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

editorialbot · 2023-05-31T17:23:15Z

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
Managing EiC: Kyle Niemeyer

Status

Status badge code:

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

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

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

editorialbot · 2023-05-31T17:23:16Z

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:

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For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

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editorialbot · 2023-05-31T17:23:19Z

Software report:

github.com/AlDanial/cloc v 1.88  T=0.04 s (1123.5 files/s, 220845.2 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Fortran 90                      15            261            416           5899
TeX                              1             21              0            695
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           7904
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

editorialbot · 2023-05-31T17:23:21Z

Wordcount for paper.md is 2761

editorialbot · 2023-05-31T17:23:22Z

Failed to discover a valid open source license

editorialbot · 2023-05-31T17:23:56Z

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
- 10.1103/PhysRevB.96.155207 is OK

MISSING DOIs

- 10.3389/fchem.2019.00377 may be a valid DOI for title: The GW compendium: A practical guide to theoretical photoemission spectroscopy
- 10.1063/1.2958921 may be a valid DOI for title: Minimax approximation for the decomposition of energy denominators in Laplace-transformed Møller–Plesset perturbation theories
- 10.1103/physrev.126.413 may be a valid DOI for title: Quantum Theory of the Dielectric Constant in Real Solids
- 10.1103/physrev.129.62 may be a valid DOI for title: Dielectric Constant with Local Field Effects Included
- 10.1063/1.462485 may be a valid DOI for title: Laplace transform techniques in Mo/ller-Plesset perturbation theory
- 10.1021/ct5001268 may be a valid DOI for title: Low scaling algorithms for the random phase approximation: Imaginary time and Laplace transformations
- 10.1103/physrevb.90.054115 may be a valid DOI for title: Cubic scaling algorithm for the random phase approximation: Self-interstitials and vacancies in Si
- 10.1021/acs.jctc.0c01282.s001 may be a valid DOI for title: Low-scaling GW with benchmark accuracy and application to phosphorene nanosheets
- 10.1103/physrev.139.a796 may be a valid DOI for title: New method for calculating the one-particle Green’s function with application to the electron-gas problem
- 10.1002/wcms.1344 may be a valid DOI for title: The GW approximation: content, successes and limitations
- 10.1021/acs.jctc.6b00380.s001 may be a valid DOI for title: GW in the Gaussian and plane waves scheme with application to linear acenes
- 10.1021/acs.jctc.0c00693.s001 may be a valid DOI for title: Low-order scaling G_0W_0 by pair atomic density fitting
- 10.1021/acs.jpclett.7b02740.s001 may be a valid DOI for title: Toward GW calculations on thousands of atoms
- 10.1021/acs.jctc.7b00770 may be a valid DOI for title: Stochastic GW calculations for molecules
- 10.1007/bf00655090 may be a valid DOI for title: Solving the Eliashberg equations by means of N-point Padé approximants
- 10.1007/jhep12(2011)071 may be a valid DOI for title: Analytic continuation of Liouville theory
- 10.1016/s0010-4655(98)00174-x may be a valid DOI for title: The GW space-time method for the self-energy of large systems
- 10.1103/physrevb.13.4274 may be a valid DOI for title: Exchange and correlation in atoms, molecules, and solids by the spin-density-functional formalism
- 10.1103/physreva.73.012511 may be a valid DOI for title: Variational energy functionals of the Green function and of the density tested on molecules
- 10.1016/j.cpc.2018.09.003 may be a valid DOI for title: Large-scale GW calculations on pre-exascale HPC systems
- 10.1016/j.cpc.2014.10.021 may be a valid DOI for title: Enabling simulation at the fifth rung of DFT: Large scale RPA calculations with excellent time to solution
- 10.1021/acs.jctc.9b01235.s001 may be a valid DOI for title: Robust Analytic-Continuation Approach to Many-Body GW Calculations
- 10.1021/acs.jctc.1c00101.s001 may be a valid DOI for title: Cubic-Scaling All-Electron GW Calculations with a Separable Density-Fitting Space–Time Approach
- 10.1021/acs.jctc.1c00308.s001 may be a valid DOI for title: GW100: A Slater-Type Orbital Perspective
- 10.3389/fchem.2021.736591 may be a valid DOI for title: Low-Order Scaling Quasiparticle Self-Consistent GW for Molecules
- 10.1021/acs.jctc.0c00600.s001 may be a valid DOI for title: Efficient Reduced-Scaling Second-Order Møller–Plesset Perturbation Theory with Cholesky-Decomposed Densities and an Attenuated Coulomb Metric
- 10.1021/acs.jctc.8b00177 may be a valid DOI for title: Accurate and Efficient Parallel Implementation of an Effective Linear-Scaling Direct Random Phase Approximation Method
- 10.1021/acs.jctc.6b01235 may be a valid DOI for title: Vanishing-Overhead Linear-Scaling Random Phase Approximation by Cholesky Decomposition and an Attenuated Coulomb-Metric
- 10.1021/acs.jctc.2c00774 may be a valid DOI for title: Efficient Method for the Computation of Frozen-Core Nuclear Gradients within the Random Phase Approximation
- 10.1063/1.5090605 may be a valid DOI for title: Separable resolution-of-the-identity with all-electron Gaussian bases: Application to cubic-scaling RPA
- 10.1016/0009-2614(91)80078-c may be a valid DOI for title: Elimination of energy denominators in Møller-Plesset perturbation theory by a Laplace transform approach
- 10.1063/1.1809602 may be a valid DOI for title: Scaled opposite-spin second order Møller–Plesset correlation energy: An economical electronic structure method
- 10.1007/s10853-012-6570-4 may be a valid DOI for title: Random-phase approximation and its applications in computational chemistry and materials science
- 10.1007/978-3-642-28445-8_12 may be a valid DOI for title: Electron correlation methods based on the random phase approximation
- 10.1021/ct4002202 may be a valid DOI for title: Electron Correlation in the Condensed Phase from a Resolution of Identity Approach Based on the Gaussian and Plane Waves Scheme
- 10.1103/revmodphys.74.601 may be a valid DOI for title: Electronic excitations: density-functional versus many-body Green’s-function approaches
- 10.1021/acs.jctc.6b00840.s001 may be a valid DOI for title: Large-scale cubic-scaling random phase approximation correlation energy calculations using a Gaussian basis
- 10.1021/acs.jctc.6b00840.s001 may be a valid DOI for title: Large-Scale Cubic-Scaling Random Phase Approximation Correlation Energy Calculations Using a Gaussian Basis
- 10.1016/j.cpc.2017.06.012 may be a valid DOI for title: Linearized self-consistent quasiparticle GW method: Application to semiconductors and simple metals

