[REVIEW]: QuaCa: an open-source library for fast calculations of steady-state quantum friction #5160

editorialbot · 2023-02-16T22:32:30Z

Submitting author: @myoelmy (Marty Oelschläger)
Repository: https://github.com/QuaCaTeam/quaca
Branch with paper.md (empty if default branch):
Version: v1.0
Editor: @lucydot
Reviewers: @arkajitmandal, @vijaymocherla
Archive: 10.5281/zenodo.8101845

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/0be711f1f5cf69cf3f6583e7f3ff254c/status.svg)](https://joss.theoj.org/papers/0be711f1f5cf69cf3f6583e7f3ff254c)

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

@arkajitmandal & @vijaymocherla, 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 @lucydot 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 @vijaymocherla

📝 Checklist for @arkajitmandal

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

editorialbot · 2023-02-16T22:32:31Z

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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editorialbot · 2023-02-16T22:32:35Z

Software report:

github.com/AlDanial/cloc v 1.88  T=0.96 s (867.7 files/s, 287717.4 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
C/C++ Header                   613          55637          17231         146954
HTML                             4            805            229          18860
C++                            119           5362           2358          16847
Markdown                        30            884              0           3394
SVG                              2              1              1           1906
make                             7            729            418           1291
CMake                           22            347            354           1012
TeX                              1             67              0            529
JSON                            20              0              0            352
JavaScript                       2             33             12            193
XML                              1              0              0            120
YAML                             5              5             10             65
Python                           2             14             13             62
INI                              2             11              0             54
CSS                              1              2              0             19
Bourne Shell                     1              6              0             17
MATLAB                           1              4              3              4
-------------------------------------------------------------------------------
SUM:                           833          63907          20629         191679
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

editorialbot · 2023-02-16T22:32:38Z

Wordcount for paper.md is 1247

editorialbot · 2023-02-16T22:34:25Z

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

editorialbot · 2023-02-16T22:34:43Z

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

OK DOIs

- 10.1103/PhysRevLett.123.120401 is OK
- 10.1103/PhysRevA.102.050203 is OK
- 10.1002/qute.202000155 is OK
- 10.1038/s41534-020-0252-x is OK
- 10.1103/PhysRevLett.123.120401 is OK
- 10.1103/PhysRevA.94.042114 is OK
- 10.1103/PhysRevLett.117.100402 is OK
- 10.1103/PhysRevA.89.050101 is OK
- 10.1002/lpor.201000045 is OK
- 10.1038/s41566-018-0246-9 is OK
- 10.1103/PhysRevLett.91.220801 is OK
- 10.1088/1367-2630/abac3a is OK
- 10.21105/joss.02011 is OK
- 10.1016/j.cpc.2009.11.008 is OK
- 10.1109/TAP.2015.2438393 is OK
- 10.1016/j.cpc.2009.11.008 is OK
- 10.1364/JOSAB.36.000C52 is OK
- 10.1063/5.0083067 is OK
- 10.1103/PhysRevA.97.062507 is OK
- 10.1134/1.1514767 is OK
- 10.1103/PhysRevA.80.042902 is OK
- 10.1007/978-3-642-20288-9_6 is OK
- 10.1103/PhysRevB.65.115419 is OK
- 10.3390/sym8050029 is OK
- 10.1103/PhysRevLett.106.094502 is OK
- 10.1103/RevModPhys.79.1291 is OK
- 10.1119/1.12552 is OK
- 10.1103/PhysRev.73.360 is OK
- 10.1103/PhysRevLett.55.2273 is OK

MISSING DOIs

- 10.1103/physreva.106.052205 may be a valid DOI for title: Electromagnetic Viscosity in Complex Structured Environments: From black-body to Quantum Friction
- 10.3367/ufne.2016.12.038006 may be a valid DOI for title: Fluctuation-electromagnetic interaction under dynamic and thermal nonequilibrium conditions
- 10.1088/0953-8984/9/47/001 may be a valid DOI for title: Shearing the vacuum - quantum friction
- 10.1103/physrevb.98.155405 may be a valid DOI for title: Internal Quantum Dynamics of a Nanoparticle in a Thermal Electromagnetic Field: A Minimal Model

