[REVIEW]: Atomic Simulation Interface (ASI): application programming interface for electronic structure codes #5186

editorialbot · 2023-02-22T16:30:11Z

Submitting author: @PavelStishenko (Pavel Stishenko)
Repository: https://gitlab.com/pvst/asi
Branch with paper.md (empty if default branch): master
Version: 1.1.0
Editor: @rkurchin
Reviewers: @xwang862, @junghans, @srmnitc
Archive: 10.5281/zenodo.7931108

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/a46f8b3148ab3fe19c0e51f620ba5815/status.svg)](https://joss.theoj.org/papers/a46f8b3148ab3fe19c0e51f620ba5815)

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

@xwang862 & @junghans & @srmnitc, 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 @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 @xwang862

📝 Checklist for @junghans

📝 Checklist for @srmnitc

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

editorialbot · 2023-02-22T16:30:14Z

Hello humans, I'm @editorialbot, a robot that can help you with some common editorial tasks.

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

@editorialbot commands

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

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editorialbot · 2023-02-22T16:30:17Z

Software report:

github.com/AlDanial/cloc v 1.88  T=0.08 s (911.0 files/s, 68823.1 lines/s)
---------------------------------------------------------------------------------------
Language                             files          blank        comment           code
---------------------------------------------------------------------------------------
C++                                      8            229             35           1357
Python                                  15            249            306           1052
TeX                                      1             42              1            350
Bourne Shell                            28            141              9            294
C/C++ Header                             4            116            190            185
Markdown                                 3            100              0            174
YAML                                     2             12              4            169
CMake                                    3             76            169             95
reStructuredText                         5             72             74             74
make                                     3             27              7             64
Windows Module Definition                3             20              0             62
DOS Batch                                1              8              1             26
TOML                                     1              2              0             25
---------------------------------------------------------------------------------------
SUM:                                    77           1094            796           3927
---------------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

editorialbot · 2023-02-22T16:30:19Z

Wordcount for paper.md is 2196

editorialbot · 2023-02-22T16:31:38Z

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

editorialbot · 2023-02-22T16:31:42Z

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

OK DOIs

- 10.1088/1361-648x/aa680e is OK
- 10.1021/acs.jctc.8b01036 is OK
- 10.1063/5.0012901 is OK
- 10.1103/PhysRevX.8.041048 is OK
- 10.1021/acs.jctc.8b00908 is OK
- 10.1103/PhysRevLett.114.096405 is OK
- 10.1126/science.aag2302 is OK
- 10.1021/acs.jctc.8b00873 is OK
- 10.1038/s41467-019-12875-2 is OK
- 10.1063/5.0004608 is OK
- 10.1063/5.0005082 is OK
- 10.1063/5.0007045 is OK
- 10.1063/1.5143190 is OK
- 10.1103/PhysRevB.71.035109 is OK
- 10.21105/jcon.00069 is OK
- 10.1021/ct400698y is OK
- 10.1021/acs.jctc.1c00751 is OK
- 10.1038/s41524-022-00843-2 is OK

MISSING DOIs

- 10.1016/j.cpc.2017.09.007 may be a valid DOI for title: ELSI: A unified software interface for Kohn–Sham electronic structure solvers

INVALID DOIs

- https://doi.org/10.1016/j.cpc.2020.107459 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/j.cpc.2012.05.007 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/j.softx.2017.11.002 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/j.cpc.2009.06.022 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1002/wcms.93 is INVALID because of 'https://doi.org/' prefix

rkurchin · 2023-02-22T16:36:11Z

@PavelStishenko, please fix the DOI issues above whenever you have a chance (not urgent to get review started, but will be necessary before we can accept the submission).

Reviewers @xwang862, @junghans, @srmnitc, please let me know if you have any questions about how to proceed!

editorialbot · 2023-02-25T19:08:16Z

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

editorialbot · 2023-02-25T19:13:19Z

Hello @PavelStishenko, 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

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

# Perform checks on the repository
@editorialbot check repository

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

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

# 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 · 2023-02-25T19:13:59Z

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

OK DOIs

- 10.1088/1361-648x/aa680e is OK
- 10.1021/acs.jctc.8b01036 is OK
- 10.1063/5.0012901 is OK
- 10.1016/j.cpc.2017.09.007 is OK
- 10.1016/j.cpc.2020.107459 is OK
- 10.1016/j.cpc.2012.05.007 is OK
- 10.1016/j.softx.2017.11.002 is OK
- 10.1103/PhysRevX.8.041048 is OK
- 10.1021/acs.jctc.8b00908 is OK
- 10.1103/PhysRevLett.114.096405 is OK
- 10.1126/science.aag2302 is OK
- 10.1021/acs.jctc.8b00873 is OK
- 10.1038/s41467-019-12875-2 is OK
- 10.1063/5.0004608 is OK
- 10.1063/5.0005082 is OK
- 10.1063/5.0007045 is OK
- 10.1016/j.cpc.2009.06.022 is OK
- 10.1063/1.5143190 is OK
- 10.1103/PhysRevB.71.035109 is OK
- 10.1002/wcms.93 is OK
- 10.21105/jcon.00069 is OK
- 10.1021/ct400698y is OK
- 10.1021/acs.jctc.1c00751 is OK
- 10.1038/s41524-022-00843-2 is OK

