[REVIEW]: PXO (Poly-XTAL Operations): Free MATLAB codebase to generate and analyse complex 2D grain structures

whedon commented 3 years ago

Submitting author: @SunilAnandatheertha (sunil anandatheertha) Repository: https://github.com/SunilAnandatheertha/PXO Version: V10.1.1 Editor: @Kevin-Mattheus-Moerman Reviewer: @yangbai90, @ksyang2013, @littlelazy6 Archive: 10.5281/zenodo.5142160

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Review checklist for @yangbai90

Conflict of interest

[x] 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.

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

General checks

[x] Repository: Is the source code for this software available at the repository url?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@SunilAnandatheertha) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

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

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

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

Review checklist for @ksyang2013

Conflict of interest

[x] 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

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

General checks

[x] Repository: Is the source code for this software available at the repository url?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@SunilAnandatheertha) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

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

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

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

Review checklist for @littlelazy6

Conflict of interest

[x] 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

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

General checks

[x] Repository: Is the source code for this software available at the repository url?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@SunilAnandatheertha) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

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

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

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

whedon commented 3 years ago

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @yangbai90, @ksyang2013, @littlelazy6 it looks like you're currently assigned to review this paper :tada:.

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whedon commented 3 years ago

Failed to discover a Statement of need section in paper

whedon commented 3 years ago

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

OK DOIs

- 10.1016/S0081-1947(08)60603-7 is OK
- 10.1016/0001-6160(84)90151-2 is OK
- 10.1016/0036-9748(89)90525-5 is OK
- 10.1016/0001-6160(84)90089-0 is OK
- 10.2355/isijinternational.38.913 is OK
- 10.1016/0956-7151(90)90177-I is OK
- 10.1016/j.actamat.2009.10.058 is OK

MISSING DOIs

- None

INVALID DOIs

- None

whedon commented 3 years ago

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.59 s (362.7 files/s, 34721.3 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
MATLAB                         205           1236           3423          15420
Markdown                         7             65              0            184
XML                              1              1              0            146
TeX                              1              7              0             89
YAML                             1              1              1             10
-------------------------------------------------------------------------------
SUM:                           215           1310           3424          15849
-------------------------------------------------------------------------------

Statistical information for the repository 'ed33fcbd1250117096d9d5d1' was
gathered on 2021/04/18.
No commited files with the specified extensions were found.

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:

Kevin-Mattheus-Moerman commented 3 years ago

@yangbai90, @ksyang2013, @littlelazy6 this is where the review takes place. Could you provide an indication as to the time you need to provide your initial review? FYI we can be flexible and it is okay if you need to take quite a bit of time. Thanks again for your help!!!!

ksyang2013 commented 3 years ago

Will return the comments within two weeks. Thanks!

Kesong YANG, Ph.D.

Associate Professor, Department of NanoEngineering, Program of Materials Science and Engineering, Center for Memory and Recording Research (CMRR), University of California San Diego 9500 Gilman Drive, Mail Code 0448 La Jolla, CA 92093-0448, USA

Office: SME 244H Tel: (858) 534-2514 E-mail: @.***
http://materials.ucsd.edu http://materials.ucsd.edu/

On Apr 28, 2021, at 8:38 AM, Kevin Mattheus Moerman @.***> wrote:

@yangbai90 https://urldefense.com/v3/__https://github.com/yangbai90__;!!Mih3wA!Twc8jCbmNKmR0OJthyOaAw0sAqUeesKDtF9jqKfdufVzI6VNvlv09dheLqHOPJQ$, @ksyang2013 https://urldefense.com/v3/__https://github.com/ksyang2013__;!!Mih3wA!Twc8jCbmNKmR0OJthyOaAw0sAqUeesKDtF9jqKfdufVzI6VNvlv09dhe8N_4YnQ$, @littlelazy6 https://urldefense.com/v3/__https://github.com/littlelazy6__;!!Mih3wA!Twc8jCbmNKmR0OJthyOaAw0sAqUeesKDtF9jqKfdufVzI6VNvlv09dheCZgtjS0$ this is where the review takes place. Could you provide an indication as to the time you need to provide your initial review? FYI we can be flexible and it is okay if you need to take quite a bit of time. Thanks again for your help!!!!

