editorialbot commented 3 months ago

Submitting author: !--author-handle-->@IonRepo@rkurchin<!--end-editor-- Reviewers: @yw-fang, @LIVazquezS Archive: 10.5281/zenodo.12771455

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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

@yw-fang & @LIVazquezS, 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:

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

📝 Checklist for @yw-fang

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

- 10.17172/NOMAD/2024.04.01-1 is OK
- 10.1039/D2MH01516A is OK
- 10.1021/jacs.3c13279 is OK
- 10.48550/arXiv.1201.0490 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.1103/PhysRevB.54.11169 is OK
- 10.1103/PhysRevLett.127.025901 is OK
- 10.1038/s41524-023-00996-8 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 3 months ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.04 s (652.9 files/s, 136820.7 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
SVG                              2              0              0           3410
Python                           9            348            436            638
Markdown                         5             76              0            161
TeX                              1              8              0             79
XML                              6              0              0             47
YAML                             1              1              4             18
Bourne Shell                     1              0              0             13
-------------------------------------------------------------------------------
SUM:                            25            433            440           4366
-------------------------------------------------------------------------------

Commit count by author:

    36  Cibrán
    15  cibran
     4  IonRepo
     3  CibranLopez

editorialbot commented 3 months ago

Paper file info:

📄 Wordcount for paper.md is 2306

🔴 Failed to discover a Statement of need section in paper

editorialbot commented 3 months ago

License info:

✅ License found: MIT 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:

LIVazquezS commented 3 months ago

Review checklist for @LIVazquezS

Conflict of interest

[x] 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

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

General checks

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

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] 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

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

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] 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?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] 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?

yw-fang commented 2 months ago

Review checklist for @yw-fang

Conflict of interest

[x] 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

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

General checks

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

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] 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

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

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] 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?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] 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?

LIVazquezS commented 2 months ago

Dear authors,

Here are some comments about your work.

General Checks

Contribution and authorship

Could the authors clarify the contributions of authors Riccardo Rurali and Claudio Cazorla? Are they sharing the git account IonRepo?

Functionality

The authors must automatize the installation of the software. I could not install it by just following the procedure described.
The authors claimed that their implementation scales linearly with different factors, such as the length of the temporal window, the total duration of the simulation, and the number of mobile ions. Evidence for this claim must be provided.
The authors mention vectorizing operations using a common library such as Numpy. However, could this be improved by using Numba? Is the code parallelized?
The authors claim that their implementation outperforms standard evaluation algorithms; evidence for this claim should be provided.

Documentation

There is no clear documentation of the code's functionalities. I had to read the source code to understand some of its key functionalities. The authors need to generate documentation for the API that is not embedded in the source code.

Statement of need: It is unclear why the authors provide a new solution to this problem. Do the authors benchmark their work against more established libraries such as MDAnalysis, MDTraj or TRAVIS?
Installation instructions: The installation does not work as described by the authors, as mentioned before.
Example usage: The examples do not work as described by the authors. I have to modify the provided commands to make them work. Additionally, it is unclear what results are obtained; it would be better if the examples were described in more detail. On the other hand, the execution time of the examples is considerably long. This is not explicitly mentioned. The first example took around 13 minutes using 8 cores. The second (analyze_correlations) did not work. The third (analyze_descriptors) yields an AttributeError. Finally, the script run.sh refers to a local path, leading to confusion.

Software paper

The paper does not contain a statement of need. Additionally, it does not describe the current state of the art or how this new software can compare with well-established codes for analyzing MD trajectories.

Summary: The authors must specify their target audience. If I understand correctly, their code can only be used to analyse trajectories from ab-initio simulations, which excludes people who make classical simulations. Even among people who make ab initio simulations, it seems their code is targeted to be used with VASP, reducing the pool of possible users considerably.
State-of-the-art: The authors must add appropriate citations to some basic concepts to develop the paper. For example, the definition of fast-ion conductors requires a reference to where it is taken. Additionally, citations to other codes that can be used for a similar task must be added if those exist.
References: As mentioned, the authors must enrich their references to cover the state-of-the-art.