MISSING DOIs

- None

INVALID DOIs

- None

rkurchin · 2023-03-03T00:10:30Z

Hi @xwang862, @junghans, @srmnitc, reminder to get this review started whenever you can!

xwang862 · 2023-03-03T20:13:58Z

@rkurchin Sorry for the delay, I'll try to get this review done by the end of next week.

xwang862 · 2023-03-10T20:24:12Z

Review checklist for @xwang862

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://gitlab.com/pvst/asi?
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 (@PavelStishenko) 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?

junghans · 2023-03-13T16:47:57Z

Review checklist for @junghans

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://gitlab.com/pvst/asi?
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 (@PavelStishenko) 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?

junghans · 2023-03-13T16:56:45Z

Re: contributing to the ASI see https://gitlab.com/pvst/asi/-/issues/2

srmnitc · 2023-03-15T07:32:00Z

Review checklist for @srmnitc

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://gitlab.com/pvst/asi?
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 (@PavelStishenko) 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?

junghans · 2023-03-17T16:38:17Z

Re: contributing to the ASI see https://gitlab.com/pvst/asi/-/issues/2

Fixed

xwang862 · 2023-03-22T01:24:39Z

@PavelStishenko thanks for the nice work. I find this software useful and the summary paper clearly written. A few comments below:

I had an installation error. Could be my own issue, but please address it.
Please add more details in your build instructions. For example, to correctly build DFTB+, one needs to clone your forked repo, switch to branch api-H-import, follow the "building from source" method, etc. To set environment variables, should one just copy and modify your envs examples? Which variables are necessary and which are optional?
Please add explanations/comments to help users better understand your usage example.
Please add documentation to the tests (in tests/ dir), as many people would learn by adapting those test files. Although the filenames indicate their usage to some extent, it would be helpful if you add descriptions within each file, e.g. what does a test do, which DFT code is used, purposes of functions/code blocks, etc.

rkurchin · 2023-04-07T16:06:22Z

@PavelStishenko, just checking in on this!

PavelStishenko · 2023-04-08T17:11:35Z

@PavelStishenko, just checking in on this!

@rkurchin We are working on the @xwang862 suggestions. Aiming to complete and respond on the next week.

PavelStishenko · 2023-04-17T15:11:22Z

@xwang862 , thanks for the review! The answers are in the quotes below:

* I had an [installation error](https://gitlab.com/pvst/asi/-/issues/4). Could be my own issue, but please address it.

Thanks for helping with debugging that issue. It turns out, that the MacOS support is not currently not available. Adding of the MacOS support is a future work. The list of currently supported and tested platforms has been added to the documentation.

* Please add more details in your [build instructions](https://gitlab.com/pvst/asi#building). For example, to correctly build DFTB+, one needs to clone your forked repo, switch to branch `api-H-import`, follow the "building from source" method, etc. To set environment variables, should one just copy and modify your `envs` examples? Which variables are necessary and which are optional?

The documentation of the building process has been significantly extended. Necessary and optional environment variables have been listed and described. The building scripts have been refactored aiming to simplicity. The envs directory is removed, because the new documentation has necessary examples and supersedes it.

* Please add explanations/comments to help users better understand your [usage example](https://pvst.gitlab.io/asi/intro.html#usage-example).

Comments have been added into the code of the usage example.

* Please add documentation to the tests (in `tests/` dir), as many people would learn by adapting those test files. Although the filenames indicate their usage to some extent, it would be helpful if you add descriptions within each file, e.g. what does a test do, which DFT code is used, purposes of functions/code blocks, etc.

The documentation has been added for tests building and running. Descriptions have been added for each test.

xwang862 · 2023-04-21T00:20:54Z

Thanks @PavelStishenko for your extensive responses. My comments have been appropriately addressed. 👍

rkurchin · 2023-04-22T18:34:35Z

Thanks, @xwang862. Checking in on @srmnitc's review progress?

rkurchin · 2023-04-28T15:38:41Z

🔔 Pinging @srmnitc again – the other two reviews are finished, so we're just waiting on you here!

rkurchin · 2023-05-12T19:49:28Z

@editorialbot set 1.1.0 as version

editorialbot · 2023-05-12T19:49:30Z

Done! version is now 1.1.0

rkurchin · 2023-05-12T19:53:03Z

@PavelStishenko it looks like the archive has a CCA4.0 license while the repo has an MIT license. Can we make those match up?

