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

[editorialbot]

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

Status

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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

@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

[editorialbot]

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

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

@editorialbot commands

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

@editorialbot generate pdf

[editorialbot]

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]

Wordcount for paper.md is 2196

[editorialbot]

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

[editorialbot]

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]

@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]

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

[editorialbot]

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]

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]

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

[xwang862]

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

[xwang862]

Review checklist for @xwang862

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://gitlab.com/pvst/asi?
• [x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• [x] 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?
• [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?

[junghans]

Review checklist for @junghans

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://gitlab.com/pvst/asi?
• [x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• [x] 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?
• [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?

[junghans]

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

[srmnitc]

Review checklist for @srmnitc

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://gitlab.com/pvst/asi?
• [x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• [x] 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?
• [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?

[junghans]

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

Fixed

[xwang862]

@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]

@PavelStishenko, just checking in on this!

[PavelStishenko]

@PavelStishenko, just checking in on this!

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

[PavelStishenko]

@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]

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

[rkurchin]

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

[rkurchin]

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

[srmnitc]

@rkurchin I apologize the delay from my side due to some other commitements. I will finish the review on by 02.05. I hope this is ok.

[srmnitc]

@rkurchin @PavelStishenko I have now finished my review. I only have few minor points about the paper for which I have started this issue. Apart from these, this submission is complete and could be useful for the community.

[rkurchin]

@editorialbot generate post-review checklist

Thanks everyone for your help on this review! The command above will generate a checklist to keep track of the last few things we need to take care of before accepting this submission.

[editorialbot]

I'm sorry human, I don't understand that. You can see what commands I support by typing:

@editorialbot commands

[rkurchin]

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

• [x] Double check authors and affiliations (including ORCIDs)
• [x] 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.
• [x] Archive the release on Zenodo/figshare/etc and post the DOI here.
• [x] Make sure that the title and author list (including ORCIDs) in the archive match those in the JOSS paper.
• [x] 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 PR)
• [x] Check the references in the paper for corrections (e.g. capitalization)
• [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]

@editorialbot check references

[editorialbot]

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]

@editorialbot generate pdf

[editorialbot]

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

[rkurchin]

A few small editorial comments (thanks also to @srmnitc for his in the aforementioned issue):

• line 26: "pluggable" feels awkward – do you mean "interoperable" here?
• line 30: I would add a "such as" into the parenthetical
• 38-39: I would rephrase the end of this to "due to their explicit dependence on the specific electronic structure code used"
• 39, 45: hyphenate "machine-learning" here; it's acting as a compound adjective
• 46: suggest rephrase to "direct prediction of energies and forces"
• 48: not certain what "addressed" means here – should it be "developed" perhaps?
• 50: change to "...set of material properties"
• 51: no need to hyphenate reinforcement learning here, but "ground-state" should be hyphenated (again, compound adjective)
• 52: hyphenate "deep-learning"
• 63-64: a few typos, should read "...do provide Python or Julia API's and thus simplify development of new functionality."
• 87: if after other edits, table 1 header is still on the previous page to the table, maybe address that too
• in table 1: hyphenate "single-point"
• also in table 1: I would put parentheses around "after ASI_init"
• table 1: "Supported partitioning schemes depend [remove S] on implementation"
• figure 1: suggest to change "...depends on a specific..." to "...depends on the particular..."
• 88: add "the" before "ASI library"
• 88: change "build" to "built"
• 90: change "overheads" to "overhead"
• 93: hyphenate "control-flow"
• 95: remove "a" from "a direct access"
• 97: missing Oxford comma in parenthetical (after "overlap")
• 107: hyphenate "density-matrix"
• 108: hyphenate "machine-learning"
• 110: missing a "to" after "expected"
• 115: I would replace "Also" with "In addition" and add a comma after
• 120: add comma after "Therefore"
• 123: add "the" before ctypes
• 124: cite numpy
• 126: cite ScaLAPACK
• 165: missing space after "example"
• 166: add comma after "files"

A few conceptual comments also since this is close enough to my own area of expertise that I feel comfortable making them 😄 :

• it would be good to add in a comparison to some of MolSSI's efforts in this area so folks can understand what's similar/different about what you've built
• in addition to the ML and QM/MM angles, I would think that AIMD could be another use case for this (e.g. "plug-and-play" between different DFT codes for forces and MD engines for time evolution). If you agree, you could mention that too!

Please also do the checks suggested in the checklist above and send me the info (version number, DOI) to attach to this submission. We're almost there! 🚀

[PavelStishenko]

@editorialbot generate pdf

[PavelStishenko]

@editorialbot check references

[editorialbot]

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
- 10.1021/acs.jctc.1c00834 is OK

MISSING DOIs

- None

INVALID DOIs

- doi.org/10.1016/j.cpc.2020.107688 is INVALID because of 'doi.org/' prefix

[editorialbot]

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

[PavelStishenko]

@editorialbot check references

[editorialbot]

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

[PavelStishenko]

@editorialbot generate pdf

[editorialbot]

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

[PavelStishenko]

@srmnitc , thanks for the review. Your comments in the issue were addressed and necessary correction has been introduced.

@rkurchin , thanks for your notes. All suggested corrections has been introduced. Thanks for the conceptual comments. The MolSSI Driver Interface is really related and should be mentioned here. The appropriate citation also was added. And yes, indeed, the ASI API really fits to facilitate AIMD workflows. The corresponding additions has been made.

[rkurchin]

@editorialbot check references

[editorialbot]

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

[rkurchin]

Great! So to finish this up, you just need to help me finish the checklist above – in particular, the items under the "author tasks" header.

[PavelStishenko]

Here are: version: 1.1.0 DOI: 10.5281/zenodo.7931108

[rkurchin]

@editorialbot set 1.1.0 as version

[editorialbot]

Done! version is now 1.1.0

[rkurchin]

@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]

@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!