Joss-reviews: [PRE REVIEW]: J2suscep: Calculation of magnetic exchange coupling and temperature dependence of magnetic susceptibility

[whedon]

Submitting author: @Swetanshu (Swetanshu Tandon)
Repository: https://github.com/WatsonGroupTCD/J2suscep
Version: 1.0
Editor: @dpsanders
Reviewers: @mturiansky, @mfherbst
Managing EiC: Daniel S. Katz

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

@Swetanshu 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

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[whedon]

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.

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[whedon]

Failed to discover a Statement of need section in paper

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.84  T=0.04 s (369.3 files/s, 78884.8 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Fortran 90                       9            165            762           2186
TeX                              1              8              0            146
Markdown                         4             13              0             94
make                             2             14              0             30
-------------------------------------------------------------------------------
SUM:                            16            200            762           2456
-------------------------------------------------------------------------------


Statistical information for the repository '2660' was gathered on 2020/09/10.
No commited files with the specified extensions were found.

[whedon]

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

OK DOIs

- 10.1002/jcc.23234 is OK
- 10.1021/ic900992r is OK
- 10.1039/B902745A is OK
- 10.1007/128_2015_645 is OK
- 10.1021/ic502651w is OK
- 10.1039/D0SE00701C is OK
- 10.1039/D0DT01404D is OK
- 10.1002/chem.201405679 is OK

MISSING DOIs

- None

INVALID DOIs

- https://doi.org/10.1016/j.ccr.2008.05.014 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/j.cpc.2010.09.007 is INVALID because of 'https://doi.org/' prefix

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[danielskatz]

👋 @Swetanshu - please add an explicit "Statement of need" section to your paper, then regenerate the PDF by adding @whedon generate pdf as a new comment here.

[danielskatz]

👋 @usethedata - I know you have a few papers already, but would you be willing to edit this one as well?

[danielskatz]

@whedon invite @usethedata as editor

[whedon]

@usethedata has been invited to edit this submission.

[whedon]

Here are some things you can ask me to do:

# List Whedon's capabilities
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# List of editor GitHub usernames
@whedon list editors

# List of reviewers together with programming language preferences and domain expertise
@whedon list reviewers

EDITORIAL TASKS

# Compile the paper
@whedon generate pdf

# Compile the paper from alternative branch
@whedon generate pdf from branch custom-branch-name

# Ask Whedon to check the references for missing DOIs
@whedon check references

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[Swetanshu]

@whedon generate pdf

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[Swetanshu]

@whedon check references

[whedon]

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

OK DOIs

- 10.1002/jcc.23234 is OK
- 10.1021/ic900992r is OK
- 10.1039/B902745A is OK
- 10.1007/128_2015_645 is OK
- 10.1016/j.ccr.2008.05.014 is OK
- 10.1021/ic502651w is OK
- 10.1016/j.cpc.2010.09.007 is OK
- 10.1039/D0SE00701C is OK
- 10.1039/D0DT01404D is OK
- 10.1002/chem.201405679 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[Swetanshu]

Hi @danielskatz,
Potential reviewers: Alex ganose (username: utf) and Benjamin Morgan (username: bjmorgan).

[danielskatz]

Thanks @Swetanshu - the next step will be assigning an editor, who will then work on reviewers

[arfon]

@whedon generate pdf

[whedon]

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

[Kevin-Mattheus-Moerman]

@pdebuyl @usethedata @pibion @dpsanders could one of you handle this submission?

[Kevin-Mattheus-Moerman]

:wave: @pdebuyl @jgostick @usethedata @pibion @dpsanders could one of you handle this submission?

[dpsanders]

👋 @Kevin-Mattheus-Moerman: I can take it on.

[Kevin-Mattheus-Moerman]

@whedon assign @dpsanders as editor

[whedon]

OK, the editor is @dpsanders

[dpsanders]

@whedon generate pdf

[whedon]

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

[dpsanders]

👋 @Swetanshu: Thanks for your submission to JOSS!
Looking over the paper and repo, I have some preliminary comments:

• It's not clear why there are two standalone codes being submitted as one submission.

