[REVIEW]: Time-frequency component of the Green-X library: minimax grids for efficient RPA and GW calculations #5570

editorialbot · 2023-06-18T18:24:31Z

Submitting author: @aziziph (Maryam Azizi)
Repository: https://github.com/nomad-coe/greenX
Branch with paper.md (empty if default branch): main
Version: v1.0.0
Editor: @lucydot
Reviewers: @mailhexu, @DarioALeonValido
Archive: 10.5281/zenodo.8321618

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/47a495c8d6c180bfb278762fc06cb992/status.svg)](https://joss.theoj.org/papers/47a495c8d6c180bfb278762fc06cb992)

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

@mailhexu & @DarioALeonValido, 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:

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The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @lucydot 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 @DarioALeonValido

📝 Checklist for @mailhexu

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

editorialbot · 2023-06-18T18:24:33Z

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editorialbot · 2023-06-18T18:24:34Z

Software report:

github.com/AlDanial/cloc v 1.88  T=0.05 s (997.6 files/s, 197311.0 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Fortran 90                      15            261            416           5899
TeX                              1             21              0            754
Markdown                        10            133              0            441
Python                           7            150            134            398
CMake                           11            116            282            388
YAML                             2             12              6             70
C/C++ Header                     1              0              0             10
TOML                             1              0              0              3
-------------------------------------------------------------------------------
SUM:                            48            693            838           7963
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

editorialbot · 2023-06-18T18:24:36Z

Wordcount for paper.md is 2761

editorialbot · 2023-06-18T18:24:36Z

Failed to discover a valid open source license

editorialbot · 2023-06-18T18:24:41Z

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

OK DOIs

- 10.1021/acs.jctc.1c00488 is OK
- 10.1103/PhysRevB.92.081104 is OK
- 10.1038/s41550-017-0220-3 is OK
- 10.2307/j.ctvc778ff is OK
- 10.1051/0004-6361/201629272 is OK
- 10.1051/0004-6361/201322068 is OK
- 10.6084/m9.figshare.828487 is OK
- 10.1007/978-3-642-61609-9 is OK
- 10.3389/fchem.2019.00377 is OK
- 10.1103/PhysRevB.78.085125 is OK
- 10.1145/1874391.187410 is OK
- 10.1007/s00791-018-00308-4 is OK
- 10.1007/s00791-018-00308-4 is OK
- 10.1103/PhysRev.126.413 is OK
- 10.1103/PhysRev.129.62 is OK
- 10.1063/1.462485 is OK
- 10.1021/ct5001268 is OK
- 10.1103/PhysRevB.90.054115 is OK
- 10.1103/PhysRevB.94.165109 is OK
- 10.1021/acs.jctc.0c01282 is OK
- 10.1103/PhysRevLett.74.1827 is OK
- 10.1103/PhysRev.139.A796 is OK
- 10.1002/wcms.1344 is OK
- 10.1103/PhysRevB.84.241201 is OK
- 10.1103/PhysRevB.71.193102 is OK
- 10.1021/acs.jctc.6b00380 is OK
- 10.1038/s41597-020-0385-y is OK
- 10.1021/acs.jctc.0c00693 is OK
- 10.1021/acs.jpclett.7b02740 is OK
- 10.1021/acs.jctc.7b00770 is OK
- 10.1088/1367-2630/14/5/053020 is OK
- 10.1007/BF00655090 is OK
- 10.48550/arXiv.1108.4417 is OK
- 10.1016/S0010-4655(98)00174-X is OK
- 10.1103/PhysRevB.13.4274 is OK
- 10.1103/PhysRevA.73.012511 is OK
- 10.1103/PhysRevB.96.155207 is OK
- 10.1016/j.cpc.2018.09.003 is OK
- 10.1016/j.cpc.2014.10.021 is OK
- 10.1021/acs.jctc.9b01235 is OK
- 10.1021/acs.jctc.1c00101 is OK
- 10.1021/acs.jctc.1c00308 is OK
- 10.48550/arXiv.2303.09979 is OK
- 10.1021/acs.jctc.0c00600 is OK
- 10.1021/acs.jctc.8b00177 is OK
- 10.1021/acs.jctc.6b01235 is OK
- 10.1021/acs.jctc.2c00774 is OK
- 10.1063/1.5090605 is OK
- 10.1016/0009-2614(91)80078-C is OK
- 10.1063/1.1809602 is OK
- 10.1103/PhysRevB.94.035118 is OK
- 10.1007/s10853-012-6570-4 is OK
- 10.1007/s00214-011-1084-8 is OK
- 10.1021/ct4002202 is OK
- 10.1103/RevModPhys.74.601 is OK
- 10.1021/acs.jctc.6b00840 is OK
- 10.1021/acs.jctc.6b00840 is OK
- 10.1103/PhysRevB.85.155129 is OK
- 10.1016/j.cpc.2017.06.012 is OK