In addition, I have the following questions:

The authors do not adequately specify the format of the MD trajectory that needs to be used in their code. This must be clarified because the code seems heavily dependent on only that specific format. Complementary, the specification of the trajectory format helps ensure the reliability of results obtained with other software.
The authors mentioned that one of the code's functionalities is analyze_descriptors. I think a more detailed description of which descriptors are obtained and how they are obtained is required.
From the technical side, the authors need to provide information about hyperparameters for the k-means algorithm or give a criterion, either empirically or physically based, for selecting those values that are known to be key to using the unsupervised method.
In the same line as above, I wonder if the authors consider using other unsupervised machine learning algorithms (see for examples, section 5 of Chem. Rev. 2021, 121, 16, 9722–9758) to do the clustering. It is mentioned that it is possible to use spectral clustering. If that is the case, an explicit example should be added.
Regarding the methods section, in equation 1, the authors mention that the ionic conductivity is a function of the number of spatial dimensions. I would like to know if the code allows the computation of the ionic conductivity in a specific dimension (i.e., in the x-axis only).
Authors need to provide information about the equation used to obtain the diffusion coefficient; equation 2 seems to be the Einstein relationship, while equation 4 seems like a discretized version of the Green-Kubo expression. To do this, I encourage the authors to review the following reference: Living J. Comput. Mol. Sci., 2019, 1, 6324.
The authors mention that they assumed that the non-diffusive particles have an isotropic behaviour in their fluctuations. What is the reason for that assumption? In which cases is this assumption fulfilled? Is the developed code still useful if the non-diffusive particles do not follow that assumption?
The authors adopt an arbitrary threshold of 0.5 $\unicode{x212B}$. What is the justification for this definition? As they mentioned, the definition of this distance is critical for obtaining the k-centers. Then, what is the effect of this value? Could the author provide information on what happens if other threshold values are used?
In the subsection regarding correlations between mobile ions, the procedure explained in the first paragraph can be illustrated as pseudocode to facilitate its comprehension.
Regarding the examples, why do you always obtain one or two clusters? Is that what we should expect? Does that mean that only one diffusion path is observed in your simulations? What is the physical meaning of the clusters obtained by the code, if there is one?

Suggested improvements

Besides the points mentioned before, I think the author could make the following improvements:

Improve the code installation using a setup.py file or a .toml file. Also, a mention of specific requirements such as Python and package version will be very useful.
Create detailed tutorials for using the code with the aid of either scripts or Jupyter notebooks that allow the user to understand what the code is doing.
The authors must provide a better description of their code's capabilities. Judging from their software's reported use, I believe this code has multiple applications. However, it is unclear to me which capabilities and how they can be applied by the MD community.
As mentioned before, documentation must be improved. I also suggest that the authors include a detailed section explaining the theory behind it. This should not be a problem because the authors explained it in their previous work. Last but not least, a section on the documentation on constructing the input files for the code must be added.
I suggest the authors add more details about generating the MD Trajectories. As these simulations are very sensitive to different factors, the user must be alerted that their results will depend on those.

Overall

I believe the presented work can be useful for analysing MD trajectories for ionic systems. However, I have several doubts about the software's functionality and applications; therefore, the paper requires major revision to have a clear view of them. Also, the state-of-the-art software must be improved, and suitable comparisons with other available software must be made. Finally, I failed to see how this work can be combined with existing frameworks as it seems to be specialized in analyzing VASP trajectories and is incompatible with classical MD. Likewise, I failed to see how this code systematically determines exact ionic migration paths and the level of coordination between mobile particles in diffusive events. To conclude, the paper and the code must go through major revision before considering its acceptance.

Best wishes, Claudio Cazorla

Dr. Claudio Cazorla "Ramón y Cajal" Researcher Department of Physics Universitat Politècnica de Catalunya (UPC) C/ Jordi Girona 1-3, Campus Nord, B4-203 08034 Barcelona (Spain) telephone: +34 93 4017066 email: @.*** website: www.claudiocazorla-physics.com

Missatge de Rachel Kurchin @.***> del dia dt., 18 de juny 2024 a les 22:52:

🔔 Hi @Claudiator7 https://github.com/Claudiator7, just checking in here!

