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[REVIEW]: 'HallThruster.jl: a Julia package for 1D Hall thruster discharge simulation' #4672

Closed editorialbot closed 1 year ago

editorialbot commented 2 years ago

Submitting author: !--author-handle-->@archermarx<!--end-author-handle-- (Thomas Marks) Repository: https://github.com/UM-PEPL/HallThruster.jl Branch with paper.md (empty if default branch): Version: v0.8.3 Editor: !--editor-->@lucydot<!--end-editor-- Reviewers: @Rupali-Sahu, @TomGoffrey, @lucydot Archive: 10.5281/zenodo.8066246

Status

status

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HTML: <a href="https://joss.theoj.org/papers/ce9cb7aa54df10d69ed248912e584f53"><img src="https://joss.theoj.org/papers/ce9cb7aa54df10d69ed248912e584f53/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/ce9cb7aa54df10d69ed248912e584f53/status.svg)](https://joss.theoj.org/papers/ce9cb7aa54df10d69ed248912e584f53)

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

@StanczakDominik & @Rupali-Sahu, 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:

@editorialbot generate my checklist

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 @Rupali-Sahu

📝 Checklist for @TomGoffrey

📝 Checklist for @lucydot

editorialbot commented 2 years ago

Hello humans, 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 commented 2 years ago 
Software report:

github.com/AlDanial/cloc v 1.88  T=0.18 s (529.3 files/s, 176500.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Julia                           53           1136            264           4705
TOML                             9            832              3           3766
Markdown                        23            510              0           1249
SVG                              3              0              0            843
TeX                              2             20              0            145
YAML                             3              5              1            105
Jupyter Notebook                 1              0          17659            100
-------------------------------------------------------------------------------
SUM:                            94           2503          17927          10913
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository
editorialbot commented 2 years ago

Wordcount for paper.md is 1229

editorialbot commented 2 years ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1063/5.0021474 is OK
- 10.2514/6.2001-3505 is OK
- 10.1088/1361-6595/ab0f70 is OK
- 10.1088/0963-0252/14/4/011 is OK
- 10.1063/1.5055750 is OK
- 10.1002/9780470436448.ch7 is OK
- 10.1063/1.4972269 is OK
- 10.1145/3511528.3511535 is OK
- 10.1137/141000671 is OK

MISSING DOIs

- None

INVALID DOIs

- None
editorialbot commented 2 years ago

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

StanczakDominik commented 2 years ago

Review checklist for @StanczakDominik

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

lucydot commented 2 years ago

@StanczakDominik - I can see you have started your review - great! - let me know if you have any queries as you progress.

@Rupali-Sahu - your first review task is to generate a checklist - there is more information at the top of this thread. Please, if you have any questions, just ask in the thread below.

I find reviews work best when it is a back-and-forth conversations between reviewers and authors, so please feel free to give your thoughts and suggestions as you are working through the checklist. In many cases, it may best to raise these as an issue on the HallThruster repository - if you do, please let us know in this thread.

Rupali-Sahu commented 2 years ago

Hi Lucy,

Thanks for the reminder. It had completely slipped my mind ever since I started my new job. I am kinda stuck since this is not a traditional review process. I have not really used Github before, so I'm confused about where to run the commands and create a review report. If there's documentation that can guide me, that would be great.

Warm regards, Rupali

On Wed, Aug 31, 2022 at 8:43 AM Lucy Whalley @.***> wrote:

@StanczakDominik https://github.com/StanczakDominik - I can see you have started your review - great! - let me know if you have any queries as you progress.

@Rupali-Sahu https://github.com/Rupali-Sahu - your first review task is to generate a checklist - there is more information at the top of this thread. Please, if you have any questions, just ask in the thread below.

I find reviews work best when it is a back-and-forth conversations between reviewers and authors, so please feel free to give your thoughts and suggestions as you are working through the checklist. In many cases, it may best to raise these as an issue on the HallThruster repository - if you do, please let us know in this thread.

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/4672#issuecomment-1233108926, or unsubscribe https://github.com/notifications/unsubscribe-auth/AX546UFYE5XHNACBG5SKMO3V354S7ANCNFSM56I255IA . You are receiving this because you were mentioned.Message ID: @.***>

-- Rupali Sahu Aerospace department

lucydot commented 2 years ago

Hi Rupali - there is some more documentation here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html.

