[PRE REVIEW]: PeriDEM - High-fidelity modeling of granular media consisting of deformable complex-shaped particles

[editorialbot]

Submitting author: !--author-handle-->@prashjha<!--end-author-handle-- (Prashant K Jha) Repository: https://github.com/prashjha/PeriDEM Branch with paper.md (empty if default branch): joss Version: v0.2.1 Editor: !--editor-->@matthewfeickert<!--end-editor-- Reviewers: @divijghose, @nrichart Managing EiC: Kyle Niemeyer

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/dd0c52ad995d506dc88c4cc9b79416d5"><img src="https://joss.theoj.org/papers/dd0c52ad995d506dc88c4cc9b79416d5/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/dd0c52ad995d506dc88c4cc9b79416d5/status.svg)](https://joss.theoj.org/papers/dd0c52ad995d506dc88c4cc9b79416d5)

Author instructions

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

@prashjha 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]

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]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.59 s (634.3 files/s, 305826.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
SVG                              4              4              4          41380
C/C++ Header                   158          11551          22547          36252
Python                          38           5991           6508          15856
C++                             57           3590           2435          13231
Markdown                        19           1879              0           6697
YAML                            23            155            184           3862
CSS                              5            506            169           2269
CMake                           34            315            566           1060
CSV                              8              0              0            901
Bourne Shell                    14            151            122            674
JavaScript                       6             72            124            280
Jupyter Notebook                 1              0            512            236
TeX                              1             15              0            143
XML                              2              0              0             36
make                             2             15              6             33
reStructuredText                 1              0              0              2
Bazel                            1              0              0              1
-------------------------------------------------------------------------------
SUM:                           374          24244          33177         122913
-------------------------------------------------------------------------------

Commit count by author:

   178  Prashant K. Jha
    11  prashjha

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 2040

✅ The paper includes a Statement of need section

[editorialbot]

License info:

✅ License found: Boost Software License 1.0 (Valid open source OSI approved license)

[editorialbot]

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

✅ OK DOIs

- 10.1007/s10704-020-00480-0 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: Introduction to peridynamics
- No DOI given, and none found for title: Finite element approximation of nonlocal dynamic f...
- No DOI given, and none found for title: METIS: A software package for partitioning unstruc...
- No DOI given, and none found for title: Peridynamic states and constitutive modeling
- No DOI given, and none found for title: nanoflann: a C++ header-only fork of FLANN, a libr...

❌ MISSING DOIs

- 10.1680/geot.1979.29.1.47 may be a valid DOI for title: A discrete numerical model for granular assemblies
- 10.1016/j.jmps.2021.104376 may be a valid DOI for title: Peridynamics-based discrete element method (PeriDE...
- 10.2172/1895 may be a valid DOI for title: Reformulation of elasticity theory for discontinui...
- 10.1137/17m1112236 may be a valid DOI for title: Numerical analysis of nonlocal fracture models in ...
- 10.1016/j.cma.2019.03.024 may be a valid DOI for title: Numerical convergence of finite difference approxi...
- 10.1002/nme.5791 may be a valid DOI for title: Numerical convergence of nonlinear nonlocal contin...
- 10.1007/s42102-019-00010-0 may be a valid DOI for title: Complex fracture nucleation and evolution with non...
- 10.1007/s10659-013-9463-0 may be a valid DOI for title: Dynamic brittle fracture as a small horizon limit ...
- 10.1016/j.powtec.2018.09.047 may be a valid DOI for title: A rheometry based calibration of a first-order DEM...
- 10.1109/tpds.2021.3104255 may be a valid DOI for title: Taskflow: A lightweight parallel and heterogeneous...

❌ INVALID DOIs

- None

[editorialbot]

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

[kyleniemeyer]

Hi @prashjha, can you address this missing DOI messages above?

@matthewfeickert could you edit this submission?

Just for full disclosure, @prashjha is a JOSS editor.