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/6616#issuecomment-2176950810, or unsubscribe https://github.com/notifications/unsubscribe-auth/BHXD4BRNZ6JPWG3HJZALTXTZICMXBAVCNFSM6AAAAABGFVF3QGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCNZWHE2TAOBRGA . You are receiving this because you were mentioned.Message ID: @.***>

yw-fang commented 2 weeks ago

Hi, editor @rkurchin and one of the leading authors @Claudiator7 , my 2nd-round review report has been ready https://github.com/IonRepo/IonDiff/issues/6! Herein, I'd like to invite @Claudiator7 and his colleagues to further improve the code. Thanks.

rkurchin commented 2 weeks ago

Thanks, @yw-fang. @LIVazquezS, take a look at the updates/responses from @Claudiator7 and team and let us know what you think, thanks!

LIVazquezS commented 2 weeks ago

Dear Authors,

Thank you very much for your detailed response to the points raised before and for solving most of them.

The paper has improved considerably. Nevertheless, I still have three points that require the authors' attention.

In their reply, the authors mention mention: "There seems to be a misunderstanding on this Reviewer’s point. The IonDiff code can be perfectly used by any scientist performing either classical molecular dynamics simulations (classical MD) or ab initio molecular dynamics simulations (AIMD). In both types of simulations, atomic trajectories are generated and this is the main input information that the IonDiff code necessitates to perform its correlation and ionic hopping analysis. In other words, the IonDiff analysis does not depend on how the atomic forces are calculated in the undertaken molecular dynamics simulations, whether these are obtained through classical force fields or quantum mechanical methods (e.g., density functional theory). As far as the output trajectory files generated by any classical MD code can be converted to the output trajectory file format of VASP, which is very simple and intuitive, the IonDiff code can be purposely employed. There is already a myriad of open-source codes and scripts that can be used for this end, namely, to convert a trajectory file generated by a classical MD code to the VASP format, like, for instance, LAVA (https://github.com/lanl/LAVA, to convert from LAMMPS format to VASP format) and the online website https://www.xfroggie.com/index.cgi/strconv (to convert from GROMACS format to VASP format). Therefore, there is not any factual limitation on the number of potential users of the IonDiff code. Likewise, there is neither a pressing need to replicate already existing codes and scripts able to perform MD files format conversions."

The authors must explicitly mention this in the documentation. Although this might be obvious for the experienced user, it might be a big headache for an inexpert user because it is not completely obvious how to convert files generated with one code to the required format by IonDiff.

The authors mention "Generation of documentation in ReadTheDocs." I have not found the link to this documentation, so I would like to kindly ask the authors to add it to the README file.
While running the examples provided by the authors, I found a minor bug in the first example with analyze_correlations.py in line 77 with the number of arguments to unpack.

Finally, I would like to acknowledge the author's effort to improve their code and the supporting manuscript.

IonRepo commented 1 week ago

Dear Reviewer,

We thank the Reviewer for their insightful comments and thorough review, as well as their nice feedback regarding our improvements in both text and package. We agree on the complexity of the mentioned task for non experienced used, which can be challengeing and discouraging. Following the reviewer's advice, we added a section explaining how to use the trajectories generated with different codes as input to IonDiff in the README (https://github.com/IonRepo/IonDiff/blob/main/README.md) and the documentation (https://iondiff.readthedocs.io/en/latest/). As well, the hyperlik to the documentation was not displaying correctly in the README file, as pointed out, which has been now fixed. Finally, we thank the reviewer for detecting that the tuple from line 77 in analyze_correlations.py could be more efficiently unpacked, which has been now improved.

Best regards, Cibrán.

Missatge de Luis Itza Vazquez-Salazar @.***> del dia dl., 8 de jul. 2024 a les 16:11:

Dear Authors,

Thank you very much for your detailed response to the points raised before and for solving most of them.

The paper has improved considerably. Nevertheless, I still have three points that require the authors' attention.

