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[REVIEW]: VOTCA: multiscale frameworks for quantum and 1 classical simulations in soft matter #6864

Open editorialbot opened 3 weeks ago

editorialbot commented 3 weeks ago

Submitting author: !--author-handle-->@junghans<!--end-author-handle-- (Christoph Junghans) Repository: https://github.com/votca/votca Branch with paper.md (empty if default branch): JOSS Version: v2024.1 Editor: !--editor-->@srmnitc<!--end-editor-- Reviewers: @gomartini-collab, @TariniHardikar Archive: Pending

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/e1e849ebf7176db5bebcaab930d55ee7"><img src="https://joss.theoj.org/papers/e1e849ebf7176db5bebcaab930d55ee7/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/e1e849ebf7176db5bebcaab930d55ee7/status.svg)](https://joss.theoj.org/papers/e1e849ebf7176db5bebcaab930d55ee7)

Reviewers and authors:

Please avoid lengthy details of difficulties in the review thread. Instead, please create a new issue in the target repository and link to those issues (especially acceptance-blockers) by leaving comments in the review thread below. (For completists: if the target issue tracker is also on GitHub, linking the review thread in the issue or vice versa will create corresponding breadcrumb trails in the link target.)

Reviewer instructions & questions

@gomartini-collab & @TariniHardikar, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review. First of all you need to run this command in a separate comment to create the checklist:

@editorialbot generate my checklist

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @srmnitc know.

✨ Please start on your review when you are able, and be sure to complete your review in the next six weeks, at the very latest ✨

Checklists

📝 Checklist for @gomartini-collab

📝 Checklist for @TariniHardikar

editorialbot commented 3 weeks ago

Hello humans, 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
editorialbot commented 3 weeks ago

Software report:

github.com/AlDanial/cloc v 1.90  T=1.96 s (772.1 files/s, 404611.5 lines/s)
--------------------------------------------------------------------------------
Language                      files          blank        comment           code
--------------------------------------------------------------------------------
XML                             254            411           1385         347375
Objective-C++                   151              0              0         267460
C++                             409          11012          12633          63765
SVG                               7              6              6          22429
C/C++ Header                    299           5335           9657          16244
Bourne Shell                    121            952           1588           4848
reStructuredText                 51           1841           1247           4479
Python                           33            995           1186           3222
Perl                             25            370            507           2192
CMake                            61            222            343           1941
PO File                          20            533            985           1487
YAML                             16             19              9            717
TeX                               6             99             11            638
HTML                              6             42              8            438
MUMPS                            20              0              0            381
Markdown                          9             93              0            353
Jupyter Notebook                  8              0           2266            210
Bourne Again Shell                2             34             39            204
ReasonML                          3              0              0             90
Dockerfile                        5             10              0             24
CSV                               1              0              0             16
CSS                               3              1              3              8
JavaScript                        2              0              0              2
--------------------------------------------------------------------------------
SUM:                           1512          21975          31873         738523
--------------------------------------------------------------------------------

Commit count by author:

  5568  Christoph Junghans
  1224  JoshuaSBrown
  1161  Jens Wehner
  1047  Votca Bot
   813  Victor Ruehle
   756  Jens
   661  Denis Andrienko
   538  Bjoern Baumeier
   430  felipez
   419  jenswehner
   304  Carl Poelking
   261  wehner
   237  12AngryMen
   216  rubengerritsen
   208  marvinbernhardt
   203  Joshua Scott Brown
   195  Jeroen van der Holst
   154  James Kirkpatrick
   135  Thorsten Vehoff
   126  Falk May
   120  Nicolas Renaud
   106  B. Baumeier
   105  felipeZ
   103  Pranav Madhikar
   103  jwehner
    97  Pascal Kordt
    90  Alexander Lukyanov
    90  JavierSijen
    86  Sebastian Fritsch
    75  Sikandar Mashayak
    73  NicoRenaud
    73  Vivek Sundaram
    58  Joshua S Brown
    52  Nico
    44  sundaramvivek10
    43  Christoph Scherer
    43  schererc
    41  Jakub Krajniak
    41  gtirimbo
    40  Konstantin Koschke
    34  Andrey Brukhno
    34  felipe
    33  Ruben Gerritsen
    30  Georg Hahn
    30  Manuel Schrader
    29  Majklikikik
    29  Rene Halver
    26  Tristan Bereau
    19  Javier
    15  Onur
    15  Yuriy Khalak
    13  Anton Melnyk
    12  Olga Bezkorovaynaya
     9  Alexander Malafeev
     9  David Rosenberger
     9  Gianluca Tirimbo
     8  Suvayu Ali
     6  drosen285
     6  floaltvater
     5  Cahit Dalgicdir
     5  b2bagher
     5  jdmoore2004
     4  Pritam Ganguly
     4  Tirimbo, G
     4  abrukhno
     3  Klaus Kaempf
     3  The Codacy Badger
     3  Tiago Espinosa
     3  Zhen-Hao Xu
     3  baumeier
     2  Jurriaan H. Spaaks
     2  Nicholas Breen
     2  Thomas Spura
     2  Torsten Sachse
     2  ipelupessy
     2  ricalessandri
     2  zch079
     1  Alexander Alexander
     1  Bernhard M. Wiedemann
     1  Codacy Badger
     1  Dominic Roehm
     1  Florian Weik
     1  Frank Zack
     1  Haoxiang Zhao
     1  Inti Pelupessy
     1  Jan Janssen
     1  Jean-Noël Grad
     1  Louis Vernon
     1  Mara Jochum
     1  Marc Barbry
     1  Marc Robinson
     1  Michael Cho
     1  Sikandar Y. Mashayak
     1  Stas Bevc
     1  Tonalli R.-L
     1  Vitaliy Starchenko
     1  Zhongquan Chen
     1  behnaz
     1  felipe zapata
     1  hx-zhao
     1  razziel89
editorialbot commented 3 weeks ago

Paper file info:

📄 Wordcount for paper.md is 3062

✅ The paper includes a Statement of need section

editorialbot commented 3 weeks ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1063/5.0006074 is OK
- 10.1063/5.0004635 is OK
- 10.1002/jcc.1056 is OK
- 10.1063/1.4986887 is OK
- 10.1016/j.softx.2017.11.002 is OK
- 10.1021/ct050190 is OK
- 10.1002/wcms.81 is OK
- 10.1103/PhysRevE.52.3730 is OK
- 10.1140/epjst/e2016-60120-1 is OK
- 10.1063/1.2646614 is OK
- 10.1039/B901511F is OK
- 10.1063/1.1543142 is OK
- 10.1021/acs.jctc.2c00665 is OK
- 10.1063/5.0038633 is OK
- 10.1080/17415977.2019.1710504 is OK
- 10.1021/acs.jpcb.7b09993 is OK
- 10.1063/1.5027645 is OK
- 10.1021/ct301019v is OK
- 10.1021/acs.jpcb.3c04473 is OK
- 10.1021/acs.jctc.9b01256 is OK
- 10.1109/TPDS.2021.3097283 is OK
- 10.21105/joss.04115 is OK

MISSING DOIs

- No DOI given, and none found for title: Fidgit: An ungodly union of GitHub and Figshare
- 10.1021/ct300544e may be a valid DOI for title: A Simple, Exact Density-Functional-Theory Embeddin...
- No DOI given, and none found for title: Intel Math Kernel Library. Reference Manual
- No DOI given, and none found for title: Libint: A library for the evaluation of molecular ...
- No DOI given, and none found for title: Eigen v3
- No DOI given, and none found for title: pybind11 – Seamless operability between C++11 and ...
- No DOI given, and none found for title: The atomic simulation environment—a Python library...
- No DOI given, and none found for title: Hierarchical Data Format, version 5
- No DOI given, and none found for title: MPI-P Fork of VOTCA

INVALID DOIs

- https://doi.org/10.1016/j.cpc.2016.06.019 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/j.cpc.2014.01.018 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1002/jcc.21717 is INVALID because of 'https://doi.org/' prefix
editorialbot commented 3 weeks ago

License info:

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

srmnitc commented 3 weeks ago

👋🏼 @junghans @gomartini-collab @TariniHardikar this is the review thread for the paper. All of our communications will happen here from now on.

As a reviewer, the first step is to create a checklist for your review by entering

@editorialbot generate my checklist

as the top of a new comment in this thread.

These checklists contain the JOSS requirements. As you go over the submission, please check any items that you feel have been satisfied. The first comment in this thread also contains links to the JOSS reviewer guidelines.

The JOSS review is different from most other journals. Our goal is to work with the authors to help them meet our criteria instead of merely passing judgment on the submission. As such, the reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention openjournals/joss-reviews#REVIEW_NUMBER so that a link is created to this thread (and I can keep an eye on what is happening). Please also feel free to comment and ask questions on this thread. In my experience, it is better to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.

