[PRE REVIEW]: SPARC-X-API: Versatile Python Interface for Real-space Density Functional Theory Calculations #7565

editorialbot · 2024-12-04T12:16:34Z

Submitting author: @alchem0x2A (Tian Tian)
Repository: https://github.com/SPARC-X/SPARC-X-API
Branch with paper.md (empty if default branch): master
Version: v1.0.5
Editor: @zhubonan
Reviewers: @jacksund, @vijaymocherla, @naik-aakash
Managing EiC: Kevin M. Moerman

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/4d0595454576663f781ac193fec76f58"><img src="https://joss.theoj.org/papers/4d0595454576663f781ac193fec76f58/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/4d0595454576663f781ac193fec76f58/status.svg)](https://joss.theoj.org/papers/4d0595454576663f781ac193fec76f58)

Author instructions

Thanks for submitting your paper to JOSS @alchem0x2A. Currently, there isn't a JOSS editor assigned to your paper.

@alchem0x2A if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). You can search the list of people that have already agreed to review and may be suitable for this submission.

Editor instructions

The JOSS submission bot @editorialbot is here to help you find and assign reviewers and start the main review. To find out what @editorialbot can do for you type:

@editorialbot commands

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

editorialbot · 2024-12-04T12:16:37Z

Hello human, 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 · 2024-12-04T12:17:09Z

⚠️ An error happened when generating the pdf.

editorialbot · 2024-12-04T12:17:40Z

Software report:

github.com/AlDanial/cloc v 1.90  T=0.16 s (826.7 files/s, 225678.9 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
SVG                              6              6              6           8162
TeX                             28           2406           1028           7831
Python                          64           1796           2519           7533
JSON                             1              0              0           2543
Markdown                        26            507              0           2156
YAML                             8             29             45            469
DOS Batch                        1              8              1             26
Bourne Shell                     1              3              3             16
make                             1              8              9             16
-------------------------------------------------------------------------------
SUM:                           136           4763           3611          28752
-------------------------------------------------------------------------------

Commit count by author:

   439	T.Tian
    58	Benjamin Michael Comer
    32	Ben Comer
     8	ltimmerman3
     4	Benjamin Comer
     3	Github Action Bot
     3	Jackson Kjar
     3	Sushree Jagriti Sahoo
     3	Yorick Andeweg
     3	benjamin
     2	AJ Medford
     2	Andeweg, Yorick
     2	Andrew Medford
     2	Lucas R Timmerman
     1	
     1	Jacob Rafael Sy Paras
     1	Nianhan Tian
     1	Timmerman
     1	ajmedford

editorialbot · 2024-12-04T12:17:45Z

Paper file info:

📄 Wordcount for paper.md is 2571

✅ The paper includes a Statement of need section

editorialbot · 2024-12-04T12:17:48Z

License info:

🟡 License found: GNU General Public License v3.0 (Check here for OSI approval)

editorialbot · 2024-12-04T23:26:09Z

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

@editorialbot commands

alchem0x2A · 2024-12-04T23:26:45Z

@editorialbot generate pdf

editorialbot · 2024-12-04T23:27:14Z

⚠️ An error happened when generating the pdf. Problem with affiliations for Tian Tian, perhaps the affiliations index need quoting?.

alchem0x2A · 2024-12-04T23:34:21Z

@editorialbot generate pdf

editorialbot · 2024-12-04T23:35:55Z

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

editorialbot · 2024-12-04T23:36:39Z

Five most similar historical JOSS papers:

Surfaxe: Systematic surface calculations
Submitting author: @brlec
Handling editor: @danielskatz (Active)
Reviewers: @pzarabadip, @eihernan
Similarity score: 0.7529

Lightshow: a Python package for generating computational x-ray absorption spectroscopy input files
Submitting author: @matthewcarbone
Handling editor: @ppxasjsm (Active)
Reviewers: @maurov, @larsenkg
Similarity score: 0.7402

solid_dmft: gray-boxing DFT+DMFT materials simulations with TRIQS
Submitting author: @the-hampel
Handling editor: @rkurchin (Active)
Reviewers: @amandadumi, @shivupa
Similarity score: 0.7364

GMP-Featurizer: A parallelized Python package for efficiently computing the Gaussian Multipole features of atomic systems
Submitting author: @RayLei-TRI
Handling editor: @rkurchin (Active)
Reviewers: @isdanni, @bdice, @yw-fang
Similarity score: 0.7324

