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[PRE REVIEW]: iharm3D: Vectorized General Relativistic Magnetohydrodynamics #3288

Closed whedon closed 3 years ago

whedon commented 3 years ago

Submitting author: @bprather (Ben S. Prather) Repository: https://github.com/AFD-Illinois/iharm3d/ Version: v3.6-alpha Editor: @eloisabentivegna Reviewers: @bgiacoma, @cpalenzuela Managing EiC: Daniel S. Katz

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Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

Status

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Markdown: [![status](https://joss.theoj.org/papers/c1516163ae242984700ebc6e3044f3f5/status.svg)](https://joss.theoj.org/papers/c1516163ae242984700ebc6e3044f3f5)

Author instructions

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

@bprather 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).

Editor instructions

The JOSS submission bot @whedon is here to help you find and assign reviewers and start the main review. To find out what @whedon can do for you type:

@whedon commands
whedon commented 3 years ago

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks.

:warning: JOSS reduced service mode :warning:

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

For a list of things I can do to help you, just type:

@whedon commands

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

@whedon generate pdf
whedon commented 3 years ago 
Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.09 s (1073.0 files/s, 166692.1 lines/s)
--------------------------------------------------------------------------------
Language                      files          blank        comment           code
--------------------------------------------------------------------------------
C                                30           1139            853           5237
Python                           31            954            756           4029
C/C++ Header                     14            185            343            643
Bourne Shell                     18            196             88            509
make                              1             32             24             91
Markdown                          1             10              0             53
Bourne Again Shell                3             28             35             19
--------------------------------------------------------------------------------
SUM:                             98           2544           2099          10581
--------------------------------------------------------------------------------

Statistical information for the repository 'a5d9b8b23b93cb5f08372a3b' was
gathered on 2021/05/14.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Ben Prather                    474         62033          36164           80.63
Ben Ryan                        12          8992           6631           12.83
Charles F Gammie                 1             8              0            0.01
Charles F. Gammie                1          5879              0            4.83
George N. Wong                   2             6              4            0.01
George Wong                      4            71             22            0.08
Josh Dolence                     6          1075            341            1.16
Vedant Dhruv                     5            73             21            0.08
cfgammie                         1             2              1            0.00
e-petersen                       1             1              1            0.00
jdolence                         2            60            399            0.38

Below are the number of rows from each author that have survived and are still
intact in the current revision:

Author                     Rows      Stability          Age       % in comments
Ben Prather               11363           18.3         32.5               13.17
Ben Ryan                   2683           29.8         42.3               16.73
George Wong                  74          104.2          7.0                5.41
Vedant Dhruv                 53           72.6          8.3                5.66
cfgammie                      1           50.0         29.7              100.00
whedon commented 3 years ago

PDF failed to compile for issue #3288 with the following error: 

 Can't find any papers to compile :-(
danielskatz commented 3 years ago

@whedon generate pdf from branch joss-paper-branch

whedon commented 3 years ago 
Attempting PDF compilation from custom branch joss-paper-branch. Reticulating splines etc...
whedon commented 3 years ago

