[REVIEW]: CAD_to_OpenMC: from CAD design to particle transport

[editorialbot]

Submitting author: @ebknudsen (Erik B Knudsen)
Repository: https://www.github.com/openmsr/CAD_to_OpenMC
Branch with paper.md (empty if default branch): paper_joss
Version: v1.0.0
Editor: @mbarzegary
Reviewers: @nasserma, @jacobmerson, @bonh
Archive: Pending

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/fc9555a355e3d399303a371bfce633f5/status.svg)](https://joss.theoj.org/papers/fc9555a355e3d399303a371bfce633f5)

Reviewers and authors:

Please avoid lengthy details of difficulties in the review thread. Instead, please create a new issue in the target repository and link to those issues (especially acceptance-blockers) by leaving comments in the review thread below. (For completists: if the target issue tracker is also on GitHub, linking the review thread in the issue or vice versa will create corresponding breadcrumb trails in the link target.)

Reviewer instructions & questions

@nasserma & @jacobmerson & @bonh, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review.
First of all you need to run this command in a separate comment to create the checklist:

@editorialbot generate my checklist

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @mbarzegary know.

✨ Please start on your review when you are able, and be sure to complete your review in the next six weeks, at the very latest ✨

Checklists

📝 Checklist for @jacobmerson

📝 Checklist for @nasserma

[editorialbot]

Hello humans, I'm @editorialbot, a robot that can help you with some common editorial tasks.

For a list of things I can do to help you, just type:

@editorialbot commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@editorialbot generate pdf

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.98  T=0.13 s (375.0 files/s, 358817.5 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
SVG                              2              2              2          41591
Python                          30            439            433           2758
TeX                              1            151              0           1584
Markdown                         3             96             11            437
YAML                             4             10              3            148
TOML                             1              2              0             33
reStructuredText                 4             19             11             31
DOS Batch                        1              8              1             26
XML                              1              0              0             17
Text                             1              0              0              9
make                             1              4              7              9
INI                              1              0              0              2
-------------------------------------------------------------------------------
SUM:                            50            731            468          46645
-------------------------------------------------------------------------------

Commit count by author:

   619	Erik B Knudsen
    49	erkn
     8	LukeLabrie
     3	dependabot[bot]
     2	Jonathan Shimwell
     2	Stephen Coleman
     1	Daniel Kozma
     1	Luke Labrie-Cleary

[editorialbot]

Paper file info:

🚨 Wordcount for paper.md is 2802

✅ The paper includes a Statement of need section

[editorialbot]

License info:

✅ License found: MIT License (Valid open source OSI approved license)

[editorialbot]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[editorialbot]