Simmate: a framework for materials science
Submitting author: @jacksund
Handling editor: @rkurchin (Active)
Reviewers: @bocklund, @utf
Similarity score: 0.7321

⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before considering asking the reviewers of these papers to review again for JOSS.

alchem0x2A · 2024-12-04T23:52:09Z

suggested reviewers

The TeX tag is probably not necessary since these lines come from TeX examples files for testing documentation parser functionality and not part of the core software.

zhubonan · 2024-12-12T09:42:50Z

Hi @Kevin-Mattheus-Moerman, I can potentially take this one.

alchem0x2A · 2025-01-07T05:46:51Z

@zhubonan @Kevin-Mattheus-Moerman Thanks for the message. It's been more than 1 month since the initial pre-review started, could the editorial team inform us whether the next steps will commence? Thx.

Kevin-Mattheus-Moerman · 2025-01-10T15:13:05Z

@editorialbot check references

editorialbot · 2025-01-10T15:13:43Z

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

✅ OK DOIs

- 10.1088/1361-651x/acdf06 is OK
- 10.1021/acs.jctc.4c00474 is OK
- 10.1063/5.0204229 is OK
- 10.1088/1361-648x/aa680e is OK
- 10.1038/s41592-019-0506-8 is OK
- 10.1103/physrevb.71.035109 is OK
- 10.1016/j.procs.2011.04.003 is OK
- 10.1063/5.0182685 is OK
- 10.1063/1.5142502 is OK
- 10.1016/0927-0256(96)00008-0 is OK
- 10.1088/1361-648x/aa8f79 is OK
- 10.1016/j.cpc.2019.107042 is OK
- 10.1016/j.cpc.2017.12.003 is OK
- 10.1103/physrevb.103.035101 is OK
- 10.1103/physreve.108.045302 is OK
- 10.1016/j.jcp.2015.12.027 is OK
- 10.1063/5.0180541 is OK
- 10.1021/acs.jctc.4c00474 is OK
- 10.1063/5.0230060 is OK
- 10.1103/revmodphys.71.1085 is OK
- 10.1088/0034-4885/75/3/036503 is OK
- 10.1016/j.cpc.2022.108594 is OK
- 10.1063/5.0006002 is OK
- 10.1088/2632-2153/ac8fe0 is OK
- 10.48550/ARXIV.2401.00096 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: i-PI 2.0: A universal force engine for advanced mo...
- No DOI given, and none found for title: i-PI 3.0: A flexible and efficient framework for a...
- No DOI given, and none found for title: M-SPARC: Matlab-Simulation Package for Ab-initio R...
- No DOI given, and none found for title: SPARC: Simulation Package for Ab-initio Real-space...
- No DOI given, and none found for title: On representing chemical environments
- No DOI given, and none found for title: Gaussian Process Regression for Materials and Mole...
- No DOI given, and none found for title: fairchem by FAIR Chemistry

❌ MISSING DOIs

- 10.1016/j.cpc.2013.10.027 may be a valid DOI for title: i-PI: A Python interface for ab initio path integr...
- 10.1016/j.softx.2022.101295 may be a valid DOI for title: Version 2.0.0 - M-SPARC: Matlab-Simulation Package...
- 10.1016/j.simpa.2024.100649 may be a valid DOI for title: SPARC v2.0.0: Spin-orbit coupling, dispersion inte...
- 10.1016/j.commatsci.2012.10.028 may be a valid DOI for title: Python Materials Genomics (pymatgen): A robust, op...

❌ INVALID DOIs

- None

Kevin-Mattheus-Moerman · 2025-01-10T15:46:44Z

@alchem0x2A Dear author, thanks for this submission. I am the AEiC on this track and here to help process the initial steps. Before we proceed, please can you have a look at the following points:

Please study the above reference check ☝️ and see if you can address any of the reported potential DOI issues. You can add/amend DOI entries in your .bib file, and call @editorialbot check references here to check them again.