PavelStishenko · 2023-05-12T20:01:57Z

@PavelStishenko it looks like the archive has a CCA4.0 license while the repo has an MIT license. Can we make those match up?

Fixed!

rkurchin · 2023-05-12T21:54:38Z

@editorialbot set 10.5281/zenodo.7931108 as archive

editorialbot · 2023-05-12T21:54:40Z

Done! archive is now 10.5281/zenodo.7931108

rkurchin · 2023-05-12T21:55:01Z

@editorialbot recommend-accept

editorialbot · 2023-05-12T21:55:02Z

Attempting dry run of processing paper acceptance...

editorialbot · 2023-05-12T21:55:07Z

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

OK DOIs

- 10.1088/1361-648x/aa680e is OK
- 10.1021/acs.jctc.8b01036 is OK
- 10.1063/5.0012901 is OK
- 10.1016/j.cpc.2017.09.007 is OK
- 10.1016/j.cpc.2020.107459 is OK
- 10.1016/j.cpc.2012.05.007 is OK
- 10.1016/j.softx.2017.11.002 is OK
- 10.1103/PhysRevX.8.041048 is OK
- 10.1021/acs.jctc.8b00908 is OK
- 10.1103/PhysRevLett.114.096405 is OK
- 10.1126/science.aag2302 is OK
- 10.1021/acs.jctc.8b00873 is OK
- 10.1038/s41467-019-12875-2 is OK
- 10.1063/5.0004608 is OK
- 10.1063/5.0005082 is OK
- 10.1063/5.0007045 is OK
- 10.1016/j.cpc.2009.06.022 is OK
- 10.1063/1.5143190 is OK
- 10.1103/PhysRevB.71.035109 is OK
- 10.1002/wcms.93 is OK
- 10.21105/jcon.00069 is OK
- 10.1021/ct400698y is OK
- 10.1021/acs.jctc.1c00751 is OK
- 10.1038/s41524-022-00843-2 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.1016/j.cpc.2020.107688 is OK
- 10.1021/acs.jctc.1c00834 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot · 2023-05-12T21:56:56Z

👋 @openjournals/bcm-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#4223, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

Kevin-Mattheus-Moerman · 2023-05-13T10:18:26Z

@PavelStishenko I'm the AEiC on this track and here to help pieces the final steps. Below are some items that require your attention.

Can you creat a tagged release on your repository with the label '1.1.0'. As listed here and on the archived version. Your repository currently lists "Tags 0".

PavelStishenko · 2023-05-13T13:23:07Z

@Kevin-Mattheus-Moerman The tag has been added

rkurchin · 2023-05-16T20:06:21Z

Ping @Kevin-Mattheus-Moerman are we good to go here?

Kevin-Mattheus-Moerman · 2023-05-17T13:32:23Z

@rkurchin @PavelStishenko sorry for the delay. Nearly there.

@PavelStishenko Can you check if ommiting auxilary should be omitting auxiliary?

PavelStishenko · 2023-05-17T14:04:03Z

Thanks @Kevin-Mattheus-Moerman ! The typo is fixed.