Github can be a bit daunting when you first use it, however you only need to think about the issue thread (there is a lot more github functionality which isn't used in this process).

You can run the commands in the Github thread itself (rather than via email) - the thread address is here: https://github.com/openjournals/joss-reviews/issues/4672. There are more instructions at the top of that page - please ask me more questions as they arise.

Rupali-Sahu commented 2 years ago

Review checklist for @Rupali-Sahu

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Rupali-Sahu commented 1 year ago

This is a good initiative and I hope it can be extended to incorporate other plasma dynamics and higher dimensions as well.

I am working remotely on a company laptop which doesn't allow third party installations, so I cannot comment on the functionality or documentation of the code. I hope that is not a problem. I have a few questions/concerns regarding the computational model and the physics being resolved:

  1. Line 25: The electron flux causing the problem is actually parallel to the applied electric field. The 'Hall' current in the direction perpendicular to both magnetic and electric fields (i.e. in the azimuthal direction), but the anomalous electron transport is primarily in the axial direction.

  2. An explanation is needed on why the lesser-known flux schemes are used instead of the more standard schemes like HLLC, Steger-Warming, Roe's method, etc.

  3. I'm not sure of JOSS, but in general it is expected that all the governing equations are presented in the paper itself, instead of referring to the documentation. It would also help to add the details of the three subcases used for comparison. Please ignore this if irrelevant.

  4. Details for the fluid model used for comparing the results should be mentioned to some extent. It is unclear at this point if the fluid models are expected to be more or less accurate than the code developed in this study.

  5. In general, a code/software presented must be evaluated for its accuracy and limitations. While the comparison results are presented, no discussion is made on the why the differences occur, and in what cases would this code not provide reliable results at all. For instance, removing the anomalous collision would bring the Knudsen number dangerously close to 1, and a fluid description is inaccurate. Also mention under what circumstances does a 1D approximation not hold for a hall thruster.

  6. The list of references seems incomplete. Many researchers have worked on fluid/hybrid models of plasma for hall thrusters. It would be helpful to place the current code in context of the existing codes.

lucydot commented 1 year ago

Hi thanks @Rupali-Sahu for your feedback so far. RE:

I'm not sure of JOSS, but in general it is expected that all the governing equations are presented in the paper itself, instead of referring to the documentation. It would also help to add the details of the three subcases used for comparison. Please ignore this if irrelevant.

This is not necessary for a JOSS submission.

@StanczakDominik are you able to take a look at this code over the next few weeks?

archermarx commented 1 year ago

Hi Rupali! Thank you for your feedback. Let me try and address some of the concerns. Note that many of these were not included in the paper due to the word limit. I don't know if you had a chance to look through the documentation, but many of these ought to be covered there.

1. Line 25: The electron flux causing the problem is actually parallel to the applied electric field. The 'Hall' current in the direction perpendicular to both magnetic and electric fields (i.e. in the azimuthal direction), but the anomalous electron transport is primarily in the axial direction.

Yes, this is a typo. It should say "perpendicular to the applied magnetic field"

2. An explanation is needed on why the lesser-known flux schemes are used instead of the more standard schemes like HLLC, Steger-Warming, Roe's method, etc.

I'm not sure these are necessarily lesser-known. Rusanov/Local Lax Friedrichs is a particularly well-known scheme in CFD, particularly within education, and the Global Lax Friedrichs is a straightforward modification of this scheme. I do agree it would be good to discuss why these fluxes were chosen, but due to wordcount limitations, I think most of this would have to be relegated to the documentation. Adding more fluxes is definitely something we'd like to do.

4. Details for the fluid model used for comparing the results should be mentioned to some extent. It is unclear at this point if the fluid models are expected to be more or less accurate than the code developed in this study.

That would be good to include. The LANDMARK benchmark code should be somewhat less accurate than our code, but it difficult to compare in detail because no numerical information is provided with the benchmark.

5. In general, a code/software presented must be evaluated for its accuracy and limitations. While the comparison results are presented, no discussion is made on the why the differences occur, and in what cases would this code not provide reliable results at all. For instance, removing the anomalous collision would bring the Knudsen number dangerously close to 1, and a fluid description is inaccurate. Also mention under what circumstances does a 1D approximation not hold for a hall thruster.

Agree. I think more discussion is warranted, but again I am unsure whether that belongs in the paper or in the documentation of the code.

