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[PRE REVIEW]: FEniCS-arclength: A numerical continuation package in FEniCS for nonlinear problems in solid mechanics #5604

Closed editorialbot closed 1 year ago

editorialbot commented 1 year ago

Submitting author: !--author-handle-->@pprachas<!--end-author-handle-- (Peerasait Prachaseree) Repository: https://github.com/pprachas/fenics_arclength Branch with paper.md (empty if default branch): Version: v0.1.0 Editor: !--editor-->@prashjha<!--end-editor-- Reviewers: @w-luo-academic, @kingyin3613 Managing EiC: Kyle Niemeyer

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Markdown: [![status](https://joss.theoj.org/papers/c4791755683fc95dd5ccd9c8e8708a08/status.svg)](https://joss.theoj.org/papers/c4791755683fc95dd5ccd9c8e8708a08)

Author instructions

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

@pprachas 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.

Editor instructions

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

@editorialbot commands
editorialbot commented 1 year ago

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:

@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 1 year ago 
Software report:

github.com/AlDanial/cloc v 1.88  T=1.64 s (21.3 files/s, 510073.0 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
XML                              1              0              0           1703
Jupyter Notebook                 7              0         829381           1133
Python                           8            373            247           1085
Markdown                         4            312              0            729
reStructuredText                 9            378            305            318
TeX                              1             22              0            225
YAML                             3              3              4             34
DOS Batch                        1              8              1             26
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                            35           1100         829945           5262
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository
editorialbot commented 1 year ago

Wordcount for paper.md is 1301

editorialbot commented 1 year ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1016/0045-7825(88)90024-2 is OK
- 10.1016/j.eml.2022.101797 is OK
- 10.21105/joss.01292 is OK
- 10.5281/zenodo.1287832 is OK

MISSING DOIs

- 10.1016/j.engstruct.2020.111755 may be a valid DOI for title: A simple extrapolated predictor for overcoming the starting and tracking issues in the arc-length method for nonlinear structural mechanics
- 10.1103/physrevb.101.064101 may be a valid DOI for title: Navigating the landscape of nonlinear mechanical metamaterials for advanced programmability
- 10.1103/physrevlett.127.138102 may be a valid DOI for title: Elastic instabilities govern the morphogenesis of the optic cup
- 10.1016/b978-0-08-027299-3.50009-1 may be a valid DOI for title: A fast incremental/iterative solution procedure that handles “snap-through”
- 10.1002/nme.2447 may be a valid DOI for title: A dissipation-based arc-length method for robust simulation of brittle and ductile failure
- 10.1016/0020-7683(79)90081-7 may be a valid DOI for title: An incremental approach to the solution of snapping and buckling problems
- 10.1061/jmcea3.0000966 may be a valid DOI for title: Large deflections and stability of elastic frame
- 10.1016/0045-7825(86)90079-4 may be a valid DOI for title: A three-dimensional finite-strain rod model. Part II: Computational aspects
- 10.21105/joss.01539 may be a valid DOI for title: pulse: A python package based on FEniCS for solving problems in cardiac mechanics
- 10.1016/j.softx.2018.10.005 may be a valid DOI for title: FEniCS mechanics: A package for continuum mechanics simulations
- 10.1002/nme.1620140811 may be a valid DOI for title: Incremental displacement algorithms for nonlinear problems
- 10.1115/1.4006992 may be a valid DOI for title: A unified library of nonlinear solution schemes
- 10.1115/1.4005960 may be a valid DOI for title: Wrinkling phenomena in neo-Hookean film/substrate bilayers
- 10.1007/bf03184638 may be a valid DOI for title: Surface instability of rubber in compression
- 10.1137/s0895479899358194 may be a valid DOI for title: A fully asynchronous multifrontal solver using distributed dynamic scheduling

INVALID DOIs

- https://doi.org/10.1016/j.cma.2018.10.002 is INVALID because of 'https://doi.org/' prefix
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:

kyleniemeyer commented 1 year ago

Hello @pprachas, as we are finding an editor and reviewers for your submission, could you take a look at the DOI issues above and address in your paper?

kyleniemeyer commented 1 year ago

@editorialbot invite @prashjha as editor

Hi @prashjha, this looks to be in your wheelhouse - could you edit this submission?

editorialbot commented 1 year ago

Invitation to edit this submission sent!

pprachas 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:

pprachas commented 1 year ago

@editorialbot check references

editorialbot commented 1 year ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1016/0045-7825(88)90024-2 is OK
- 10.1016/j.eml.2022.101797 is OK
- 10.1103/PhysRevB.101.064101 is OK
- 10.1103/PhysRevLett.127.138102 is OK
- 10.21105/joss.01292 is OK
- 10.1061/JMCEA3.0000966 is OK
- 10.5281/zenodo.1287832 is OK
- 10.21105/joss.01539 is OK
- 10.1115/1.4006992 is OK
- 10.1115/1.4005960 is OK
- 10.1098/rsta.2016.0163 is OK
- 10.1137/S0895479899358194 is OK

MISSING DOIs

- None

INVALID DOIs

- https://doi.org/10.1016/j.engstruct.2020.111755 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/j.cma.2018.10.002 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/0045-7949(81)90108-5 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1002/nme.2447 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/0020-7683(79)90081-7 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/0045-7825(86)90079-4 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/j.softx.2018.10.005 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1002/nme.1620140811 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1007/BF03184638 is INVALID because of 'https://doi.org/' prefix
pprachas commented 1 year ago

