bsc_thesis/ref/bookmarks.md

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