MISSING DOIs

- None

INVALID DOIs

- -- is INVALID
- 10.33892Ffchem.2021.736591 is INVALID

editorialbot · 2023-06-18T18:26:05Z

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

AlexBuccheri · 2023-06-18T22:42:49Z

@aziziph My suggestion is wait for the reviewer feedback, then open an MR off of this issue, which addresses the points. The reviewers can then check diff and confirm we have sufficiently addressed points/concerns.

DarioALeonValido · 2023-06-21T07:50:10Z

Review checklist for @DarioALeonValido

Conflict of interest

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

I confirm that I read and will adhere to the JOSS code of conduct.

General checks

Repository: Is the source code for this software available at the https://github.com/nomad-coe/greenX?
License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
Contribution and authorship: Has the submitting author (@aziziph) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
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.
Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
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

Installation: Does installation proceed as outlined in the documentation?
Functionality: Have the functional claims of the software been confirmed?
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

A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
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

Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
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?
State of the field: Do the authors describe how this software compares to other commonly-used packages?
Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
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?

DarioALeonValido · 2023-06-21T13:43:33Z

@aziziph

Dear Maryam and other authors, I find this library potentially very useful. However, my main concern so far is regarding validation and performance, that are left to an unpublished paper (Azizi et al 2023).

I suggest you to include here at lest a simple example illustrating the efficiency of the minimax grids. Maybe it could be done by integrating a toy function, but I also would like to see if you can get an estimate of how much it is reduced the prefactor of low-scaling MP2/RPA/GW calculations to justify the exclusive use of this particular quadrature.

Another related question. In line 150 of the pdf you specify that the number of time/frequency points in the library ranges from 2 to 64, how are these values related to the final accuracy of correlation and quasi-particle energies?

lucydot · 2023-06-28T08:40:40Z

Hi @aziziph, re-pinging the message above.

The review process in JOSS is different from other journals in that it is more of a conversation back and forth (rather than a review that is completed in one go, which is then responded to in one go). My advice would be to start responding to points as they are raised. Usually the review process will include several merged PRs, and the reviewers keep track using the checklist.

As mentioned in the pre-review, I suggest renaming the license file to LICENSE.txt as that is standard for gh repos (and will be automatically recognised as a license by gh), and there are a couple of invalid DOIs reported in the thread above.

mailhexu · 2023-06-30T14:58:09Z

Review checklist for @mailhexu

Conflict of interest

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

I confirm that I read and will adhere to the JOSS code of conduct.

General checks

Repository: Is the source code for this software available at the https://github.com/nomad-coe/greenX?
License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
Contribution and authorship: Has the submitting author (@aziziph) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
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.
Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
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

Installation: Does installation proceed as outlined in the documentation?
Functionality: Have the functional claims of the software been confirmed?
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

A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
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

Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
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?
State of the field: Do the authors describe how this software compares to other commonly-used packages?
Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
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?

lucydot · 2023-07-02T19:42:42Z

Hello @mailhexu @aziziph @DarioALeonValido
Just to let you know that I am at a conference for the next week; will check in again w/c 10th July.

mailhexu · 2023-07-02T21:29:49Z

@aziziph Dear Mariam and other authors,

Thanks for making this library available! I think it can be very useful.

I found a few minor issues during the reviewing procedure:
I opened a few minor issues:
nomad-coe/greenX#48
nomad-coe/greenX#49
nomad-coe/greenX#51
nomad-coe/greenX#52
And a PR:
nomad-coe/greenX#50

I have some minor suggestions below:

I find it unclear whether some part of the Summary is referring to GreenX as a whole or specifically discussing its time-frequency component. For instance, in line 22, "the package" appears to refer to the GreenX library, while the subsequent sentences seem to focus more on the time-frequency component. Using an acronym like GXTF for the component could potentially provide clarity even though the time-frequency library is currently the only functional component in GreenX, based on the presence of multiple directories with the prefix "GreenX-" with only "README" files inside the main branch (correct me if the other components are already developped). This might confuse the fut
I didn't find the mentioning of the documentation of the API in the manuscript. The method of compiling and opening the documentation is indeed in the README.md, but it doesn't seem straightforward to know what is inside. Some introduction of the contents should be helpful. To put it online (e.g. in github pages or readthedocs.io) can also be helpful.
An example code of using it (as provided in the doxygen documentation) is helpful if it is made more easily accessible (e.g. in an example directory).

