[REVIEW]: HylleraasMD: Massively parallel hybrid particle-field molecular dynamics in python

[whedon]

Submitting author: @mortele (Morten Ledum)
Repository: https://github.com/Cascella-Group-UiO/HyMD
Branch with paper.md (empty if default branch):
Version: v1.0.9
Editor: @rkurchin
Reviewers: @blakeaw, @yhtang, @abb58
Archive: 10.5281/zenodo.7839898

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General checks

• Repository: Is the source code for this software available at the repository url?
• 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 (@mortele) 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

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). #5308
• 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 and who the target audience is?
• 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?

[whedon]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @blakeaw, @yhtang it looks like you're currently assigned to review this paper 🎉.

⚠️ JOSS reduced service mode ⚠️

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

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If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/joss-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿

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@whedon commands

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

@whedon generate pdf

[whedon]

Wordcount for paper.md is 1103

[whedon]

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

OK DOIs

- 10.1016/j.cpc.2014.01.018 is OK
- 10.5281/zenodo.1051254 is OK
- 10.1137/120885887 is OK
- 10.1021/ct900457z is OK
- 10.1021/ct800122x is OK
- 10.1063/5.0020733 is OK
- 10.1002/jcc.23365 is OK
- 10.1002/jcc.22883 is OK
- 10.1021/acs.jctc.7b01160 is OK
- 10.1002/anie.202004522 is OK
- 10.26434/chemrxiv.6264644.v1 is OK
- 10.1080/00268976.2020.1785571 is OK
- 10.26434/chemrxiv.7398719 is OK
- 10.1016/j.bbagen.2020.129570 is OK
- 10.1063/5.0007445 is OK
- 10.1021/acs.jctc.5b00485 is OK
- 10.26434/chemrxiv.12388772.v1 is OK
- 10.1088/1361-648X/abef25 is OK
- 10.1021/acs.jctc.0c00954 is OK
- 10.1063/1.881812 is OK
- 10.1063/1.3142103 is OK
- 10.1088/1478-3975/10/4/045007 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.46 s (174.4 files/s, 36350.8 lines/s)
--------------------------------------------------------------------------------
Language                      files          blank        comment           code
--------------------------------------------------------------------------------
Python                           35           1581           2641           7857
Fortran 90                       11            216            239            791
reStructuredText                 15            618            856            729
TeX                               2             30              0            335
YAML                              4              9              1            139
Markdown                          2             36              0            128
Bourne Again Shell                1              9              2             80
CSS                               1             19              0             72
make                              2             15              7             57
Bourne Shell                      3             28             47             48
DOS Batch                         1              8              1             26
HTML                              1              3              0             24
Dockerfile                        1              5              2             17
TOML                              1              0              0              2
--------------------------------------------------------------------------------
SUM:                             80           2577           3796          10305
--------------------------------------------------------------------------------


Statistical information for the repository 'cd260c8f9501c121e7084c81' was
gathered on 2022/02/10.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Manuel Carrer                   78          6610           2959           33.79
Morten Ledum                   182         11012           4039           53.14
Sigbjørn Bore                   29           806            644            5.12
Yu Feng                          5           119             55            0.61
sigbjorn.loland.bore             3           519             63            2.05
xinmeng2020                     18          1135            362            5.29

Below are the number of rows from each author that have survived and are still
intact in the current revision:

Author                     Rows      Stability          Age       % in comments
Manuel Carrer              4440           67.2          6.2               13.02
Morten Ledum               7409           67.3          9.1                4.27
Sigbjørn Bore                93           11.5         18.2               21.51
sigbjorn.loland.bore         22            4.2          6.7                9.09
xinmeng2020                 112            9.9          9.7                0.00

[whedon]

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

[yhtang]

I found another article on ChemRxiv titled HylleraasMD: A Domain Decomposition-Based Hybrid Particle-Field Software for Multi-Scale Simulations of Soft Matter from the same group of authors.

It seems that both papers focus on the HylleraasMD software and the ChenRxiv one is more elaborated. Is it meant for a more traditional platform?