INVALID DOIs

- https://doi.org/10.1002/andp.19103381603 is INVALID because of 'https://doi.org/' prefix
- http://dx.doi.org/10.18452/22412 is INVALID because of 'https://doi.org/' prefix

myoelmy · 2023-02-20T08:05:41Z

The DOIs should be fixed now.

lucydot · 2023-02-20T10:20:39Z

@editorialbot check references

editorialbot · 2023-02-20T10:22:06Z

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

OK DOIs

- 10.1103/PhysRevLett.123.120401 is OK
- 10.1103/PhysRevA.102.050203 is OK
- 10.1002/qute.202000155 is OK
- 10.1038/s41534-020-0252-x is OK
- 10.1002/andp.19103381603 is OK
- 10.1103/PhysRevLett.123.120401 is OK
- 10.1103/PhysRevA.94.042114 is OK
- 10.1103/PhysRevLett.117.100402 is OK
- 10.1103/PhysRevA.89.050101 is OK
- 10.1002/lpor.201000045 is OK
- 10.1038/s41566-018-0246-9 is OK
- 10.1103/PhysRevLett.91.220801 is OK
- 10.1088/1367-2630/abac3a is OK
- 10.21105/joss.02011 is OK
- 10.1016/j.cpc.2009.11.008 is OK
- 10.1109/TAP.2015.2438393 is OK
- 10.1016/j.cpc.2009.11.008 is OK
- 10.1103/physreva.106.052205 is OK
- 10.1364/JOSAB.36.000C52 is OK
- 10.1063/5.0083067 is OK
- 10.18452/22412 is OK
- 10.1103/PhysRevA.97.062507 is OK
- 10.3367/ufne.2016.12.038006 is OK
- 10.1134/1.1514767 is OK
- 10.1088/0953-8984/9/47/001 is OK
- 10.1103/PhysRevA.80.042902 is OK
- 10.1007/978-3-642-20288-9_6 is OK
- 10.1103/PhysRevB.65.115419 is OK
- 10.3390/sym8050029 is OK
- 10.1103/PhysRevLett.106.094502 is OK
- 10.1103/RevModPhys.79.1291 is OK
- 10.1119/1.12552 is OK
- 10.1103/PhysRev.73.360 is OK
- 10.1103/PhysRevLett.55.2273 is OK
- 10.1103/physrevb.98.155405 is OK

MISSING DOIs

- None

INVALID DOIs

- None

lucydot · 2023-02-20T10:33:58Z

@vijaymocherla @arkajitmandal here is the review thread. Please read the instructions at the top of the thread re: starting the review. Your first task is to generate your review checklists ✅ .

If you any questions, please just ask - it is quite a different review process than other journals.

vijaymocherla · 2023-02-23T04:07:08Z

Review checklist for @vijaymocherla

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/QuaCaTeam/quaca?
License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
Contribution and authorship: Has the submitting author (@myoelmy) 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?

lucydot · 2023-02-28T15:06:53Z

@arkajitmandal a gentle reminder of the review.

@vijaymocherla I can see you have started your review, and that you have raised issues QuaCaTeam/quaca#79, QuaCaTeam/quaca#78) in the repo, excellent!

editorialbot · 2023-02-28T16:24:44Z

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

vijaymocherla · 2023-03-03T06:34:16Z

Hi @lucydot,

I'm mostly done with my review. I didn't have any problems installing and testing the package on Linux environments. I've tested it on a few configurations and most didn't have any major issues that I couldn't easily resolve. But, I suggest the authors include a section in the documentation with known installation issues (like the one pointed out by @arkajitmandal).

Apart from that, I just have a few comments and suggestions for the authors. Also, this is the first time I'm reviewing a software paper for JOSS, so please let me know if I'm missing on any counts.

