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

editorialbot · 2024-06-10T14:10:21Z

Submitting author: @junghans (Christoph Junghans)
Repository: https://github.com/votca/votca
Branch with paper.md (empty if default branch): master
Version: v2024.1
Editor: @srmnitc
Reviewers: @gomartini-collab, @TariniHardikar
Archive: 10.5281/zenodo.12750697

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

The text was updated successfully, but these errors were encountered:

editorialbot · 2024-06-10T14:10:24Z

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:

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

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editorialbot · 2024-06-10T14:10:49Z

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 · 2024-06-10T14:10:52Z

Paper file info:

📄 Wordcount for paper.md is 3062

✅ The paper includes a Statement of need section

editorialbot · 2024-06-10T14:10:58Z

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 · 2024-06-10T14:10:58Z

License info:

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

srmnitc · 2024-06-10T14:12:01Z

👋🏼 @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 · 2024-06-10T14:12:23Z

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

editorialbot · 2024-06-10T16:50:05Z

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

editorialbot · 2024-06-10T16:57:12Z

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 · 2024-06-10T16:58:07Z

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 · 2024-06-10T17:56:58Z

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 · 2024-06-10T18:01:08Z

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 · 2024-06-10T20:34:41Z

@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 · 2024-06-11T00:20:53Z

@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 · 2024-06-11T16:06:40Z

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 · 2024-06-11T19:03:26Z

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 · 2024-06-13T07:42:22Z

Review checklist for @gomartini-collab

Conflict of interest

I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

I confirm that I read and will adhere to the JOSS code of conduct.

General checks

Repository: Is the source code for this software available at the https://github.com/votca/votca?
License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
Contribution and authorship: Has the submitting author (@junghans) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
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.

Functionality

Installation: Does installation proceed as outlined in the documentation?
Functionality: Have the functional claims of the software been confirmed?
Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
State of the field: Do the authors describe how this software compares to other commonly-used packages?
Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

gomartini-collab · 2024-06-13T07:50:32Z

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 · 2024-06-13T14:55:56Z

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 · 2024-06-13T16:01:25Z

Review checklist for @TariniHardikar

Conflict of interest

I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

I confirm that I read and will adhere to the JOSS code of conduct.

General checks

Repository: Is the source code for this software available at the https://github.com/votca/votca?
License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
Contribution and authorship: Has the submitting author (@junghans) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
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.

Functionality

Installation: Does installation proceed as outlined in the documentation?
Functionality: Have the functional claims of the software been confirmed?
Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
State of the field: Do the authors describe how this software compares to other commonly-used packages?
Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

srmnitc · 2024-06-26T07:59:54Z

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

gomartini-collab · 2024-07-03T18:51:52Z

I think I completed my review.

TariniHardikar · 2024-07-03T18:53:43Z

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

srmnitc · 2024-07-08T10:10:23Z

I think I completed my review.

thanks a lot @gomartini-collab . I see that there are some unchecked boxes. If it is not applicable to the paper, please check it. If you feel the code needs improvement, could you please open an issue at the code repository, and mention here. We would need all boxes checked to go forward. Thanks once again!

gomartini-collab · 2024-07-08T12:47:26Z

This is the kind of things I am not sure:

Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.

If I click here, I am accepting the paper has NO original data. This is how I understood this part. Now you asked me to click on it. I am very much confuse.

DRosen285 · 2024-07-22T14:21:04Z

Looks good to me.

kyleniemeyer · 2024-07-22T14:24:00Z

@junghans I believe the paper converter will add first initials when needing to distinguish multiple citations from the same first author; it should be able to handle the author = {Last, First and Last2, First2} format just fine.

junghans · 2024-07-22T14:32:05Z

@junghans I believe the paper converter will add first initials when needing to distinguish multiple citations from the same first author; it should be able to handle the author = {Last, First and Last2, First2} format just fine.