AlexBuccheri · 2023-07-05T13:36:28Z

@mailhexu Not sure it will let me tag you as a reviewer, but here's the MR addressing issues 49 and 51:

nomad-coe/greenX#54

mailhexu · 2023-07-05T15:35:09Z

@mailhexu Not sure it will let me tag you as a reviewer, but here's the MR addressing issues 49 and 51:

nomad-coe/greenX#54

It seems I cannot review the MR. But I had a look and it seems the issues are well addressed.

aziziph · 2023-07-12T09:45:04Z

@aziziph

Dear Maryam and other authors, I find this library potentially very useful. However, my main concern so far is regarding validation and performance, that are left to an unpublished paper (Azizi et al 2023).

I suggest you to include here at lest a simple example illustrating the efficiency of the minimax grids. Maybe it could be done by integrating a toy function, but I also would like to see if you can get an estimate of how much it is reduced the prefactor of low-scaling MP2/RPA/GW calculations to justify the exclusive use of this particular quadrature.

Another related question. In line 150 of the pdf you specify that the number of time/frequency points in the library ranges from 2 to 64, how are these values related to the final accuracy of correlation and quasi-particle energies?

We thank the referee for the suggestion. The editor already remarked on the length of the paper "JOSS papers are short advertisements for the software package, and as a guideline the word count is 250-1000 words. Your paper currently exceeds this guideline by a significant amount." Since it is not possible to shorten the paper without sacrificing clarity, it seems that adding further material to the paper is not appropriate. However, we agree that it is highly interesting to compare minimax grids against standard time and frequency grids, which we will report extensively in an unpublished work, referenced as Azizi2023. We are happy to provide here an example. In this test, we evaluate the RPA total energy of CH4 using a Gauss-Legendre grid, a modified Gauss-Legendre grid (so far the standard in FHI-aims and abinit), and minimax grids. An accuracy of 10^-6 eV is reached with 10 minimax grid points while the modified Gauss-Legendre grids requires 36 points for this accuracy (Please see the following figure).

Error differences of the total RPA energy [eV] of methane calculated using the Gauss-Legendre, modified Gauss-Legendre and minimax imaginary frequency grid points. These differences were calculated with respect to the lowest RPA energy obtained with 34 minimax grid points. The ground state energy was calculated using the PBE exchange correlation functional in combination of the Tier2 basis set. The global resolution of identity (RI-V) approach was used for the calculation of the exact exchange and RPA correlation energy. The auxiliary basis functions for the RI-V method were generated automatically on the fly. #

DarioALeonValido · 2023-07-13T08:17:02Z

@aziziph

Dear Maryam, thanks for providing this example. These results seem very promising indeed. Since you are using the minimax grid as a reference, I wonder if the Gauss-Legendre grid is converging to a different value around 10^-3 eV. I guess you will comment on this in the benchmarking paper.

I see that all the issues raised by the other referee have been corrected, so I am happy to recommend the paper for publication without further ado.

All the best,
Dario A. Leon

lucydot · 2023-07-13T10:25:33Z

Hi @DarioALeonValido - thanks for your expertise in reviewing the paper.

Hi @aziziph @AlexBuccheri - I agree that there is not space for the efficiency comparison in the JOSS paper. As this is the key performance claim of the software, a link to this comparison in the documentation or in a paper published elsewhere is required. Ideally it would be both. I note that the paper you link to is currently unpublished - is there a pre-print available?

I agree with @mailhexu that the documentation is quite inaccessible in its current form; requiring user installation to access (I think, it is not clear) function-level documentation. It is not easy for potential users to understand the software capabilities and use cases without reading the JOSS paper, which requires pdf download.

I suggest you make this information (software capabilities, use cases, API docs) available as webpages. This could be hosted on github pages, for example. At a minimum, this information (minus the API docs) need to be available on the README.md.