Kevin-Mattheus-Moerman · 2025-01-10T15:46:58Z

@editorialbot assign @zhubonan as editor

editorialbot · 2025-01-10T15:47:01Z

Assigned! @zhubonan is now the editor

alchem0x2A · 2025-01-11T05:22:17Z

@editorialbot check references

editorialbot · 2025-01-11T05:22:36Z

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

✅ OK DOIs

- 10.1016/j.cpc.2013.10.027 is OK
- 10.1063/5.0215869 is OK
- 10.1016/j.softx.2020.100423 is OK
- 10.1016/j.softx.2022.101295 is OK
- 10.1016/j.softx.2021.100709 is OK
- 10.1016/j.simpa.2024.100649 is OK
- 10.1088/1361-651x/acdf06 is OK
- 10.1021/acs.jctc.4c00474 is OK
- 10.1063/5.0204229 is OK
- 10.1088/1361-648x/aa680e is OK
- 10.1103/PhysRevB.87.184115 is OK
- 10.1021/acs.chemrev.1c00022 is OK
- 10.1016/j.commatsci.2012.10.028 is OK
- 10.1038/s41592-019-0506-8 is OK
- 10.1103/physrevb.71.035109 is OK
- 10.1016/j.procs.2011.04.003 is OK
- 10.1063/5.0182685 is OK
- 10.1063/1.5142502 is OK
- 10.1016/0927-0256(96)00008-0 is OK
- 10.1088/1361-648x/aa8f79 is OK
- 10.1016/j.cpc.2019.107042 is OK
- 10.1016/j.cpc.2017.12.003 is OK
- 10.1103/physrevb.103.035101 is OK
- 10.1103/physreve.108.045302 is OK
- 10.1016/j.jcp.2015.12.027 is OK
- 10.1063/5.0180541 is OK
- 10.1021/acs.jctc.4c00474 is OK
- 10.1063/5.0230060 is OK
- 10.1103/revmodphys.71.1085 is OK
- 10.1088/0034-4885/75/3/036503 is OK
- 10.1016/j.cpc.2022.108594 is OK
- 10.1063/5.0006002 is OK
- 10.1088/2632-2153/ac8fe0 is OK
- 10.48550/ARXIV.2401.00096 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: i-PI 2.0: A universal force engine for advanced mo...
- No DOI given, and none found for title: fairchem by FAIR Chemistry

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

alchem0x2A · 2025-01-11T05:28:00Z

@editorialbot check references

editorialbot · 2025-01-11T05:28:18Z

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

✅ OK DOIs

- 10.1016/j.cpc.2013.10.027 is OK
- 10.1016/j.cpc.2018.09.020 is OK
- 10.1063/5.0215869 is OK
- 10.1016/j.softx.2020.100423 is OK
- 10.1016/j.softx.2022.101295 is OK
- 10.1016/j.softx.2021.100709 is OK
- 10.1016/j.simpa.2024.100649 is OK
- 10.1088/1361-651x/acdf06 is OK
- 10.1021/acs.jctc.4c00474 is OK
- 10.1063/5.0204229 is OK
- 10.1088/1361-648x/aa680e is OK
- 10.1103/PhysRevB.87.184115 is OK
- 10.1021/acs.chemrev.1c00022 is OK
- 10.1016/j.commatsci.2012.10.028 is OK
- 10.1038/s41592-019-0506-8 is OK
- 10.1103/physrevb.71.035109 is OK
- 10.1016/j.procs.2011.04.003 is OK
- 10.1063/5.0182685 is OK
- 10.1063/1.5142502 is OK
- 10.1016/0927-0256(96)00008-0 is OK
- 10.1088/1361-648x/aa8f79 is OK
- 10.1016/j.cpc.2019.107042 is OK
- 10.1016/j.cpc.2017.12.003 is OK
- 10.1103/physrevb.103.035101 is OK
- 10.1103/physreve.108.045302 is OK
- 10.1016/j.jcp.2015.12.027 is OK
- 10.1063/5.0180541 is OK
- 10.1021/acs.jctc.4c00474 is OK
- 10.1063/5.0230060 is OK
- 10.1103/revmodphys.71.1085 is OK
- 10.1088/0034-4885/75/3/036503 is OK
- 10.1016/j.cpc.2022.108594 is OK
- 10.1063/5.0006002 is OK
- 10.1088/2632-2153/ac8fe0 is OK
- 10.48550/ARXIV.2401.00096 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: fairchem by FAIR Chemistry

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

alchem0x2A · 2025-01-11T05:29:33Z

@editorialbot generate pdf

editorialbot · 2025-01-11T05:31:15Z

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

editorialbot · 2025-01-11T05:31:59Z

Five most similar historical JOSS papers:

Surfaxe: Systematic surface calculations
Submitting author: @brlec
Handling editor: @danielskatz (Active)
Reviewers: @pzarabadip, @eihernan
Similarity score: 0.7556