Comments

Modular structure
- Since most scientific software is modular, I would request the author to elaborate more on the modularity of QuaCa and discuss any intentional choices made from a software design perspective to make the package extensible. This was briefly mentioned in lines 67-73, but a more clear justification would be helpful.
Optimized version $F_\text{fric}$
- Though the authors have cited MEEP, I would like the authors to clearly describe the current state of other open-source packages and the exact gap that QuaCa is trying to address.
- Specifically, they have mentioned that QuaCa uses a numerically optimized version of $F_\text{fric}$. I would request the authors briefly describe the approach that is unique to QuaCa when compared with other FDTD packages that offer subroutines to calculate the Casimir force.
- Additionally, I would request the authors to comment on the applicability of the implemented optimizations and limitations of the same, if any.
Performance
- It is mentioned that QuaCa is meant for efficient computation of $F_\text{fric}$ on any regular personal computer, but providing a few performance benchmarks and minimum prescribed hardware configuration would be ideal.

Suggestions

To make it more accessible, I would recommend the authors consider improvising the documentation to provide more detailed information on creating the input file and reduce the code snippets (C++ class structures) in their documentation. Additionally, they could consider adding more information about arguments of their class methods.
I would also suggest setting a default value for the no. of threads (OMP_NUM_THREADS) to 1 (when no environment variable is set) within the package to prevent high CPU usage or oversubscription of processors which could risk crashing the system.

arkajitmandal · 2023-03-03T17:32:17Z

@lucydot to clarify : the issues that you mentioned were mine -- seems there is some issues with macs and said package. I am trying to get hold on to a linux machine -- to finish the review.

lucydot · 2023-03-05T18:00:13Z

thanks @arkajitmandal - please do create a checklist for you to check off when you next come back to review ✔️ - instructions at the top of this thread.

arkajitmandal · 2023-03-05T20:38:01Z

Review checklist for @arkajitmandal

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/QuaCaTeam/quaca?
License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
Contribution and authorship: Has the submitting author (@myoelmy) 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?

arkajitmandal · 2023-03-10T04:09:06Z

Hi @lucydot, I have checked the software and used it following the documentation provided by the authors.
The package is well written and it is undoubtedly an important contribution to the field. Presently I have the following comment that the authors should address (in addition to those mentioned by @vijaymocherla) before I can recommend this work for publication.

Installation: Presently package is nearly very difficult to install on a mac (I have tried three macs one with M1, two with intel) in all of them I have faced issued in installing. However such an issue do not arise in a linux (I tried this in Ubuntu). I think the authors have two options: (1) modify cmake to make sure the package is installable in mac (or (2) To clearly state that they do not support mac in the readme. On mac due to the problem of installation (most likely due to some issue with openmp) sometimes when it is installed the many of the test fail. The tests pass on Ubuntu.
[JOSS Review] Unit tests are failing QuaCaTeam/quaca#78 (comment)
Readme: For installing the package on linux, I see that the authors use the following line in workflows/build_and_test.yml

sudo apt-get update && sudo apt-get install libblas-dev liblapack-dev cmake make g++ libboost-filesystem-dev libboost-program-options-dev

which is very convenient. In the readme however they provide an alternate route with conda. I would suggest the author to also add this alternate installation approach in the readme.

Minor Issue : Some links do not work:
[JOSS Review] Minor Issues QuaCaTeam/quaca#79 (comment)

lucydot · 2023-03-13T10:11:57Z

Thank you very much @arkajitmandal and @vijaymocherla for your expertise, and timely reviews.

@myoelmy over to you! It looks like you have several points to act on, both from comment above ☝️ and earlier (#5160 (comment)). I expect you will not be able to resolve everything in one sitting, but please do keep us updated with your work in this thread as you progress.

lucydot · 2023-03-20T10:39:24Z

@myoelmy a gentle reminder - please see comment above ☝️

myoelmy · 2023-03-20T15:58:05Z

Hi @lucydot ,
we created some issues with respect to the comments/suggestions from @arkajitmandal and @vijaymocherla and will try to resolve them soon. And many thanks to @arkajitmandal and @vijaymocherla for reviewing!

lucydot · 2023-03-28T12:43:31Z

Thanks @myoelmy for the update, please keep in touch with how things progress. If you see updates and responses taking a significant amount of time (roughly > fortnight), please let us know. Good luck!