@kyleniemeyer thanks. In our case there is no distinguish needed, I think we are missing a middle initial somewhere, so let me see if that fixes it.

junghans · 2024-07-22T15:50:36Z

Ok fixed in votca/votca#1153

junghans · 2024-07-22T16:14:00Z

Looks good now!

kyleniemeyer · 2024-07-23T08:32:13Z

@editorialbot generate pdf

editorialbot · 2024-07-23T08:32:57Z

⚠️ An error happened when generating the pdf.

kyleniemeyer · 2024-07-23T08:36:01Z

@editorialbot set master as branch

editorialbot · 2024-07-23T08:36:03Z

Done! branch is now master

kyleniemeyer · 2024-07-23T08:36:09Z

@editorialbot generate pdf

editorialbot · 2024-07-23T08:37:50Z

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

kyleniemeyer · 2024-07-23T10:14:04Z

@junghans can you review and merge votca/votca#1154 ? It fixes some small issues I noticed.

baumeier · 2024-07-23T10:26:01Z

@kyleniemeyer done, thanks for fixing

junghans · 2024-07-23T12:48:21Z

@kyleniemeyer thanks!

kyleniemeyer · 2024-07-23T13:28:50Z

@editorialbot generate pdf

editorialbot · 2024-07-23T13:30:50Z

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

kyleniemeyer · 2024-07-23T13:33:16Z

@editorialbot accept

editorialbot · 2024-07-23T13:33:19Z

Doing it live! Attempting automated processing of paper acceptance...

editorialbot · 2024-07-23T13:40:49Z

Ensure proper citation by uploading a plain text CITATION.cff file to the default branch of your repository.

If using GitHub, a Cite this repository menu will appear in the About section, containing both APA and BibTeX formats. When exported to Zotero using a browser plugin, Zotero will automatically create an entry using the information contained in the .cff file.

You can copy the contents for your CITATION.cff file here:

CITATION.cff

cff-version: "1.2.0"
authors:
- family-names: Baumeier
  given-names: Björn
  orcid: "https://orcid.org/0000-0002-6077-0467"
- family-names: Wehner
  given-names: Jens
  orcid: "https://orcid.org/0000-0003-1203-5000"
- family-names: Renaud
  given-names: Nicolas
  orcid: "https://orcid.org/0000-0001-9589-2694"
- family-names: Ruiz
  given-names: Felipe Zapata
  orcid: "https://orcid.org/0000-0001-8286-677X"
- family-names: Halver
  given-names: Rene
  orcid: "https://orcid.org/0000-0002-4895-3762"
- family-names: Madhikar
  given-names: Pranav
  orcid: "https://orcid.org/0000-0003-3658-3685"
- family-names: Gerritsen
  given-names: Ruben
  orcid: "https://orcid.org/0000-0003-0738-8952"
- family-names: Tirimbo
  given-names: Gianluca
  orcid: "https://orcid.org/0000-0002-6641-0761"
- family-names: Sijen
  given-names: Javier
- family-names: Rosenberger
  given-names: David
  orcid: "https://orcid.org/0000-0001-6620-6499"
- family-names: Brown
  given-names: Joshua S.
  orcid: "https://orcid.org/0000-0003-1227-6429"
- family-names: Sundaram
  given-names: Vivek
  orcid: "https://orcid.org/0000-0002-9986-8461"
- family-names: Krajniak
  given-names: Jakub
  orcid: "https://orcid.org/0000-0001-9372-6975"
- family-names: Bernhardt
  given-names: Marvin
  orcid: "https://orcid.org/0000-0001-6520-5208"
- family-names: Junghans
  given-names: Christoph
  orcid: "https://orcid.org/0000-0003-0925-1458"
contact:
- family-names: Baumeier
  given-names: Björn
  orcid: "https://orcid.org/0000-0002-6077-0467"
- family-names: Junghans
  given-names: Christoph
  orcid: "https://orcid.org/0000-0003-0925-1458"
doi: 10.5281/zenodo.12750697
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Baumeier
    given-names: Björn
    orcid: "https://orcid.org/0000-0002-6077-0467"
  - family-names: Wehner
    given-names: Jens
    orcid: "https://orcid.org/0000-0003-1203-5000"
  - family-names: Renaud
    given-names: Nicolas
    orcid: "https://orcid.org/0000-0001-9589-2694"
  - family-names: Ruiz
    given-names: Felipe Zapata
    orcid: "https://orcid.org/0000-0001-8286-677X"
  - family-names: Halver
    given-names: Rene
    orcid: "https://orcid.org/0000-0002-4895-3762"
  - family-names: Madhikar
    given-names: Pranav
    orcid: "https://orcid.org/0000-0003-3658-3685"
  - family-names: Gerritsen
    given-names: Ruben
    orcid: "https://orcid.org/0000-0003-0738-8952"
  - family-names: Tirimbo
    given-names: Gianluca
    orcid: "https://orcid.org/0000-0002-6641-0761"
  - family-names: Sijen
    given-names: Javier
  - family-names: Rosenberger
    given-names: David
    orcid: "https://orcid.org/0000-0001-6620-6499"
  - family-names: Brown
    given-names: Joshua S.
    orcid: "https://orcid.org/0000-0003-1227-6429"
  - family-names: Sundaram
    given-names: Vivek
    orcid: "https://orcid.org/0000-0002-9986-8461"
  - family-names: Krajniak
    given-names: Jakub
    orcid: "https://orcid.org/0000-0001-9372-6975"
  - family-names: Bernhardt
    given-names: Marvin
    orcid: "https://orcid.org/0000-0001-6520-5208"
  - family-names: Junghans
    given-names: Christoph
    orcid: "https://orcid.org/0000-0003-0925-1458"
  date-published: 2024-07-23
  doi: 10.21105/joss.06864
  issn: 2475-9066
  issue: 99
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 6864
  title: "VOTCA: multiscale frameworks for quantum and classical
    simulations in soft matter"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.06864"
  volume: 9
title: "VOTCA: multiscale frameworks for quantum and classical
  simulations in soft matter"