We aim for reviews to be completed within about 2-4 weeks. Please let me know if any of you require some more time. We can also use EditorialBot (our bot) to set automatic reminders if you know you'll be away for a known period of time.

Please feel free to ping me (@srmnitc ) if you have any questions/concerns, thanks again for the submission, and for thr reviews

editorialbot commented 3 weeks 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 weeks 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 weeks ago

Hello @junghans, here are the things you can ask me to do:


# List all available commands
@editorialbot commands

# Get a list of all editors's GitHub handles
@editorialbot list editors

# Adds a checklist for the reviewer using this command
@editorialbot generate my checklist

# Set a value for branch
@editorialbot set joss-paper as branch

# Run checks and provide information on the repository and the paper file
@editorialbot check repository

# Check the references of the paper for missing DOIs
@editorialbot check references

# Generates the pdf paper
@editorialbot generate pdf

# Generates a LaTeX preprint file
@editorialbot generate preprint

# Get a link to the complete list of reviewers
@editorialbot list reviewers
editorialbot commented 3 weeks ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1063/5.0006074 is OK
- 10.1063/5.0004635 is OK
- 10.1002/jcc.1056 is OK
- 10.1016/j.cpc.2016.06.019 is OK
- 10.1021/ct300544e is OK
- 10.1063/1.4986887 is OK
- 10.1016/j.softx.2017.11.002 is OK
- 10.1021/ct050190 is OK
- 10.1002/wcms.81 is OK
- 10.1103/PhysRevE.52.3730 is OK
- 10.1140/epjst/e2016-60120-1 is OK
- 10.1063/1.2646614 is OK
- 10.1039/B901511F is OK
- 10.1063/1.1543142 is OK
- 10.1021/acs.jctc.2c00665 is OK
- 10.1063/5.0038633 is OK
- 10.1080/17415977.2019.1710504 is OK
- 10.1016/j.cpc.2014.01.018 is OK
- 10.1021/acs.jpcb.7b09993 is OK
- 10.1063/1.5027645 is OK
- 10.1002/jcc.21717 is OK
- 10.1021/ct301019v is OK
- 10.1021/acs.jpcb.3c04473 is OK
- 10.1021/acs.jctc.9b01256 is OK
- 10.1109/TPDS.2021.3097283 is OK
- 10.21105/joss.04115 is OK

MISSING DOIs

- No DOI given, and none found for title: Fidgit: An ungodly union of GitHub and Figshare
- No DOI given, and none found for title: Intel Math Kernel Library. Reference Manual
- No DOI given, and none found for title: Libint: A library for the evaluation of molecular ...
- No DOI given, and none found for title: Eigen v3
- No DOI given, and none found for title: pybind11 – Seamless operability between C++11 and ...
- No DOI given, and none found for title: The atomic simulation environment—a Python library...
- No DOI given, and none found for title: Hierarchical Data Format, version 5
- No DOI given, and none found for title: MPI-P Fork of VOTCA

INVALID DOIs

- None
editorialbot commented 3 weeks ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1063/5.0006074 is OK
- 10.1063/5.0004635 is OK
- 10.1002/jcc.1056 is OK
- 10.1016/j.cpc.2016.06.019 is OK
- 10.1021/ct300544e is OK
- 10.1007/978-3-319-06486-4_7 is OK
- 10.1063/1.4986887 is OK
- 10.1016/j.softx.2017.11.002 is OK
- 10.1021/ct050190 is OK
- 10.1002/wcms.81 is OK
- 10.1103/PhysRevE.52.3730 is OK
- 10.1140/epjst/e2016-60120-1 is OK
- 10.1063/1.2646614 is OK
- 10.1039/B901511F is OK
- 10.1063/1.1543142 is OK
- 10.1021/acs.jctc.2c00665 is OK
- 10.1063/5.0038633 is OK
- 10.1080/17415977.2019.1710504 is OK
- 10.1088/1361-648X/aa680e is OK
- 10.1016/j.cpc.2014.01.018 is OK
- 10.1007/978-1-4419-7719-9_10 is OK
- 10.1021/acs.jpcb.7b09993 is OK
- 10.1063/1.5027645 is OK
- 10.1002/jcc.21717 is OK
- 10.1021/ct301019v is OK
- 10.1021/acs.jpcb.3c04473 is OK
- 10.1021/acs.jctc.9b01256 is OK
- 10.1109/TPDS.2021.3097283 is OK
- 10.21105/joss.04115 is OK

