Started updating references

Author: MarJMue

paper/paper.bib

@@ -111,7 +111,7 @@ @online{rii
   author = {Mikhail N. Polyanskiy},
   title = {Refractive index database},
   url = {https://refractiveindex.info},
-  urldate = {2024-07-02}
+  urldate = {2025-03-11}
 }
 
 @online{castany,
@@ -239,7 +239,7 @@ @Inbook{Hilfiker2018
 url="https://doi.org/10.1007/978-3-319-75377-5_5"
 }
 
-@software{matt_newville_2023_7810964,
+@software{matt_newville_2024_12785036,
   author       = {Matt Newville and
                   Renee Otten and
                   Andrew Nelson and
@@ -251,32 +251,32 @@ @software{matt_newville_2023_7810964
                   Michał and
                   Ray Osborn and
                   Dima Pustakhod and
-                  lneuhaus and
                   Sebastian Weigand and
+                  lneuhaus and
                   Andrey Aristov and
                   Glenn and
-                  Christoph Deil and
-                  mgunyho and
                   Mark and
+                  mgunyho and
+                  Christoph Deil and
                   Allan L. R. Hansen and
                   Gustavo Pasquevich and
                   Leon Foks and
                   Nicholas Zobrist and
                   Oliver Frost and
                   Stuermer and
-                  azelcer and
-                  Anthony Polloreno and
-                  Arun Persaud and
-                  Jens Hedegaard Nielsen and
+                  Jean-Christophe Jaskula and
+                  Shane Caldwell and
+                  Pieter Eendebak and
                   Matteo Pompili and
-                  Shane Caldwell},
-  title        = {lmfit/lmfit-py: 1.2.0},
-  month        = apr,
-  year         = 2023,
+                  Jens Hedegaard Nielsen and
+                  Arun Persaud},
+  title        = {lmfit/lmfit-py: 1.3.2},
+  month        = jul,
+  year         = 2024,
   publisher    = {Zenodo},
-  version      = {1.2.0},
-  doi          = {10.5281/zenodo.7810964},
-  url          = {https://doi.org/10.5281/zenodo.7810964}
+  version      = {1.3.2},
+  doi          = {10.5281/zenodo.12785036},
+  url          = {https://doi.org/10.5281/zenodo.12785036},
 }
 
 @article{eberheim2022,
@@ -385,3 +385,27 @@ @manual{WVASEguide
   organization={J. A. Woollam Co., Inc.},
   address={Lincoln, NE}
 }
+
+@software{tmmax,
+  author = {Bahrem Serhat Danis, Esra Zayim},
+  title = {tmmax: transfer matrix method with jax},
+  version = {1.0.0},
+  url = {https://github.com/bahremsd/tmmax},
+  year = {2025}
+}
+
+@article{Langevin:24,
+author = {Denis Langevin and Pauline Bennet and Abdourahman Khaireh-Walieh and Peter Wiecha and Olivier Teytaud and Antoine Moreau},
+journal = {J. Opt. Soc. Am. B},
+keywords = {Deep learning; Optical computing; Optical filters; Optical properties; Resonant modes; Wavelength division multiplexing},
+number = {2},
+pages = {A67--A78},
+publisher = {Optica Publishing Group},
+title = {PyMoosh: a comprehensive numerical toolkit for computing the optical properties of multilayered structures},
+volume = {41},
+month = {Feb},
+year = {2024},
+url = {https://opg.optica.org/josab/abstract.cfm?URI=josab-41-2-A67},
+doi = {10.1364/JOSAB.506175},
+abstract = {We present PyMoosh, a Python-based simulation library designed to provide a comprehensive set of numerical tools allowing the computation of essentially all optical characteristics of multilayered structures, ranging from reflectance and transmittance to guided modes and photovoltaic efficiency. PyMoosh is designed not just for research purposes, but also for use cases in education. To this end, we have invested significant effort in ensuring the user-friendliness and simplicity of the interface. PyMoosh has been developed in line with the principles of open science and considering the fact that multilayered structures are increasingly being used as a testing ground for optimization and deep learning approaches. We provide in this paper the theoretical basis at the core of PyMoosh, an overview of its capabilities, as well as a comparison between the different numerical methods implemented in terms of speed and stability. We are convinced such a versatile tool will be useful for the community in many ways.},
+}