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

✅ OK DOIs

- 10.1016/j.fusengdes.2010.05.030 is OK
- 10.1016/j.net.2024.01.052 is OK
- 10.1145/3272127.3275006 is OK
- 10.1016/S0168-9002(03)01368-8 is OK
- 10.2172/1889957 is OK
- 10.1016/j.nds.2014.07.049 is OK
- 10.2172/4237975 is OK
- 10.1016/j.anucene.2012.06.040 is OK
- 10.1051/epjconf/202023918002 is OK
- 10.1787/7e0ebc50-en is OK
- 10.1080/00295639.2021.1947103 is OK
- 10.3769/radioisotopes.56.497 is OK
- 10.1080/00223131.2015.1062812 is OK
- 10.1016/j.nucengdes.2021.111381 is OK
- 10.1016/j.pnucene.2006.07.005 is OK
- 10.1107/S0021889813007991 is OK
- 10.1145/2487228.2487235 is OK
- 10.1145/2487228.2487235 is OK
- 10.1107/S0021889813007991 is OK
- 10.1016/j.pnucene.2006.07.005 is OK
- 10.1016/j.nucengdes.2021.111381 is OK
- 10.1080/00223131.2015.1062812 is OK
- 10.3769/radioisotopes.56.497 is OK
- 10.1080/00295639.2021.1947103 is OK
- 10.1787/7e0ebc50-en is OK
- 10.1051/epjconf/202023918002 is OK
- 10.1145/2487228.2487235 is OK
- 10.1107/S0021889813007991 is OK
- 10.1016/j.pnucene.2006.07.005 is OK
- 10.1016/j.nucengdes.2021.111381 is OK
- 10.1080/00223131.2015.1062812 is OK
- 10.3769/radioisotopes.56.497 is OK
- 10.1080/00295639.2021.1947103 is OK
- 10.1787/7e0ebc50-en is OK
- 10.1051/epjconf/202023918002 is OK
- 10.1016/j.anucene.2012.06.040 is OK
- 10.2172/4237975 is OK
- 10.1016/j.nds.2014.07.049 is OK
- 10.2172/1889957 is OK
- 10.1016/S0168-9002(03)01368-8 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: Zur Theori der Interferenzen der Röntgenstrahlen i...
- No DOI given, and none found for title: Benchmark for Neutronic Analysis of Sodium-cooled ...
- No DOI given, and none found for title: Benchmark for Neutronic Analysis of Sodium-cooled ...
- No DOI given, and none found for title: Highly birefringent index-guiding photonic crystal...
- No DOI given, and none found for title: Macro-bending loss properties of photonic crystal ...
- No DOI given, and none found for title: High-birefringent photonic crystal fiber
- No DOI given, and none found for title: Photonic crystal fiber modelling and applications
- No DOI given, and none found for title: Crystal fibre technology
- No DOI given, and none found for title: Coupling to photonic crystal fibers
- No DOI given, and none found for title: Mapping grains and their dynamics in three dimensi...
- No DOI given, and none found for title: Photonic Crystal Fibres-the State-of-the-Art
- No DOI given, and none found for title: Component Manual for the Neutron Ray-Tracing Packa...
- No DOI given, and none found for title: Cut-off properties of index-guiding photonic cryst...
- No DOI given, and none found for title: Optical waveguide, method of its production, and i...
- No DOI given, and none found for title: Micro-structured optical fiber
- No DOI given, and none found for title: Modeling photonic crystal fibers with localized fu...
- No DOI given, and none found for title: User and programmers guide to the x-ray-tracing pa...
- No DOI given, and none found for title: Modelling of photonic crystal fibres
- No DOI given, and none found for title: Users’ and Programmers’ Guide to the X-ray tracing...
- No DOI given, and none found for title: McXtrace: a Monte Carlo software package for simul...
- No DOI given, and none found for title: McXtrace-An X-ray Monte Carlo Ray-tracing software...
- No DOI given, and none found for title: ESS technical design report
- No DOI given, and none found for title: Component Manual for the Xray-Tracing Package McXt...
- No DOI given, and none found for title: Simulation and modeling of silicon pore optics for...
- No DOI given, and none found for title: McXtrace 1.4: latest developments in the new relea...
- No DOI given, and none found for title: A Monte Carlo simulation of scattering reduction i...
- No DOI given, and none found for title: Monte Carlo Ray Tracing of Scanning Coherent Diffr...
- No DOI given, and none found for title: Coherent X-ray Diffractive Imaging Simulated by Mo...
- No DOI given, and none found for title: Sådan får vi en (endnu) bedre læreruddannelse
- No DOI given, and none found for title: Simulating the optical performances of the ATHENA ...
- No DOI given, and none found for title: Optical simulations for design, alignment, and per...
- No DOI given, and none found for title: Three dimensional polarimetric neutron tomography-...
- No DOI given, and none found for title: McXtrace anno 2020-complex sample geometries and G...
- No DOI given, and none found for title: Magic Analyzer Simulation Report
- No DOI given, and none found for title: Simulations of foil-based spin-echo (modulated) sm...
- No DOI given, and none found for title: Iridium thin-film coatings for the BabyIAXO hybrid...
- No DOI given, and none found for title: AstroX/McXtrace 2021: an update on simulation exam...
- No DOI given, and none found for title: Effect of mirror curvature on the angular resoluti...
- No DOI given, and none found for title: Modelling diffractive effects in silicon pore opti...
- No DOI given, and none found for title: The effect of mirror curvature and wedging on the ...
- No DOI given, and none found for title: Real-time imaging of acoustic waves in bulk materi...
- No DOI given, and none found for title: International Tables for Crystallography (2019). V...
- No DOI given, and none found for title: Photon. Technol. Lett.
- No DOI given, and none found for title: Simultaneous bright-and dark-field X-ray microscop...
- No DOI given, and none found for title: Benchmark for Neutronic Analysis of Sodium-cooled ...
- No DOI given, and none found for title: Zur Theori der Interferenzen der Röntgenstrahlen i...
- No DOI given, and none found for title: Industrial automation systems and integration—Prod...
- No DOI given, and none found for title: OCCT3D Collaborative development portal
- No DOI given, and none found for title: MSRE Design and Operations Report, Part I, Descrip...

