[REVIEW]: Mold: a LAMMPS package to compute interfacial free energies and nucleation rates

[editorialbot]

Submitting author: !--author-handle-->@AndresRTejedor<!--end-author-handle-- (Andrés R. Tejedor) Repository: https://github.com/AndresRTejedor/Mold Branch with paper.md (empty if default branch): joss Version: v1.0.0 Editor: !--editor-->@lucydot<!--end-editor-- Reviewers: @mattwthompson, @marjanalbooyeh Archive: 10.5281/zenodo.10843863

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/f9584c967fb2437c95819d590e4bf3d7"><img src="https://joss.theoj.org/papers/f9584c967fb2437c95819d590e4bf3d7/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/f9584c967fb2437c95819d590e4bf3d7/status.svg)](https://joss.theoj.org/papers/f9584c967fb2437c95819d590e4bf3d7)

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

@mattwthompson & @marjanAlbouye, 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 @lucydot 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 @marjanAlbouye

📝 Checklist for @mattwthompson

[AndresRTejedor]

Thanks @lucydot - I have checked the title and author list and now it matches those in the JOSS paper. Please let me know if you need anything else.

[lucydot]

Great!

[lucydot]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

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

OK DOIs

- 10.1063/1.4896621 is OK
- 10.1063/5.0139699 is OK
- 10.1039/C4CP03948C is OK
- 10.1063/1.5018303 is OK
- 10.1039/C1CP22167A is OK
- 10.1016/j.bpj.2023.03.006 is OK
- 10.1063/1.1747248 is OK
- 10.1038/s41598-021-94309-y is OK
- 10.1039/C6FD00141F is OK
- 10.1016/j.softx.2015.06.001 is OK
- 10.1063/1.3578182 is OK
- 10.1016/j.cossms.2011.07.003 is OK
- 10.1063/1.3153843 is OK
- 10.1080/00268978300100971 is OK
- 10.1039/D1CP01784E is OK
- 10.1103/PhysRevLett.130.118001 is OK
- 10.1063/1.4921185 is OK
- 10.1021/acs.jpcc.5b11221 is OK
- 10.1021/ie50510a027 is OK
- 10.1016/j.actamat.2008.10.020 is OK
- 10.1063/5.0101746 is OK
- 10.1016/j.jcis.2022.05.029 is OK
- 10.1063/5.0101383 is OK
- 10.1063/1.5098551 is OK
- 10.1073/pnas.1917569117 is OK
- 10.1016/j.bpj.2021.01.031 is OK
- 10.3390/biom11020278 is OK
- 10.1063/5.0101529 is OK
- 10.1063/1.1563248 is OK
- 10.1016/j.cpc.2021.108171 is OK
- 10.1063/1.445633 is OK
- 10.1063/5.0028219 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

:wave: @openjournals/bcm-eics, this paper is ready to be accepted and published.

Check final proof :point_right::page_facing_up: Download article

If the paper PDF and the deposit XML files look good in https://github.com/openjournals/joss-papers/pull/5160, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[Kevin-Mattheus-Moerman]

@AndresRTejedor as AEiC for JOSS I will now help to process this submission for acceptance in JOSS. I have checked this review, your repository, the archive link, and the paper. Most seems in order, however the below are some points that require your attention:

• [x] Please manually edit the archive listed license to match your software license (it currently says Creative Commons Attribution 4.0 International).
• [x] Check minor typo: perfomed -> performed

[AndresRTejedor]

@Kevin-Mattheus-Moerman thank you for your help. I have corrected the typo, but I don't find the Creative Commons Attribution 4.0 International line you mention. Where can I find it? What should I exactly put instead?

@AndresRTejedor as AEiC for JOSS I will now help to process this submission for acceptance in JOSS. I have checked this review, your repository, the archive link, and the paper. Most seems in order, however the below are some points that require your attention:

• [x] Please manually edit the archive listed license to match your software license (it currently says Creative Commons Attribution 4.0 International).
• [x] Check minor typo: perfomed -> performed

[AndresRTejedor]

@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:

[Kevin-Mattheus-Moerman]

@AndresRTejedor I have not done this myself in a while but I think if you manually edit the archive there is a field called "Rights" or "License" (I can check for you tomorrow if you're still stuck). Instead of the CC-BY license it should list your actual open source software license. Hope this helps.

[AndresRTejedor]

@Kevin-Mattheus-Moerman you mean in the Zenodo release?

[Kevin-Mattheus-Moerman]

@AndresRTejedor Yes this is for the ZENODO archive. I highlighted where the license is listed here in red:

Here is an animation (for some reason my cursor was not captured) of me editing one of my project entries, you go to edit then to license, then delete the CC-BY license and select your software license.

[AndresRTejedor]

@Kevin-Mattheus-Moerman many thanks for your help. I have already changed the license in the Zenodo release. Let me know if you need any further information.

[Kevin-Mattheus-Moerman]

@AndresRTejedor okay, thanks. In that case I think all looks good now.

[Kevin-Mattheus-Moerman]

@editorialbot accept

[editorialbot]

Doing it live! Attempting automated processing of paper acceptance...

[editorialbot]

Ensure proper citation by uploading a plain text CITATION.cff file to the default branch of your repository.

