[PRE REVIEW]: State-Averaged Orbital-Optimized VQE: A quantum algorithm for the democratic description of ground and excited electronic states

[editorialbot]

Submitting author: !--author-handle-->@MartinBeseda<!--end-author-handle-- (Martin Beseda) Repository: https://gitlab.com/MartinBeseda/sa-oo-vqe-qiskit.git Branch with paper.md (empty if default branch): Version: v1.0.0 Editor: !--editor-->@matthewfeickert<!--end-editor-- Reviewers: @alejandrogallo, @erikkjellgren Managing EiC: Kevin M. Moerman

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/adbd388232798291d6d3613b7059bee9"><img src="https://joss.theoj.org/papers/adbd388232798291d6d3613b7059bee9/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/adbd388232798291d6d3613b7059bee9/status.svg)](https://joss.theoj.org/papers/adbd388232798291d6d3613b7059bee9)

Author instructions

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

@MartinBeseda 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

[editorialbot]

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]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.08 s (469.0 files/s, 143195.8 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
SVG                              5              0             72           4401
Python                          18            887           1171           2655
Jupyter Notebook                 2              0            579            677
Markdown                         4            137              0            327
TeX                              1             17              0            176
YAML                             3              7              0             38
reStructuredText                 2             25             44             29
DOS Batch                        1              8              1             26
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                            37           1085           1874           8338
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 1152

[editorialbot]

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

OK DOIs

- 10.1051/0004-6361/201629272 is OK
- 10.1051/0004-6361/201322068 is OK

MISSING DOIs

- 10.1016/0009-2614(89)85347-3 may be a valid DOI for title: The CASSCF state interaction method
- 10.1021/acs.jctc.3c00182.s001 may be a valid DOI for title: The OpenMolcas Web: A Community-Driven Approach to Advancing Computational Chemistry
- 10.1021/acs.jctc.1c00995 may be a valid DOI for title: Analytical nonadiabatic couplings and gradients within the state-averaged orbital-optimized variational quantum eigensolver
- 10.1088/2058-9565/abd334 may be a valid DOI for title: A state-averaged orbital-optimized hybrid quantum–classical algorithm for a democratic description of ground and excited states
- 10.1103/physrevx.10.011004 may be a valid DOI for title: Increasing the representation accuracy of quantum simulations of chemistry without extra quantum resources
- 10.1021/acs.jctc.9b00919.s001 may be a valid DOI for title: Analytical gradient theory for quasidegenerate N-electron valence state perturbation theory (QD-NEVPT2)
- 10.1063/1.3596699 may be a valid DOI for title: Extended multi-configuration quasi-degenerate perturbation theory: The new approach to multi-state multi-reference perturbation theory
- 10.1063/1.5096217 may be a valid DOI for title: Trajectory surface hopping molecular dynamics simulation by spin-flip time-dependent density functional theory
- 10.1073/pnas.1619152114 may be a valid DOI for title: Elucidating reaction mechanisms on quantum computers

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]

@MartinBeseda thanks for this submission. I am the AEiC on this track and here to help with the initial steps. For the moment can you try to address the above potentially missing DOIs? You can add them to your .bib file where possible (and where correct, our system is may be wrong), and use the following to check the references again:

@editorialbot check references

And the following to update the paper draft:

@editorialbot generate pdf

[MartinBeseda]

@Kevin-Mattheus-Moerman Thank you very much, I'll have a look at it.

[MartinBeseda]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.1016/0009-2614(89)85347-3 is OK
- 10.1021/acs.jctc.3c00182 is OK
- 10.1021/acs.jctc.1c00995 is OK
- 10.1088/2058-9565/abd334 is OK
- 10.1103/PhysRevX.10.011004 is OK
- 10.1021/acs.jctc.9b00919 is OK
- 10.1063/1.3596699 is OK
- 10.1063/1.5096217 is OK
- 10.1021/acs.chemrev.9b00829 is OK
- 10.1073/pnas.1619152114 is OK
- 10.48550/arXiv.1703.04627 is OK
- 10.1051/0004-6361/201629272 is OK
- 10.1051/0004-6361/201322068 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[MartinBeseda]

@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:

[Kevin-Mattheus-Moerman]

@editorialbot invite @richardjgowers as editor

[editorialbot]

Invitation to edit this submission sent!

[Kevin-Mattheus-Moerman]

@richardjgowers :wave:

[Kevin-Mattheus-Moerman]

@editorialbot invite @richardjgowers as editor

[editorialbot]

Invitation to edit this submission sent!