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

danielskatz commented 3 years ago

@whedon check references from branch joss-paper-branch

whedon commented 3 years ago 
Attempting to check references... from custom branch joss-paper-branch
whedon commented 3 years ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1186/s40668-017-0020-2 is OK
- 10.1093/mnras/stx364 is OK
- 10.1086/374594 is OK
- 10.1086/422244 is OK
- 10.1086/154565 is OK
- 10.1088/0004-637X/807/1/31 is OK
- 10.1126/sciadv.aaz1310 is OK
- 10.1111/j.1365-2966.2012.22002.x is OK
- 10.1006/jcph.2000.6519 is OK
- 10.3847/0067-0049/225/2/22 is OK
- 10.1093/mnras/sts632 is OK
- 10.1093/mnras/stt2479 is OK
- 10.1007/BF00165988 is OK
- 10.1093/mnras/stw1526 is OK
- 10.3847/2041-8213/ab1141 is OK
- 10.3847/2041-8213/ab0f43 is OK
- 10.3847/2041-8213/ab0e85 is OK
- 10.3847/2041-8213/ab0c57 is OK
- 10.3847/2041-8213/ab0c96 is OK
- 10.3847/2041-8213/ab0ec7 is OK
- 10.1146/annurev-astro-082812-141003 is OK
- 10.1093/mnras/stx3162 is OK
- 10.1086/500349 is OK
- 10.1093/mnras/208.4.721 is OK
- 10.3847/1538-4357/aa6a52 is OK
- 10.3847/1538-4365/ab29fd is OK
- 10.12942/lrr-2013-1 is OK
- 10.1111/j.1745-3933.2010.00958.x is OK
- 10.3847/1538-4357/ab86ac is OK
- 10.1146/annurev.aa.19.090181.001033 is OK
- 10.1146/annurev.aa.33.090195.002445 is OK
- 10.1146/annurev.astro.34.1.703 is OK
- 10.1086/170270 is OK
- 10.1016/j.jpdc.2014.07.003 is OK
- 10.1093/pasj/55.6.L69 is OK
- 10.1007/s41115-017-0002-8 is OK
- 10.1093/mnras/staa826 is OK
- 10.1086/176343 is OK
- 10.1088/0264-9381/24/12/S17 is OK
- 10.1007/BF00642237 is OK
- 10.1088/0004-637X/701/2/1175 is OK
- 10.1088/0004-637X/752/2/123 is OK
- 10.1051/0004-6361/201526630 is OK
- 10.3847/0004-637X/822/1/34 is OK
- 10.1088/0264-9381/32/17/175009 is OK
- 10.1093/mnras/stv2084 is OK
- 10.1088/0067-0049/201/2/9 is OK
- 10.1088/0004-637X/796/1/22 is OK
- 10.1086/497294 is OK
- 10.1086/308344 is OK
- 10.1016/j.jcp.2003.09.016 is OK
- 10.1086/500349 is OK
- 10.1088/0004-637X/755/1/51 is OK
- 10.1088/0004-637X/692/1/411 is OK
- 10.1088/0264-9381/31/6/065013 is OK
- 10.3847/2041-8213/aaa756 is OK
- 10.3847/2041-8213/ab0ec7 is OK
- 10.3847/2041-8213/ab0c96 is OK
- 10.3847/2041-8213/ab0c57 is OK
- 10.3847/2041-8213/ab0e85 is OK
- 10.3847/2041-8213/ab0f43 is OK
- 10.3847/2041-8213/ab1141 is OK
- 10.3847/2041-8213/abe4de is OK
- 10.3847/1538-4357/ab96c6 is OK
- 10.3847/2041-8213/abe71d is OK
- 10.3847/1538-4357/abac0d is OK

MISSING DOIs

- 10.3847/1538-4357/abee13 may be a valid DOI for title: The Role of Adaptive Ray Tracing in Analyzing Black Hole Structure
- 10.1093/mnras/staa955 may be a valid DOI for title: Large-Scale Poloidal Magnetic Field Dynamo Leads to Powerful Jets in GRMHD Simulations of Black Hole Accretion with Toroidal Field
- 10.1073/pnas.1812491116 may be a valid DOI for title: Thermal disequilibration of ions and electrons by collisionless plasma turbulence
- 10.3847/1538-4357/ab0c0c may be a valid DOI for title: A Resolution Study of Magnetically Arrested Disks
- 10.1093/mnras/staa2692 may be a valid DOI for title: Decomposing the Internal Faraday Rotation of Black Hole Accretion Flows
- 10.1109/tpds.2020.3010016 may be a valid DOI for title: K-Athena: a performance portable structured grid finite volume magnetohydrodynamics code

INVALID DOIs

- None
danielskatz commented 3 years ago

@bprather - if you have time, you could work on the possibly missing DOIs that whedon suggests, but note that some may be incorrect. You could also remove any entries from your bib file that are not actually referenced, if there are any, which will make this process easier. Please feel free to make changes to your .bib file, then use the command @whedon check references to check again, and the command @whedon generate pdf when the references are right to make a new PDF. Whedon commands need to be the first entry in a new comment.

danielskatz commented 3 years ago

👋 @eloisabentivegna - would you be able to edit this submission?

danielskatz commented 3 years ago

@whedon invite @eloisabentivegna as editor

whedon commented 3 years ago

@eloisabentivegna has been invited to edit this submission.

bprather commented 3 years ago

@whedon check references from branch joss-paper-branch

eloisabentivegna commented 3 years ago

👋 @eloisabentivegna - would you be able to edit this submission?

