[PRE REVIEW]: ASIMTools: A lightweight workflow and simulation manager for reproducible atomistic simulations

[editorialbot]

Submitting author: !--author-handle-->@mkphuthi<!--end-author-handle-- (Mgcini Keith Phuthi) Repository: https://github.com/BattModels/asimtools.git Branch with paper.md (empty if default branch): Version: v0.0.0 Editor: !--editor-->@HaoZeke<!--end-editor-- Reviewers: @abhishektiwari, @imtambovtcev Managing EiC: Daniel S. Katz

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Thanks for submitting your paper to JOSS @mkphuthi. Currently, there isn't a JOSS editor assigned to your paper.

@mkphuthi if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). You can search the list of people that have already agreed to review and may be suitable for this submission.

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[editorialbot]

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[editorialbot]

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

OK DOIs

- 10.5281/zenodo.8317316 is OK
- 10.1016/j.commatsci.2021.110731 is OK
- 10.1038/s41597-020-00638-4 is OK
- 10.1016/j.cpc.2021.108171 is OK
- 10.1038/s41563-023-01699-7 is OK
- 10.1002/cpe.3505 is OK
- 10.1016/j.commatsci.2012.10.028 is OK
- 10.1088/1361-648X/aa680e is OK
- 10.5281/zenodo.8317316 is OK
- 10.1016/j.commatsci.2021.110731 is OK
- 10.1038/s41597-020-00638-4 is OK
- 10.1021/acsomega.3c10014 is OK

MISSING DOIs

- No DOI given, and none found for title: Vibrational Entropy and Free Energy of Solid Lithi...

INVALID DOIs

- None

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.08 s (2218.5 files/s, 130276.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          53            771           1399           4417
YAML                            73             44             95           1414
Markdown                         3            101              0            440
reStructuredText                19            279            557            430
TeX                              1             13              0            203
Bourne Shell                    29             89            159            100
DOS Batch                        1              8              1             26
make                             1              5              7             12
-------------------------------------------------------------------------------
SUM:                           180           1310           2218           7042
-------------------------------------------------------------------------------

Commit count by author:

   150  mkphuthi
     6  emilannevelink
     3  Keith Phuthi

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 2071

✅ The paper includes a Statement of need section

[editorialbot]

License info:

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

[editorialbot]

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

[editorialbot]

Five most similar historical JOSS papers:

strucscan: A lightweight Python-based framework for high-throughput material simulation Submitting author: @thohamm Handling editor: @ppxasjsm (Active) Reviewers: @mturiansky, @wcwitt Similarity score: 0.7614

Simmate: a framework for materials science Submitting author: @jacksund Handling editor: @rkurchin (Active) Reviewers: @bocklund, @utf Similarity score: 0.7469

excitingtools: An exciting Workflow Tool Submitting author: @AlexBuccheri Handling editor: @richardjgowers (Active) Reviewers: @fjmartinmartinez, @hmacdope Similarity score: 0.7426

FHI-vibes: Ab Initio Vibrational Simulations Submitting author: @flokno Handling editor: @jgostick (Active) Reviewers: @keipertk, @ajjackson Similarity score: 0.7332

matscipy: materials science at the atomic scale with Python Submitting author: @pastewka Handling editor: @diehlpk (Active) Reviewers: @rashatwi, @mbarzegary, @mastricker Similarity score: 0.7277

⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before considering asking the reviewers of these papers to review again for JOSS.

[danielskatz]

👋 @mkphuthi - thanks for your submission.

Can you please add the countries to the author affiliations?

Also, JOSS papers are requested to be around 1000 words at most, and this is 2000, so you will have to reduce the content somewhat. Sometimes, there are parts of the paper that either duplicate documentation in the repo, or that could move into documentation in the repo (in this case, perhaps one or both of the examples).

Finally, you need to add a references header at the end of the .md file, so that when the references are added to the PDF, they have a header in front of them.

After you make changes in your .md file, you can then use the command @editorialbot generate pdf to make a new PDF and recount the word length. editorialbot commands need to be the first entry in a new comment.

[mkphuthi]

@editorialbot generate pdf

[editorialbot]

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

[editorialbot]

Five most similar historical JOSS papers:

excitingtools: An exciting Workflow Tool Submitting author: @AlexBuccheri Handling editor: @richardjgowers (Active) Reviewers: @fjmartinmartinez, @hmacdope Similarity score: 0.8011

Atomic Simulation Interface (ASI): application programming interface for electronic structure codes Submitting author: @PavelStishenko Handling editor: @rkurchin (Active) Reviewers: @xwang862, @junghans, @srmnitc Similarity score: 0.7607

ShakeNBreak: Navigating the defect configurational landscape Submitting author: @ireaml Handling editor: @rkurchin (Active) Reviewers: @obaica, @mkhorton Similarity score: 0.7524

Surfaxe: Systematic surface calculations Submitting author: @brlec Handling editor: @danielskatz (Active) Reviewers: @pzarabadip, @eihernan Similarity score: 0.7474

GIMS: Graphical Interface for Materials Simulations Submitting author: @kokookster Handling editor: @jgostick (Active) Reviewers: @marshallmcdonnell, @jgostick Similarity score: 0.7443

⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before considering asking the reviewers of these papers to review again for JOSS.

