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arxiv: 2512.18091 · v2 · submitted 2025-12-19 · ⚛️ physics.plasm-ph

MCPlas, a MATLAB toolbox for reproducible plasma modelling with COMSOL

Marjan N. Stankov , Daan Boer , Wouter Graef , Kevin van 't Veer , Aleksandar P. Jovanovi\'c , Florian Sigeneger , Detlef Loffhagen , Jan van Dijk
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Markus M. Becker
This is my paper

Pith reviewed 2026-05-16 20:38 UTC · model grok-4.3

classification ⚛️ physics.plasm-ph
keywords plasma modellingCOMSOLMATLAB toolboxfluid-Poissonnon-thermal plasmaargon dischargereproducible workflowJSON input
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The pith

MCPlas toolbox generates transparent fluid-Poisson plasma models in COMSOL from JSON data.

A machine-rendered reading of the paper's core claim, the machinery that carries it, and where it could break.

The paper presents MCPlas as a collection of MATLAB functions that automatically create equation-based fluid-Poisson models for non-thermal plasmas inside COMSOL. Inputs are supplied in structured JSON format that follows interoperable schemas, and the code remains fully editable with support for advanced electron transport descriptions. The toolbox handles one- and two-dimensional geometries in Cartesian, polar, and cylindrical coordinates. Verification occurs through direct comparison with COMSOL's Plasma Module on reference DC and RF argon glow discharges, confirming that the generated models reproduce standard results while exposing the influence of transport and boundary choices.

Core claim

MCPlas supplies MATLAB functions that translate structured JSON plasma kinetic data into COMSOL equation-based fluid-Poisson models, incorporating flexible electron transport and boundary conditions across one- and two-dimensional Cartesian, polar, and cylindrical geometries. When applied to low-pressure DC and RF argon discharges, the resulting simulations match outputs from COMSOL's Plasma Module, confirming implementation reliability and illustrating the impact of the chosen transport treatment.

What carries the argument

The MCPlas toolbox of editable MATLAB functions that convert JSON-formatted plasma data into COMSOL equation-based fluid-Poisson simulations.

If this is right

  • Complex reaction sets can be managed by direct editing of the JSON input files.
  • Input data remain reusable across different simulation platforms through the shared JSON schema.
  • The transparent MATLAB code lets users inspect and alter every equation and boundary condition.
  • Verification against the Plasma Module establishes baseline reliability for low-pressure argon cases.

Where Pith is reading between the lines

These are editorial extensions of the paper, not claims the author makes directly.

  • Adoption of the same JSON format could simplify data exchange between plasma codes written in different environments.
  • The explicit code structure may reduce hidden implementation errors when users extend models to new gases or pressures.
  • Similar automation layers could be built for other multiphysics solvers once the JSON schema is fixed.
  • Extensions to three-dimensional geometries would follow directly from the existing coordinate handling.

Load-bearing premise

The fluid-Poisson approximation with the selected electron transport description and boundary conditions sufficiently represents the physics of the tested low-pressure glow discharges.

What would settle it

A clear mismatch between MCPlas-generated results and either the Plasma Module or measured data on a well-documented argon discharge would show the model fails to capture the intended physics.

Figures

Figures reproduced from arXiv: 2512.18091 by Aleksandar P. Jovanovi\'c, Daan Boer, Detlef Loffhagen, Florian Sigeneger, Jan van Dijk, Kevin van 't Veer, Marjan N. Stankov, Markus M. Becker, Wouter Graef.