Happy to discuss this more if anything is unclear. Exploring previous repos published in JOSS can be a good way to find strong documentation examples. I can see this is being discussed on the issue here.

lucydot · 2023-07-13T10:28:22Z

A follow on note to say that by having a documentation webpage you will be able to cut the details in your JOSS paper. The JOSS paper is an advert for the repo, it does not need to go into details of the implementation (it is not the place for the e.g. mathematical framework section). This is better in the online docs.

DarioALeonValido · 2023-07-13T19:15:01Z

@lucydot

Dear Lucy, thank you very much for providing this possible solution. I coincide with you that an illustrative example in support of the claims of the library should be available at a preprint of the benchmarking reference or somewhere else beside this thread.

lucydot · 2023-07-20T08:59:07Z

Dear @aziziph @AlexBuccheri @Panadestein -

A heads up that I am going on annual leave until the 8th of August.

The primary outstanding issue relates to documentation, which I can see is under discussion (nomad-coe/greenX#59). If you have any questions relating to this I will briefly have access to internet this Monday 24th, otherwise I will be off-grid!

There are also some more minor issues raised by @mailhexu (nomad-coe/greenX#48 nomad-coe/greenX#49 nomad-coe/greenX#51 nomad-coe/greenX#52).

Hopefully this gives a good timeline for completion; I will check back here ASAP after returning from AL as I think we are getting close to the end!

Lucy

editorialbot · 2023-10-02T08:47:14Z

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

OK DOIs

- 10.1038/s41550-017-0220-3 is OK
- 10.2307/j.ctvc778ff is OK
- 10.1051/0004-6361/201629272 is OK
- 10.1051/0004-6361/201322068 is OK
- 10.6084/m9.figshare.828487 is OK
- 10.1007/978-3-642-61609-9 is OK
- 10.3389/fchem.2019.00377 is OK
- 10.1103/PhysRevB.78.085125 is OK
- 10.1145/1874391.187410 is OK
- 10.1007/s00791-018-00308-4 is OK
- 10.1021/acs.jctc.3c00555 is OK
- 10.1007/s00791-018-00308-4 is OK
- 10.1103/PhysRev.126.413 is OK
- 10.1103/PhysRev.129.62 is OK
- 10.1063/1.462485 is OK
- 10.1021/ct5001268 is OK
- 10.1103/PhysRevB.90.054115 is OK
- 10.1103/PhysRevB.94.165109 is OK
- 10.1021/acs.jctc.0c01282 is OK
- 10.1103/PhysRevLett.74.1827 is OK
- 10.1103/PhysRev.139.A796 is OK
- 10.1002/wcms.1344 is OK
- 10.1103/PhysRevB.84.241201 is OK
- 10.1103/PhysRevB.71.193102 is OK
- 10.1021/acs.jctc.6b00380 is OK
- 10.1038/s41597-020-0385-y is OK
- 10.1021/acs.jctc.0c00693 is OK
- 10.1021/acs.jpclett.7b02740 is OK
- 10.1021/acs.jctc.7b00770 is OK
- 10.1088/1367-2630/14/5/053020 is OK
- 10.1007/BF00655090 is OK
- 10.48550/arXiv.1108.4417 is OK
- 10.1016/S0010-4655(98)00174-X is OK
- 10.1103/PhysRevB.13.4274 is OK
- 10.1103/PhysRevA.73.012511 is OK
- 10.1103/PhysRevB.96.155207 is OK
- 10.1016/j.cpc.2018.09.003 is OK
- 10.1016/j.cpc.2014.10.021 is OK
- 10.1021/acs.jctc.9b01235 is OK
- 10.1021/acs.jctc.1c00101 is OK
- 10.1021/acs.jctc.1c00308 is OK
- 10.3389/fchem.2021.736591 is OK
- 10.1021/acs.jctc.3c00512 is OK
- 10.1021/acs.jctc.0c00600 is OK
- 10.1021/acs.jctc.8b00177 is OK
- 10.1021/acs.jctc.6b01235 is OK
- 10.1021/acs.jctc.2c00774 is OK
- 10.1063/1.5090605 is OK
- 10.1016/0009-2614(91)80078-C is OK
- 10.1063/1.1809602 is OK
- 10.1103/PhysRevB.94.035118 is OK
- 10.1007/s10853-012-6570-4 is OK
- 10.1007/s00214-011-1084-8 is OK
- 10.1021/ct4002202 is OK
- 10.1103/RevModPhys.74.601 is OK
- 10.1021/acs.jctc.6b00840 is OK
- 10.1103/PhysRevB.85.155129 is OK
- 10.1016/j.cpc.2017.06.012 is OK
- 10.48550/arXiv.2306.16066 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot · 2023-10-02T08:48:26Z

👋 @openjournals/pe-eics, this paper is ready to be accepted and published.