In their reply, the authors mention mention: "There seems to be a misunderstanding on this Reviewer’s point. The IonDiff code can be perfectly used by any scientist performing either classical molecular dynamics simulations (classical MD) or ab initio molecular dynamics simulations (AIMD). In both types of simulations, atomic trajectories are generated and this is the main input information that the IonDiff code necessitates to perform its correlation and ionic hopping analysis. In other words, the IonDiff analysis does not depend on how the atomic forces are calculated in the undertaken molecular dynamics simulations, whether these are obtained through classical force fields or quantum mechanical methods (e.g., density functional theory). As far as the output trajectory files generated by any classical MD code can be converted to the output trajectory file format of VASP, which is very simple and intuitive, the IonDiff code can be purposely employed. There is already a myriad of open-source codes and scripts that can be used for this end, namely, to convert a trajectory file generated by a classical MD code to the VASP format, like, for instance, LAVA (https://github.com/lanl/LAVA https://github.com/lanl/LAVA, to convert from LAMMPS format to VASP format) and the online website https://www.xfroggie.com/index.cgi/strconv https://www.xfroggie.com/index.cgi/strconv (to convert from GROMACS format to VASP format). Therefore, there is not any factual limitation on the number of potential users of the IonDiff code. Likewise, there is neither a pressing need to replicate already existing codes and scripts able to perform MD files format conversions."

The authors must explicitly mention this in the documentation. Although this might be obvious for the experienced user, it might be a big headache for an inexpert user because it is not completely obvious how to convert files generated with one code to the required format by IonDiff.

2.

The authors mention "Generation of documentation in ReadTheDocs." I have not found the link to this documentation, so I would like to kindly ask the authors to add it to the README file. 3.

While running the examples provided by the authors, I found a minor bug in the first example with analyze_correlations.py in line 77 with the number of arguments to unpack.

Finally, I would like to acknowledge the author's effort to improve their code and the supporting manuscript.

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/6616#issuecomment-2214189430, or unsubscribe https://github.com/notifications/unsubscribe-auth/A6TPLNPSYWABNZLUALT4JS3ZLKMZZAVCNFSM6AAAAABGFVF3QGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEMJUGE4DSNBTGA . You are receiving this because you were mentioned.Message ID: @.***>

LIVazquezS commented 1 week ago

Dear Authors,

Thanks for your efforts to improve the code. I am fine with the manuscript associated with the code. Nevertheless, I still have two problems with the code.

The bug in the first example with analyze_correlations.py in line 77 with the number of arguments to unpack. I am using python 3.8.19. Adjuncted a screenshot of the mentioned problem.
Thanks for adding the link to the read-the-docs page with the documentation; it works fine. Nevertheless, to fullfil the requirements of JOSS, you need to add API level documentation. This should not be a problem as all functions in the code are adequately documented, so any automatic API generator like sphinx [https://www.sphinx-doc.org/en/master/man/sphinx-apidoc.html] can do it. This is a minor point, but it will improve the user experience as the arguments of each function can be checked from the documentation instead of reading the source code.

Again, thanks for your effort. Once those two points are sorted, I will gladly recommend accepting your work.

IonRepo commented 1 week ago

Dear Reviewer,

We sincerely appreciate your efforts in reviewing this article, which has greatly enhanced its quality. The problem that has been raised is based on the fact that correlations can not be drawn from one single simulation. In response, and following both Reviewers' advice, we have added an additional example to the repository. This ensures that all functionalities can now be run adequately (please see the updated examples folder and README file). Additionally, we have improved the API documentation (please see the updated documentation, which now contains the docstrings of the libraries). We thank the Reviewer for suggesting the Sphinx package, which we have utilized for this end.

Best regards, Cibrán.

Missatge de Luis Itza Vazquez-Salazar @.***> del dia dj., 11 de jul. 2024 a les 14:44:

Dear Authors,

Thanks for your efforts to improve the code. I am fine with the manuscript associated with the code. Nevertheless, I still have two problems with the code.

The bug in the first example with analyze_correlations.py in line 77 with the number of arguments to unpack. I am using python 3.8.19. Adjuncted a screenshot of the mentioned problem.