[mkphuthi]

Potential reviewers based on my search from the JOSS list are given below. I have no strong preferences.

yw-fang ericfell RMeli ml-evs jfaraudo

[danielskatz]

@editorialbot check repository

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.08 s (2229.5 files/s, 130055.2 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          53            771           1399           4417
YAML                            73             44             95           1414
reStructuredText                19            279            557            430
Markdown                         3             86              0            385
TeX                              1             13              0            203
Bourne Shell                    29             89            159            100
DOS Batch                        1              8              1             26
make                             1              5              7             12
-------------------------------------------------------------------------------
SUM:                           180           1295           2218           6987
-------------------------------------------------------------------------------

Commit count by author:

   152  mkphuthi
     6  emilannevelink
     3  Keith Phuthi

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 1690

✅ The paper includes a Statement of need section

[editorialbot]

License info:

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

[danielskatz]

thanks @mkphuthi - we're just having a short discussion about which JOSS track this best fits in, then we'll start the process

[danielskatz]

👋 @mkphuthi - we've moved this, as you can see, and you should hear from the new track editor next

[Kevin-Mattheus-Moerman]

@editorialbot invite @HaoZeke as editor

[editorialbot]

Invitation to edit this submission sent!

[HaoZeke]

@editorialbot assign @HaoZeke as editor

Thanks for the invite @Kevin-Mattheus-Moerman, I'm happy to accept

@mkphuthi thanks for the suggestions, I will start sending out invitations by the end of this week.

[editorialbot]

Assigned! @HaoZeke is now the editor

[HaoZeke]

hi @utf @Andrew-S-Rosen @janosh 👋 would you be interested in and available to review this JOSS submission? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: joss.readthedocs.io/en/latest/review_criteria.html

If not, could you recommend any potential reviewers? I was hoping to have your insights because of your work on atomate and jobflow.

[HaoZeke]

hi @askhl 👋 would you be interested in and available to review this JOSS submission? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: joss.readthedocs.io/en/latest/review_criteria.html

If not, could you recommend any potential reviewers? I was hoping to have your insights because of your work on ASE and ASE workflows...

[HaoZeke]

hi @PavelStishenko @thohamm 👋 would you be interested in and available to review this JOSS submission? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: joss.readthedocs.io/en/latest/review_criteria.html

If not, could you recommend any potential reviewers? I was hoping to have your insights because of your work on ASI woskflows and strucscan..

[Andrew-S-Rosen]

@HaoZeke: Thank you for reaching out. Unfortunately, I will have to decline, as I have too much of a conflict of interest due to https://github.com/Quantum-Accelerators/quacc.

[janosh]

I also have to decline due to CoI.

[thohamm]

I'm sorry but I have to decline due to time constraints.

[HaoZeke]

Hi @imtambovtcev 👋 would you be interested in and available to review this JOSS submission? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: joss.readthedocs.io/en/latest/review_criteria.html

[askhl]

Hi Rohit,

I'm very sorry, but there is no way I will have time to review.

Best regards Ask

Am Di., 9. Juli 2024 um 19:54 Uhr schrieb Rohit Goswami < @.***>:

hi @askhl https://github.com/askhl 👋 would you be interested in and available to review this JOSS submission? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: joss.readthedocs.io/en/latest/review_criteria.html

If not, could you recommend any potential reviewers? I was hoping to have your insights because of your work on ASE and ASE workflows...

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/6929#issuecomment-2218321618, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAMVG2J5GREUBCANW6WXCKLZLQPUJAVCNFSM6AAAAABJ4RLA2KVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEMJYGMZDCNRRHA . You are receiving this because you were mentioned.Message ID: @.***>

[abhishektiwari]

@HaoZeke I will be open to review this submission. Feel free to tag me as additional reviewer.

[HaoZeke]

@editorialbot add @abhishektiwari as reviewer

@abhishektiwari thanks for volunteering :)

[editorialbot]

@abhishektiwari added to the reviewers list!

[imtambovtcev]

@HaoZeke, I just came from vacation and am ready to review

[HaoZeke]

@editorialbot add @imtambovtcev as reviewer

@imtambovtcev thanks stepping up :)

[editorialbot]

@imtambovtcev added to the reviewers list!

[HaoZeke]

@editorialbot start review

[editorialbot]

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/7085.