Figure 1
Figure 1. Figure 1: Modelling geometries supported by MCPlas toolbox ( [PITH_FULL_IMAGE:figures/full_fig_p007_1.png] view at source ↗
Figure 2
Figure 2. Figure 2: Illustration of the MCPlas workflows including the provision of input data (1), [PITH_FULL_IMAGE:figures/full_fig_p014_2.png] view at source ↗
Figure 3
Figure 3. Figure 3: Schematic representation of the top-level structure of an LXCat JSON document [PITH_FULL_IMAGE:figures/full_fig_p016_3.png] view at source ↗
Figure 4
Figure 4. Figure 4: Example of a JSON object representing a reference, as defined by the CSL-JSON [PITH_FULL_IMAGE:figures/full_fig_p017_4.png] view at source ↗
Figure 5
Figure 5. Figure 5: Example of a key-value pair from the states property. The JSON object defines the argon 1s5 metastable state using the J1L2 coupling scheme. The info property stores an array of different data related to the species, some possible options are Mass, Energy, Mobility, and DiffusionCoefficient. The Ar[1s5] key can be used to reference this state in other parts of the document. its accompanying data using mult… view at source ↗
Figure 6
Figure 6. Figure 6: Examples of JSON objects for the different supported data storage types. [PITH_FULL_IMAGE:figures/full_fig_p019_6.png] view at source ↗
Figure 7
Figure 7. Figure 7: Example of a JSON object entry in the processes property. This object defines an electron-impact ionisation reaction from the argon ground state: e − + Ar 1S0  → 2e− + Ar+. The reaction property stores the basic definition of the reaction. The electron, Ar[1S_0] and Ar[+] strings are keys in the states object that reference the electron, argon ground state, and the argon ion, respectively. The info proper… view at source ↗
Figure 8
Figure 8. Figure 8: Sketch of the discharge geometry used in the modelling studies with DC (test [PITH_FULL_IMAGE:figures/full_fig_p022_8.png] view at source ↗
Figure 9
Figure 9. Figure 9: Verification of the MCPlas toolbox for a DC glow discharge in argon. Com [PITH_FULL_IMAGE:figures/full_fig_p024_9.png] view at source ↗
Figure 10
Figure 10. Figure 10: Comparison of particle number densities a) as well as mean electron energy [PITH_FULL_IMAGE:figures/full_fig_p025_10.png] view at source ↗
Figure 11
Figure 11. Figure 11: Verification of MCPlas toolbox for an RF glow discharge in argon. Comparison [PITH_FULL_IMAGE:figures/full_fig_p025_11.png] view at source ↗
Figure 12
Figure 12. Figure 12: Comparison of period-averaged particle number densities a) and mean electron [PITH_FULL_IMAGE:figures/full_fig_p026_12.png] view at source ↗
Figure 13
Figure 13. Figure 13: Comparison of number densities of electrons and atomic argon ions, as well [PITH_FULL_IMAGE:figures/full_fig_p027_13.png] view at source ↗
Figure 14
Figure 14. Figure 14: Comparison of period-averaged number densities of electrons and [PITH_FULL_IMAGE:figures/full_fig_p027_14.png] view at source ↗
Figure 15
Figure 15. Figure 15: Number densities of excited molecular states and the molecular ion calculated [PITH_FULL_IMAGE:figures/full_fig_p028_15.png] view at source ↗
Figure 16
Figure 16. Figure 16: Comparison of modelling results obtained with MCPlas, PLASIMO and FEDM [PITH_FULL_IMAGE:figures/full_fig_p030_16.png] view at source ↗
Figure 17
Figure 17. Figure 17: Comparison of modelling results obtained with MCPlas, PLASIMO and FEDM [PITH_FULL_IMAGE:figures/full_fig_p031_17.png] view at source ↗
read the original abstract

The MCPlas toolbox represents a collection of MATLAB functions for the automated generation of an equation-based fluid-Poisson model for non-thermal plasmas in the multiphysics simulation software COMSOL. Following the development of the new generation of the LXCat platform, all input data are prepared in a structured and interoperable JSON format and can be supplied and validated using existing JSON schemas. The toolbox includes fully transparent, editable MATLAB source code and offers an advanced description of electron transport in addition to commonly used approaches in the plasma modelling community. It supports one-dimensional and two-dimensional modelling geometries employing Cartesian, polar and cylindrical coordinate systems. MCPlas is tested on two reference cases: DC- and RF-driven low-pressure glow discharges in argon. Comparison of MCPlas results with results obtained by employing COMSOL's Plasma Module verifies the reliability of the plasma model implemented by MCPlas and demonstrates the significance of electron transport treatment and boundary conditions applied in the toolbox. Using the same examples, the easy handling of complex reaction kinetic models in MCPlas and the reusability of its JSON input data across different modelling platforms are illustrated. This demonstrates that MCPlas provides a transparent and reproducible workflow for the simulation of non-thermal plasmas using COMSOL.

Editorial analysis

A structured set of objections, weighed in public.

Desk editor's note, referee report, simulated authors' rebuttal, and a circularity audit. Tearing a paper down is the easy half of reading it; the pith above is the substance, this is the friction.

Referee Report

3 major / 2 minor

Summary. The paper presents MCPlas, a MATLAB toolbox that automates generation of equation-based fluid-Poisson models for non-thermal plasmas inside COMSOL. Input data are supplied in structured JSON format from the LXCat platform; the toolbox supports advanced electron transport closures, 1D/2D geometries in Cartesian/polar/cylindrical coordinates, and is demonstrated on DC- and RF-driven low-pressure argon glow discharges. Results are compared to COMSOL's Plasma Module to verify reliability of the implemented model and to illustrate the role of transport treatment and boundary conditions; reusability of the JSON kinetics data across platforms is also shown.