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://urldefense.com/v3/__https://github.com/openjournals/joss-reviews/issues/3190*issuecomment-828557919__;Iw!!Mih3wA!Twc8jCbmNKmR0OJthyOaAw0sAqUeesKDtF9jqKfdufVzI6VNvlv09dheG6d7B4M$, or unsubscribe https://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/AEHTG3HZR7XSCSTVSAUZTY3TLATYVANCNFSM43EGUGCA__;!!Mih3wA!Twc8jCbmNKmR0OJthyOaAw0sAqUeesKDtF9jqKfdufVzI6VNvlv09dheIUpBBxg$.

littlelazy6 commented 3 years ago

Hi

I propose to revert next weekend, no later than 14th May. Hope this suits.

Regards Yuhui

From: YANG Research Group@UC San Diego @.> Sent: 2021年4月28日 18:41 To: openjournals/joss-reviews @.> Cc: Yuhui Tu @.>; Mention @.> Subject: Re: [openjournals/joss-reviews] [REVIEW]: PXO (Poly-XTAL Operations): Free MATLAB codebase to generate and analyse complex 2D grain structures (#3190)

Will return the comments within two weeks. Thanks!

Kesong YANG, Ph.D.

Associate Professor, Department of NanoEngineering, Program of Materials Science and Engineering, Center for Memory and Recording Research (CMRR), University of California San Diego 9500 Gilman Drive, Mail Code 0448 La Jolla, CA 92093-0448, USA

Office: SME 244H Tel: (858) 534-2514 E-mail: @.*** http://materials.ucsd.edu http://materials.ucsd.edu/

On Apr 28, 2021, at 8:38 AM, Kevin Mattheus Moerman @.***> wrote:

@yangbai90 https://urldefense.com/v3/__https://github.com/yangbai90__;!!Mih3wA!Twc8jCbmNKmR0OJthyOaAw0sAqUeesKDtF9jqKfdufVzI6VNvlv09dheLqHOPJQ$, @ksyang2013 https://urldefense.com/v3/__https://github.com/ksyang2013__;!!Mih3wA!Twc8jCbmNKmR0OJthyOaAw0sAqUeesKDtF9jqKfdufVzI6VNvlv09dhe8N_4YnQ$, @littlelazy6 https://urldefense.com/v3/__https://github.com/littlelazy6__;!!Mih3wA!Twc8jCbmNKmR0OJthyOaAw0sAqUeesKDtF9jqKfdufVzI6VNvlv09dheCZgtjS0$ this is where the review takes place. Could you provide an indication as to the time you need to provide your initial review? FYI we can be flexible and it is okay if you need to take quite a bit of time. Thanks again for your help!!!!

― You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://urldefense.com/v3/__https://github.com/openjournals/joss-reviews/issues/3190*issuecomment-828557919__;Iw!!Mih3wA!Twc8jCbmNKmR0OJthyOaAw0sAqUeesKDtF9jqKfdufVzI6VNvlv09dheG6d7B4M$, or unsubscribe https://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/AEHTG3HZR7XSCSTVSAUZTY3TLATYVANCNFSM43EGUGCA__;!!Mih3wA!Twc8jCbmNKmR0OJthyOaAw0sAqUeesKDtF9jqKfdufVzI6VNvlv09dheIUpBBxg$.

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yangbai90 commented 3 years ago

I will return the comments within two weeks. Thanks!

whedon commented 3 years ago

:wave: @yangbai90, please update us on how your review is going (this is an automated reminder).

whedon commented 3 years ago

:wave: @ksyang2013, please update us on how your review is going (this is an automated reminder).

whedon commented 3 years ago

:wave: @littlelazy6, please update us on how your review is going (this is an automated reminder).

yangbai90 commented 3 years ago

@SunilAnandatheertha Hi sunil, except for the Limitations in the wiki, is there any more text about the performance part for your code?

ksyang2013 commented 3 years ago

Hello there,

Is the review process for this code still active?

I encountered following message "Sorry, we couldn't find that repository invitation. It is possible that the invitation was revoked or that you are not logged into the invited account.”

Thanks,

Kesong YANG, Ph.D.

Associate Professor, Department of NanoEngineering, Program of Materials Science and Engineering, Center for Memory and Recording Research (CMRR), University of California San Diego 9500 Gilman Drive, Mail Code 0448 La Jolla, CA 92093-0448, USA

Office: SME 244H Tel: (858) 534-2514 E-mail: @.***
http://materials.ucsd.edu http://materials.ucsd.edu/

On May 2, 2021, at 6:10 AM, whedon @.***> wrote:

👋 @ksyang2013 https://urldefense.com/v3/__https://github.com/ksyang2013__;!!Mih3wA!XNLE3fVSIlS4xdgkhLSnAJxwfuduLw0XD1FD_QlsKkFjRFuUqPdKoMY0VPLq92s$, please update us on how your review is going (this is an automated reminder).