Lightshow: a Python package for generating computational x-ray absorption spectroscopy input files
Submitting author: @matthewcarbone
Handling editor: @ppxasjsm (Active)
Reviewers: @maurov, @larsenkg
Similarity score: 0.7423

solid_dmft: gray-boxing DFT+DMFT materials simulations with TRIQS
Submitting author: @the-hampel
Handling editor: @rkurchin (Active)
Reviewers: @amandadumi, @shivupa
Similarity score: 0.7367

Simmate: a framework for materials science
Submitting author: @jacksund
Handling editor: @rkurchin (Active)
Reviewers: @bocklund, @utf
Similarity score: 0.7359

GMP-Featurizer: A parallelized Python package for efficiently computing the Gaussian Multipole features of atomic systems
Submitting author: @RayLei-TRI
Handling editor: @rkurchin (Active)
Reviewers: @isdanni, @bdice, @yw-fang
Similarity score: 0.7334

⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before considering asking the reviewers of these papers to review again for JOSS.

alchem0x2A · 2025-01-11T16:43:59Z

@zhubonan I hope the above issue with missing DOIs has been fixed. Please kindly let me know if there's anything we need to take action before the pre-review starts. Thanks!

zhubonan · 2025-01-13T02:30:25Z

Hi @jacksund @RayLei-TRI and @lancekavalsky Would you be able to review this submission for JOSS?

JOSS is unique and takes place on GitHub. This involves reviewing the manuscript and installing/testing/reading the underlying code. You can learn more about it here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html#reviewing-for-joss

Please let me know if you are able/unable to review. Your response is greatly appreciated. Thanks in advance.

RayLei-TRI · 2025-01-16T21:12:37Z

Hi Bonan, Thank you so much for the invitation! I would very much love to contribute to JOSS, but for this particular group and project I think there is a conflict of interest, as I am a former member of that team. I would love to help with other reviews down the line though. Best, Ray

…

On Sun, Jan 12, 2025 at 6:30 PM Bonan Zhu ***@***.***> wrote: Hi @jacksund <https://github.com/jacksund> @RayLei-TRI <https://github.com/RayLei-TRI> and @lancekavalsky <https://github.com/lancekavalsky> Would you be able to review this submission for JOSS? JOSS is unique and takes place on GitHub. This involves reviewing the manuscript and installing/testing/reading the underlying code. You can learn more about it here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html#reviewing-for-joss Please let me know if you are able/unable to review. Your response is greatly appreciated. Thanks in advance. — Reply to this email directly, view it on GitHub <#7565 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AV52DLQXET4J5PWXFDSAPCT2KMQNRAVCNFSM6AAAAABTAA5P6CVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDKOBWGA3DMOJXG4> . You are receiving this because you were mentioned.Message ID: ***@***.***>

-- Confidential or protected information may be contained in this email and/or attachment. Unless otherwise marked, all TRI email communications are considered "PROTECTED" and should not be shared or distributed. Thank you.

jacksund · 2025-01-17T01:50:56Z

yep! I'd be happy to review

zhubonan · 2025-01-17T06:02:02Z

@editorialbot add @jacksund as reviewer

editorialbot · 2025-01-17T06:02:05Z

@jacksund added to the reviewers list!

zhubonan · 2025-01-17T06:11:21Z

Hi Bonan,

Thank you so much for the invitation! I would very much love to
contribute to JOSS, but for this particular group and project I think there
is a conflict of interest, as I am a former member of that team.

I would love to help with other reviews down the line though.

Best,
Ray

Thanks for letting me know and disclosing the conflict of interest. 👏
It is possible to waive the conflict if you think you make impartial judgement of this work.
The policy and some examples can be found here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html#joss-conflict-of-interest-policy

zhubonan · 2025-02-04T05:01:21Z

Hi @utf, @naik-aakash and @vijaymocherla Would you be able to review this submission for JOSS?