INVALID DOIs

- None

editorialbot · 2023-05-31T17:24:40Z

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

kyleniemeyer · 2023-05-31T17:27:28Z

Hello @aziziph, thanks for your submission to JOSS. We will use this pre-review issue to assign an editor and find reviewers. Any suggestions for the latter would be welcome!

In the meantime, can you look at those missing DOI messages above for the paper?

kyleniemeyer · 2023-05-31T17:27:50Z

@editorialbot invite @lucydot as editor

Hi @lucydot, this looks to be in your wheelhouse—can you edit this submission?

editorialbot · 2023-05-31T17:27:51Z

Invitation to edit this submission sent!

lucydot · 2023-06-01T10:52:26Z

Hi @kyleniemeyer it is indeed!

lucydot · 2023-06-01T10:52:42Z

@editorialbot assign me as editor

editorialbot · 2023-06-01T10:52:45Z

Assigned! @lucydot is now the editor

lucydot · 2023-06-01T11:00:10Z

Hi @aziziph, thank you for your submission to JOSS.

I'll start looking for reviewers. If you could do the following it will help move things along:

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.
please fix the missing doi's list above ☝️
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. I suggest that the mathematical framework section is moved online; you can then link to this from the paper.

aziziph · 2023-06-01T11:40:34Z

Hi @lucydot

We would like to thank you for reviewing the paper.
Here are my suggestions for potential reviewers:
@vijaymocherla
@rangsimanketkaew
@yw-fang
@RMeli
@richardjgowers

The DOI has been fixed and will appear in pdf as soon as the pull request will be accepted.

aziziph · 2023-06-01T11:57:43Z

Dear @lucydot

Is it possible to propose a person who is not listed in the list of reviewers?

RMeli · 2023-06-03T07:51:52Z

Thanks for suggesting me. Unfortunately I don't have bandwidth to take this on, and there might be a conflict of interest with @AlexBuccheri (although it's been more than 4 years...).

lucydot · 2023-06-05T14:50:13Z

Hello @aziziph yes, you can suggest someone not in the list of reviewers. Please do not include the @ sign so as to avoid pinging potential reviewers without reason.

lucydot · 2023-06-05T14:50:29Z

@editorialbot generate pdf

lucydot · 2023-06-05T14:50:42Z

@editorialbot check references

editorialbot · 2023-06-05T14:51:11Z

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
- 10.1007/978-3-642-61609-9 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
- https://doi.org/10.6084/m9.figshare.828487 is INVALID because of 'https://doi.org/' prefix
- 10.33892Ffchem.2021.736591 is INVALID

lucydot · 2023-06-05T14:52:11Z

@aziziph I can see that the JOSS editorial bot and github have not automatically detected the license file. I suggest renaming this to the more standard LICENSE.txt so that it is automatically detected.

editorialbot · 2023-06-05T14:52:14Z

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

lucydot · 2023-06-05T14:53:21Z

@aziziph please also take a look at the three invalid DOI's listed above; you can check yourself if they compile correctly using @editorialbot check references.

aziziph · 2023-06-05T14:56:43Z

Dear @lucydot
I suggest Merzuk Kaltak "mkaltak85" as a potential reviewer.

