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[PRE REVIEW]: HySoP: Hybrid Simulation with Particles #7483

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editorialbot opened this issue Nov 14, 2024 · 32 comments
Open

[PRE REVIEW]: HySoP: Hybrid Simulation with Particles #7483

editorialbot opened this issue Nov 14, 2024 · 32 comments
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Fortran Meson pre-review Python Track: 3 (PE) Physics and Engineering

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editorialbot commented Nov 14, 2024 •
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Submitting author: @jmetancelin (Jean-Matthieu Etancelin)
Repository: https://gricad-gitlab.univ-grenoble-alpes.fr/particle_methods/hysop
Branch with paper.md (empty if default branch): joss
Version: 2024.11
Editor: @ppxasjsm
Reviewers: Pending
Managing EiC: Daniel S. Katz

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/735fee5b21e2c53e8198a33a387aef21"><img src="https://joss.theoj.org/papers/735fee5b21e2c53e8198a33a387aef21/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/735fee5b21e2c53e8198a33a387aef21/status.svg)](https://joss.theoj.org/papers/735fee5b21e2c53e8198a33a387aef21)

Author instructions

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

@jmetancelin if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). You can search the list of people that have already agreed to review and may be suitable for this submission.

Editor instructions

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

@editorialbot commands
@editorialbot editorialbot added pre-review Track: 7 (CSISM) Computer science, Information Science, and Mathematics labels Nov 14, 2024
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Hello human, I'm @editorialbot, a robot that can help you with some common editorial tasks.

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

@editorialbot commands

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

@editorialbot generate pdf

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Software report:

github.com/AlDanial/cloc v 1.90  T=0.95 s (564.2 files/s, 189289.4 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                         397          19597          24897         110274
Fortran 90                      40           2967           6472          10521
Meson                           69            154            179           1245
Markdown                         4            216              0            506
Bourne Shell                    11             63            255            380
YAML                             5             52            189            377
TeX                              1              0              0            197
Dockerfile                       2             41             67            146
JSON                             1              1              0            123
C++                              2             26             86             44
TOML                             1              3              4             18
C/C++ Header                     1             10             21             14
-------------------------------------------------------------------------------
SUM:                           534          23130          32170         123845
-------------------------------------------------------------------------------

Commit count by author:

  1293	Jean-Baptiste Keck
   578	Jean-Matthieu Etancelin
   479	Franck Pérignon
   200	Keck Jean-Baptiste
   135	JM Etancelin
    79	Chloe Mimeau
    54	Nicolas Grima
    36	Eric Dalissier
    28	Jean-Baptiste Lagaert
    21	Jean-Baptiste Keck [email protected]
    19	GRIMA NICOLAS
    17	Chloé Mimeau
    16	Christophe Picard
    11	EXT Jean-Matthieu Etancelin
     8	Nicolas G
     7	mimeau
     6	Adrien Magni
     6	Nicolas Grm
     4	EXT GRIMA Nicolas
     4	Georges-Henri Cottet
     1	JME

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Paper file info:

📄 Wordcount for paper.md is 2887

✅ The paper includes a Statement of need section

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License info:

✅ License found: Apache License 2.0 (Valid open source OSI approved license)

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

✅ OK DOIs

- 10.1103/PhysRevFluids.6.L022301 is OK
- 10.1016/j.compfluid.2021.104946 is OK
- 10.3390/fluids6020068 is OK
- 10.1016/j.advwatres.2020.103780 is OK
- 10.1016/j.euromechflu.2017.03.002 is OK
- 10.1051/m2an/2014009 is OK
- 10.1016/j.compfluid.2016.06.020 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: MURPHY – A scalable multiresolution framework for ...
- No DOI given, and none found for title: Numerical modelling and High Performance Computing...
- No DOI given, and none found for title: Conception et mise en oeuvre de méthodes vortex hy...
- No DOI given, and none found for title: Couplage de modèles, algorithmes multi-échelles et...

❌ MISSING DOIs

- 10.1016/j.compfluid.2024.106287 may be a valid DOI for title: Large-Eddy Simulations with remeshed Vortex method...