Could the authors (@mortele) please clarify this, especially if the ChemRxiv version is still under review somewhere?

[mortele]

Hi @yhtang. The ChemRxiv manuscript is one we prepared simultaneously with the submitted JOSS manuscript describing the application of the Hamiltoninan hPF scheme on realistic soft matter chemical assemblies. The focus in the ChemRxiv paper, which is currently under J. Chem. Theory Comput. peer review, is the development of the algorithms and the parallelization decomposition used in general for the filtered hPF approach. Whereas this JOSS paper pertains to the actual implementation and development of the code and the tutorial, user guide, etc.

We prepared two manuscripts in accord with what we think is accepted practice for JOSS according to the author guidelines; one describing the application of the software on numerous bio/soft-matter systems, and one describing the software itself.

We notified the editor-in-chief about the other manuscript and how it was (then newly) submitted (now under review) to JCTC when we submitted this manuscript to JOSS in the short cover letter. I believe the cover letter should be available somewhere as part of the open review process, but I am not sure where to find it.

[yhtang]

@mortele Thanks for the clarification! That's very helpful.

[yhtang]

I noticed that the automated test coverage is around 50%. Should this be considered something that needs improvement? @rkurchin @blakeaw

[yhtang]

I am now stuck at the functionality and performance check due to a difficulty in installing h5py in Fedora as already documented in Cascella-Group-UiO/HyMD#157. I will resume as soon as a workaround has been found.

ValueError: h5py was built without MPI support, can't use mpio driver

[blakeaw]

Hi @yhtang, it looks like core functionality and things important for accuracy such as energy/force evaluation and integration are covered in the automated tests, so I think the ~50% automated test coverage is probably acceptable.

[rkurchin]

I would agree with @blakeaw's perspective – JOSS doesn't include specific coverage requirements for this reason. That being said, @yhtang, if you see lack of coverage in areas crucial to functionality, that could certainly be an argument for suggesting additional tests!

[blakeaw]

Ran into a problem/errors when running automated tests: Cascella-Group-UiO/HyMD#160

[mortele]

Hi @yhtang and @blakeaw. I apologize for the slow response from our end on the issues opened so far. With the slight delay after being waitlisted in the JOSS system, this review ended up coinciding with the last 10 days of my PhD contract. As such I am incredibly busy and need to have my focus mostly elsewhere for a little while. I will try to offload the review-response work as much as possible on the other members of my team, but unfortunately, I need to ask for some patience from you guys as the response time will probably still be long.

I apologize again for the inconvenience and hope you understand.

[yhtang]

@mortele Totally understand. Good luck on your defense!

[rkurchin]

Absolutely – take your time, and congratulations on finishing up!

[blakeaw]

No problem, @mortele. Good luck!

[rkurchin]

Oh, great, thanks!

[rkurchin]

@editorialbot set 1.0.9 as version

[editorialbot]

Done! version is now 1.0.9

[rkurchin]

@editorialbot set 10.5281/zenodo.7839898 as archive

[editorialbot]

Done! Archive is now 10.5281/zenodo.7839898

[rkurchin]

@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

- 10.1016/j.cpc.2014.01.018 is OK
- 10.5281/zenodo.1051254 is OK
- 10.1137/120885887 is OK
- 10.1021/ct900457z is OK
- 10.1021/ct800122x is OK
- 10.1063/5.0020733 is OK
- 10.1002/jcc.23365 is OK
- 10.1002/jcc.22883 is OK
- 10.1021/acs.jctc.7b01160 is OK
- 10.1002/anie.202004522 is OK
- 10.26434/chemrxiv.6264644.v1 is OK
- 10.1080/00268976.2020.1785571 is OK
- 10.26434/chemrxiv.7398719 is OK
- 10.1016/j.bbagen.2020.129570 is OK
- 10.1063/5.0007445 is OK
- 10.1021/acs.jctc.5b00485 is OK
- 10.26434/chemrxiv.12388772.v1 is OK
- 10.1088/1361-648X/abef25 is OK
- 10.1021/acs.jctc.0c00954 is OK
- 10.1063/1.881812 is OK
- 10.1063/1.3142103 is OK
- 10.1088/1478-3975/10/4/045007 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

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

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#4140, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[Kevin-Mattheus-Moerman]

@editorialbot set v1.0.9 as version

[editorialbot]

Done! version is now v1.0.9

[Kevin-Mattheus-Moerman]

@mortele I am the AEiC for this track and here to help process final steps. I have checked the archive and the paper and have the below minor comments that require your attention:

On the archive:

• Please manually edit the ZENODO archive title to match the JOSS paper title.

