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

editorialbot commented 3 months ago

Submitting author: !--author-handle-->@gezelter@srmnitc<!--end-editor-- Reviewers: @samwaseda, @blackspur Managing EiC: Kevin M. Moerman

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editorialbot commented 3 months ago

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editorialbot commented 3 months ago

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 commented 3 months ago

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 commented 3 months ago

Paper file info:

📄 Wordcount for paper.md is 2781

✅ The paper includes a Statement of need section

editorialbot commented 3 months ago

License info:

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

editorialbot commented 3 months ago

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

editorialbot commented 3 months ago

Five most similar historical JOSS papers:

PAPRECA: A parallel hybrid off-lattice kinetic Monte Carlo/molecular dynamics simulator Submitting author: @sntioudis Handling editor: @srmnitc (Active) Reviewers: @liamhuber, @jfaraudo Similarity score: 0.7450

HylleraasMD: Massively parallel hybrid particle-field molecular dynamics in Python Submitting author: @mortele Handling editor: @rkurchin (Active) Reviewers: @blakeaw, @yhtang, @abb58 Similarity score: 0.7350

MetalWalls: A classical molecular dynamics software dedicated to the simulation of electrochemical systems Submitting author: @salanne Handling editor: @richardjgowers (Active) Reviewers: @mattwthompson, @hmacdope Similarity score: 0.7138

polypy - Analysis Tools for Solid State Molecular Dynamics and Monte Carlo Trajectories Submitting author: @symmy596 Handling editor: @richardjgowers (Active) Reviewers: @hmacdope, @lscalfi Similarity score: 0.7103

PorousFlow: a multiphysics simulation code for coupled problems in porous media Submitting author: @WilkAndy Handling editor: @jedbrown (Active) Reviewers: @jbrezmorf, @rpodgorney Similarity score: 0.7100

⚠️ 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 commented 2 months ago

@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 :point_up: 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 commented 2 months ago

@editorialbot invite @srmnitc as editor

editorialbot commented 2 months ago

Invitation to edit this submission sent!

crdrisko commented 2 months ago

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 commented 2 months ago

@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.