❌ INVALID DOIs

- https://doi.org/10.1016/j.cpc.2019.03.007 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/j.jcp.2013.12.026 is INVALID because of 'https://doi.org/' prefix

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

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Five most similar historical JOSS papers:

RHEA: an open-source Reproducible Hybrid-architecture flow solver Engineered for Academia
Submitting author: @lluisjofre
Handling editor: @diehlpk (Active)
Reviewers: @ctdegroot, @thomasgillis
Similarity score: 0.7174

PyMPDATA v1: Numba-accelerated implementation of MPDATA with examples in Python, Julia and Matlab
Submitting author: @slayoo
Handling editor: @arfon (Active)
Reviewers: @Chiil, @wdeconinck
Similarity score: 0.7154

SiSyPHE: A Python package for the Simulation of Systems of interacting mean-field Particles with High Efficiency
Submitting author: @antoinediez
Handling editor: @pdebuyl (Active)
Reviewers: @lorenzo-rovigatti, @junghans
Similarity score: 0.7066

NebulaSEM: A high-order discontinuous Galerkin spectral element code for atmospheric modeling
Submitting author: @dshawul
Handling editor: @observingClouds (Active)
Reviewers: @capitalaslash, @esclapez
Similarity score: 0.7065

OpenCMP: An Open-Source Computational Multiphysics Package
Submitting author: @nasserma
Handling editor: @lucydot (Active)
Reviewers: @bonh, @WilkAndy
Similarity score: 0.7036

⚠️ 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.

@danielskatz
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@jmetancelin - thanks for your submission. However, note that JOSS submissions are expected to be 250-1000 words, roughly, and yours is about 3 times that long. Can you remove text, which could potentially be moved to the documentation or the repo, with the paper pointing to this for more detail? Alternatively, JOSS might not be the right journal for your submission if you want all of the details in the paper.

In addition, you could work on the possibly missing DOI and incorrectly formatted DOIs that editorialbot suggests, but note that some may be incorrect. Please feel free to make changes to your .bib file, then use the command @editorialbot check references to check again, and the command @editorialbot generate pdf when the references are right to make a new PDF. editorialbot commands need to be the first entry in a new comment.

You can also use @editorialbot check repository to check the paper length.

@editorialbot editorialbot added Track: 3 (PE) Physics and Engineering and removed Track: 7 (CSISM) Computer science, Information Science, and Mathematics labels Nov 14, 2024
@danielskatz
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Also, we've switched the track for this, so another track editor will continue working with you.

@kyleniemeyer
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Unfortunately @jmetancelin, we do not have any editors available to handle this right now, so I have to put this in our queue until someone frees up. Please do address @danielskatz's comments in the meantime. Thanks for your patience!

@kyleniemeyer kyleniemeyer added the waitlisted Submissions in the JOSS backlog due to reduced service mode. label Nov 18, 2024
@jmetancelin
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@editorialbot check references

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

✅ OK DOIs

- 10.1016/j.cpc.2019.03.007 is OK
- 10.48550/arXiv.2112.07537 is OK
- 10.1103/PhysRevFluids.6.L022301 is OK
- 10.1016/j.compfluid.2021.104946 is OK
- 10.3390/fluids6020068 is OK
- 10.1016/j.advwatres.2020.103780 is OK
- 10.1016/j.euromechflu.2017.03.002 is OK
- 10.1051/m2an/2014009 is OK
- 10.1016/j.compfluid.2016.06.020 is OK
- 10.1016/j.jcp.2013.12.026 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: Numerical modelling and High Performance Computing...
- No DOI given, and none found for title: Conception et mise en oeuvre de méthodes vortex hy...
- No DOI given, and none found for title: Couplage de modèles, algorithmes multi-échelles et...

❌ MISSING DOIs

- None

❌ INVALID DOIs

- 10.1016/j.compfluid.2024.10628 is INVALID

@jmetancelin
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@editorialbot check references

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

✅ OK DOIs

- 10.1016/j.cpc.2019.03.007 is OK
- 10.48550/arXiv.2112.07537 is OK
- 10.1016/j.compfluid.2024.106287 is OK
- 10.1103/PhysRevFluids.6.L022301 is OK
- 10.1016/j.compfluid.2021.104946 is OK
- 10.3390/fluids6020068 is OK
- 10.1016/j.advwatres.2020.103780 is OK
- 10.1016/j.euromechflu.2017.03.002 is OK
- 10.1051/m2an/2014009 is OK
- 10.1016/j.compfluid.2016.06.020 is OK
- 10.1016/j.jcp.2013.12.026 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: Numerical modelling and High Performance Computing...
- No DOI given, and none found for title: Conception et mise en oeuvre de méthodes vortex hy...
- No DOI given, and none found for title: Couplage de modèles, algorithmes multi-échelles et...