Sure thing!

eloisabentivegna commented 3 years ago

@whedon assign @eloisabentivegna as editor

whedon commented 3 years ago

OK, the editor is @eloisabentivegna

bprather commented 3 years ago

@eloisabentivegna Thanks for taking this on!

@danielskatz is there something I'm missing activating whedon? In any case I've taken another look at the references and I believe all the missing DOIs should be fixed in 'joss-paper-branch'

danielskatz commented 3 years ago

@whedon check references from branch joss-paper-branch

I'm not sure why this didn't work - let's just try it again. If it fails, there's perhaps a problem in the bib file that is causing it to fail silently. If this happens, we might try to generate the PDF and see if that tells us the error

whedon commented 3 years ago 
Attempting to check references... from custom branch joss-paper-branch
whedon commented 3 years ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.3847/1538-4365/ab29fd is OK
- 10.12942/lrr-2013-1 is OK
- 10.1093/mnras/sts632 is OK
- 10.1093/mnras/stt2479 is OK
- 10.1007/BF00165988 is OK
- 10.1093/mnras/stw1526 is OK
- 10.3847/2041-8213/ab1141 is OK
- 10.3847/2041-8213/ab0f43 is OK
- 10.3847/2041-8213/ab0e85 is OK
- 10.3847/2041-8213/ab0c57 is OK
- 10.3847/2041-8213/ab0c96 is OK
- 10.3847/2041-8213/ab0ec7 is OK
- 10.1146/annurev-astro-082812-141003 is OK
- 10.1093/mnras/stx3162 is OK
- 10.1086/500349 is OK
- 10.1093/mnras/208.4.721 is OK
- 10.3847/1538-4357/aa6a52 is OK
- 10.1006/jcph.2000.6519 is OK
- 10.3847/0067-0049/225/2/22 is OK
- 10.1186/s40668-017-0020-2 is OK
- 10.1093/mnras/stx364 is OK
- 10.1086/374594 is OK
- 10.1086/422244 is OK
- 10.1086/154565 is OK
- 10.1088/0004-637X/807/1/31 is OK
- 10.1111/j.1365-2966.2012.22002.x is OK
- 10.1126/sciadv.aaz1310 is OK
- 10.1111/j.1745-3933.2010.00958.x is OK
- 10.3847/1538-4357/ab86ac is OK
- 10.1088/0264-9381/32/17/175009 is OK
- 10.3847/0004-637X/822/1/34 is OK
- 10.1051/0004-6361/201526630 is OK
- 10.1088/0004-637X/752/2/123 is OK
- 10.1088/0004-637X/701/2/1175 is OK
- 10.1007/BF00642237 is OK
- 10.1088/0264-9381/24/12/S17 is OK
- 10.1086/176343 is OK
- 10.1093/mnras/staa826 is OK
- 10.1007/s41115-017-0002-8 is OK
- 10.1093/pasj/55.6.L69 is OK
- 10.1016/j.jpdc.2014.07.003 is OK
- 10.1086/170270 is OK
- 10.1146/annurev.astro.34.1.703 is OK
- 10.1146/annurev.aa.33.090195.002445 is OK
- 10.1146/annurev.aa.19.090181.001033 is OK
- 10.3847/2041-8213/aaa756 is OK
- 10.1088/0264-9381/31/6/065013 is OK
- 10.1088/0004-637X/692/1/411 is OK
- 10.1088/0004-637X/755/1/51 is OK
- 10.1016/j.jcp.2003.09.016 is OK
- 10.1086/308344 is OK
- 10.1086/497294 is OK
- 10.1088/0004-637X/796/1/22 is OK
- 10.1088/0067-0049/201/2/9 is OK
- 10.1093/mnras/stv2084 is OK
- 10.1093/mnras/staa955 is OK
- 10.1073/pnas.1812491116 is OK
- 10.3847/1538-4357/ab0c0c is OK
- 10.1093/mnras/staa2692 is OK
- 10.1109/TPDS.2020.3010016 is OK
- 10.3847/1538-4357/abee13 is OK
- 10.3847/2041-8213/ab0ec7 is OK
- 10.3847/2041-8213/ab0c96 is OK
- 10.3847/2041-8213/ab0c57 is OK
- 10.3847/2041-8213/ab0e85 is OK
- 10.3847/2041-8213/ab0f43 is OK
- 10.3847/2041-8213/ab1141 is OK
- 10.3847/2041-8213/abe4de is OK
- 10.3847/1538-4357/ab96c6 is OK
- 10.3847/2041-8213/abe71d is OK
- 10.3847/1538-4357/abac0d is OK