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SunilAnandatheertha commented 3 years ago

@yangbai90 Thank you for the comment. Will include the performance related limitations in the code in the wiki page and will update here.

SunilAnandatheertha commented 3 years ago

@ksyang2013 Thank you for the update. I think @Kevin-Mattheus-Moerman would be the best person to help you in this issue.

yangbai90 commented 3 years ago

@whedon commands

whedon commented 3 years ago

Here are some things you can ask me to do:

# List Whedon's capabilities
@whedon commands

# 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

# Ask Whedon to check repository statistics for the submitted software
@whedon check repository

yangbai90 commented 3 years ago

@whedon check references

whedon commented 3 years ago

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

OK DOIs

- 10.1016/S0081-1947(08)60603-7 is OK
- 10.1016/0001-6160(84)90151-2 is OK
- 10.1016/0036-9748(89)90525-5 is OK
- 10.1016/0001-6160(84)90089-0 is OK
- 10.2355/isijinternational.38.913 is OK
- 10.1016/0956-7151(90)90177-I is OK
- 10.1016/j.actamat.2009.10.058 is OK

MISSING DOIs

- None

INVALID DOIs

- None

yangbai90 commented 3 years ago

@whedon check repository

whedon commented 3 years ago

Failed to discover a Statement of need section in paper

whedon commented 3 years ago

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.27 s (811.1 files/s, 77654.7 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
MATLAB                         205           1236           3423          15420
Markdown                         7             65              0            184
XML                              1              1              0            146
TeX                              1              7              0             89
YAML                             1              1              1             10
-------------------------------------------------------------------------------
SUM:                           215           1310           3424          15849
-------------------------------------------------------------------------------

Statistical information for the repository '25aefe23aa693626ee2a25d8' was
gathered on 2021/05/17.
No commited files with the specified extensions were found.

yangbai90 commented 3 years ago

@SunilAnandatheertha Hi sunil, please also add the Statement of need section in your manuscript. BR Yang

littlelazy6 commented 3 years ago

Installation & general test case manual: Please give definition for CNT, SLSP and SLSPC at the first instance. I firstly saw them in Limitations. Where is the STEP 5 in the installation instruction?

Functionality documentation: As a starting point, test case 01 is like a basic tutorial and I am referring to https://github.com/SunilAnandatheertha/PXO/wiki/Test-case---01 It could assist an easier and quicker start given that more details were added into this documentation.

Voronoi tessellation (VT) model generating method. The first section highlights the regions A to E, to explain the generated resulting files. Could you add in a section explaining where to change the key VT setting in source code, such as seed (number of grain), aspect ratio (grain morphology), model size, mesh density? I think this is one core capability of PXO.
Could you also briefly explain where in the source code to modify the kernel parameters for Monte Carlo MC simulation? It would be great to indicate what specific material you are simulating for the test case.

littlelazy6 commented 3 years ago

State of the field: Functions comparing to other software. This part seems to be missing in the current paper draft. Based on my knowledge, there are several open-access packages available for MC based grain growth (GG) simulation solver, such as MCPM. VT generating tools include Python, NEPER, DREAM3D. Could you please add in few lines showing what distinguish your developed tool from other similar software? For e.g., do you use improved MC theory, grain size measurement or VT algorithm? Linkage to MTEX and ABAQUS could be a strong novelty in this work and is worth emphasizing when compared to other tools.

Generally speaking, this is a handy and useful software from my perspective. Below is just a suggestion for future development. PXO currently provides plenty of output channels to EBSD, FE mesh data. It would be beneficial to offer more choice for inputs source. If the user generates polycrystalline map from 3rd party tool and convert the nodal, phase, and orientation info into a PXO supported format, such structure can then be imported into PXO and enjoy all functions. This capability may broaden the popularity of this tool.

SunilAnandatheertha commented 3 years ago

Thank you for the feedback and review. I will address these soon and post it here.

