From ac84d8fca237d6f158c34c0a5dd9acb0006ccd63 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sofus=20Albert=20H=C3=B8gsbro=20Rose?= Date: Mon, 29 Jan 2024 14:33:17 +0100 Subject: [PATCH] init: Thesis repository. --- .editorconfig | 11 ++ .gitattributes | 39 ++++++ .gitignore | 300 +++++++++++++++++++++++++++++++++++++++++++++++ ref/.gitignore | 2 + ref/bookmarks.md | 137 ++++++++++++++++++++++ thesis.qmd | 0 6 files changed, 489 insertions(+) create mode 100644 .editorconfig create mode 100644 .gitattributes create mode 100644 .gitignore create mode 100644 ref/.gitignore create mode 100644 ref/bookmarks.md create mode 100644 thesis.qmd diff --git a/.editorconfig b/.editorconfig new file mode 100644 index 0000000..ba2807a --- /dev/null +++ b/.editorconfig @@ -0,0 +1,11 @@ +[*] +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 diff --git a/.gitattributes b/.gitattributes new file mode 100644 index 0000000..56f6924 --- /dev/null +++ b/.gitattributes @@ -0,0 +1,39 @@ +# 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 diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..267ace0 --- /dev/null +++ b/.gitignore @@ -0,0 +1,300 @@ +#################### +# - 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 diff --git a/ref/.gitignore b/ref/.gitignore new file mode 100644 index 0000000..fb1b230 --- /dev/null +++ b/ref/.gitignore @@ -0,0 +1,2 @@ +fem +chiroptics diff --git a/ref/bookmarks.md b/ref/bookmarks.md new file mode 100644 index 0000000..1422011 --- /dev/null +++ b/ref/bookmarks.md @@ -0,0 +1,137 @@ +# Articles +## Wave Optics +Fourier Modal Method: +- + + + +## FDTD + + + + +## Maxwell-Bloch + + + + +## Diffraction + + + + +## Chiroptical Properties +**Chiroptical Properties Overview** +- +- *Also PDF*. + +Circular Dichroism Spectroscopy +- + +Absolute Configuration +- Spatial arrangement of atoms within a chiral molecular entity +- + +Optical Rotary Dispersion +- Variation in the optical rotation of a substance with a change in the wavelength of light. +- + + + +## 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. +- + +Coupling of translational and rotational motion in chiral liquids in electromagnetic and circularly polarised electric fields +- + + + +## General PDE Learning +Intro to Maxwell PDE Solutions +- Slides: + +## FEM Tool Aggregators +Resume of This Guy: +- + +Blog Post of This Guy: +- + +Differentiable Solvers (fluid-focused): +- + +Survey of Julia-Based PDE Solvers: +- + +## Geometry Tools +pygmsh +- Nice abstraction on top of `gmsh`. +- PyPi: + +## FEM Learning +Wikipedia: + +Finite Element Encyclopedia +- Home: +- Nedelec: + +Introduction to FEM for Maxwell +- + +## FEM Solvers +COMSOL +- **NOT Open Source**. Pedatory license. +- General-purpose PDE solver. +- Limited Python Interface: + +FEniCS +- **NO GPU** +- Extremely advanced Python muliphysics solver. +- Project: +- Sphere EM Scattering: +- Finite Elements for Maxwell Solvers: +- Maxwell Eigenvalue FEM Solver: +- JAX Integration for Autograd: +- Tutorial: +- Multiphysics Models in FEniCS: +- Gallery of FEM Solvers: +- The FEniCS Tutorial Volume 1: + +FreeFEM: +- Domain-specific C++-like language +- Documentation: +- + +Elmer: +- Project: +- Models: +- Python Interface: +- Docker: + +jax-fem: +- Doesn't seem to do much (if any) wave stuff. +- Repo: +- Paper: +- Sister Project for Additive Manufacturing: + +deal.II: +- A crazy C++ library. +- + +## Julia FEM Solvers +BEAST: +- + +## FEM Fluid Solvers + + +## FEM Theory +Matrix-Free FEM Solver +- Paper: + +## Topological Optimization +FreeFEM-based Topology Optimization +- Paper: diff --git a/thesis.qmd b/thesis.qmd new file mode 100644 index 0000000..e69de29