If using GitHub, a Cite this repository menu will appear in the About section, containing both APA and BibTeX formats. When exported to Zotero using a browser plugin, Zotero will automatically create an entry using the information contained in the .cff file.

You can copy the contents for your CITATION.cff file here:

CITATION.cff

``` cff-version: "1.2.0" authors: - family-names: Tejedor given-names: Andres R. orcid: "https://orcid.org/0000-0002-9437-6169" - family-names: Sanchez-Burgos given-names: Ignacio orcid: "https://orcid.org/0000-0002-1160-3945" - family-names: Sanz given-names: Eduardo orcid: "https://orcid.org/0000-0001-6474-5835" - family-names: Vega given-names: Carlos orcid: "https://orcid.org/0000-0002-2417-9645" - family-names: Blas given-names: Felipe J. orcid: "https://orcid.org/0000-0001-9030-040X" - family-names: Davidchack given-names: Ruslan L. orcid: "https://orcid.org/0000-0001-9418-5322" - family-names: Pasquale given-names: Nicodemo Di orcid: "https://orcid.org/0000-0001-5676-8527" - family-names: Ramirez given-names: Jorge orcid: "https://orcid.org/0000-0002-8946-3786" - family-names: Espinosa given-names: Jorge R. orcid: "https://orcid.org/0000-0001-9530-2658" contact: - family-names: Ramirez given-names: Jorge orcid: "https://orcid.org/0000-0002-8946-3786" - family-names: Espinosa given-names: Jorge R. orcid: "https://orcid.org/0000-0001-9530-2658" doi: 10.5281/zenodo.10843863 message: If you use this software, please cite our article in the Journal of Open Source Software. preferred-citation: authors: - family-names: Tejedor given-names: Andres R. orcid: "https://orcid.org/0000-0002-9437-6169" - family-names: Sanchez-Burgos given-names: Ignacio orcid: "https://orcid.org/0000-0002-1160-3945" - family-names: Sanz given-names: Eduardo orcid: "https://orcid.org/0000-0001-6474-5835" - family-names: Vega given-names: Carlos orcid: "https://orcid.org/0000-0002-2417-9645" - family-names: Blas given-names: Felipe J. orcid: "https://orcid.org/0000-0001-9030-040X" - family-names: Davidchack given-names: Ruslan L. orcid: "https://orcid.org/0000-0001-9418-5322" - family-names: Pasquale given-names: Nicodemo Di orcid: "https://orcid.org/0000-0001-5676-8527" - family-names: Ramirez given-names: Jorge orcid: "https://orcid.org/0000-0002-8946-3786" - family-names: Espinosa given-names: Jorge R. orcid: "https://orcid.org/0000-0001-9530-2658" date-published: 2024-03-26 doi: 10.21105/joss.06083 issn: 2475-9066 issue: 95 journal: Journal of Open Source Software publisher: name: Open Journals start: 6083 title: "Mold: a LAMMPS package to compute interfacial free energies and nucleation rates" type: article url: "https://joss.theoj.org/papers/10.21105/joss.06083" volume: 9 title: "Mold: a LAMMPS package to compute interfacial free energies and nucleation rates" ```

If the repository is not hosted on GitHub, a .cff file can still be uploaded to set your preferred citation. Users will be able to manually copy and paste the citation.

Find more information on .cff files here and here.

[editorialbot]

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

[editorialbot]

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

0. Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/joss-papers/pull/5179
1. Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.06083
2. If everything looks good, then close this review issue.
3. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

[Kevin-Mattheus-Moerman]

@AndresRTejedor congratulations on this JOSS publication!

@lucydot thanks for editing! And a special thank you to the reviewers: @mattwthompson, @marjanAlbouye !!!

[editorialbot]

:tada::tada::tada: Congratulations on your paper acceptance! :tada::tada::tada:

If you would like to include a link to your paper from your README use the following code snippets:

Markdown:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.06083/status.svg)](https://doi.org/10.21105/joss.06083)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.06083">
  <img src="https://joss.theoj.org/papers/10.21105/joss.06083/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.06083/status.svg
   :target: https://doi.org/10.21105/joss.06083

This is how it will look in your documentation:

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[Kevin-Mattheus-Moerman]

@editorialbot remove @marjanAlbouye as reviewer

[editorialbot]

@marjanAlbouye is not in the reviewers list

[Kevin-Mattheus-Moerman]

@editorialbot add @marjanalbooyeh as reviewer

[editorialbot]

@marjanalbooyeh is already included in the reviewers list

[Kevin-Mattheus-Moerman]

@editorialbot re-accept

[editorialbot]

I'm sorry human, I don't understand that. You can see what commands I support by typing:

@editorialbot commands

[Kevin-Mattheus-Moerman]

@editorialbot reaccept

[editorialbot]

Rebuilding paper!

[Kevin-Mattheus-Moerman]

@lucydot @marjanalbooyeh there was something wrong with your reviewer name (the one listed was not a GitHub handle), so I updated it now and the paper should now update so you are properly listed as a reviewer.

[editorialbot]

🌈 Paper updated!

New PDF and metadata files :point_right: https://github.com/openjournals/joss-papers/pull/5180