On the paper:

• One affiliation says United States, this is fine. However, most JOSS papers seem to feature: United States of America, so perhaps consider conforming to this too.
• Check if backend should be written instead as back-end

[mortele]

@mortele I am the AEiC for this track and here to help process final steps. I have checked the archive and the paper and have the below minor comments that require your attention:

On the archive:

• Please manually edit the ZENODO archive title to match the JOSS paper title.

On the paper:

• One affiliation says United States, this is fine. However, most JOSS papers seem to feature: United States of America, so perhaps consider conforming to this too.
• Check if backend should be written instead as back-end

Hi @Kevin-Mattheus-Moerman, I have changed the Zenodo archive title to match the paper title and added of America to Sigbjørn's affiliation in the archive and in the paper.

As for the last point, I think that back end and backend are acceptable forms when used as a noun, with back-end reserved for usage as a compound adjective. However, I have absolutely no strong feelings about this and would not mind at all changing it if anyone with a stronger background in the English language disagrees.

[mortele]

@editorialbot generate pdf

[editorialbot]

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

[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: Ledum
  given-names: Morten
  orcid: "https://orcid.org/0000-0003-4244-4876"
- family-names: Carrer
  given-names: Manuel
  orcid: "https://orcid.org/0000-0002-8777-4310"
- family-names: Sen
  given-names: Samiran
  orcid: "https://orcid.org/0000-0002-1922-7796"
- family-names: Li
  given-names: Xinmeng
  orcid: "https://orcid.org/0000-0002-6863-6078"
- family-names: Cascella
  given-names: Michele
  orcid: "https://orcid.org/0000-0003-2266-5399"
- family-names: Bore
  given-names: Sigbjørn Løland
  orcid: "https://orcid.org/0000-0002-8620-4885"
contact:
- family-names: Ledum
  given-names: Morten
  orcid: "https://orcid.org/0000-0003-4244-4876"
doi: 10.5281/zenodo.7839898
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Ledum
    given-names: Morten
    orcid: "https://orcid.org/0000-0003-4244-4876"
  - family-names: Carrer
    given-names: Manuel
    orcid: "https://orcid.org/0000-0002-8777-4310"
  - family-names: Sen
    given-names: Samiran
    orcid: "https://orcid.org/0000-0002-1922-7796"
  - family-names: Li
    given-names: Xinmeng
    orcid: "https://orcid.org/0000-0002-6863-6078"
  - family-names: Cascella
    given-names: Michele
    orcid: "https://orcid.org/0000-0003-2266-5399"
  - family-names: Bore
    given-names: Sigbjørn Løland
    orcid: "https://orcid.org/0000-0002-8620-4885"
  date-published: 2023-04-22
  doi: 10.21105/joss.04149
  issn: 2475-9066
  issue: 84
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 4149
  title: "HylleraasMD: Massively parallel hybrid particle-field
    molecular dynamics in Python"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.04149"
  volume: 8
title: "HylleraasMD: Massively parallel hybrid particle-field molecular
  dynamics in Python"

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]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[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 👉 Creating pull request for 10.21105.joss.04149 joss-papers#4167
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.04149
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]

@mortele congratulations on this publication in JOSS!

@rkurchin thanks for editing!

And a special thanks to the reviewers: @blakeaw, @yhtang, @abb58

[editorialbot]

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

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

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[![DOI](https://joss.theoj.org/papers/10.21105/joss.04149/status.svg)](https://doi.org/10.21105/joss.04149)

HTML:
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  <img src="https://joss.theoj.org/papers/10.21105/joss.04149/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.04149/status.svg
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This is how it will look in your documentation:

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