Kevin-Mattheus-Moerman · 2023-05-17T20:52:20Z

@editorialbot generate pdf

editorialbot · 2023-05-17T20:53:37Z

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

Kevin-Mattheus-Moerman · 2023-05-17T20:55:24Z

@editorialbot accept

editorialbot · 2023-05-17T20:55:26Z

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

editorialbot · 2023-05-17T20:57:42Z

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: Stishenko
  given-names: Pavel V.
  orcid: "https://orcid.org/0000-0003-4653-9899"
- family-names: Keal
  given-names: Thomas W.
  orcid: "https://orcid.org/0000-0001-8747-3975"
- family-names: Woodley
  given-names: Scott M.
  orcid: "https://orcid.org/0000-0003-3418-9043"
- family-names: Blum
  given-names: Volker
  orcid: "https://orcid.org/0000-0001-8660-7230"
- family-names: Hourahine
  given-names: Benjamin
  orcid: "https://orcid.org/0000-0002-7667-7101"
- family-names: Maurer
  given-names: Reinhard J.
  orcid: "https://orcid.org/0000-0002-3004-785X"
- family-names: Logsdail
  given-names: Andrew J.
  orcid: "https://orcid.org/0000-0002-2277-415X"
contact:
- family-names: Stishenko
  given-names: Pavel V.
  orcid: "https://orcid.org/0000-0003-4653-9899"
- family-names: Logsdail
  given-names: Andrew J.
  orcid: "https://orcid.org/0000-0002-2277-415X"
doi: 10.5281/zenodo.7931108
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Stishenko
    given-names: Pavel V.
    orcid: "https://orcid.org/0000-0003-4653-9899"
  - family-names: Keal
    given-names: Thomas W.
    orcid: "https://orcid.org/0000-0001-8747-3975"
  - family-names: Woodley
    given-names: Scott M.
    orcid: "https://orcid.org/0000-0003-3418-9043"
  - family-names: Blum
    given-names: Volker
    orcid: "https://orcid.org/0000-0001-8660-7230"
  - family-names: Hourahine
    given-names: Benjamin
    orcid: "https://orcid.org/0000-0002-7667-7101"
  - family-names: Maurer
    given-names: Reinhard J.
    orcid: "https://orcid.org/0000-0002-3004-785X"
  - family-names: Logsdail
    given-names: Andrew J.
    orcid: "https://orcid.org/0000-0002-2277-415X"
  date-published: 2023-05-17
  doi: 10.21105/joss.05186
  issn: 2475-9066
  issue: 85
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 5186
  title: "Atomic Simulation Interface (ASI): application programming
    interface for electronic structure codes"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.05186"
  volume: 8
title: "Atomic Simulation Interface (ASI): application programming
  interface for electronic structure codes"

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editorialbot · 2023-05-17T20:57:48Z

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Kevin-Mattheus-Moerman · 2023-05-18T07:50:03Z

Congratulations on this paper @PavelStishenko

Thanks for editing @rkurchin, and a special thanks to the reviewers: @xwang862, @junghans, @srmnitc

editorialbot · 2023-05-18T07:50:05Z

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editorialbot added CMake Makefile review Shell Track: 2 (BCM) Biomedical Engineering, Biosciences, Chemistry, and Materials labels Feb 22, 2023

editorialbot assigned rkurchin Feb 22, 2023

editorialbot mentioned this issue Feb 22, 2023

[PRE REVIEW]: Atomic Simulation Interface (ASI): application programming interface for electronic structure codes #5011

Closed

editorialbot added the recommend-accept Papers recommended for acceptance in JOSS. label May 12, 2023

editorialbot added accepted published Papers published in JOSS labels May 17, 2023

Kevin-Mattheus-Moerman closed this as completed May 18, 2023

editorialbot mentioned this issue Jun 25, 2024

[PRE REVIEW]: ASIMTools: A lightweight workflow and simulation manager for reproducible atomistic simulations #6929

Closed

[REVIEW]: Atomic Simulation Interface (ASI): application programming interface for electronic structure codes #5186

[REVIEW]: Atomic Simulation Interface (ASI): application programming interface for electronic structure codes #5186

Comments

editorialbot commented Feb 22, 2023 • edited Loading

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editorialbot commented Feb 22, 2023

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rkurchin commented Feb 22, 2023

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rkurchin commented Mar 3, 2023

xwang862 commented Mar 3, 2023

xwang862 commented Mar 10, 2023 • edited Loading

Review checklist for @xwang862

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junghans commented Mar 13, 2023 • edited Loading

Review checklist for @junghans

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Software paper

junghans commented Mar 13, 2023

srmnitc commented Mar 15, 2023 • edited Loading

Review checklist for @srmnitc

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

junghans commented Mar 17, 2023

xwang862 commented Mar 22, 2023

rkurchin commented Apr 7, 2023

PavelStishenko commented Apr 8, 2023

PavelStishenko commented Apr 17, 2023

xwang862 commented Apr 21, 2023

rkurchin commented Apr 22, 2023

rkurchin commented Apr 28, 2023 • edited Loading

rkurchin commented May 12, 2023

editorialbot commented May 12, 2023

rkurchin commented May 12, 2023

PavelStishenko commented May 12, 2023

rkurchin commented May 12, 2023

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rkurchin commented May 12, 2023

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Kevin-Mattheus-Moerman commented May 13, 2023 • edited Loading

PavelStishenko commented May 13, 2023

rkurchin commented May 16, 2023

Kevin-Mattheus-Moerman commented May 17, 2023

PavelStishenko commented May 17, 2023

Kevin-Mattheus-Moerman commented May 17, 2023

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Kevin-Mattheus-Moerman commented May 17, 2023

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Kevin-Mattheus-Moerman commented May 18, 2023

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editorialbot commented Feb 22, 2023 •

edited

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xwang862 commented Mar 10, 2023 •

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junghans commented Mar 13, 2023 •

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srmnitc commented Mar 15, 2023 •

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rkurchin commented Apr 28, 2023 •

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Kevin-Mattheus-Moerman commented May 13, 2023 •

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