@editorialbot check references

editorialbot commented 1 year ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1016/0045-7825(88)90024-2 is OK
- 10.1016/j.eml.2022.101797 is OK
- 10.1016/j.engstruct.2020.111755 is OK
- 10.1103/PhysRevB.101.064101 is OK
- 10.1103/PhysRevLett.127.138102 is OK
- 10.1016/j.cma.2018.10.002 is OK
- 10.21105/joss.01292 is OK
- 10.1016/0045-7949(81)90108-5 is OK
- 10.1002/nme.2447 is OK
- 10.1016/0020-7683(79)90081-7 is OK
- 10.1061/JMCEA3.0000966 is OK
- 10.1016/0045-7825(86)90079-4 is OK
- 10.5281/zenodo.1287832 is OK
- 10.21105/joss.01539 is OK
- 10.1016/j.softx.2018.10.005 is OK
- 10.1002/nme.1620140811 is OK
- 10.1115/1.4006992 is OK
- 10.1115/1.4005960 is OK
- 10.1098/rsta.2016.0163 is OK
- 10.1007/BF03184638 is OK
- 10.1137/S0895479899358194 is OK

MISSING DOIs

- None

INVALID DOIs

- None
pprachas 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:

prashjha commented 1 year ago

@editorialbot assign me as editor

editorialbot commented 1 year ago

Assigned! @prashjha is now the editor

prashjha commented 1 year ago

@pprachas, interesting library! To speed up the process, could you provide the names of a few potential reviewers from this list?

prashjha commented 1 year ago

@kyleniemeyer thanks for the invite :)

pprachas commented 1 year ago

Hi @prashjha! Thanks for editing this submission!

I looked at the list of reviewers with key words "Finite Element" and "Solid Mechanics" and listed the names of potential reviewers below. In addition, anyone with FEniCS experience would be great but I don’t want to overburden anyone who is currently already reviewing another FEniCS submission.

Potential List of reviewers:

prashjha commented 1 year ago

Hi @w-luo-academic, would you be interested in reviewing this JOSS submission? You can read the draft and also check out their software repository.

The JOSS review process is detailed in this link. I will be happy to help with other questions. Let me know if this interests you.

prashjha commented 1 year ago

Hi @kingyin3613, would you be interested in reviewing this JOSS submission? You can read the draft and also check out their software repository.

The JOSS review process is detailed in this link. I will be happy to help with other questions. Let me know if this interests you.

w-luo-academic commented 1 year ago

Yes, I am happy to review the submission.

Wen

On Tue, Aug 1, 2023 at 11:25 AM Prashant K. Jha @.***> wrote:

Hi @kingyin3613 https://github.com/kingyin3613, would you be interested in reviewing this JOSS submission? You can read the draft https://github.com/openjournals/joss-papers/blob/joss.05604/joss.05604/10.21105.joss.05604.pdf and also check out their software repository https://github.com/pprachas/fenics_arclength.

The JOSS review process is detailed in this link https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. I will be happy to help with other questions. Let me know if this interests you.

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/5604#issuecomment-1660669886, or unsubscribe https://github.com/notifications/unsubscribe-auth/AE7GLMA3AF5342DZCEQUU4LXTEUXXANCNFSM6AAAAAAZYWDEMM . You are receiving this because you were mentioned.Message ID: @.***>

--

Wen Luo

Ph.D., Theoretical and Applied Mechanics

Northwestern University

Evanston IL

prashjha commented 1 year ago

@w-luo-academic, great. Adding you as a reviewer.

prashjha commented 1 year ago

@editorialbot add @w-luo-academic as reviewer

editorialbot commented 1 year ago

@w-luo-academic added to the reviewers list!

w-luo-academic commented 1 year ago

Could you please add my new email address: @.***? My Northwestern email was no longer being used for quite a while.

Thanks, Wen

On Tue, Aug 1, 2023 at 11:37 AM The Open Journals editorial robot < @.***> wrote:

Assigned #5604 https://github.com/openjournals/joss-reviews/issues/5604 to @w-luo-academic https://github.com/w-luo-academic.

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/5604#event-9978894289, or unsubscribe https://github.com/notifications/unsubscribe-auth/AE7GLMERPERGQ74HT7HS7UTXTEWE3ANCNFSM6AAAAAAZYWDEMM . You are receiving this because you were assigned.Message ID: @.***>

--

Wen Luo

Ph.D., Theoretical and Applied Mechanics

Northwestern University

Evanston IL

prashjha commented 1 year ago

@w-luo-academic, I think you need to update your GitHub profile. I don't think I have control over this.

kingyin3613 commented 1 year ago

Hi @kingyin3613, would you be interested in reviewing this JOSS submission? You can read the draft and also check out their software repository.

The JOSS review process is detailed in this link. I will be happy to help with other questions. Let me know if this interests you.

Yes, I am willing to review this interesting package!

prashjha commented 1 year ago

@kingyin3613, great. Thanks for confirming.

prashjha commented 1 year ago

@editorialbot add @kingyin3613 as reviewer

editorialbot commented 1 year ago

@kingyin3613 added to the reviewers list!

prashjha commented 1 year ago

@pprachas, we now have two reviewers, @w-luo-academic and @kingyin3613. I will close this issue and create a new issue where the review will take place.

prashjha commented 1 year ago

@editorialbot start review

editorialbot commented 1 year ago

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/5727.