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

@jmetancelin
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@editorialbot check repository

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Software report:

github.com/AlDanial/cloc v 1.90  T=0.95 s (560.9 files/s, 187992.4 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                         397          19597          24897         110274
Fortran 90                      40           2967           6472          10521
Meson                           69            154            179           1245
Bourne Shell                    11             63            255            380
YAML                             5             52            189            377
Markdown                         4            180              0            376
TeX                              1              0              0            199
Dockerfile                       2             41             67            146
JSON                             1              1              0            123
C++                              2             26             86             44
TOML                             1              3              4             18
C/C++ Header                     1             10             21             14
-------------------------------------------------------------------------------
SUM:                           534          23094          32170         123717
-------------------------------------------------------------------------------

Commit count by author:

  1293	Jean-Baptiste Keck
   578	Jean-Matthieu Etancelin
   481	Franck Pérignon
   200	Keck Jean-Baptiste
   139	JM Etancelin
    79	Chloe Mimeau
    54	Nicolas Grima
    36	Eric Dalissier
    28	Jean-Baptiste Lagaert
    21	Jean-Baptiste Keck [email protected]
    19	GRIMA NICOLAS
    17	Chloé Mimeau
    16	Christophe Picard
    11	EXT Jean-Matthieu Etancelin
     8	Nicolas G
     8	mimeau
     6	Adrien Magni
     6	Nicolas Grm
     4	EXT GRIMA Nicolas
     4	Georges-Henri Cottet
     1	JME

@editorialbot
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Paper file info:

📄 Wordcount for paper.md is 1199

✅ The paper includes a Statement of need section

@editorialbot
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License info:

✅ License found: Apache License 2.0 (Valid open source OSI approved license)

@jmetancelin
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@editorialbot check repository

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Software report:

github.com/AlDanial/cloc v 1.90  T=0.95 s (560.3 files/s, 187796.9 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                         397          19597          24897         110274
Fortran 90                      40           2967           6472          10521
Meson                           69            154            179           1245
Bourne Shell                    11             63            255            380
YAML                             5             52            189            377
Markdown                         4            179              0            367
TeX                              1              0              0            199
Dockerfile                       2             41             67            146
JSON                             1              1              0            123
C++                              2             26             86             44
TOML                             1              3              4             18
C/C++ Header                     1             10             21             14
-------------------------------------------------------------------------------
SUM:                           534          23093          32170         123708
-------------------------------------------------------------------------------

Commit count by author:

  1293	Jean-Baptiste Keck
   578	Jean-Matthieu Etancelin
   481	Franck Pérignon
   200	Keck Jean-Baptiste
   139	JM Etancelin
    79	Chloe Mimeau
    54	Nicolas Grima
    36	Eric Dalissier
    28	Jean-Baptiste Lagaert
    21	Jean-Baptiste Keck [email protected]
    19	GRIMA NICOLAS
    17	Chloé Mimeau
    16	Christophe Picard
    11	EXT Jean-Matthieu Etancelin
     9	mimeau
     8	Nicolas G
     6	Adrien Magni
     6	Nicolas Grm
     4	EXT GRIMA Nicolas
     4	Georges-Henri Cottet
     1	JME

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Paper file info:

📄 Wordcount for paper.md is 1061

✅ The paper includes a Statement of need section

@editorialbot
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License info:

✅ License found: Apache License 2.0 (Valid open source OSI approved license)

@jmetancelin
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Hi @danielskatz, we address the issues for invalid DOIs and paper length. Some of our references do not have DOIs, as they are French PhD theses available in the HAL database (similar to arXiv in France).

@danielskatz
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👋 @jmetancelin - Thanks. However, I thought everything in HAL was given a DOI?

Also, @kyleniemeyer is now the track editor, so any comments should go to him, at least until an editor is assigned.

@kyleniemeyer
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@editorialbot invite @ppxasjsm as editor

Hi @ppxasjsm, could you edit this submission? Thanks!

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Invitation to edit this submission sent!

@ppxasjsm
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@editorialbot add @ppxasjsm as editor

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Assigned! @ppxasjsm is now the editor

@ppxasjsm ppxasjsm removed the waitlisted Submissions in the JOSS backlog due to reduced service mode. label Jan 16, 2025
@ppxasjsm
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Hi @jmetancelin, I will be editing your submssion. Would you be able to suggest some reviewers for this? Either, you can search the list of people that have already agreed to review and may be suitable for this submission or suggest other possibly suitable people however they need to be aware that the review process will be on github and will require a github account to carry out the review.

@jmetancelin
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Dear editor @ppxasjsm,
Here is a first set of possible reviewers from the joss' list:

  • thomasgillis : He work on close numerical methods and applications to fluid dynamic but in C++
  • bastorer : fluid dynamic and Python
  • upsj : HPC+GPU
  • jacobmerson : HPC+GPU

@ppxasjsm
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ppxasjsm commented Feb 2, 2025

Hi @thomasgillis, is there any chance you have capacities to review this submission?

@ppxasjsm
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ppxasjsm commented Feb 2, 2025

Hi @bastorer, I am looking for a reviewer for this JOSS submission. Is there any chance you'd be available?

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