[richardjgowers]

@Kevin-Mattheus-Moerman this is a little out of my area

[MartinBeseda]

@Kevin-Mattheus-Moerman I see, that so far there's no other reviewer. Should we start looking for somebody?

[Kevin-Mattheus-Moerman]

@MartinBeseda apologies for the delays encountered so far. The editors in this domain are handling other submissions. Hence I have just waitlisted this submission now. We'll assign an editor as soon as one becomes available.

[MartinBeseda]

@Kevin-Mattheus-Moerman Of course, let's wait :)

[Kevin-Mattheus-Moerman]

@matthewfeickert do you think you could help edit this one? Thanks

[Kevin-Mattheus-Moerman]

@editorialbot invite @matthewfeickert as editor

[editorialbot]

Invitation to edit this submission sent!

[matthewfeickert]

@editorialbot assign me as editor

[editorialbot]

Assigned! @matthewfeickert is now the editor

[matthewfeickert]

:wave: @MartinBeseda, before I start looking for reviewers I've noticed that:

• No public docs are listed on https://gitlab.com/MartinBeseda/sa-oo-vqe-qiskit. Please link them here (this should also be addressed generally).
• There is no published distribution of saoovqe on PyPI or conda-forge. We generally expect that software submitted to JOSS that have methods for installation via language specific package managers have distributions. There may be valid reasons for this to not be the case. Can you publish to PyPI?

[MartinBeseda]

@matthewfeickert The public docs are now mentioned in README. Also, it's published on PyPi, although, because of the dependency on Psi4 I'm thinking also about publishing on Conda-forge...

[matthewfeickert]

The public docs are now mentioned in README.

Great and thanks, @MartinBeseda. I'll note though that the docs currently won't pass the JOSS review criteria as is. In particular https://sa-oo-vqe-qiskit.readthedocs.io/en/latest/saoovqe.html isn't a suitable API reference.

As I don't want to asign reviewer time to something that at a glance isn't quite ready yet I'll make the following suggestion. First read through the Submitting a paper to JOSS and Reviewing for JOSS docs to have a good idea of what reviewers will be asked to address in advance. I would then suggest spending some time stepping through revising the docs to make sure that things are covered comprehensivley and that all reviewr questions can be answered quickly.

I can apprecaite that you're quite busy and that this isn't something that you can probably turn around in a week or so. If you think you can, that's great, and we can keep this open while you do that. If you (very reasonably) think this will take more than a couple weeks of time I would suggest that you withdraw this submission for now and then just resbumit whenever things are ready. Resubmissions are not a problem at all for JOSS and we welcome them if they allow for everyones time to be better focused in the review.

Also, it's published on PyPi, although, because of the dependency on Psi4 I'm thinking also about publishing on Conda-forge...

Nice on getting it up on PyPI (https://pypi.org/project/saoovqe/). :+1: I appreciate that you're trying to ensure that things are easily installable, as I take it that https://github.com/psi4/psi4 doesn't have bindings available on PyPI and is only installable via conda-forge (https://github.com/conda-forge/psi4-feedstock). If that's the case, it isn't required that you also package things and distribute them on conda-forge, just that the installation of all external dependencies is clearly documented, but it would be enocuraged.

[MartinBeseda]

@matthewfeickert Thank you for your warning! The documentation is written, unfortunately, during the last commits, it failed to build and I didn't get an error message, thus assuming it's OK...

Now it should be fixed on RTD. Also, if it helps, I'll put the software also on conda-forge during the next few days. Considering the dependency, it's literally listed and described both in the RTD documentation and in README.

Thank you for your work once more!

[Kevin-Mattheus-Moerman]

@matthewfeickert can you review the author's feedback here? :point_up:

[matthewfeickert]

@MartinBeseda Sorry I saw your response on the mobile app and thought I had replied, but apparently not :grimacing:, so I'll give the normal response here now. I've been looking for reviewers for your paper for the last several week without much luck, so I will continue on that this week via email.

If you have any suggestions for potential reviewers please mention them here (without tagging them with an @, e.g. matthewfeickert).

[MartinBeseda]

@matthewfeickert Hi Matthew! Don't worry, happens to all of us :smile:

I'd suggest the following guys, all with extensive experience in development of scientific software:

• J. S. Kottmann (kottmanj)
• Erik Kjellgren (erikkjellgren)
• Piotr Gawron (pgawron)

[matthewfeickert]

👋 @kottmanj As you've been recommended to as someone in the field with expertise in software development, quantum computing, quantum chemistry, and Python would you be available and willing to review this submission? If you are interested in reviewing we would like reviewers to aim to have their preliminary reviews (not fully finished!) completed within 3-4 weeks. We understand that everyone is busy and so even if you are interested your schedule might prohibit you from accepting this review at this time. Please let me know if you have any questions.