On Fri, May 21, 2021, 1:22 PM Yuhui Tu @.***> wrote:

State of the field: Functions comparing to other software. This part seems to be missing in the current paper draft. Based on my knowledge, there are several open-access packages available for MC based grain growth (GG) simulation solver, such as MCPM. VT generating tools include Python, NEPER, DREAM3D. Could you please add in few lines showing what distinguish your developed tool from other similar software? For e.g., do you use improved MC theory, grain size measurement or VT algorithm? Linkage to MTEX and ABAQUS could be a strong novelty in this work and is worth emphasizing when compared to other tools.

Generally speaking, this is a handy and useful software from my perspective. Below is just a suggestion for future development. PXO currently provides plenty of output channels to EBSD, FE mesh data. It would be beneficial to offer more choice for inputs source. If the user generates polycrystalline map from 3rd party tool and convert the nodal, phase, and orientation info into a PXO supported format, such structure can then be imported into PXO and enjoy all functions. This capability may broaden the popularity of this tool.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/3190#issuecomment-845912827, or unsubscribe https://github.com/notifications/unsubscribe-auth/APY25RVMYDJOVWFBMW7HM3DTOZGA7ANCNFSM43EGUGCA .

SunilAnandatheertha commented 3 years ago

@whedon generate pdf

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:

SunilAnandatheertha commented 3 years ago

@whedon check references

whedon commented 3 years ago

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

OK DOIs

- 10.1186/2193-9772-3-5 is OK
- 10.1016/S0081-1947(08)60603-7 is OK
- 10.1016/0001-6160(84)90151-2 is OK
- 10.1016/0036-9748(89)90525-5 is OK
- 10.1016/0001-6160(84)90089-0 is OK
- 10.2355/isijinternational.38.913 is OK
- 10.1016/0956-7151(90)90177-I is OK
- 10.1016/j.actamat.2009.10.058 is OK

MISSING DOIs

- None

INVALID DOIs

- https://doi.org/10.1016/j.actamat.2014.08.063 is INVALID because of 'https://doi.org/' prefix

SunilAnandatheertha commented 3 years ago

@whedon check references

whedon commented 3 years ago

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

OK DOIs

- 10.1016/j.actamat.2014.08.063 is OK
- 10.1186/2193-9772-3-5 is OK
- 10.1016/S0081-1947(08)60603-7 is OK
- 10.1016/0001-6160(84)90151-2 is OK
- 10.1016/0036-9748(89)90525-5 is OK
- 10.1016/0001-6160(84)90089-0 is OK
- 10.2355/isijinternational.38.913 is OK
- 10.1016/0956-7151(90)90177-I is OK
- 10.1016/j.actamat.2009.10.058 is OK

MISSING DOIs

- None

INVALID DOIs

- None

SunilAnandatheertha commented 3 years ago

Hi, thank you again for the review. Based on it, I have implemented the following.

Performance details have been updated at: https://github.com/SunilAnandatheertha/PXO/wiki/Performance
Statement of need: included in the paper
State of the field: Included in the paper
Step 5 of the installation instruction: This must have been a typo. I have corrected the list numbering at https://github.com/SunilAnandatheertha/PXO/wiki/Test-cases
Material specificity: Simulations are currently not material specific. As of date, it is up to the user to correlate Monte-Carlo length scale and Monte-Carlo time scale to physical length scale and physical time scale. This is a matter of active research in the community. As far as texture is concerned, the user is free to assign any texture distributions by using the in-built PXO scripts making use of mtex package. However, it would be much far-fetched to make the simulations material specific as the parameter space is just too vast and spans multiple time and size scales.
Functionality documentation: Control parameters of the simulation may be modified as guided in the link: https://github.com/SunilAnandatheertha/PXO/wiki/Test-cases#start-here-for-test-cases
Assessing Kernel function parameters: Kernel function parameters as of this moment, can only be assessed from within those functions “KERNELLOOP_MC_2D__ALGORITHM_XXX” using Kernel function. These will be fully elaborated once the research paper outlining these Kernel functions gets published.
Definitions and details of “CNT”, “SLSP”, “SLSPC” have been included in the page https://github.com/SunilAnandatheertha/PXO/wiki/Material-defs.-and-params
The following changes have been made to the paper.md A. Statement of need added B. State of the field added C. To account for the change, the paper has been slightly modified in wording and structure D. Four additional references have been added (1 for mathematical use: this was missing in the first submission), (3 for state of the field) E. A back-up of the original paper has been made in paper_bu.md

SunilAnandatheertha commented 3 years ago

Sorry, I used check references command, which is an editorial command. Did not know about it.