lucydot · 2023-07-14T08:37:37Z

@editorialbot check references

editorialbot · 2023-07-14T08:37:48Z

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

OK DOIs

- 10.1103/PhysRevLett.123.120401 is OK
- 10.1103/PhysRevA.102.050203 is OK
- 10.1002/qute.202000155 is OK
- 10.1038/s41534-020-0252-x is OK
- 10.1002/andp.19103381603 is OK
- 10.1103/PhysRevLett.123.120401 is OK
- 10.1103/PhysRevA.94.042114 is OK
- 10.1103/PhysRevLett.117.100402 is OK
- 10.18452/21484 is OK
- 10.1103/PhysRevA.89.050101 is OK
- 10.1002/lpor.201000045 is OK
- 10.1038/s41566-018-0246-9 is OK
- 10.1103/PhysRevLett.91.220801 is OK
- 10.1088/1367-2630/abac3a is OK
- 10.21105/joss.02011 is OK
- 10.1016/j.cpc.2009.11.008 is OK
- 10.1109/TAP.2015.2438393 is OK
- 10.1103/physreva.106.052205 is OK
- 10.1364/JOSAB.36.000C52 is OK
- 10.1063/5.0083067 is OK
- 10.18452/22412 is OK
- 10.1103/PhysRevA.97.062507 is OK
- 10.3367/ufne.2016.12.038006 is OK
- 10.1134/1.1514767 is OK
- 10.1088/0953-8984/9/47/001 is OK
- 10.1103/PhysRevA.80.042902 is OK
- 10.1007/978-3-642-20288-9_6 is OK
- 10.1103/PhysRevB.65.115419 is OK
- 10.3390/sym8050029 is OK
- 10.1103/PhysRevLett.106.094502 is OK
- 10.1103/RevModPhys.79.1291 is OK
- 10.1119/1.12552 is OK
- 10.1103/PhysRev.73.360 is OK
- 10.1103/PhysRevLett.55.2273 is OK
- 10.1103/physrevb.98.155405 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot · 2023-07-14T08:39:01Z

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

lucydot · 2023-07-14T08:44:25Z

I think we are good to go! 🎈

lucydot · 2023-07-14T08:44:28Z

@editorialbot recommend-accept

editorialbot · 2023-07-14T08:44:30Z

Attempting dry run of processing paper acceptance...

editorialbot · 2023-07-14T08:44:36Z

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

OK DOIs

- 10.1103/PhysRevLett.123.120401 is OK
- 10.1103/PhysRevA.102.050203 is OK
- 10.1002/qute.202000155 is OK
- 10.1038/s41534-020-0252-x is OK
- 10.1002/andp.19103381603 is OK
- 10.1103/PhysRevLett.123.120401 is OK
- 10.1103/PhysRevA.94.042114 is OK
- 10.1103/PhysRevLett.117.100402 is OK
- 10.18452/21484 is OK
- 10.1103/PhysRevA.89.050101 is OK
- 10.1002/lpor.201000045 is OK
- 10.1038/s41566-018-0246-9 is OK
- 10.1103/PhysRevLett.91.220801 is OK
- 10.1088/1367-2630/abac3a is OK
- 10.21105/joss.02011 is OK
- 10.1016/j.cpc.2009.11.008 is OK
- 10.1109/TAP.2015.2438393 is OK
- 10.1103/physreva.106.052205 is OK
- 10.1364/JOSAB.36.000C52 is OK
- 10.1063/5.0083067 is OK
- 10.18452/22412 is OK
- 10.1103/PhysRevA.97.062507 is OK
- 10.3367/ufne.2016.12.038006 is OK
- 10.1134/1.1514767 is OK
- 10.1088/0953-8984/9/47/001 is OK
- 10.1103/PhysRevA.80.042902 is OK
- 10.1007/978-3-642-20288-9_6 is OK
- 10.1103/PhysRevB.65.115419 is OK
- 10.3390/sym8050029 is OK
- 10.1103/PhysRevLett.106.094502 is OK
- 10.1103/RevModPhys.79.1291 is OK
- 10.1119/1.12552 is OK
- 10.1103/PhysRev.73.360 is OK
- 10.1103/PhysRevLett.55.2273 is OK
- 10.1103/physrevb.98.155405 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot · 2023-07-14T08:45:41Z

The paper's PDF and metadata files generation produced some warnings that could prevent the final paper from being published. Please fix them before the end of the review process.