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#4641, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

arfon · 2023-10-02T08:53:19Z

Looks like this is fixed now. I'll let @kyleniemeyer take over from here.

lucydot · 2023-10-02T10:21:04Z

Thanks @Panadestein and the rest of the team, got there in the end!

dgolze · 2023-10-02T12:47:55Z

@lucydot is action required from our side? Do we have to reply in openjournals/joss-papers#4641

kyleniemeyer · 2023-10-03T17:05:30Z

@dgolze nothing at the moment - I'm going to do some final checks before publishing. I'll let you know if we need any changes. You could review the final PDF, though!

kyleniemeyer · 2023-10-03T17:33:22Z

@dgolze just a question: can you explain why GW is italicized in the title and text, while other acronyms like RPA are not?

aziziph · 2023-10-03T18:08:13Z

It's in Italic because of convention.
@kyleniemeyer

kyleniemeyer · 2023-10-03T18:16:57Z

OK, thanks @aziziph!

kyleniemeyer · 2023-10-03T18:17:11Z

@editorialbot accept

editorialbot · 2023-10-03T18:17:13Z

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

editorialbot · 2023-10-03T18:19:26Z

Ensure proper citation by uploading a plain text CITATION.cff file to the default branch of your repository.

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CITATION.cff

cff-version: "1.2.0"
authors:
- family-names: Azizi
  given-names: Maryam
  orcid: "https://orcid.org/0000-0001-9089-1043"
- family-names: Wilhelm
  given-names: Jan
  orcid: "https://orcid.org/0000-0001-8678-8246"
- family-names: Golze
  given-names: Dorothea
  orcid: "https://orcid.org/0000-0002-2196-9350"
- family-names: Giantomassi
  given-names: Matteo
  orcid: "https://orcid.org/0000-0002-7007-9813"
- family-names: Panadés-Barrueta
  given-names: Ramón L.
  orcid: "https://orcid.org/0000-0003-4239-0978"
- family-names: Delesma
  given-names: Francisco A.
  orcid: "https://orcid.org/0000-0001-6912-7745"
- family-names: Buccheri
  given-names: Alexander
  orcid: "https://orcid.org/0000-0001-5983-8631"
- family-names: Gulans
  given-names: Andris
  orcid: "https://orcid.org/0000-0001-7304-1952"
- family-names: Rinke
  given-names: Patrick
  orcid: "https://orcid.org/0000-0003-1898-723X"
- family-names: Draxl
  given-names: Claudia
  orcid: "https://orcid.org/0000-0003-3523-6657"
- family-names: Gonze
  given-names: Xavier
  orcid: "https://orcid.org/0000-0002-8377-6829"
doi: 10.5281/zenodo.8321618
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Azizi
    given-names: Maryam
    orcid: "https://orcid.org/0000-0001-9089-1043"
  - family-names: Wilhelm
    given-names: Jan
    orcid: "https://orcid.org/0000-0001-8678-8246"
  - family-names: Golze
    given-names: Dorothea
    orcid: "https://orcid.org/0000-0002-2196-9350"
  - family-names: Giantomassi
    given-names: Matteo
    orcid: "https://orcid.org/0000-0002-7007-9813"
  - family-names: Panadés-Barrueta
    given-names: Ramón L.
    orcid: "https://orcid.org/0000-0003-4239-0978"
  - family-names: Delesma
    given-names: Francisco A.
    orcid: "https://orcid.org/0000-0001-6912-7745"
  - family-names: Buccheri
    given-names: Alexander
    orcid: "https://orcid.org/0000-0001-5983-8631"
  - family-names: Gulans
    given-names: Andris
    orcid: "https://orcid.org/0000-0001-7304-1952"
  - family-names: Rinke
    given-names: Patrick
    orcid: "https://orcid.org/0000-0003-1898-723X"
  - family-names: Draxl
    given-names: Claudia
    orcid: "https://orcid.org/0000-0003-3523-6657"
  - family-names: Gonze
    given-names: Xavier
    orcid: "https://orcid.org/0000-0002-8377-6829"
  date-published: 2023-10-03
  doi: 10.21105/joss.05570
  issn: 2475-9066
  issue: 90
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 5570
  title: "Time-frequency component of the GreenX library: minimax grids
    for efficient RPA and GW calculations"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.05570"
  volume: 8
title: "Time-frequency component of the GreenX library: minimax grids
  for efficient RPA and *GW* calculations"

