[REVIEW]: PeleLMeX: An AMR Low Mach Number Reactive Flow Simulation Code Without Level Sub-cycling about joss-reviews HOT 12 OPEN

👋 @esclapez @mameehan5 @xzz105 the actual review will take place in here. Thanks!

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Software report:

github.com/AlDanial/cloc v 1.88  T=0.18 s (1504.0 files/s, 252976.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
C++                             76           2418           1807          17324
C/C++ Header                    87           2016            867          10380
CSS                              8            339            110           1348
Python                          11            285            451           1253
reStructuredText                 8            526            239           1000
YAML                             8             37             28            681
make                            30            164            124            607
SVG                              1              0              0            520
Markdown                         7            125              0            394
HTML                             4             42             38            369
Bourne Shell                    13             80             96            341
TeX                              1             14              0            161
JavaScript                       5              8             12             84
JSON                             1              0              0             40
CMake                            3              6              3             34
DOS Batch                        1              8              1             26
-------------------------------------------------------------------------------
SUM:                           264           6068           3776          34562
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

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Wordcount for paper.md is 956

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

OK DOIs

- 10.21105/joss.01370 is OK
- 10.1177/10943420221121151 is OK
- 10.1088/1364-7830/4/4/309 is OK
- 10.1080/00102208508960376 is OK
- 10.1145/1089014.1089020 is OK
- 10.1145/3539801 is OK
- 10.1016/j.parco.2021.102836 is OK
- 10.1080/13647830.2012.701019 is OK
- 10.1080/13647830.2017.1390610 is OK
- 10.1006/jcph.1998.5890 is OK
- 10.1080/00102209808915770 is OK
- 10.1016/j.jcp.2022.111305 is OK
- 10.1016/j.combustflame.2022.112286 is OK

MISSING DOIs

- None

INVALID DOIs

- None

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

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@editorialbot add @muellerm-pu as reviewer

Hi all, happy to report that @muellerm-pu (Michael Mueller) has agreed to provide a third review for this submission.

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@muellerm-pu added to the reviewers list!

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Thank you all !

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Review checklist for @mameehan5

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://github.com/AMReX-Combustion/PeleLMeX?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@esclapez) 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?

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Hi @esclapez ,

I finished my first pass at a review. Overall, the paper and codebase look great! Below, I have a few comments with a few minor revisions before acceptance.

General checks:

• All of the required checks here pass, no major concerns or questions.

Functionality:

• There is a small bug installation instructions. I think there is a typo in the README where cd PeleLMeX/Exec/RegTest/HotBubble should be cd PeleLMeX/Exec/RegTests/HotBubble, right? Otherwise, all works well.
• I have personally confirmed key functionality and performance claims, at least at a superficial level (e.g., it runs combustion simulations, highly scalable, etc.). Of course, given the enormous scope of combustion scenarios, I cannot test everything, and would recommend the authors continue adding tests that integrate different functionalities beyond this publication.

Documentation:

• A statement of need is needed in the repository, likely a couple of sentences in the README.
• Installation, examples, and functionality are all great.
• Automated tests are also good, but refer to previous comments.
• A small piece of documentation is needed specifically stating where to report issues and seek support. 1-2 sentences in the README should do the trick.

Software paper:

• The authors provide a great summary. One minor comment is there is an issue with the references on lines 35-36 producing double parentheses.
• The statement of need is in good shape but it should be expanded, particularly the last paragraph. Why do we need, specifically, PeleLMeX to study these fine scale interactions? What next-generation combustion devices are you referring to? Who is the target audience? While I think most readers may be able to infer these (e.g., AMR is required for dynamic, spatially-local flow features which sets it apart), these goals should be more clearly stated.
• The authors do a great job explaining the underlying software that supports PeleLMeX, but I think a little more context would be good, specifically including a couple other pieces of software that do similar things (e.g., PeleLM, OpenFOAM, Sierra/Fuego, Chord, etc.). Obviously this does not need to be a complete list, but there should be enough so the reader has a rough idea where PeleLMeX fits into combustion codes.

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Review checklist for @xzz105

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://github.com/AMReX-Combustion/PeleLMeX?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@esclapez) 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?

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