F_{\rm CP}
       ^
unexpected control sequence \rm
expecting "%", "\\label", "\\tag", "\\nonumber" or whitespace

F_{\rm fric}
       ^
unexpected control sequence \rm
expecting "%", "\\label", "\\tag", "\\nonumber" or whitespace

editorialbot · 2023-07-14T08:46:25Z

👋 @openjournals/pe-eics, this paper is ready to be accepted and published.

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#4403, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

kyleniemeyer · 2023-07-14T20:28:11Z

Hi @chegerland, I'm doing some final checks on the paper before accepting.

To address the warning messages above, please update all the instances where you are using \rm{xx} for text in math mode; I believe the correct command is \text{xx} or \textrm{xx}.

For some other minor edits in the paper: our preferred citation style does not treat references as proper objects in sentences. You have a few instances with this (e.g., "refer to Ref. (Oelschlager 2019)" and similar on the first page). Can you revise those sentences to treat the references as footnotes instead? My suggested edits are:

Replace For a comprehensive review of quantum friction in various contexts as well as related effects in dynamical nonequilibrium, we refer, for example, to the reviews in Refs. [@volokitin2007;@dedkov2017;@reiche2022] and the references therein. with For a comprehensive review of quantum friction in various contexts as well as related effects in dynamical nonequilibrium, we refer, for example, to the reviews by @volokitin2007, @dedkov2017, and @reiche2022.
Replace For details of the procedure, we refer to Ref. [@oelschlager2019]. with @oelschlager2019 provides details of the procedure.

chegerland · 2023-07-15T11:31:58Z

Hello @kyleniemeyer, I have included all proposed changes.

kyleniemeyer · 2023-07-15T20:26:23Z

@editorialbot generate pdf

editorialbot · 2023-07-15T20:28:03Z

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

kyleniemeyer · 2023-07-15T20:34:45Z

@editorialbot recommend-accept

editorialbot · 2023-07-15T20:34:46Z

Attempting dry run of processing paper acceptance...

editorialbot · 2023-07-15T20:34:52Z

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

OK DOIs

- 10.1103/PhysRevLett.123.120401 is OK
- 10.1103/PhysRevA.102.050203 is OK
- 10.1002/qute.202000155 is OK
- 10.1038/s41534-020-0252-x is OK
- 10.1002/andp.19103381603 is OK
- 10.1103/PhysRevLett.123.120401 is OK
- 10.1103/PhysRevA.94.042114 is OK
- 10.1103/PhysRevLett.117.100402 is OK
- 10.18452/21484 is OK
- 10.1103/PhysRevA.89.050101 is OK
- 10.1002/lpor.201000045 is OK
- 10.1038/s41566-018-0246-9 is OK
- 10.1103/PhysRevLett.91.220801 is OK
- 10.1088/1367-2630/abac3a is OK
- 10.21105/joss.02011 is OK
- 10.1016/j.cpc.2009.11.008 is OK
- 10.1109/TAP.2015.2438393 is OK
- 10.1103/physreva.106.052205 is OK
- 10.1364/JOSAB.36.000C52 is OK
- 10.1063/5.0083067 is OK
- 10.18452/22412 is OK
- 10.1103/PhysRevA.97.062507 is OK
- 10.3367/ufne.2016.12.038006 is OK
- 10.1134/1.1514767 is OK
- 10.1088/0953-8984/9/47/001 is OK
- 10.1103/PhysRevA.80.042902 is OK
- 10.1007/978-3-642-20288-9_6 is OK
- 10.1103/PhysRevB.65.115419 is OK
- 10.3390/sym8050029 is OK
- 10.1103/PhysRevLett.106.094502 is OK
- 10.1103/RevModPhys.79.1291 is OK
- 10.1119/1.12552 is OK
- 10.1103/PhysRev.73.360 is OK
- 10.1103/PhysRevLett.55.2273 is OK
- 10.1103/physrevb.98.155405 is OK

MISSING DOIs

- None

INVALID DOIs

- None

kyleniemeyer · 2023-07-15T20:36:03Z

@editorialbot accept

editorialbot · 2023-07-15T20:36:05Z

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

editorialbot · 2023-07-15T20:36:15Z

👋 @openjournals/pe-eics, this paper is ready to be accepted and published.