❌ MISSING DOIs

- 10.2172/1463583 may be a valid DOI for title: Updating the GODIVA-IV benchmark
- 10.2172/877507 may be a valid DOI for title: FLUKA: a multi-particle transport code
- 10.1107/s002188980601939x may be a valid DOI for title: A discrete tomography algorithm for improving the ...
- 10.1109/jlt.2003.808668 may be a valid DOI for title: Quantitative estimates of mode coupling and differ...
- 10.1049/ip-opt:20020713 may be a valid DOI for title: Spectral macro-bending loss considerations for pho...
- 10.1107/s0021889807001288 may be a valid DOI for title: A stochastic algorithm for reconstruction of grain...
- 10.4028/www.scientific.net/msf.467-470.1363 may be a valid DOI for title: 3DXRD–Mapping grains and their dynamics in 3 dimen...
- 10.1088/1464-4258/2/6/314 may be a valid DOI for title: Polarization properties of honeycomb-structured ph...
- 10.1016/s0030-4018(03)01451-2 may be a valid DOI for title: Modelling photonic crystal fibres with Hermite–Gau...
- 10.1016/j.endm.2005.05.076 may be a valid DOI for title: Resolving ambiguities in reconstructed grain maps ...
- 10.1117/1.2390680 may be a valid DOI for title: Optimized algebraic reconstruction technique for g...
- 10.1080/10238160902819684 may be a valid DOI for title: Virtual experiments: the ultimate aim of neutron r...
- 10.1007/978-0-8176-4543-4_13 may be a valid DOI for title: Discrete tomography for generating grain maps of p...
- 10.3233/jnr-130004 may be a valid DOI for title: McStas: Past, present and future
- 10.1016/j.endm.2005.05.077 may be a valid DOI for title: Discrete tomographic reconstruction of 2D polycrys...
- 10.1109/ecoc.2001.989089 may be a valid DOI for title: Photonic crystal fibres and effective index approa...
- 10.3934/ipi.2009.3.69 may be a valid DOI for title: A greedy method for reconstructing polycrystals fr...
- 10.1117/12.2302167 may be a valid DOI for title: Macro-bending loss estimation for air-guiding phot...
- 10.1109/icsens.2003.1278941 may be a valid DOI for title: Photonic crystal fibers; fundamental properties an...
- 10.1109/ecoc.2001.989648 may be a valid DOI for title: Microbending in photonic crystal fibres-An ultimat...
- 10.1117/12.559602 may be a valid DOI for title: Optimization of an algebraic reconstruction techni...
- 10.1107/s0021889810034114 may be a valid DOI for title: DART: a robust algorithm for fast reconstruction o...
- 10.1117/12.894179 may be a valid DOI for title: McXtrace: a modern ray-tracing package for x-ray i...
- 10.1016/j.nima.2010.06.212 may be a valid DOI for title: Using McStas for modelling complex optics, using s...
- 10.1016/j.nima.2010.06.235 may be a valid DOI for title: Analysing neutron scattering data using McStas vir...
- 10.1016/j.nima.2010.06.261 may be a valid DOI for title: Eliminating line of sight in elliptic guides using...
- 10.1179/174328405x71684 may be a valid DOI for title: 3D grainmap generation with the algebraic reconstr...
- 10.1117/12.894520 may be a valid DOI for title: A monte carlo approach for simulating the propagat...
- 10.4028/0-87849-443-x.389 may be a valid DOI for title: Mapping partially recrystallised structures by 3DX...
- 10.1117/12.893343 may be a valid DOI for title: Advanced simulations of x-ray beam propagation thr...
- 10.1016/j.physb.2010.11.060 may be a valid DOI for title: McStas-model of the delft SESANS
- 10.1109/icton.2002.1007862 may be a valid DOI for title: Photonic crystal fibers: a variety of applications
- 10.1107/s0021889813000150 may be a valid DOI for title: FabIO: easy access to two-dimensional X-ray detect...
- 10.3233/jnr-130003 may be a valid DOI for title: Investigation of propagation algorithms for ray-tr...
- 10.1063/1.4803167 may be a valid DOI for title: Simulation of a suite of generic long-pulse neutro...
- 10.1088/1742-6596/528/1/012032 may be a valid DOI for title: Application of the MCNPX-McStas interface for shie...
- 10.1016/j.nima.2013.11.071 may be a valid DOI for title: McStas event logger: Definition and applications
- 10.1088/1742-6596/528/1/012035 may be a valid DOI for title: New developments in the McStas neutron instrument ...
- 10.1117/12.2061411 may be a valid DOI for title: Novel applications of the x-ray tracing software p...
- 10.1016/j.nimb.2014.10.015 may be a valid DOI for title: Prediction of beam hardening artefacts in computed...
- 10.1117/12.2233060 may be a valid DOI for title: Simulating X-ray telescopes with McXtrace: A case ...
- 10.1016/j.cpc.2017.04.012 may be a valid DOI for title: Monte Carlo particle lists: MCPL
- 10.3233/jnr-150023 may be a valid DOI for title: Simulation of waviness in neutron guides
- 10.1103/physreva.95.023618 may be a valid DOI for title: Zero-order filter for diffractive focusing of de B...
- 10.1038/s41598-017-09717-w may be a valid DOI for title: Time-of-flight three dimensional neutron diffracti...
- 10.1016/j.physb.2018.03.025 may be a valid DOI for title: Simulation tools for detector and instrument desig...
- 10.1117/1.oe.57.3.037105 may be a valid DOI for title: Simulation tools for scattering corrections in spe...
- 10.1117/12.2312272 may be a valid DOI for title: The McXtrace AstroX toolbox: a general ray tracing...
- 10.1080/10448632.2018.1551000 may be a valid DOI for title: Molecular (and lattice) dynamics to analyze neutro...
- 10.1088/1361-6463/ab0aba may be a valid DOI for title: Three dimensional polarimetric neutron tomography—...
- 10.1117/12.2529113 may be a valid DOI for title: Simulating the effects of thermoelastic deformatio...
- 10.1107/s1600576719012858 may be a valid DOI for title: Full-field neutron microscopy based on refractive ...
- 10.1107/s1600577519014425 may be a valid DOI for title: A Monte Carlo ray-tracing simulation of coherent X...
- 10.1109/ecoc.2001.989675 may be a valid DOI for title: Macrobending loss properties of photonic crystal f...
- 10.1117/12.2561372 may be a valid DOI for title: Example telescope simulations with the AstroX tele...
- 10.1117/12.2594461 may be a valid DOI for title: Open-source simulator for ATHENA X-ray telescope o...
- 10.1107/s1600576721012760 may be a valid DOI for title: X-ray free-electron laser based dark-field X-ray m...
- 10.3233/jnr-150023 may be a valid DOI for title: Simulation of waviness in neutron guides
- 10.1117/12.2622220 may be a valid DOI for title: A fully-analytical treatment of stray light in sil...
- 10.1038/s41598-024-59506-5 may be a valid DOI for title: Neutron Instrument Concepts for a High Intensity M...
- 10.2172/877507 may be a valid DOI for title: FLUKA: a multi-particle transport code
- 10.2172/1463583 may be a valid DOI for title: Updating the GODIVA-IV benchmark

