencedirect.com/science/article/pii/S266709922300004X#sec0020>
+- Gallery of FEM Solvers: <https://fenicsproject.org/pub/tutorial/sphinx1/._ftut1004.html>
+- The FEniCS Tutorial Volume 1: <https://fenicsproject.org/pub/tutorial/sphinx1/>
+
+FreeFEM: 
+- Domain-specific C++-like language
+- Documentation: <https://doc.freefem.org/introduction/index.html>
+- <https://freefem.org/>
+
+Elmer:
+- Project: <https://www.elmerfem.org/blog/>
+- Models: <https://www.nic.funet.fi/pub/sci/physics/elmer/doc/ElmerModelsManual.pdf>
+- Python Interface: <https://pypi.org/project/pyelmer/>
+- Docker: <https://hub.docker.com/r/nwrichmond/elmerice/>
+
+jax-fem:
+- Doesn't seem to do much (if any) wave stuff.
+- Repo: <https://github.com/tianjuxue/jax-fem>
+- Paper: <https://www.sciencedirect.com/science/article/pii/S0010465523001479#kws0010>
+- Sister Project for Additive Manufacturing: <https://github.com/tianjuxue/jax-am>
+
+deal.II:
+- A crazy C++ library.
+- <https://www.dealii.org/>
+
+## Julia FEM Solvers
+BEAST:
+- <https://github.com/krcools/BEAST.jl>
+
+## FEM Fluid Solvers
+<https://github.com/tum-pbs/PhiFlow>
+
+## FEM Theory
+Matrix-Free FEM Solver
+- Paper: <https://www.iitg.ac.in/dsharma/papers/journal/2020_EBE_SYM_FEA.pdf>
+
+## Topological Optimization
+FreeFEM-based Topology Optimization
+- Paper: <https://link.springer.com/article/10.1007/s00158-023-03529-5#Sec7>