[PRE REVIEW]: OpenMD: A parallel molecular dynamics engine for complex systems and interfaces

[editorialbot]

Submitting author: @gezelter (J. Daniel Gezelter)
Repository: https://github.com/OpenMD/OpenMD/
Branch with paper.md (empty if default branch):
Version: v3.1
Editor: @srmnitc
Reviewers: @samwaseda, @blackspur
Managing EiC: Kevin M. Moerman

Status

Status badge code:

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[editorialbot]

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

OK DOIs

- 10.1063/1.439486 is OK
- 10.1145/235815.235821 is OK
- 10.1103/PhysRevB.99.094106 is OK
- 10.1103/PhysRevB.29.6443 is OK
- 10.1021/acs.jctc.4c00182 is OK
- 10.1145/174462.156635 is OK
- 10.1103/physreva.34.2499 is OK
- 10.1007/BF00977785 is OK
- 10.1063/1.473271 is OK
- 10.1021/ja01299a050 is OK
- 10.1021/j100161a070 is OK
- 10.1063/1.468398 is OK
- 10.1063/1.480502 is OK
- 10.1021/ct100670m is OK
- 10.1063/1.478738 is OK
- 10.1021/jp025949h is OK
- 10.1063/1.2206581 is OK
- 10.1063/1.4896627 is OK
- 10.1063/1.4896628 is OK
- 10.1063/1.4960957 is OK
- 10.1002/jcc.20161 is OK
- 10.1080/00268976.2012.680512 is OK
- 10.1103/PhysRevE.59.4894 is OK
- 10.1063/1.3276454 is OK
- 10.1063/1.3499947 is OK
- 10.1021/ct500221u is OK
- 10.1038/sdata.2016.18 is OK

MISSING DOIs

- No DOI given, and none found for title: Sur la sphère vide: A la mémoire de Georges Vorono...
- No DOI given, and none found for title: Point multipoles in the Ewald summation
- No DOI given, and none found for title: Point multipoles in the Ewald summation (revisited...

INVALID DOIs

- None

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.78 s (1361.8 files/s, 283430.9 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
C++                            448          19096          27991          94418
C/C++ Header                   561           9094          31941          31555
CMake                           14            207            281           1667
Python                           9            225            154           1011
Markdown                        21            317              0            911
ANTLR Grammar                    2            143             52            799
TeX                              1              0              0            327
Perl                             1             63            105            239
YAML                             3             23             21            103
Bourne Shell                     1             12             20             48
-------------------------------------------------------------------------------
SUM:                          1061          29180          60565         131078
-------------------------------------------------------------------------------

Commit count by author:

  1566	Dan Gezelter
   426	Teng Lin
   316	Charles Vardeman
   199	Christopher Fennell
   171	Patrick Louden
    61	Hematna Bhattarai
    57	crdrisko
    33	Cody Drisko
    27	Xiuquan Sun
    25	Joseph Michalka
    14	Hemanta-Bhattarai
    14	Shenyu Kuang
    12	Soren Holm
    11	Chunlei Li
    11	Kelsey Stocker
     9	Hemanta
     9	James Marr
     8	Sydney Shavalier
     7	Hemanta Bhattarai
     7	Kyle Daily
     6	Christie Puglis
     6	Cody R. Drisko
     6	sshavali
     5	Anderson
     4	Hythem Sidky
     4	Martin Vala
     3	123manudai
     3	OpenMD
     3	Patrick-Louden
     3	adasilv3
     2	C.R. Drisko
     2	Kenneth Fletcher
     2	gezelter
     1	Alexander Joseph Mazanek
     1	Alexander Mazanek
     1	Anderson Da Silva Duraes
     1	Benjamin Harless
     1	Cody Ryan Drisko
     1	Gianluca Puliti
     1	Julien Nabet
     1	Madan Lamichhane
     1	Minh Nhat Pham

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 2781

✅ The paper includes a Statement of need section

[editorialbot]

License info:

✅ License found: BSD 3-Clause "New" or "Revised" License (Valid open source OSI approved license)

[editorialbot]

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

[editorialbot]

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⚠️ 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.

[Kevin-Mattheus-Moerman]

@gezelter, thanks for this submission. I am the AEiC on this track and here to help process the initial steps. Before we proceed, please can you have a look at the following points:

• Please study the above reference check ☝️ and see if you can address any of the reported potential DOI issues. You can add/amend DOI entries in your .bib file, and call @editorialbot check references here to check them again. If the references truly do not have DOI's you may leave them.
• Your project appears to lack contributing guidelines at the moment. Please work to add these and to mention/link to them in your README. You could for instance create a CONTRIBUTING.md file (see here for some examples: https://contributing.md/example/).

[Kevin-Mattheus-Moerman]

@editorialbot invite @srmnitc as editor

[editorialbot]

Invitation to edit this submission sent!

[crdrisko]

Hello @Kevin-Mattheus-Moerman, we have verified that the three articles mentioned do not have DOI's associated with them. In lieu of this, we've included urls for these articles, but we can remove them if it goes against the journal's formatting. Also, our CONTRIBUTING.md is located in the .github directory, here.

[gezelter]

@crdrisko mentions the DOI issue - the three papers are from journals that ceased publishing prior to the DOI system. Two of the papers are in the Computational Collaboration Project No 5 (CCP5) information newsletter which does have a digital archive and the Delaunay paper was influential enough that it has been archived at MathNet.

[srmnitc]

@editorialbot assign me as editor

[editorialbot]

Assigned! @srmnitc is now the editor

[srmnitc]

@gezelter @crdrisko Thanks for this nice submission, I will be handling editor here. The next step would be to find some reviewers. If you have suggestions, please feel free to post their Github usernames without @, eg, srmnitc instead of @srmnitc. I will also take a look, and start finding some reviewers in the next few days. Meanwhile feel free to ask any questions that you might have.

[gezelter]

For reviewers: jpotoff and blackspur seem like good matches.

[srmnitc]

👋🏽 @samwaseda @jpotoff would any of you have time and be willing to review this submission for JOSS? As you might know, we carry out our checklist-driven reviews here in GitHub issues and follow these guidelines. Thanks for your time!

[samwaseda]

Yes I can do it

[srmnitc]

Yes I can do it

@samwaseda thanks! I will start a review issue once I find another reviewer.

[srmnitc]

@editorialbot add @samwaseda as reviewer

[editorialbot]

@samwaseda added to the reviewers list!

[srmnitc]

👋🏽 @blackspur would you have time and be willing to review this submission for JOSS? As you might know, we carry out our checklist-driven reviews here in GitHub issues and follow these guidelines. Thanks for your time!

[blackspur]

Yes I would be happy to review

[srmnitc]

@blackspur thanks a lot!

[srmnitc]

@editorialbot add @blackspur as reviewer

[editorialbot]

@blackspur added to the reviewers list!

[srmnitc]

@editorialbot start review

[editorialbot]

OK, I've started the review over in #7004.