❌ INVALID DOIs

- None

[mbarzegary]

@nasserma, @jacobmerson, @bonh thanks for your help reviewing this work! This is where the review happens. I kindly ask you to now formally start the review. Follow the instructions above ☝️ to generate a check box list for yourself here to guide you through the process. Let me know if you have any questions. When posting issues on the software repository, I appreciate it if you mention openjournals/joss-reviews/issues/7710 so that a link is created to this thread and I can keep track of what is happening.

[mbarzegary]

@ebknudsen this is where the review takes place. Please keep an eye out for comments here from the reviewers, as well as any issues opened by them on your software repository. I recommend you aim to respond to these as soon as possible, and you can address them straight away as they come in if you like, to ensure we do not loose track of the reviewers.

I suggest that you start by removing the uncited references from your bib file. It will help us later to spot the invalid entries with missing DOIs according to the reference check above, otherwise you may need to fix them all.

[ebknudsen]

@mbarzegary Thanks for the comment - I have now cleaned up the bib file.

[ebknudsen]

@editorialbot generate pdf

[editorialbot]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[jacobmerson]

Review checklist for @jacobmerson

Conflict of interest

• I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

• I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• Repository: Is the source code for this software available at the https://www.github.com/openmsr/CAD_to_OpenMC?
• License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@ebknudsen) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
• Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
• Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

• Installation: Does installation proceed as outlined in the documentation?
• Functionality: Have the functional claims of the software been confirmed?
• Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
• Community guidelines: Are there clear guidelines for third parties wishing to 1. Contribute to the software 2. Report issues or problems with the software 3. Seek support

Software paper

• Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
• State of the field: Do the authors describe how this software compares to other commonly-used packages?
• Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

[nasserma]

Review checklist for @nasserma

Conflict of interest

• I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

• I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• Repository: Is the source code for this software available at the https://www.github.com/openmsr/CAD_to_OpenMC?
• License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@ebknudsen) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
• Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
• Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

• Installation: Does installation proceed as outlined in the documentation?
• Functionality: Have the functional claims of the software been confirmed?
• Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
• Community guidelines: Are there clear guidelines for third parties wishing to 1. Contribute to the software 2. Report issues or problems with the software 3. Seek support

Software paper

• Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
• State of the field: Do the authors describe how this software compares to other commonly-used packages?
• Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?