MISSING DOIs

- No DOI given, and none found for title: Libint: A library for the evaluation of molecular ...
- No DOI given, and none found for title: Eigen v3
- No DOI given, and none found for title: pybind11 – Seamless operability between C++11 and ...
- No DOI given, and none found for title: MPI-P Fork of VOTCA

INVALID DOIs

- None
junghans commented 3 weeks ago
  • No DOI given, and none found for title: Libint: A library for the evaluation of molecular ...
  • No DOI given, and none found for title: Eigen v3
  • No DOI given, and none found for title: pybind11 – Seamless operability between C++11 and ...

We cited those 3 as suggested in their documents, no DOI available.

  • No DOI given, and none found for title: MPI-P Fork of VOTCA

This one has no DOI either, and the repo is also currently unavailable, still investigating, but if that persists we might drop this citation.

srmnitc commented 3 weeks ago

@junghans thanks! My recommendation would be add the url field in the software citations which would ensure that link appears in the paper. Without a direct link in the paper, it could be hard to find.

junghans commented 3 weeks ago

@junghans thanks! My recommendation would be add the url field in the software citations which would ensure that link appears in the paper. Without a direct link in the paper, it could be hard to find.

That was already the case.

junghans commented 3 weeks ago
  • No DOI given, and none found for title: MPI-P Fork of VOTCA

This one has no DOI either, and the repo is also currently unavailable, still investigating, but if that persists we might drop this citation.

The repo is back online.

editorialbot commented 3 weeks ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1063/5.0006074 is OK
- 10.1063/5.0004635 is OK
- 10.1002/jcc.1056 is OK
- 10.1016/j.cpc.2016.06.019 is OK
- 10.1021/ct300544e is OK
- 10.1007/978-3-319-06486-4_7 is OK
- 10.1063/1.4986887 is OK
- 10.5281/zenodo.10780719 is OK
- 10.1016/j.softx.2017.11.002 is OK
- 10.1021/ct050190 is OK
- 10.1002/wcms.81 is OK
- 10.1103/PhysRevE.52.3730 is OK
- 10.1140/epjst/e2016-60120-1 is OK
- 10.1063/1.2646614 is OK
- 10.1039/B901511F is OK
- 10.1063/1.1543142 is OK
- 10.1021/acs.jctc.2c00665 is OK
- 10.1063/5.0038633 is OK
- 10.1080/17415977.2019.1710504 is OK
- 10.5281/zenodo.5807779 is OK
- 10.1088/1361-648X/aa680e is OK
- 10.1016/j.cpc.2014.01.018 is OK
- 10.1007/978-1-4419-7719-9_10 is OK
- 10.1021/acs.jpcb.7b09993 is OK
- 10.1063/1.5027645 is OK
- 10.1002/jcc.21717 is OK
- 10.1021/ct301019v is OK
- 10.1021/acs.jpcb.3c04473 is OK
- 10.1021/acs.jctc.9b01256 is OK
- 10.1109/TPDS.2021.3097283 is OK
- 10.21105/joss.04115 is OK
- 10.1016/j.cpc.2021.108171 is OK
- 10.1016/j.cpc.2018.12.017 is OK
- 10.1140/epjst/e2019-800186-9 is OK

MISSING DOIs

- No DOI given, and none found for title: Eigen v3
- No DOI given, and none found for title: MPI-P Fork of VOTCA

INVALID DOIs

- None
gomartini-collab commented 3 weeks ago

Review checklist for @gomartini-collab

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

gomartini-collab commented 3 weeks ago

This is a bit ambiguous: Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item. So what to do: check if it is affirmative and check if it not affirmative? @srmnitc

srmnitc commented 3 weeks ago

This is a bit ambiguous: Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item. So what to do: check if it is affirmative and check if it not affirmative? @srmnitc

In this case, since there is on human/animal research, checking the box would be the appropriate response.

TariniHardikar commented 3 weeks ago

Review checklist for @TariniHardikar

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

srmnitc commented 1 week ago

@gomartini-collab and @TariniHardikar just a small reminder from my side about the review! Thanks once again for your efforts.

gomartini-collab commented 1 day ago

I think I completed my review.

TariniHardikar commented 1 day ago

Sorry, I was traveling! Will get my full review in by July 12th.