• Please expand the README in the repo with usage instructions and links to the documentation.

• It is not clear where the data from the DFT calculations comes from or what format it should be in. Please give a complete example.

• I do not see the source for the documentation -- this should be provided. It would be preferable for the docs to be available as web pages etc., rather than a monolithic PDF.

• Ideally, please include a simple usage example in the paper.

Thanks!

[dpsanders]

Also I forgot to mention that the software will need some kind of tests to make sure that it is working correctly.

[Swetanshu]

Hi @dpsanders: Thank you for your comments and apologies for the late reply. I have tried to address your comments and the changes are described below:

• It's not clear why there are two standalone codes being submitted as one submission.
The codes “EJ_calc” and “suscep” together provide a means to use the data obtained from density functional theory calculations for simulating the magnetic susceptibility. This requires the calculation of J-values (obtained from EJ_calc) followed by their use in the simulation of the susceptibility (obtained from the suscep code). Although, the two codes complement each other, the calculation of both J-values and susceptibility together is not always required. Additionally, the time required for the calculation of susceptibility can vary from seconds to hours. Keeping these things in mind, we decided to tackle the problem by developing two standalone codes instead of coupling them together.

• Please expand the README in the repo with usage instructions and links to the documentation.
The readme file in the repository provides a brief description of the package. The detailed documentation has been provided in the github wiki pages. The README has been modified to indicate this.

• It is not clear where the data from the DFT calculations comes from or what format it should be in. Please give a complete example.
An example has been included in the wiki pages in the example sections.

• I do not see the source for the documentation -- this should be provided. It would be preferable for the docs to be available as web pages etc., rather than a monolithic PDF.
The documentation in the pdf format has been left in the repo but all the information contained in the pdf files is also available in the github wiki pages.

• Ideally, please include a simple usage example in the paper.
Considering the length of the input files, the example covered in the paper is only briefly described. A detailed description of the same example is provided in the wiki pages. The input and output files for the same example are provided in the respective directories.

• the software will need some kind of tests to make sure that it is working correctly.
A few example input and output files are provided for this purpose. One can compare their output files with the provided ones to test the working of the code.

Let me know if you want me to modify anything else.
Thank you once again!

[dpsanders]

@Swetanshu At a glance that looks good, thanks!

Do you have any suggestions for reviewers from the list linked above?

[Swetanshu]

@dpsanders From the list: Alex ganose (username: utf) and Benjamin Morgan (username: bjmorgan).
Prof. Julian Gale ( [email protected]) would be extremely suitable but I could not find his name in the list.

[dpsanders]

👋 @utf and @mturiansky: Would you be willing and able to review this submission for JOSS, the Journal of Open Source Software? Thanks!

[mturiansky]

@dpsanders I'd be happy to. This would be my first review for JOSS though, so please excuse my naivety.

[dpsanders]

@mturiansky Thanks! No problem, let me know if you have any questions once the review starts.

[dpsanders]

👋 @mfherbst: Would you be willing and able to review this submission for JOSS, the Journal of Open Source Software? Thanks!

[mfherbst]

@dpsanders Sure, I'm happy to take it up. But same as @mturiansky it would be my first time reviewing for JOSS.

[dpsanders]

@whedon add @mturiansky as reviewer

[whedon]

OK, @mturiansky is now a reviewer

[dpsanders]

@whedon add @mfherbst as reviewer

[whedon]

OK, @mfherbst is now a reviewer

[dpsanders]

@whedon start review

[whedon]

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/2838.

[dpsanders]

Many thanks @mturiansky and @mfherbst!

Please head over to the review issue, where there's a checklist to orient your review.
The guidelines can be found in https://joss.readthedocs.io/en/latest/reviewer_guidelines.html

Please don't hesitate to ask if you have any questions. Thanks!