If the repository is not hosted on GitHub, a .cff file can still be uploaded to set your preferred citation. Users will be able to manually copy and paste the citation.

Find more information on .cff files here and here.

editorialbot · 2023-10-03T18:19:31Z

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot · 2023-10-03T18:19:32Z

🚨🚨🚨 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 👉 Creating pull request for 10.21105.joss.05570 joss-papers#4650
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.05570
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

Panadestein · 2023-10-03T18:23:40Z

@kyleniemeyer thanks for accepting the manuscript. The title seems to have been rendered incorrectly though, I can see in my mobile device \textit{GW}, should simply be this in italics.

kyleniemeyer · 2023-10-03T18:24:53Z

@openjournals/dev looks like some LaTeX markup got caught in the title at https://doi.org/10.21105/joss.05570, does that need to be fixed manually?

dgolze · 2023-10-05T16:43:03Z

@kyleniemeyer is there a chance that the title on the website gets fixed --> \textit{GW}

Panadestein · 2023-10-07T12:42:13Z

@kyleniemeyer the article already got indexed by Google Scholar and ResearchGate with this latex code in the title. That does not look good for anybody. Would you mind taking a look at this issue? Thanks

kyleniemeyer · 2023-10-07T16:39:35Z

@openjournals/dev @arfon can the title for this paper be fixed manually? I don't think I can do this myself.

arfon · 2023-10-08T07:20:14Z

@aziziph – please merge this PR. @kyleniemeyer then you can run reaccept here: https://joss.readthedocs.io/en/latest/editorial_bot.html?highlight=reaccept#updating-an-already-accepted-paper

kyleniemeyer · 2023-10-09T03:12:50Z

@editorialbot reaccept

editorialbot · 2023-10-09T03:12:52Z

Rebuilding paper!

editorialbot · 2023-10-09T03:18:29Z

🌈 Paper updated!

New PDF and metadata files 👉 openjournals/joss-papers#4662

kyleniemeyer · 2023-10-09T03:20:36Z

Thanks, @arfon. I thought fixing this would involve some manual magic on the website.

@Panadestein @dgolze the website appears correct for me now, and indexers should update after some time as well.

editorialbot · 2023-10-09T03:20:40Z

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

If you would like to include a link to your paper from your README use the following code snippets:

Markdown:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.05570/status.svg)](https://doi.org/10.21105/joss.05570)

HTML:
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  <img src="https://joss.theoj.org/papers/10.21105/joss.05570/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.05570/status.svg
   :target: https://doi.org/10.21105/joss.05570

This is how it will look in your documentation:

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editorialbot added CMake Fortran Python review Track: 3 (PE) Physics and Engineering labels Jun 18, 2023

editorialbot assigned lucydot Jun 18, 2023

editorialbot mentioned this issue Jun 18, 2023

[PRE REVIEW]: Time-frequency component of the Green-X library: minimax grids for efficient RPA and GW calculations #5509

Closed

AlexBuccheri mentioned this issue Jul 5, 2023

JOSS Issues: PyGreenX Clarity and README Update nomad-coe/greenX#54

Merged

AlexBuccheri mentioned this issue Jul 6, 2023

Rename License File nomad-coe/greenX#56

Merged

editorialbot added the recommend-accept Papers recommended for acceptance in JOSS. label Oct 2, 2023

editorialbot added accepted published Papers published in JOSS labels Oct 3, 2023

kyleniemeyer closed this as completed Oct 9, 2023

RMeli mentioned this issue Feb 14, 2024

[PRE REVIEW]: HofstadterTools: A Python package for analyzing the Hofstadter model #6195

Closed

[REVIEW]: Time-frequency component of the Green-X library: minimax grids for efficient RPA and GW calculations #5570

[REVIEW]: Time-frequency component of the Green-X library: minimax grids for efficient RPA and GW calculations #5570

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