SunilAnandatheertha commented 3 years ago

@whedon generate pdf

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:

SunilAnandatheertha commented 3 years ago

@yangbai90 @littlelazy6 @ksyang2013 Hi I have incorporated changes accroding to your comments and replied above. Thank you.

Kevin-Mattheus-Moerman commented 3 years ago

@yangbai90 @littlelazy6 @ksyang2013 the author has implemented changes that need your attention. Are you able to review them? Thanks.

Kevin-Mattheus-Moerman commented 3 years ago

@ksyang2013 can you please update me on review progress? Are you able to tick the boxes at the top of this issue? Thanks.

ksyang2013 commented 3 years ago

Hi Kevin, thanks for your message. I am not able to finish the checklist and I keep getting the message "Sorry, we couldn't find that repository invitation. It is possible that the invitation was revoked or that you are not logged into the invited account." I guess I need to remove my assignment first.

In spite of the unfinished checklist, I am glad to share some general comments. i) The generation and analysis of complex two-dimensional grain structures is indeed one important subject in computational materials science. The generated grain structures and corresponding analysis from the developed code are oriented at a macroscale modeling. It is fundamentally different from the existing codes or algorithms to build and/or model grain boundaries of materials at an atomic scale. Therefore, the application scene of the code should be clearly indicated and emphasized. This can be achieved by appropriately modifying the statements of need and summary in the article AND by adding application examples.
ii) The author is strongly encouraged to add some typical application examples that are best able to reflect the functionalities of the developed code, along with detailed instructions. A best practice could be that one application example (in one folder) only contains one major functionality.

Best,

Kesong YANG, Ph.D.

Associate Professor, Department of NanoEngineering, Program of Materials Science and Engineering, Center for Memory and Recording Research (CMRR), University of California San Diego 9500 Gilman Drive, Mail Code 0448 La Jolla, CA 92093-0448, USA

Office: SME 244H Tel: (858) 534-2514 E-mail: @.***
http://materials.ucsd.edu http://materials.ucsd.edu/

On Jun 17, 2021, at 1:11 PM, Kevin Mattheus Moerman @.***> wrote:

@ksyang2013 https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_ksyang2013&d=DwMCaQ&c=-35OiAkTchMrZOngvJPOeA&r=45Q83Sy6H1-CqyoctWnD6w&m=0qzDKDROZFmUyYfSJ31t42lplWJC-l0pAU-Jz-oHAsU&s=_QQTWBc22Cn2UFxZ1jm0dDT0yQQfIYPd_pQM3LoRVzY&e= can you please update me on review progress? Are you able to tick the boxes at the top of this issue? Thanks.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_openjournals_joss-2Dreviews_issues_3190-23issuecomment-2D863531695&d=DwMCaQ&c=-35OiAkTchMrZOngvJPOeA&r=45Q83Sy6H1-CqyoctWnD6w&m=0qzDKDROZFmUyYfSJ31t42lplWJC-l0pAU-Jz-oHAsU&s=rmR3Dx1NZ0aZzqv8_s4tq9LmQDvtMPvvUIdSfsxcIkk&e=, or unsubscribe https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_AEHTG3ACFTI4KXXB6JNFSILTTJJIPANCNFSM43EGUGCA&d=DwMCaQ&c=-35OiAkTchMrZOngvJPOeA&r=45Q83Sy6H1-CqyoctWnD6w&m=0qzDKDROZFmUyYfSJ31t42lplWJC-l0pAU-Jz-oHAsU&s=vrD3MoMQqRF33EM2rO9qSxrFWTYWpO-eY9FcWpFZlN8&e=.

Kevin-Mattheus-Moerman commented 3 years ago

@whedon re-invite @ksyang2013 as reviewer

whedon commented 3 years ago

OK, the reviewer has been re-invited.

@ @ksyang2013 please accept the invite by clicking this link: https://github.com/openjournals/joss-reviews/invitations

Kevin-Mattheus-Moerman commented 3 years ago

@ksyang2013 thanks for the update, and sorry you had trouble ticking those boxes. Yes, I think it did time out. Can you accept this new invitation :point_up: ?

Kevin-Mattheus-Moerman commented 3 years ago

@littlelazy6 can you provide an update on the review process? Are there still remaining issues that prevent you from ticking the last boxes? If so, could you summarize them? Thanks!

ksyang2013 commented 3 years ago

I still have trouble ticking these boxes. Can you remove my assignment and re-assign it?