MISSING DOIs

- None

INVALID DOIs

- None
bprather commented 3 years ago

Thanks! I guess @whedon just doesn't like me...

eloisabentivegna commented 3 years ago

@bgiacoma, @pmoesta, would you be able to review this submission?

bgiacoma commented 3 years ago

@bgiacoma, @pmoesta, would you be able to review this submission?

@eloisabentivegna can I have more details? Do I have to review a paper or the code? What is the deadline?

eloisabentivegna commented 3 years ago

@bgiacoma, I will send you an email with all the details. In the meantime, you can take a look here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html

bgiacoma commented 3 years ago

@eloisabentivegna I received the email and I also had a look at the guidelines. Are the authors the same ones listed as contributors in the github repository of the code? Just to be sure that there are no conflict of interests.

eloisabentivegna commented 3 years ago

@bgiacoma, you can take a look at the paper draft. The author list usually coincides with the set of code authors, but sometimes there are reasons why it does not. The author list in the paper is the one you should keep in mind (although check the JOSS COI policy for sources of conflict that go beyond direct collaboration with the individual authors).

bgiacoma commented 3 years ago

@eloisabentivegna thanks, I checked the list of authors in the draft and I do not see any conflict of interests.

eloisabentivegna commented 3 years ago

@TomGoffrey, would you be able to provide a review for this submission?

eloisabentivegna commented 3 years ago

@tomidakn, @felker, would you be able to provide a review for this submission to JOSS?

felker commented 3 years ago

Unfortunately I cannot, but I would suggest to the authors to change the reference for Athena++: https://ui.adsabs.harvard.edu/abs/2020ApJS..249....4S/abstract

See details here: https://github.com/PrincetonUniversity/athena

bprather commented 3 years ago

@whedon generate pdf from branch joss-paper-branch

@felker Thanks! Apologies for the omission, it should be fixed now.

whedon commented 3 years ago 
Attempting PDF compilation from custom branch joss-paper-branch. Reticulating splines etc...
whedon commented 3 years ago

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

tomidakn commented 3 years ago

I'm sorry but I am very busy and cannot review it.

eloisabentivegna commented 3 years ago

@felker, @tomidakn, thanks for letting us know.

pmoesta commented 3 years ago

sorry for the delay but I am currently also unable to review this.

Philipp

On Wed, May 26, 2021 at 9:20 AM Eloisa Bentivegna @.***> wrote:

@felker https://github.com/felker, @tomidakn https://github.com/tomidakn, thanks for letting us know.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/3288#issuecomment-848531218, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAJEOZMGWLO2CZHI5E5BZC3TPSOKDANCNFSM445AODQA .

eloisabentivegna commented 3 years ago

@whedon add @bgiacoma as reviewer

whedon commented 3 years ago

OK, @bgiacoma is now a reviewer

eloisabentivegna commented 3 years ago

@whedon add @cpalenzuela as reviewer

whedon commented 3 years ago

OK, @cpalenzuela is now a reviewer

eloisabentivegna commented 3 years ago

@bgiacoma, @cpalenzuela, thanks for accepting to review this submission! I will now close the pre-review issue and start the actual review.

eloisabentivegna commented 3 years ago

@whedon start review

whedon commented 3 years ago

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/3336.