6. The list of references seems incomplete. Many researchers have worked on fluid/hybrid models of plasma for hall thrusters. It would be helpful to place the current code in context of the existing codes.

Yes. I think adding more references would definitely be good. @lucydot do references count toward the word limit?

lucydot commented 1 year ago

@archermarx apologies for my late reply on this. The word limit is a soft word limit, so do not worry if the references take you over.

archermarx commented 1 year ago

Thanks! I'll revise my paper with some additional references and to address some of the changes suggested by Dr. Sahu in the next few days.

StanczakDominik commented 1 year ago

Hey! I'm terribly sorry, but I think I overestimated the time I'd have available for now, so I don't think I'm going to be able to do this review promptly. Sincerest apologies :(

lucydot commented 1 year ago

Hi @StanczakDominik and thanks for the update, do you have a rough timeline for when you may be able to do the review?

lucydot commented 1 year ago

This review seems to have taken a bit of a stall.

@archermarx we are waiting on your revisions in response to the changes suggested by @Rupali-Sahu

@StanczakDominik can you give an estimate for when (if at all?) you can do the review?

I will start reaching out to additional reviewers - we need someone who can install and run the code to verify functionality.

lucydot commented 1 year ago

@Datseris @jameshclrk @matbesancon - I'm aware that I have already asked you to review this submission (and I received your earlier responses), however that was a few months back - so I'm re-asking in case you have any more give in your schedule and are now able to review. No problems if not!

Datseris commented 1 year ago

Hello @lucydot , thanks for the (re-)invite. Unfortunately once again I must decline :( I'm in a worst state than previously, finishing my job soon before leaving for a month long leave. Unlikely I would have the capacity to deliver something here. Sorry! Wish best of luck to the authors!

archermarx commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

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

archermarx commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

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

@editorialbot commands

archermarx commented 1 year ago

@lucydot I've updated the paper. Not sure why the editorialbot can't generate the pdf, but it generates correctly when triggered via github actions.

StanczakDominik commented 1 year ago

I can probably get back to this in mid November, but not likely earlier. Apologies :(

lucydot commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

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

lucydot commented 1 year ago

@StanczakDominik I think mid-November is fine, especially given that we are struggling to find alternative reviewers - thank you for the update. Although all checkboxes on the reviewer list are important, particular emphasis should be given to Functionality as @Rupali-Sahu has not been able to verify this.

@Rupali-Sahu I can see there are some items still ticked off on your list that do not require installation of the software (under Documentation and Software paper). Please do continue to work through these items and tick-off if/when met. @archermarx has updated the paper since you last updated the review thread (see link to paper above).

lucydot commented 1 year ago

@StanczakDominik @Rupali-Sahu - any updates on your reviews? or indicative timeline for when next updates will be? ---> I'm keen to keep this review moving along..

remember, if there are any uncertainties, we can use this thread as a place for discussion..

Rupali-Sahu commented 1 year ago

Hi Lucy!

I am happy with the author's response on my comments. I would recommend this work for publication in JOSS as it would provide an easily accessible tool to test many hypotheses for anomalous electron transport.

lucydot commented 1 year ago

Hi @Rupali-Sahu can you update the tick boxes so I can see which parts of the review you have completed (as I know there were some parts you have not assessed as you could not install the software - is this still correct?)

Rupali-Sahu commented 1 year ago

Hi Lucy! I updated my checklist. I could also download and run the software on my new personal laptop so I have ticked off a few boxes in the documentation and functionality section as well. In the documentation,

  1. Few equations, such as that for electron heat conduction and two-zone Bohm collision frequency are not printing in math mode, possibly a missing bracket or something like that.
  2. In the tutorial, it is unclear how an anomalous electron transport model is selected.

I could not find a statement of need and community guidelines in the documentation. If the authors could add that, or point me to where its located, I can tick off the corresponding boxes. Other than that, the documentation looks quite detailed and informative :)

lucydot commented 1 year ago

@archermarx please see comments from @Rupali-Sahu above ☝️

lucydot commented 1 year ago

@StanczakDominik a reminder for your review 🕐

archermarx commented 1 year ago

Hi Lucy! I updated my checklist. I could also download and run the software on my new personal laptop so I have ticked off a few boxes in the documentation and functionality section as well. In the documentation,

1. Few equations, such as that for electron heat conduction and two-zone Bohm collision frequency are not printing in math mode, possibly a missing bracket or something like that.