Captura.de.pantalla.2024-07-11.a.la.s.14.31.10.png (view on web) https://github.com/openjournals/joss-reviews/assets/59973237/7540ac9a-6b24-4629-965a-d8998eb6c4b4

Thanks for adding the link to the read-the-docs page with the documentation; it works fine. Nevertheless, to fullfil the requirements of JOSS, you need to add API level documentation. This should not be a problem as all functions in the code are adequately documented, so any automatic API generator like sphinx [ https://www.sphinx-doc.org/en/master/man/sphinx-apidoc.html] can do it. This is a minor point, but it will improve the user experience as the arguments of each function can be checked from the documentation instead of reading the source code.

Again, thanks for your effort. Once those two points are sorted, I will gladly recommend accepting your work.

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/6616#issuecomment-2222840170, or unsubscribe https://github.com/notifications/unsubscribe-auth/A6TPLNMXZ3LXXMW7CGXI3WLZLZ4ZXAVCNFSM6AAAAABGFVF3QGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEMRSHA2DAMJXGA . You are receiving this because you were mentioned.Message ID: @.***>

yw-fang commented 1 week ago

Dear editor @rkurchin

The authors have addressed my raised issues. Thus, I recommend its accept for the publication at JOSS. Thank you!

LIVazquezS commented 1 week ago

Dear authors,

Thanks for your effort. All my points have been resolved.

@rkurchin I am happy to recommend this work for publication.

rkurchin commented 1 week ago

@yw-fang, if you're satisfied on all points, could you please check off the rest of your checklist items?

yw-fang commented 6 days ago

@yw-fang, if you're satisfied on all points, could you please check off the rest of your checklist items?

Done! Thank you for your kind reminder!

rkurchin commented 6 days ago

@editorialbot check references

editorialbot commented 6 days ago

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

OK DOIs

- 10.17172/NOMAD/2024.04.01-1 is OK
- 10.1039/D2MH01516A is OK
- 10.1021/jacs.3c13279 is OK
- 10.48550/arXiv.1201.0490 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.1103/PhysRevB.54.11169 is OK
- 10.1103/PhysRevLett.127.025901 is OK
- 10.1038/s41524-023-00996-8 is OK
- 10.1088/0034-4885/67/7/R05 is OK
- 10.1021/acsami.7b11687 is OK

MISSING DOIs

- None

INVALID DOIs

- None

rkurchin commented 6 days ago

@editorialbot generate pdf

editorialbot commented 6 days ago

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

rkurchin commented 6 days ago

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

Double check authors and affiliations (including ORCIDs)
Make a release of the software with the latest changes from the review and post the version number here. This is the version that will be used in the JOSS paper.
Archive the release on Zenodo/figshare/etc and post the DOI here.
Make sure that the title and author list (including ORCIDs) in the archive match those in the JOSS paper.
Make sure that the license listed for the archive is the same as the software license.

Editor Tasks Prior to Acceptance

[x] Read the text of the paper and offer comments/corrections (as either a list or a pull request)
[x] Check that the archive title, author list, version tag, and the license are correct
[x] Set archive DOI with @editorialbot set <DOI here> as archive
[x] Set version with @editorialbot set <version here> as version
[x] Double check rendering of paper with @editorialbot generate pdf
[x] Specifically check the references with @editorialbot check references and ask author(s) to update as needed
[x] Recommend acceptance with @editorialbot recommend-accept

rkurchin commented 6 days ago

Thanks everyone! @IonRepo, I'll do an editorial pass over the manuscript and send any comments shortly. In the meantime, the next steps for you are shown in the comment above, so you can work on those checks and send me version number and DOI information whenever you can. Almost there!