tpurcell90 · 2023-06-05T15:35:07Z

I can review this, but I have a conflict of interest because I am a deputy leader on another WP for the NOMAD CoE.

alejandrogallo · 2023-06-05T20:36:01Z

I could also review this, but I could also be biased as I am also part of the NOMAD CoE, I would suggest Merzuk as a better candidate. (https://www.nomad-coe.eu/nomad-coe/about-coe/team-nomad-coe)

aziziph · 2023-06-06T16:43:58Z

Hello,
Here is another possible reviewer mailhexu.

lucydot · 2023-06-07T08:51:30Z

Ah ok thanks @tpurcell90 and @alejandrogallo, we will avoid any CoIs.

lucydot · 2023-06-07T08:51:52Z

Hello @mailhexu are you available to review this submission to JOSS?

mailhexu · 2023-06-08T09:08:45Z

Hello @mailhexu are you available to review this submission to JOSS?

Yes, I can review this.

aziziph · 2023-06-09T15:32:01Z

The other potential reviewers in case it is needed:
daniele-varsano

lucydot · 2023-06-13T11:39:03Z

Excellent @mailhexu, thank-you!

@daniele-varsano are you available to review this submission to JOSS?

lucydot · 2023-06-13T11:39:14Z

@editorialbot add @mailhexu as reviewer

editorialbot · 2023-06-13T11:39:15Z

@mailhexu added to the reviewers list!

daniele-varsano · 2023-06-13T11:51:08Z

Excellent @mailhexu, thank-you!

@daniele-varsano are you available to review this submission to JOSS?

Many thanks for suggesting me as a reviewer, but unfortunately I have to decline for lack of time due to some deadlines approaching. I can anyway suggest the following reviewer:

andrea-ferretti
DarioALeonValido
sangallidavide
attacc

lucydot · 2023-06-14T15:53:18Z

@andrea-ferretti @DarioALeonValido - hello 👋 - are you available to review this submission to JOSS?

andrea-ferretti · 2023-06-15T16:58:53Z

@lucydot: Dear Lucy, thanks for writing. Unfortunately I am not able to accept the review at present (overwhelmed by other commitments). Best regards.
Andrea

DarioALeonValido · 2023-06-16T11:24:31Z

@lucydot: Dear Lucy, thanks for the invitation, I am available to do the review.
Best regards,
Dario

lucydot · 2023-06-18T18:19:07Z

Excellent, thanks @DarioALeonValido 🎈

lucydot · 2023-06-18T18:19:53Z

@editorialbot add @DarioALeonValido as reviewer

editorialbot · 2023-06-18T18:19:54Z

@DarioALeonValido added to the reviewers list!

lucydot · 2023-06-18T18:24:22Z

OK, thanks for agreeing to review @mailhexu and @DarioALeonValido ⭐

ping @aziziph

I'll ask @editorialbot to start the review proper (which will be on a separate thread). There will be more instructions there - the first reviewer task will be to generate a review checklist to work through. The process is different from traditional journals - it is an on-going conversation between reviewers, authors, editors and our bot. So I recommend starting the review early and keeping us updated as things progress rather than trying to complete the review or response to a review in a single-shot. If you have any questions, you can raise them on the review thread.

lucydot · 2023-06-18T18:24:30Z

@editorialbot start review

editorialbot · 2023-06-18T18:24:33Z

OK, I've started the review over in #5570.

aziziph · 2023-07-12T09:29:22Z

@editorialbot generate pdf

editorialbot · 2023-07-12T09:30:42Z

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

aziziph · 2023-07-12T09:37:53Z

@editorialbot check references

editorialbot · 2023-07-12T09:38:09Z

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
- 10.3389/fchem.2021.736591 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

editorialbot added pre-review Track: 3 (PE) Physics and Engineering labels May 31, 2023

editorialbot added the CMake label May 31, 2023

editorialbot added Fortran Python labels May 31, 2023

editorialbot assigned lucydot Jun 1, 2023

editorialbot assigned mailhexu Jun 13, 2023

openjournals deleted a comment from editorialbot Jun 13, 2023

openjournals deleted a comment from editorialbot Jun 18, 2023

editorialbot assigned DarioALeonValido Jun 18, 2023

editorialbot closed this as completed Jun 18, 2023

dgolze mentioned this issue Jul 12, 2023

Answer to the referee's comment about the example nomad-coe/greenX#60

Closed

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

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

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RMeli commented Jun 3, 2023

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lucydot commented Jun 13, 2023

lucydot commented Jun 13, 2023

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daniele-varsano commented Jun 13, 2023

lucydot commented Jun 14, 2023

andrea-ferretti commented Jun 15, 2023

DarioALeonValido commented Jun 16, 2023

lucydot commented Jun 18, 2023

lucydot commented Jun 18, 2023

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editorialbot commented May 31, 2023 •

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alejandrogallo commented Jun 5, 2023 •

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