Significance. A transparent, editable MATLAB implementation with reusable JSON reaction data could improve reproducibility and ease of modification in the plasma-modeling community, particularly for users who prefer equation-based COMSOL workflows over the built-in Plasma Module. The provision of an advanced electron-transport description is potentially useful, but its practical advantage remains to be quantified.

major comments (3)
  1. [Abstract] Abstract and verification section: the statement that comparison with COMSOL's Plasma Module 'verifies the reliability of the plasma model implemented by MCPlas' is circular. Because MCPlas constructs equation-based models inside the identical COMSOL environment and draws from the same LXCat JSON data, agreement on the DC and RF argon cases primarily confirms consistent equation setup and boundary-condition implementation rather than independent validation of the fluid-Poisson closure or chosen transport coefficients.
  2. [Verification] Verification section: no quantitative discrepancy metrics (L2 norms, maximum relative errors, or point-wise differences on ne, Te, or E profiles) are reported for the two reference cases. Only qualitative agreement is stated, which prevents readers from judging the numerical fidelity of the generated models.
  3. [Electron transport] Electron-transport discussion: the claim that the toolbox 'demonstrates the significance of electron transport treatment' is not supported by explicit side-by-side comparisons (e.g., figures or tables) showing how the advanced description alters discharge characteristics relative to the standard mobility/diffusion approach on the same DC/RF cases.
minor comments (2)
  1. [Abstract] The abstract states that 'fully transparent, editable MATLAB source code' is included, yet no repository URL, supplementary-material link, or licensing statement is provided.
  2. [Figures] All comparison figures should include quantitative axis scales, error bars or difference plots, and clear legends distinguishing MCPlas from Plasma Module results.

Simulated Author's Rebuttal

3 responses · 0 unresolved

We thank the referee for the constructive and detailed comments on our manuscript. We have addressed each major point below and will revise the paper accordingly to improve clarity and rigor.

read point-by-point responses

  1. Referee: [Abstract] Abstract and verification section: the statement that comparison with COMSOL's Plasma Module 'verifies the reliability of the plasma model implemented by MCPlas' is circular. Because MCPlas constructs equation-based models inside the identical COMSOL environment and draws from the same LXCat JSON data, agreement on the DC and RF argon cases primarily confirms consistent equation setup and boundary-condition implementation rather than independent validation of the fluid-Poisson closure or chosen transport coefficients.

    Authors: We agree that the comparison primarily confirms consistent implementation of equations and boundary conditions within the same COMSOL framework rather than providing independent validation of the fluid-Poisson model. In the revised manuscript we will rephrase the abstract and verification section to state that the agreement demonstrates correct setup of the generated models and boundary conditions, without claiming independent verification of the underlying physics or transport coefficients. revision: yes

  2. Referee: [Verification] Verification section: no quantitative discrepancy metrics (L2 norms, maximum relative errors, or point-wise differences on ne, Te, or E profiles) are reported for the two reference cases. Only qualitative agreement is stated, which prevents readers from judging the numerical fidelity of the generated models.

    Authors: We acknowledge the absence of quantitative metrics. The revised version will include L2 norms and maximum relative errors for electron density, electron temperature, and electric field profiles for both DC and RF cases. These metrics will be added to the verification section, accompanied by a table summarizing the discrepancies to allow readers to assess numerical fidelity. revision: yes

  3. Referee: [Electron transport] Electron-transport discussion: the claim that the toolbox 'demonstrates the significance of electron transport treatment' is not supported by explicit side-by-side comparisons (e.g., figures or tables) showing how the advanced description alters discharge characteristics relative to the standard mobility/diffusion approach on the same DC/RF cases.

    Authors: We agree that explicit side-by-side comparisons are required to substantiate the claim. The revised manuscript will add dedicated figures and/or tables directly comparing results obtained with the advanced electron transport description versus the standard mobility/diffusion approach for the same DC and RF argon cases, quantifying the differences in key discharge parameters such as density and temperature profiles. revision: yes

Circularity Check

0 steps flagged

No circularity: software verification against external COMSOL module

full rationale

The paper describes a MATLAB toolbox (MCPlas) that generates equation-based fluid-Poisson models inside COMSOL and verifies correctness by direct numerical comparison against COMSOL's built-in Plasma Module on reference DC and RF argon cases. No derivation chain, first-principles predictions, parameter fitting presented as prediction, or self-citation load-bearing steps exist. The comparison serves as an external benchmark within the shared platform, and the central claim of providing a transparent, reusable workflow is self-contained against that benchmark without reducing to its own inputs by construction.

Axiom & Free-Parameter Ledger

0 free parameters · 1 axioms · 0 invented entities

The central claim rests on standard domain assumptions of fluid plasma modeling rather than new postulates.

axioms (1)
  • domain assumption Fluid approximation remains valid for the low-pressure argon glow discharges considered
    Invoked implicitly when the toolbox generates fluid-Poisson models for the reference cases.

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