[matthewfeickert]

@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:

[editorialbot]

Five most similar historical JOSS papers:

FHI-vibes: Ab Initio Vibrational Simulations Submitting author: @flokno Handling editor: @jgostick (Active) Reviewers: @keipertk, @ajjackson Similarity score: 0.8234

ShakeNBreak: Navigating the defect configurational landscape Submitting author: @ireaml Handling editor: @rkurchin (Active) Reviewers: @obaica, @mkhorton Similarity score: 0.8227

Interface to high-performance periodic coupled-cluster theory calculations with atom-centered, localized basis functions Submitting author: @Evmoerman Handling editor: @rkurchin (Active) Reviewers: @awvwgk, @wcwitt Similarity score: 0.8164

QComms QKD Software Toolkit Submitting author: @richardcollins Handling editor: @brainstorm (Retired) Reviewers: @arturgs Similarity score: 0.8152

Ising_OPV v4.0: Experimental Tomography Data Import, Interpretation, and Analysis Submitting author: @MikeHeiber Handling editor: @katyhuff (Retired) Reviewers: @myousefi2016, @stuartcampbell, @mdoucet Similarity score: 0.8110

⚠️ 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 before considering asking the reviewers of these papers to review again for JOSS.

[matthewfeickert]

👋 @flokno As someone who has published in JOSS before in a broadly related area would you be available and willing to review this submission? If you are interested in reviewing we would like reviewers to aim to have their preliminary reviews (not fully finished!) completed within 3-4 weeks. We understand that everyone is busy and so even if you are interested your schedule might prohibit you from accepting this review at this time. Please let me know if you have any questions.

[matthewfeickert]

@MartinBeseda @Kevin-Mattheus-Moerman As a heads up I will be traveling without cell phone or internet access next week, so if potential reviewers that I've emailed show up with questions or if anything urgent comes up between now and 2023-10-21, @Kevin-Mattheus-Moerman can you please either ask them to hold or help out with some decision making?

[MartinBeseda]

@matthewfeickert Hi Matthew! Aside from the reviewers I'd like to ask you about adding affiliations both for me and S. Illesova - during the work on the paper we've both changed positions from ICGM to IT4Innovations and we need to list that. I've added the affiliations to the paper draft, if it's not a problem. Is there anything else we need to do now or is it OK like this?

[MartinBeseda]

@matthewfeickert @Kevin-Mattheus-Moerman I see, that addressed reviewers probably didn't respond so far... Should I look for another set of experts to recommend?

[matthewfeickert]

Aside from the reviewers I'd like to ask you about adding affiliations both for me and S. Illesova - during the work on the paper we've both changed positions from ICGM to IT4Innovations and we need to list that. I've added the affiliations to the paper draft, if it's not a problem. Is there anything else we need to do now or is it OK like this?

Thanks for the notice, and apologies on the delay given my travel, @MartinBeseda, but that all sounds fine and as long as you've updated it in the paper and your ORCIDs are also updated that should be fine.

I see, that addressed reviewers probably didn't respond so far.

Yes, I'm having some issues getting any response here, and as this is outside of my field of expertise I'm assuming that my work email address isn't getting much notice. I'll ask for some additional recommendations from other editors.

[matthewfeickert]

👋 @vijaymocherla As you're a JOSS reviewer in the field with expertise in software development, quantum chemistry, and Python would you be available and willing to review this submission? If you are interested in reviewing we would like reviewers to aim to have their preliminary reviews (not fully finished!) completed within 3-4 weeks. We understand that everyone is busy and so even if you are interested your schedule might prohibit you from accepting this review at this time. Please let me know if you have any questions.

[matthewfeickert]

@editorialbot add @alejandrogallo as reviewer

[editorialbot]

@alejandrogallo added to the reviewers list!

[MartinBeseda]

Thank you very much @matthewfeickert ! If you'll need anything else, I'm ready to make the modifications ASAP.

[matthewfeickert]

@editorialbot add @erikkjellgren as reviewer

[editorialbot]

@erikkjellgren added to the reviewers list!

[matthewfeickert]

@MartinBeseda We now have two reviewers (@alejandrogallo, @erikkjellgren) so I'll start the review.

We need a minimum of two reviewers, but additional reviews are very welcome, so if I get responses from other possible reviewers I may add a third later.

[matthewfeickert]

@editorialbot start review

[editorialbot]

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/6036.