Joss paper #88
Joss paper #88
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@MarJMue I worked a bit on the introductory part and I am quite happy with it. Do you like to have a look and see if you are fine with it, too? I also added a basic example for building a simple model, to give readers a feeling for how building a model looks like. I would add a bit of text around this in a few days. Other than that I just think that the Statement of need and Software with similar functionalities need some refinement, but then we should be able to hand this in. What do you think? |
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Hey @domna, One thing is odd, your name still gets our affiliations even tho it is not set in the file. |
| Currently, two algorithms using different formulations are available: a fast algorithm based on a 2x2 matrix formulation [@byrnes2020multilayer] and a more complex 4x4 matrix formulation [@Berreman72; @berreman4x4_doku; @berreman4x4_software]. | ||
| The 2x2 matrix algorithm divides the light into two perpendicular linearly polarized beams, which are solved separately. | ||
| One of its limitations is eliminating the possibility to include birefringent materials. | ||
| The 4x4 matrix approach fully solves Maxwell's equations. |
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I wouldn't say it solves them fully. It solves them fully in the frame of a 1D model. For modelling 2D or 3D interaction one would need to use RCWA or other algorithms to solve this.
| For SE, optical models vary between manufacturers and translation can be difficult without comprehensive documentation. | ||
| **PyElli's** open-source nature makes optical models extendable, auditable, and fully comprehensive. | ||
| Each version of **PyElli** is associated with a DOI and a Zenodo upload, allowing for reliable referencing and reproducibility of analysis results. | ||
| It supports [NXellipsometry](https://fairmat-experimental.github.io/nexus-fairmat-proposal/9636feecb79bb32b828b1a9804269573256d7696/classes/contributed_definitions/NXellipsometry.html#nxellipsometry), a recent advancement in SE data standardization. |
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The link is outdated. This would be the official one: https://manual.nexusformat.org/classes/contributed_definitions/NXellipsometry.html and this the latest dev https://fairmat-nfdi.github.io/nexus_definitions/classes/contributed_definitions/NXellipsometry.html#nxellipsometry .
However, I'm not sure we still support the latest version so we might have to leave this part out or at least check that it still works (I'm not sure if there were relevant changes).
| Each version of **PyElli** is associated with a DOI and a Zenodo upload, allowing for reliable referencing and reproducibility of analysis results. | ||
| It supports [NXellipsometry](https://fairmat-experimental.github.io/nexus-fairmat-proposal/9636feecb79bb32b828b1a9804269573256d7696/classes/contributed_definitions/NXellipsometry.html#nxellipsometry), a recent advancement in SE data standardization. | ||
| This standard is developed by the German consortium [FAIRmat](https://www.fair-di.eu/fairmat) within the German National Research Data Infrastructure (NFDI) and is accepted by the [NeXus International Advisory Committee (NIAC)](https://www.nexusformat.org/NIAC.html), which has been maintaining beamline standards in the [NeXus format](https://www.nexusformat.org) for over 20 years [@Konnecke2015]. | ||
| **PyElli** is also available as an [example](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-remote-tools-hub/-/tree/develop/docker/ellips/example) and a cloud-based [analysis tool](https://nomad-lab.eu/prod/v1/staging/gui/analyze/north) in the research data management software [NOMAD](https://nomad-lab.eu/nomad-lab/) [@Scheffler2022]. |
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The example also changed places and is now here: https://gitlab.mpcdf.mpg.de/nomad-lab/north/ellips/-/tree/main/example?ref_type=heads
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Thank you for the update! I went through it and have some small remarks. Mainly concerning the FAIRmat part. We might leave this out since I don't know whether this is still compatible. Otherwise it's good to go from my side.
I think it might to try to set something if there is nothing specified. Anyways, I talked to Sangam and we agreed that it's fine if I still use the Gießen affiliation (since I don't know what to use otherwise). |
Hey @MarJMue,
I started to write some text for the paper. I'll just create this as a PR to enable easier commenting and reviewing of changes. However, I think we're not supposed to merge this in the end (and I would also argue against it).