[PRE 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 Version: v1.0.3 Editor: @rkurchin Reviewers: @blakeaw, @yhtang Managing EiC: Daniel S. Katz

:warning: JOSS reduced service mode :warning:

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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Author instructions

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

@mortele if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). In addition, this list of people have already agreed to review for JOSS and may be suitable for this submission (please start at the bottom of the list).

Editor instructions

The JOSS submission bot @whedon is here to help you find and assign reviewers and start the main review. To find out what @whedon can do for you type:

@whedon commands

[whedon]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks.

:warning: JOSS reduced service mode :warning:

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.

For a list of things I can do to help you, just type:

@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 1101

[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=0.14 s (567.7 files/s, 117723.8 lines/s)
--------------------------------------------------------------------------------
Language                      files          blank        comment           code
--------------------------------------------------------------------------------
Python                           35           1570           2627           7794
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           2566           3782          10242
--------------------------------------------------------------------------------

Statistical information for the repository '5356999f10528877cc620d1f' was
gathered on 2022/01/08.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Manuel Carrer                   77          6609           2953           33.89
Morten Ledum                   179         10915           4035           52.99
Sigbjørn Bore                   29           806            644            5.14
Yu Feng                          5           119             55            0.62
sigbjorn.loland.bore             3           519             63            2.06
xinmeng2020                     18          1135            362            5.31

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          5.3               13.02
Morten Ledum               7321           67.1          8.3                4.32
Sigbjørn Bore                93           11.5         17.4               21.51
sigbjorn.loland.bore         22            4.2          6.4                9.09
xinmeng2020                 112            9.9          8.8                0.00

[whedon]

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

[danielskatz]

@mortele - please change "python" in your paper's title and text to "Python"

[mortele]

Will do @danielskatz

[danielskatz]

👋 @jgostick - would you be able to edit this submission for JOSS?

[danielskatz]

@whedon invite @jgostick as editor

[whedon]

@jgostick has been invited to edit this submission.

[jgostick]

Hi @danielskatz, I am really sorry, but I have pledged to avoid editoring all MD simulations after what happened last time. I had a 'challenging' review and was unable to mediate the situation because I was not familiar enough with MD code and simulations.

[mortele]

@whedon generate pdf

[whedon]

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

[danielskatz]

👋 @mortele - I'm going to put your paper on our waiting list - we have three potential editors for it, but all are currently unavailable due to other assignments, so when one of those is completed, this will be able to start.

[mortele]

Thank you for the update @danielskatz 🙏

[arfon]

@whedon invite @rkurchin as editor

:wave: @rkurchin – would you be able to edit this submission for JOSS?

[whedon]

@rkurchin has been invited to edit this submission.

[rkurchin]

@whedon add me as editor

[whedon]

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

@whedon commands

[rkurchin]

@whedon assign @rkurchin as editor

[whedon]

OK, the editor is @rkurchin

[rkurchin]

👋 @blakeaw and @govarguz, would you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

[blakeaw]

Hi @rkurchin, sure. I can review it.

[rkurchin]

@whedon add @blakeaw as reviewer

[whedon]

OK, @blakeaw is now a reviewer

[rkurchin]

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

[rkurchin]

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

[yhtang]

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

@rkurchin Happy to help!

[rkurchin]

@whedon add @yhtang as reviewer

[whedon]

OK, @yhtang is now a reviewer

[rkurchin]

@whedon start review

[whedon]

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/4149.