rkurchin commented 6 days ago

Editorial remarks:

line 11: First sentence of Summary doesn't make sense as written – perhaps "conforming" should be "comprising" instead?
12: add "techniques" after "analysis"
13: add hyphen to "high-throughput"
14: rewrite as "determination of exact ionic migration paths"
15: "have" -> "has"
17: add hyphen to "high-performance"
19: rewrite as "which particles diffuse and when"
20: "migrating" -> "migration"
22: remove comma and final clause in sentence (it's clear that you're citing examples)
30: "simulations" -> "simulation"
33: rewrite as "can describe in detail the diffusion and vibration of the constituent ions"
34: replace "painstaking" with "notable" and "handy" with either "user-friendly" or "convenient"
47: "migrating" -> "migration"
59: remove extra )
86, 88, and several equations: subscripts that are not variables (e.g. "self" and "distinct" and also "B" in Boltzmann's constant) should be rendered \mathrm so they're not italicized
88: "many-atoms" -> "many-atom"
90: "many-ions" -> "many-ion"
91: add "and" before "hence"
93: add "calculation" after "coefficient"
93: "matricial" -> "matrix"
94: "like" -> "as"
99: "diffusses" -> "diffuses"
101: "tensor" -> "array" and add comma after
101: remove "very much"
103: remove "number of"
105: "four rank tensor" -> "four-dimensional array"
105: I think $n_d$ should just be $d$ the way you've defined your notation?
117: This sentence doesn't really make sense, I think perhaps "conforms" should be "constructs" here?
equation 7: what do the upper-case I and J mean?

IonRepo commented 5 days ago

Dear Editor,

We would like to thank the Editor for their careful remarks; we have addressed all of them.

In our notation, $n_d$ represents the number of dimensions considered, while $d$ denotes the specific spatial dimension along which the ionic-diffusion coefficient is computed. For example, in three dimensions, $n_d = 3$ while $d$ can be any of the Cartesian directions.

In equation 7, the upper-case I and J are cluster indexes. To improve readability, we have slightly modified the notation in equations 5-7. For reference, please see the section on the silhouette coefficient in the scikit-learn documentation: scikit-learn clustering https://scikit-learn.org/stable/modules/clustering.html#silhouette-coefficient . Best regards, Cibrán.

Missatge de Rachel Kurchin @.***> del dia dt., 16 de jul. 2024 a les 20:40:

Editorial remarks:

line 11: First sentence of Summary doesn't make sense as written – perhaps "conforming" should be "comprising" instead?

12: add "techniques" after "analysis"

13: add hyphen to "high-throughput"

14: rewrite as "determination of exact ionic migration paths"

15: "have" -> "has"

17: add hyphen to "high-performance"

19: rewrite as "which particles diffuse and when"

20: "migrating" -> "migration"

22: remove comma and final clause in sentence (it's clear that you're citing examples)

30: "simulations" -> "simulation"

33: rewrite as "can describe in detail the diffusion and vibration of the constituent ions"

34: replace "painstaking" with "notable" and "handy" with either "user-friendly" or "convenient"

47: "migrating" -> "migration"

59: remove extra )

86, 88, and several equations: subscripts that are not variables (e.g. "self" and "distinct" and also "B" in Boltzmann's constant) should be rendered \mathrm so they're not italicized

88: "many-atoms" -> "many-atom"

90: "many-ions" -> "many-ion"

91: add "and" before "hence"

93: add "calculation" after "coefficient"

93: "matricial" -> "matrix"

94: "like" -> "as"

99: "diffusses" -> "diffuses"

101: "tensor" -> "array" and add comma after

101: remove "very much"

103: remove "number of"

105: "four rank tensor" -> "four-dimensional array"

105: I think $n_d$ should just be $d$ the way you've defined your notation?

117: This sentence doesn't really make sense, I think perhaps "conforms" should be "constructs" here?

equation 7: what do the upper-case I and J mean?

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/6616#issuecomment-2231575215, or unsubscribe https://github.com/notifications/unsubscribe-auth/A6TPLNKLNRMWUNRBYIOLGILZMVSJNAVCNFSM6AAAAABGFVF3QGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEMZRGU3TKMRRGU . You are receiving this because you were mentioned.Message ID: @.***>

rkurchin commented 5 days ago

@editorialbot generate pdf

editorialbot commented 5 days ago

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

rkurchin commented 5 days ago

@IonRepo, awesome, manuscript looks great. So all we need is the version number of the release with all the changes from the review and the DOI of the deposit, then we should be ready to go!

IonRepo commented 4 days ago

Dear Editor,

This would be the release 1.6 with DOI: 10.5281/zenodo.12771455.

Best regards, Cibrán.