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#4404, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

editorialbot · 2023-07-15T20:38:04Z

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: Oelschläger
  given-names: Marty
  orcid: "https://orcid.org/0000-0002-0120-9733"
- family-names: Hermann
  given-names: Simon
- family-names: Egerland
  given-names: Christoph H.
  orcid: "https://orcid.org/0000-0002-1099-6433"
- family-names: Reiche
  given-names: Daniel
  orcid: "https://orcid.org/0000-0002-6788-9794"
doi: 10.5281/zenodo.8101845
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Oelschläger
    given-names: Marty
    orcid: "https://orcid.org/0000-0002-0120-9733"
  - family-names: Hermann
    given-names: Simon
  - family-names: Egerland
    given-names: Christoph H.
    orcid: "https://orcid.org/0000-0002-1099-6433"
  - family-names: Reiche
    given-names: Daniel
    orcid: "https://orcid.org/0000-0002-6788-9794"
  date-published: 2023-07-15
  doi: 10.21105/joss.05160
  issn: 2475-9066
  issue: 87
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 5160
  title: "QuaCa: an open-source library for fast calculations of
    steady-state quantum friction"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.05160"
  volume: 8
title: "QuaCa: an open-source library for fast calculations of
  steady-state quantum friction"

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 · 2023-07-15T20:38:10Z

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot · 2023-07-15T20:38:11Z

🚨🚨🚨 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.05160 joss-papers#4405
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.05160
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

kyleniemeyer · 2023-07-15T21:59:43Z

Congratulations @myoelmy on your article's publication in JOSS! Please consider signing up as a reviewer for JOSS, if you haven't already.

Many thanks to @arkajitmandal and @vijaymocherla for reviewing this, and @lucydot for editing.

editorialbot · 2023-07-15T21:59:44Z

🎉🎉🎉 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.05160/status.svg)](https://doi.org/10.21105/joss.05160)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.05160">
  <img src="https://joss.theoj.org/papers/10.21105/joss.05160/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.05160/status.svg
   :target: https://doi.org/10.21105/joss.05160

This is how it will look in your documentation:

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editorialbot added C++ CMake Makefile review Track: 3 (PE) Physics and Engineering labels Feb 16, 2023

editorialbot assigned lucydot Feb 16, 2023

editorialbot mentioned this issue Feb 16, 2023

[PRE REVIEW]: QuaCa: an open-source library for fast calculations of steady-state quantum friction #5051

Closed

myoelmy mentioned this issue Mar 20, 2023

[JOSS Review] Comments on Modular structure and Optimized Version QuaCaTeam/quaca#80

Closed

myoelmy mentioned this issue Mar 20, 2023

[JOSS Review] Performance QuaCaTeam/quaca#81

Closed

editorialbot added the recommend-accept Papers recommended for acceptance in JOSS. label Jul 14, 2023

editorialbot added accepted published Papers published in JOSS labels Jul 15, 2023

kyleniemeyer closed this as completed Jul 15, 2023

openjournals deleted a comment from editorialbot Jul 17, 2023

[REVIEW]: QuaCa: an open-source library for fast calculations of steady-state quantum friction #5160

[REVIEW]: QuaCa: an open-source library for fast calculations of steady-state quantum friction #5160

Comments

editorialbot commented Feb 16, 2023 • edited

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Reviewer instructions & questions

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lucydot commented Feb 20, 2023

vijaymocherla commented Feb 23, 2023 • edited

Review checklist for @vijaymocherla

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Software paper

lucydot commented Feb 28, 2023

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vijaymocherla commented Mar 3, 2023

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arkajitmandal commented Mar 3, 2023 • edited

lucydot commented Mar 5, 2023

arkajitmandal commented Mar 5, 2023 • edited

Review checklist for @arkajitmandal

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

arkajitmandal commented Mar 10, 2023

lucydot commented Mar 13, 2023

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lucydot commented Mar 28, 2023

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editorialbot commented Feb 16, 2023 •

edited

vijaymocherla commented Feb 23, 2023 •

edited

arkajitmandal commented Mar 3, 2023 •

edited

arkajitmandal commented Mar 5, 2023 •

edited