paper/paper.md

@@ -9,15 +9,13 @@ tags:
 authors:
   - name: Marius J. Müller
     orcid: 0009-0005-2187-0122
-    equal-contrib: true
     affiliation: 1
   - name: Florian Dobener
     orcid: 0000-0003-1987-6224
-    equal-contrib: true
 affiliations:
   - name: Institute of Experimental Physics I and Center for Materials Research (ZfM/LaMa), Justus Liebig University Giessen, Heinrich-Buff-Ring 16, Giessen, D-35392 Germany
     index: 1
-date: 24 April 2023
+date: 11 March 2025
 bibliography: paper.bib
 ---
 
@@ -28,7 +26,7 @@ The code primarily targets spectroscopic ellipsometry (SE) but is adaptable to v
 
 Various scientific fields use SE to determine the optical constants of materials and layered material stacks.
 The as-measured SE experimental requires numerical analysis to deduce commonly used, physically meaningful material parameters.
-A typical approach uses transfer-matrix methods (TMM) [@tompkins2005, @WVASEguide].
+A typical approach uses transfer-matrix methods (TMM) [@tompkins2005; @WVASEguide].
 Here, an interaction matrix describes the optical response of each individual material layer.
 The full optical response of a multilayer system is then determined by matrix multiplication of the layers' matrices.
 
@@ -89,11 +87,8 @@ Other notable Python open-source software for solving transfer-matrices is avail
 - [PyLlama](https://pyllama.readthedocs.io) [@Bay2022] focuses on the simulation of liquid crystals and uses non-vectorized TMM and a scattering matrix algorithm (rigorous coupled-wave analysis, RCWA).
 - [RayFlare](https://rayflare.readthedocs.io) [@Pearce2021] is a complete toolkit to simulate the physical and electrical properties of solar cells. It provides the same 2x2 algorithm[@byrnes2020multilayer] and a scattering matrix approach (S4).
 - [tmm_fast](https://github.com/MLResearchAtOSRAM/tmm_fast) [@Luce22] is a vectorized variant of Byrnes' algorithm for artificial intelligence-based analysis of multilayer stacks.
-- Additional mentions:
-  - [refellips](https://refellips.readthedocs.io/en/latest/)
-  - [EMpy](http://lbolla.github.io/EMpy/)
-  - [dtmm](https://github.com/IJSComplexMatter/dtmm)
-  - [py_matrix](https://github.com/gevero/py_matrix)
+- [tmmax](https://github.com/bahremsd/tmmax) [tmmax] is a JIT-compilable version of the 2x2 matrix method, leveraging the JAX toolkit.
+- [PyMoosh](https://github.com/AnMoreau/PyMoosh) [Langevin:24]
 
 # Example: Building a model for an oxide layer on silicon
 
@@ -102,7 +97,7 @@ Here, we will demonstrate by creating a standard model for SiO$_2$ on Si.
 We will use a Cauchy dispersion function for SiO$_2$ and tabulated literature values for Si loaded from the refractiveindex.info database.
 
 We need to import the necessary libraries before building the model:
-PyElli is imported from the module `elli`, and we want to use our parameters wrapper `ParamsHist`, which is imported from `elli.fitting`. `ParamsHist` is a wrapper around the `Parameters` class from [lmfit](https://lmfit.github.io/lmfit-py/index.html) [@matt_newville_2023_7810964], adding history to it so you can revert your model to an earlier set of parameters.
+PyElli is imported from the module `elli`, and we want to use our parameters wrapper `ParamsHist`, which is imported from `elli.fitting`. `ParamsHist` is a wrapper around the `Parameters` class from [lmfit](https://lmfit.github.io/lmfit-py/index.html) [matt_newville_2024_12785036], adding history to it so you can revert your model to an earlier set of parameters.
 We also import `linspace` from `numpy` for generating a wavelength axis.
 
 ```python