Missatge de Rachel Kurchin @.***> del dia dc., 17 de jul. 2024 a les 18:47:

@IonRepo https://github.com/IonRepo, awesome, manuscript looks great. So all we need is the version number of the release with all the changes from the review and the DOI of the deposit, then we should be ready to go!

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/6616#issuecomment-2233750163, or unsubscribe https://github.com/notifications/unsubscribe-auth/A6TPLNK7K7ENZM6ZPHOUK73ZM2NYPAVCNFSM6AAAAABGFVF3QGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEMZTG42TAMJWGM . You are receiving this because you were mentioned.Message ID: @.***>

rkurchin commented 4 days ago

@editorialbot set 1.6 as version

editorialbot commented 4 days ago

Done! version is now 1.6

rkurchin commented 4 days ago

@IonRepo, can you please make sure that the title and author list of the archive match the paper?

Also, the repo seems to have an MIT license, while the archive is CC, so please make those consistent as well.

IonRepo commented 4 days ago

Dear Editor,

Do you mean the title and author list that appears in the README.md file of the repository?

As well, I am not quite sure how to modify the license in the draft, as it seems to be predetermined by the JOSS template (I did not explicit the CC license in the draft).

Best regards, Cibrán.

Missatge de Rachel Kurchin @.***> del dia dj., 18 de jul. 2024 a les 16:00:

@IonRepo https://github.com/IonRepo, can you please make sure that the title and author list of the archive match the paper?

Also, the repo seems to have an MIT license, while the archive is CC, so please make those consistent as well.

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/6616#issuecomment-2236606508, or unsubscribe https://github.com/notifications/unsubscribe-auth/A6TPLNMFCINNKQFS5DCCLF3ZM7C67AVCNFSM6AAAAABGFVF3QGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEMZWGYYDMNJQHA . You are receiving this because you were mentioned.Message ID: @.***>

rkurchin commented 4 days ago

I'm referring to the title of the Zenodo archive.

Similarly, for the license, I'm talking about the license listed on Zenodo vs. the one in your repository; they do not currently match each other.

IonRepo commented 4 days ago

Hi again,

Thank you, all the information has been updated in Zenodo accordingly.

Best regards, Cibrán.

Missatge de Rachel Kurchin @.***> del dia dj., 18 de jul. 2024 a les 17:09:

I'm referring to the title of the Zenodo archive.

Similarly, for the license, I'm talking about the license listed on Zenodo vs. the one in your repository; they do not currently match each other.

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/6616#issuecomment-2236820040, or unsubscribe https://github.com/notifications/unsubscribe-auth/A6TPLNLYB6OIKHKILJTZOX3ZM7LB3AVCNFSM6AAAAABGFVF3QGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEMZWHAZDAMBUGA . You are receiving this because you were mentioned.Message ID: @.***>

rkurchin commented 3 days ago

@editorialbot set 10.5281/zenodo.12771455 as archive

editorialbot commented 3 days ago

Done! archive is now 10.5281/zenodo.12771455

rkurchin commented 3 days ago

@editorialbot recommend-accept

editorialbot commented 3 days ago

Attempting dry run of processing paper acceptance...

editorialbot commented 3 days ago

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

OK DOIs

- 10.17172/NOMAD/2024.04.01-1 is OK
- 10.1039/D2MH01516A is OK
- 10.1021/jacs.3c13279 is OK
- 10.48550/arXiv.1201.0490 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.1103/PhysRevB.54.11169 is OK
- 10.1103/PhysRevLett.127.025901 is OK
- 10.1038/s41524-023-00996-8 is OK
- 10.1088/0034-4885/67/7/R05 is OK
- 10.1021/acsami.7b11687 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 3 days ago

:wave: @openjournals/bcm-eics, this paper is ready to be accepted and published.

Check final proof :point_right::page_facing_up: Download article

If the paper PDF and the deposit XML files look good in https://github.com/openjournals/joss-papers/pull/5651, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

openjournals / joss-reviews

[REVIEW]: IonDiff: command-line tool to identify ionic diffusion events and hopping correlations in molecular dynamics simulations #6616

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Best wishes, Claudio Cazorla

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