If the repository is not hosted on GitHub, a .cff file can still be uploaded to set your preferred citation. Users will be able to manually copy and paste the citation.

Find more information on .cff files here and here.

editorialbot · 2024-07-23T13:40:53Z

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot · 2024-07-23T13:40:54Z

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.06864 joss-papers#5660
Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.06864
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

junghans · 2024-07-23T16:44:20Z

@srmnitc And before we close this, could you remove the auxiliary "1" from the title of the issue.

@kyleniemeyer before closing, could you update the title?

srmnitc · 2024-07-23T20:07:23Z

@srmnitc And before we close this, could you remove the auxiliary "1" from the title of the issue.

@kyleniemeyer before closing, could you update the title?

I did, sorry I missed before!

kyleniemeyer · 2024-07-24T07:13:00Z

Congratulations @junghans on your article's publication in JOSS!

Many thanks to @gomartini-collab and @TariniHardikar for reviewing this submission, and @srmnitc for editing.

editorialbot · 2024-07-24T07:13:02Z

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

If you would like to include a link to your paper from your README use the following code snippets:

Markdown:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.06864/status.svg)](https://doi.org/10.21105/joss.06864)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.06864">
  <img src="https://joss.theoj.org/papers/10.21105/joss.06864/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.06864/status.svg
   :target: https://doi.org/10.21105/joss.06864

This is how it will look in your documentation:

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Volunteering to review for us sometime in the future. You can add your name to the reviewer list here: https://reviewers.joss.theoj.org/join
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editorialbot added review Track: 2 (BCM) Biomedical Engineering, Biosciences, Chemistry, and Materials labels Jun 10, 2024

editorialbot assigned srmnitc Jun 10, 2024

editorialbot mentioned this issue Jun 10, 2024

[PRE REVIEW]: VOTCA: multiscale frameworks for quantum and classical simulations in soft matter #6795

Closed

junghans mentioned this issue Jun 10, 2024

Add v2024.1 JOSS paper votca/votca#1132

Merged

editorialbot added accepted published Papers published in JOSS labels Jul 23, 2024

junghans mentioned this issue Jul 23, 2024

Update CITATION.cff votca/votca#1155

Merged

srmnitc changed the title ~~[REVIEW]: VOTCA: multiscale frameworks for quantum and 1 classical simulations in soft matter~~ [REVIEW]: VOTCA: multiscale frameworks for quantum and classical simulations in soft matter Jul 23, 2024

kyleniemeyer closed this as completed Jul 24, 2024

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

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

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