[REVIEW]: pyCADMium: Chemical Atoms in Diatomic Molecules. A prolate spheroidal Python module for embedding calculations.

editorialbot commented 2 years ago

Submitting author: !--author-handle-->@VHchavez@lucydot<!--end-editor-- Reviewers: @raghurama123, @srmnitc Archive: 10.5281/zenodo.7039713

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Reviewer instructions & questions

@raghurama123 & @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 @lucydot know.

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📝 Checklist for @raghurama123

lucydot commented 2 years ago

Ok @VHchavez, looks good to me now - I'll ping the editors-in-chief team

VHchavez commented 2 years ago

Awesome. Thank you :) @lucydot

lucydot commented 2 years ago

@editorialbot set 10.5281/zenodo.7039713 as archive

editorialbot commented 2 years ago

Done! Archive is now 10.5281/zenodo.7039713

lucydot commented 2 years ago

@editorialbot set v0.9.1 as version

editorialbot commented 2 years ago

Done! version is now v0.9.1

lucydot commented 2 years ago

@editorialbot reocommend-accept

editorialbot commented 2 years ago

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

@editorialbot commands

lucydot commented 2 years ago

@editorialbot recommend-accept

editorialbot commented 2 years ago

Attempting dry run of processing paper acceptance...

editorialbot commented 2 years ago

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

OK DOIs

- 10.18257/raccefyn.960 is OK
- 10.1103/physreva.82.024501 is OK
- 10.1021/jp504058s is OK
- 10.1021/acs.jctc.6b01050 is OK
- 10.1063/1.5051455 is OK
- 10.1002/qua.25425 is OK
- 10.1002/wcms.1617 is OK
- 10.1126/science.1158722 is OK
- 10.1103/physrevlett.91.146401 is OK
- 10.1016/j.cpc.2012.05.007 is OK
- 10.1021/ct800485v is OK
- 10.1063/1.1535422 is OK
- 10.1016/c2009-1-28537-6 is OK
- 10.1002/qua.24355 is OK
- 10.1039/C5CP00351B is OK
- 10.1063/1.5003825 is OK
- 10.1063/1.442958 is OK

MISSING DOIs

- Errored finding suggestions for "Modern quantum chemistry: introduction to advanced...", please try later

INVALID DOIs

- None

editorialbot commented 2 years ago

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

Check final proof :point_right::page_facing_up: Download article

If the paper PDF and the deposit XML files look good in https://github.com/openjournals/joss-papers/pull/3510, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

danielskatz commented 2 years ago

@VHchavez - I'm the AEiC who will finalize this. I see a few changes needed, as shown in https://github.com/wasserman-group/pyCADMium/pull/11 - please merge this, or let me know what you disagree with, then we can continue to acceptance and publication.

VHchavez commented 2 years ago

Hello @danielskatz. Merged.

danielskatz commented 2 years ago

@editorialbot recommend-accept

editorialbot commented 2 years ago

Attempting dry run of processing paper acceptance...

editorialbot commented 2 years ago

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

OK DOIs

- 10.18257/raccefyn.960 is OK
- 10.1103/physreva.82.024501 is OK
- 10.1021/jp504058s is OK
- 10.1021/acs.jctc.6b01050 is OK
- 10.1063/1.5051455 is OK
- 10.1002/qua.25425 is OK
- 10.1002/wcms.1617 is OK
- 10.1126/science.1158722 is OK
- 10.1103/physrevlett.91.146401 is OK
- 10.1016/j.cpc.2012.05.007 is OK
- 10.1021/ct800485v is OK
- 10.1063/1.1535422 is OK
- 10.1016/c2009-1-28537-6 is OK
- 10.1002/qua.24355 is OK
- 10.1039/C5CP00351B is OK
- 10.1063/1.5003825 is OK
- 10.1063/1.442958 is OK

MISSING DOIs

- Errored finding suggestions for "Modern quantum chemistry: introduction to advanced...", please try later

INVALID DOIs

- None

editorialbot commented 2 years ago

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

Check final proof :point_right::page_facing_up: Download article

If the paper PDF and the deposit XML files look good in https://github.com/openjournals/joss-papers/pull/3512, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

danielskatz commented 2 years ago

@editorialbot accept

editorialbot commented 2 years ago

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

editorialbot commented 2 years ago

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

editorialbot commented 2 years ago

🚨🚨🚨 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 :point_right: https://github.com/openjournals/joss-papers/pull/3513
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.04459
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

danielskatz commented 2 years ago

Congratulations to @VHchavez (Victor Hugo Gonzalez Chavez) and co-authors!!

And thanks to @raghurama123 and @srmnitc for reviewing, and @lucydot for editing! We couldn't do this without you

editorialbot commented 2 years ago

:tada::tada::tada: Congratulations on your paper acceptance! :tada::tada::tada:

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susilehtola commented 2 years ago

@lucydot

The current reference to Libxc is not Marques et al 2012 but

S. Lehtola, C. Steigemann, M. J. T. Oliveira, and M. A. L. Marques, Recent developments in LIBXC — a comprehensive library of functionals for density functional theory, SoftwareX 7, 1 (2018). doi:10.1016/j.softx.2017.11.002

Fully numerical calculations on atoms and diatomic molecules have been recently reviewed in

S. Lehtola, A review on non-relativistic fully numerical electronic structure calculations on atoms and diatomic molecules, Int. J. Quantum Chem. 119, e25968 (2019). doi:10.1002/qua.25968

An open-source implementation of the finite element method for diatomic molecules in the prolate spheroidal coordinate system has been described in

S. Lehtola, Fully numerical Hartree–Fock and density functional calculations. II. Diatomic molecules, Int. J. Quantum Chem. 119, e25944 (2019). doi:10.1002/qua.25944

Note that HelFEM is open source, as well, and includes a full interface to Libxc.

I also I do not see any writeup of the algorithms or method of solution used in the code.

VHchavez commented 2 years ago

Thanks for the additional references!

choochoo-bot commented 2 years ago

Thanks @susilehtola I'll ask other editors if it is possible to update the Libxc reference somehow.

RE: algorithms,methods of solutions: I don't know if you have seen the more extensive documentation online - perhaps not? (https://wasserman-group.github.io/pyCADMium/coordinate_system.html). A JOSS paper is designed to give a more high-level overview of functionality rather than dig into the details of underlying methods.

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