2. In the tutorial, it is unclear how an anomalous electron transport model is selected.

I could not find a statement of need and community guidelines in the documentation. If the authors could add that, or point me to where its located, I can tick off the corresponding boxes. Other than that, the documentation looks quite detailed and informative :)

Thanks for the comments! I will address these in the next week.a

lucydot commented 1 year ago

Hi @archermarx, any upates or timescales for completion?

@StanczakDominik a reminder for your review, or timescale for when you will be able to review this?

Also a note here that I will be on holiday from today until the 4th of January 🎄 though I may check in between the mince pies, we'll see!

archermarx commented 1 year ago

I will also be on holiday until around then. Apologies for the delay, busy time of year for me.

Thomas Marks

Ph.D. Candidate Department of Aerospace Engineering Plasmadynamics and Electric Propulsion Laboratory University of Michigan, Ann Arbor Email: @.*** Phone: 480-532-1189 Office: FXB 1216 G-5

On Wed, Dec 21, 2022 at 4:34 AM Lucy Whalley @.***> wrote:

Hi @archermarx https://github.com/archermarx, any upates or timescales for completion?

@StanczakDominik https://github.com/StanczakDominik a reminder for your review, or timescale for when you will be able to review this?

Also a note here that I will be on holiday from today until the 4th of January 🎄 though I may check in between the mince pies, we'll see!

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/4672#issuecomment-1361203045, or unsubscribe https://github.com/notifications/unsubscribe-auth/AOP3QGSFRNPPD6BXBVUBIVDWOLTNHANCNFSM56I255IA . You are receiving this because you were mentioned.Message ID: @.***>

archermarx commented 1 year ago

I'm back and will address these comments in a new version of the code and documentation that I will hopefully push today.

archermarx commented 1 year ago

I've updated the documentation and tutorial. Let me know if there's anything else I should change or anything I missed.

lucydot commented 1 year ago

@StanczakDominik a reminder for your review, or timescale for when you will be able to review this? nb, I've emailed Dominik with a prompt.

@Rupali-Sahu can you take a look at the latest changes from @archermarx ?

archermarx commented 1 year ago

If i might suggest alternate/additional reviewer(s), Maryam Reza (m.reza20@imperial.ac.uk) and Farbod Faraji (f.faraji20@imperial.ac.uk) both recently published work using a Hall thruster code written in Julia. I think either would be well-qualified to review the code. I have no affiliation with either researcher and have not met them, but I was impressed by their recent work on reduced-order particle in cell methods.

Rupali-Sahu commented 1 year ago

I see that the authors have addressed all my concerns. I have updated my checklist. I hope it helps :)

StanczakDominik commented 1 year ago

I sincerely apologize, but it might still be a while for me. If Maryam Reza or Farbod Faraji would be available, it would probably be best for the prompt review of this article if they could take over.

lucydot commented 1 year ago

@archermarx thank you for the suggestions, and @StanczakDominik for the update - I'll contact Maryam first to ask if available for review.

lucydot commented 1 year ago

@Rupali-Sahu excellent, thanks for your update and spending your valuable time reviewing for JOSS ✨

lucydot commented 1 year ago

A note that I have also contacted Farbod to ask if available to review.

archermarx commented 1 year ago

Thank you Lucy!

Thomas Marks

Ph.D. Candidate Department of Aerospace Engineering Plasmadynamics and Electric Propulsion Laboratory University of Michigan, Ann Arbor Email: @.*** Phone: 480-532-1189 Office: FXB 1216 G-5

On Tue, Jan 24, 2023 at 6:42 AM Lucy Whalley @.***> wrote:

A note that I have also contacted Farbod to ask if available to review.

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/4672#issuecomment-1401802114, or unsubscribe https://github.com/notifications/unsubscribe-auth/AOP3QGV6QS5QSRVPO6NS2ATWT6525ANCNFSM56I255IA . You are receiving this because you were mentioned.Message ID: @.***>

lucydot commented 1 year ago

I'm afraid I'm still having trouble securing reviewers, with no response from those that have been suggested to me via email (Farbod was unavailable but kindly pointed me to others). I will keep on trying, @StanczakDominik or @Rupali-Sahu do you have any suggestions for an additional reviewer?

archermarx commented 1 year ago

Thanks for your persistence on this Lucy. I will think of some other reviewers.