JOSS is unique and takes place on GitHub. This involves reviewing the manuscript and installing/testing/reading the underlying code. You can learn more about it here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html#reviewing-for-joss

Please let me know if you are able/unable to review. Your response is greatly appreciated. Thanks in advance.

vijaymocherla · 2025-02-04T07:32:47Z

@zhubonan Yes, I'd be happy to review this. However, I'd need about a week or so, to take out some time to look into the package and check a couple of tests before I can send out my comments.

utf · 2025-02-04T08:32:56Z

Hi @zhubonan, unfortunately, I don't have much time at the moment to complete this review.

zhubonan · 2025-02-04T09:08:30Z

@editorialbot add @vijaymocherla as reviewer

editorialbot · 2025-02-04T09:08:32Z

@vijaymocherla added to the reviewers list!

naik-aakash · 2025-02-04T09:25:52Z

Hi @zhubonan, I see two reviewers have already been assigned to this submission. Is a third reviewer needed?

zhubonan · 2025-02-04T09:43:03Z

Hi @zhubonan, I see two reviewers have already been assigned to this submission. Is a third reviewer needed?

Yes, having a third reviewer would be great. We usually have two to three reviewers for each submission. Two is the minimum.

naik-aakash · 2025-02-04T10:23:12Z

Hi @zhubonan, I see two reviewers have already been assigned to this submission. Is a third reviewer needed?

Yes, having a third reviewer would be great. We usually have two to three reviewers for each submission. Two is the minimum.

Then, I am also available and glad to review this submission.

zhubonan · 2025-02-05T01:07:55Z

@editorialbot add @naik-aakash as reviewer

editorialbot · 2025-02-05T01:07:58Z

@naik-aakash added to the reviewers list!

zhubonan · 2025-02-05T01:08:08Z

@editorialbot start review

editorialbot · 2025-02-05T01:08:12Z

OK, I've started the review over in #7747.

editorialbot added pre-review Track: 2 (BCM) Biomedical Engineering, Biosciences, Chemistry, and Materials labels Dec 4, 2024

editorialbot added Python TeX labels Dec 4, 2024

editorialbot assigned zhubonan Jan 10, 2025

editorialbot assigned jacksund Jan 17, 2025

editorialbot assigned vijaymocherla Feb 4, 2025

editorialbot assigned naik-aakash Feb 5, 2025

editorialbot closed this as completed Feb 5, 2025

[PRE REVIEW]: SPARC-X-API: Versatile Python Interface for Real-space Density Functional Theory Calculations #7565

[PRE REVIEW]: SPARC-X-API: Versatile Python Interface for Real-space Density Functional Theory Calculations #7565

Comments

editorialbot commented Dec 4, 2024 • edited Loading

Status

editorialbot commented Dec 4, 2024

editorialbot commented Dec 4, 2024

editorialbot commented Dec 4, 2024

editorialbot commented Dec 4, 2024

editorialbot commented Dec 4, 2024

editorialbot commented Dec 4, 2024

alchem0x2A commented Dec 4, 2024

editorialbot commented Dec 4, 2024

alchem0x2A commented Dec 4, 2024

editorialbot commented Dec 4, 2024

editorialbot commented Dec 4, 2024

alchem0x2A commented Dec 4, 2024 • edited Loading

zhubonan commented Dec 12, 2024

alchem0x2A commented Jan 7, 2025

Kevin-Mattheus-Moerman commented Jan 10, 2025

editorialbot commented Jan 10, 2025

Kevin-Mattheus-Moerman commented Jan 10, 2025

Kevin-Mattheus-Moerman commented Jan 10, 2025

editorialbot commented Jan 10, 2025

alchem0x2A commented Jan 11, 2025

editorialbot commented Jan 11, 2025

alchem0x2A commented Jan 11, 2025

editorialbot commented Jan 11, 2025

alchem0x2A commented Jan 11, 2025

editorialbot commented Jan 11, 2025

editorialbot commented Jan 11, 2025

alchem0x2A commented Jan 11, 2025

zhubonan commented Jan 13, 2025

RayLei-TRI commented Jan 16, 2025 via email

jacksund commented Jan 17, 2025

zhubonan commented Jan 17, 2025

editorialbot commented Jan 17, 2025

zhubonan commented Jan 17, 2025

zhubonan commented Feb 4, 2025

vijaymocherla commented Feb 4, 2025

utf commented Feb 4, 2025

zhubonan commented Feb 4, 2025

editorialbot commented Feb 4, 2025

naik-aakash commented Feb 4, 2025

zhubonan commented Feb 4, 2025

naik-aakash commented Feb 4, 2025

zhubonan commented Feb 5, 2025

editorialbot commented Feb 5, 2025

zhubonan commented Feb 5, 2025

editorialbot commented Feb 5, 2025

editorialbot commented Dec 4, 2024 •

edited

Loading

alchem0x2A commented Dec 4, 2024 •

edited

Loading