Sorry, we couldn't find that repository invitation. It is possible that the invitation was revoked or that you are not logged into the invited account.

Kesong YANG, Ph.D.

Associate Professor, Department of NanoEngineering, Program of Materials Science and Engineering, Center for Memory and Recording Research (CMRR), University of California San Diego 9500 Gilman Drive, Mail Code 0448 La Jolla, CA 92093-0448, USA

Office: SME 244H Tel: (858) 534-2514 E-mail: @.***
http://materials.ucsd.edu http://materials.ucsd.edu/

On Jun 23, 2021, at 11:04 AM, Kevin Mattheus Moerman @.***> wrote:

@ksyang2013 https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_ksyang2013&d=DwMFaQ&c=-35OiAkTchMrZOngvJPOeA&r=45Q83Sy6H1-CqyoctWnD6w&m=LcS5ELFRzeDZqVy9stlvCg0DIBX8ZtdVnhkb0Nl3Lb0&s=NMJ8vNJyVS4GCFdiXud2BfxwpLe5vTQCw2bRuOxUpzE&e= thanks for the update, and sorry you had trouble ticking those boxes. Yes, I think it did time out. Can you accept this new invitation ☝️ ?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_openjournals_joss-2Dreviews_issues_3190-23issuecomment-2D867048231&d=DwMFaQ&c=-35OiAkTchMrZOngvJPOeA&r=45Q83Sy6H1-CqyoctWnD6w&m=LcS5ELFRzeDZqVy9stlvCg0DIBX8ZtdVnhkb0Nl3Lb0&s=Z1cdA6RD_ZO4d0I_JsZARpygjJ7ONCE3CFsQL-_pZEo&e=, or unsubscribe https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_AEHTG3DQUWCNI4WVWAIGUXLTUIO2PANCNFSM43EGUGCA&d=DwMFaQ&c=-35OiAkTchMrZOngvJPOeA&r=45Q83Sy6H1-CqyoctWnD6w&m=LcS5ELFRzeDZqVy9stlvCg0DIBX8ZtdVnhkb0Nl3Lb0&s=hF3j3mtPde3pDWT6dP20uxunMRndwz2kTV3DpKjPiYk&e=.

littlelazy6 commented 3 years ago

Thanks for the prompt revision. Just one issue with the documentation finishing level: Could you please remind me where in wiki or document do you introduce how to define the initial VT generation parameters, such as:

The size and length_scale of the whole model (2D square)
The total number of grains, or mean and standard deviation used to define the grain size distribution The above two is important when modelling the grain growth problem. If applicable, please also define
How to define the initial VT aspect ratio or texture?

SunilAnandatheertha commented 3 years ago

@littlelazy6 Thank you for the review comment. Will post back soon.

SunilAnandatheertha commented 3 years ago

@ksyang2013 Thank you for the comments and suggestions. I will update accordingly and post here soon.

SunilAnandatheertha commented 3 years ago

@littlelazy6

In PXO, simulation of grain growth is carried out by using importance sampling Monte-Carlo (MC) schemes. Equivalent VT grain structures may also be produced. But, the equivalence is defined by the grain structure statistics as contained in the grain structure, as the grain structure evolves in the state-time space. The function of the codes for this, is to allow VT computation. Two types of VT computations can be generated. These are:

VT over a user defined lattice. Currently, only 2D is available. Three types of lattices are possible, and these are random, rectangular and triangular. Together, they allow Voronoi tessellated random, rectangular and hexagonal grains respectively. Number of grains, size of grains, and aspect ratio of grains can be generated. Hexagonal grains with zigzag or armchair chirality may be generated. Rectangular grains can be made square grains as well, as the latter is subset of former. Long edge of a rectangular grain can be made to align either with x or y. These changes can be introduced by giving different values to a set of defining parameters for each case. A gradient may also be introduced if desired in each of these cases. Values of these parameters to obtain the grain structures have been detailed at https://github.com/SunilAnandatheertha/PXO/wiki/Voronoi-tessellation.
VT equivalent of a MC generated grain structure at any of the allowed temporal slices. This is being refined and integrated. It will be included in PXO distribution in the subsequent releases.

However, as of now, PXO lacks the capability of generating either a MC grain structure or a VT grain structure to match a given grain structure statistics. This is a functionality present in the software DREAM3D and is being worked on to be introduced in PXO as well.

openjournals / joss-reviews