[PRE REVIEW]: QMCTorch: a PyTorch Implementation of Real-Space Quantum Monte Carlo Simulations of Molecular Systems

[editorialbot]

Submitting author: !--author-handle-->@NicoRenaud<!--end-author-handle-- (Nicolas Renaud) Repository: https://github.com/NLESC-JCER/QMCTorch Branch with paper.md (empty if default branch): master Version: v0.3.0 Editor: !--editor-->@jarvist<!--end-editor-- Reviewers: @tonnylou44853, @scemama, @AbdAmmar Managing EiC: Kevin M. Moerman

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

@NicoRenaud if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). In addition, this list of people have already agreed to review for JOSS and may be suitable for this submission (please start at the bottom of the list).

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.22 s (1200.1 files/s, 127985.7 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                         153           5719           5360          11789
reStructuredText                86            338            506            528
Jupyter Notebook                10              0           2743            211
TeX                              1             19              0            140
YAML                             3             19              9             93
Markdown                         5             40              0             87
make                             1              4              6             10
-------------------------------------------------------------------------------
SUM:                           259           6139           8624          12858
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 1627

[editorialbot]

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

OK DOIs

- 10.1103/physrevb.99.085121 is OK
- 10.1088/1361-648X/aab9c3 is OK
- 10.1063/5.0139024 is OK
- 10.1103/PhysRevResearch.2.033429 is OK
- 10.1038/s41557-020-0544-y is OK
- 10.1002/jcc.1056 is OK
- 10.1063/1.4948778 is OK

MISSING DOIs

- 10.1007/978-3-642-38718-0_14 may be a valid DOI for title: QMC=Chem: A Quantum Monte Carlo Program for Large-Scale Simulations in Chemistry at the Petascale Level and beyond

INVALID DOIs

- None

[editorialbot]

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

[Kevin-Mattheus-Moerman]

@NicoRenaud thanks for this submission. I am the AEiC for this track and here to help process initial steps. I have just assigned the waitlisted label, since the editors in this domain are currently preoccupied with other submissions. I'll assign an editor as soon as one becomes available. In the mean time, could you address the above potentially missing DOI ☝️ You can fix the .bib file if needed, and call @editorialbot check references to check them again, and use @editorialbot generate pdf to update the paper draft.

[Kevin-Mattheus-Moerman]

@jarvist this seems like your cup of tea 🍵 , however you are handling several other submissions already. I've waitlisted this for now, but let me know if this could be something you can help handle when the time comes. Thanks.

[NicoRenaud]

@editorialbot check references

[editorialbot]

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

@editorialbot commands

[NicoRenaud]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.1103/physrevb.99.085121 is OK
- 10.1088/1361-648X/aab9c3 is OK
- 10.1007/978-3-642-38718-0_14 is OK
- 10.1063/5.0139024 is OK
- 10.1103/PhysRevResearch.2.033429 is OK
- 10.1038/s41557-020-0544-y is OK
- 10.1002/jcc.1056 is OK
- 10.1063/1.4948778 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[NicoRenaud]

@editorialbot generate pdf

[editorialbot]

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

@editorialbot commands

[NicoRenaud]

@editorialbot commands

[editorialbot]

Hello @NicoRenaud, here are the things you can ask me to do:

# List all available commands
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@editorialbot list editors

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@editorialbot check references

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[NicoRenaud]

@editorialbot generate pdf

[NicoRenaud]

@Kevin-Mattheus-Moerman I think the references are correct now ! Looking forward to the review

[editorialbot]

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

[jarvist]

@editorialbot assign @jarvist as editor

This is indeed in my vague area, so I should take it!

@NicoRenaud - any suggestions for reviewers? Are you associated with any of the Ferminet / Paulinet researchers?

Generally I'd say from skim reading the Article, it seems quite early to have a JOSS paper on this package. Have you published any scientific research with it yet? It was a bit unclear to me what the statement of need encoded: is the key thing having the variational ansatz automatically differentiable? Or an efficient GPU implementation of QMC? Also, what flavour of QMC do you implement? Just VMC?

Separately, on a technical note, your Article PDF is > 12MB, which we need to do something about. Probably this is due to high resolution PNGs being used as figures.

[editorialbot]

Assigned! @jarvist is now the editor

[NicoRenaud]

@jarvist Thanks for being an editor on this.

@NicoRenaud - any suggestions for reviewers? Are you associated with any of the Ferminet / Paulinet researchers?

I quickly talked to the Paulinet authors but we are not associated in any way.

Generally I'd say from skim reading the Article, it seems quite early to have a JOSS paper on this package. Have you published any scientific research with it yet?

I haven't published a scientific paper about it, the main reason being a lack of time for this project on my side. Ideally it would be great to have both a scientific and a JOSS paper but the former will come much later ...

It was a bit unclear to me what the statement of need encoded: is the key thing having the variational ansatz automatically differentiable? Or an efficient GPU implementation of QMC?

The key idea is that we have a way of encoding well tested wave function encoded in a differentiable model, which allows to easily explore different flavor of jastrow/backflow etc ... On top of that we have GPU implementation that is not so prevalent in the QMC world. I can make both points more clear in the statement of need.

Also, what flavour of QMC do you implement? Just VMC?

It is only VMC and now that you are pointing that out I notice it's not mentionned. I will add it to the text.

Separately, on a technical note, your Article PDF is > 12MB, which we need to do something about. Probably this is due to high resolution PNGs being used as figures.

I'll reduce the figure size and reupload everything

Thanks !

[NicoRenaud]

@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:

[NicoRenaud]

@jarvist I've slightly modified the text/figures to address your initial comments.

As a potential reviewer, I would suggest Anthony Scemama who is the main developer of QMC=CHEM and an excellent software engineer. We have interacted in the past, trying to organize a workshop with other people, but we never worked together otherwise.

You also mentionned that you though it was quite early for a JOSS paper, I'm wondering why and how to adress this concern.

Thanks !

[jarvist]

Thanks for the suggestions, I've sent an email to Anthony, and have a provisional yes from someone who works on Ferminet.

[jarvist]

You also mentionned that you though it was quite early for a JOSS paper, I'm wondering why and how to adress this concern.

It's basically this bit, under 'substantial scholarly effort': https://joss.readthedocs.io/en/latest/submitting.html#substantial-scholarly-effort

It's much easier to justify this if the code is already used in scientific papers, already used by groups outside the originator etc. In this case, I suppose you will have to explain quite directly the unique features that mean that this code will go on to be used in the future.

[jarvist]

@editorialbot add @tonnylou44853 to reviewers

Thank you Tonny for offering to review 🎉

[editorialbot]

@tonnylou44853 added to the reviewers list!

[jarvist]

@editorialbot add @scemama to reviewers

[editorialbot]

@scemama added to the reviewers list!

[jarvist]

@editorialbot add @AbdAmmar to reviewers

[editorialbot]

@AbdAmmar added to the reviewers list!

[jarvist]

Thank you Abdallah Ammar and Anthony Scemama for offering to review!

[jarvist]

@editorialbot start review

Let's get this party started! 🎉

[editorialbot]

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/5472.