[editorialbot]

Five most similar historical JOSS papers:

NLMech: Implementation of finite difference/meshfree discretization of nonlocal fracture models Submitting author: @diehlpk Handling editor: @Kevin-Mattheus-Moerman (Active) Reviewers: @vijaysm, @chennachaos Similarity score: 0.6909

Stokesian Dynamics in Python Submitting author: @Pecnut Handling editor: @philipcardiff (Active) Reviewers: @rajeshrinet, @szwiep Similarity score: 0.6557

$hp\mathrm{3D}$: A Scalable MPI/OpenMP $hp$-Adaptive Finite Element Software Library for Complex Multiphysics Applications Submitting author: @stefanhenneking Handling editor: @jedbrown (Active) Reviewers: @peterrum, @likask Similarity score: 0.6553

Akantu: an HPC finite-element library for contact and dynamic fracture simulations Submitting author: @nrichart Handling editor: @diehlpk (Active) Reviewers: @vijaysm, @chennachaos Similarity score: 0.6542

cRacklet: a spectral boundary integral method library for interfacial rupture simulation Submitting author: @tiburoch Handling editor: @diehlpk (Active) Reviewers: @srmnitc, @kylebeggs Similarity score: 0.6528

⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before considering asking the reviewers of these papers to review again for JOSS.

[kyleniemeyer]

@editorialbot invite @matthewfeickert as editor

[editorialbot]

Invitation to edit this submission sent!

[prashjha]

@editorialbot generate pdf

[editorialbot]

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

[prashjha]

@editorialbot check references

[editorialbot]

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

✅ OK DOIs

- 10.1680/geot.1979.29.1.47 is OK
- 10.1007/s10704-020-00480-0 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: Introduction to peridynamics
- No DOI given, and none found for title: METIS: A software package for partitioning unstruc...
- No DOI given, and none found for title: nanoflann: a C++ header-only fork of FLANN, a libr...

❌ MISSING DOIs

- None

❌ INVALID DOIs

- https://doi.org/10.1016/j.jmps.2021.104376 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/S0022-5096(99)00029-0 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1137/17M1112236 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/j.cma.2019.03.024 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1002/nme.5791 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1007/s42102-019-00010-0 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.3934/dcdsb.2020178 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1007/s10659-013-9463-0 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1007/s10659-007-9125-1 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/j.powtec.2018.09.047 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1109/TPDS.2021.3104255 is INVALID because of 'https://doi.org/' prefix

[editorialbot]

Five most similar historical JOSS papers:

NLMech: Implementation of finite difference/meshfree discretization of nonlocal fracture models Submitting author: @diehlpk Handling editor: @Kevin-Mattheus-Moerman (Active) Reviewers: @vijaysm, @chennachaos Similarity score: 0.6791

Stokesian Dynamics in Python Submitting author: @Pecnut Handling editor: @philipcardiff (Active) Reviewers: @rajeshrinet, @szwiep Similarity score: 0.6498

cRacklet: a spectral boundary integral method library for interfacial rupture simulation Submitting author: @tiburoch Handling editor: @diehlpk (Active) Reviewers: @srmnitc, @kylebeggs Similarity score: 0.6492

Tamaas: a library for elastic-plastic contact of periodic rough surfaces Submitting author: @prs513rosewood Handling editor: @Kevin-Mattheus-Moerman (Active) Reviewers: @likask, @agshvarts, @srmnitc, @chennachaos Similarity score: 0.6471

Akantu: an HPC finite-element library for contact and dynamic fracture simulations Submitting author: @nrichart Handling editor: @diehlpk (Active) Reviewers: @vijaysm, @chennachaos Similarity score: 0.6406

⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before considering asking the reviewers of these papers to review again for JOSS.

[prashjha]

@editorialbot check references

[editorialbot]

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

✅ OK DOIs

- 10.1680/geot.1979.29.1.47 is OK
- 10.1016/j.jmps.2021.104376 is OK
- 10.1016/S0022-5096(99)00029-0 is OK
- 10.1137/17M1112236 is OK
- 10.1016/j.cma.2019.03.024 is OK
- 10.1002/nme.5791 is OK
- 10.1007/s10704-020-00480-0 is OK
- 10.1007/s42102-019-00010-0 is OK
- 10.3934/dcdsb.2020178 is OK
- 10.1007/s10659-013-9463-0 is OK
- 10.1007/s10659-007-9125-1 is OK
- 10.1016/j.powtec.2018.09.047 is OK
- 10.1109/TPDS.2021.3104255 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: Introduction to peridynamics
- No DOI given, and none found for title: METIS: A software package for partitioning unstruc...
- No DOI given, and none found for title: nanoflann: a C++ header-only fork of FLANN, a libr...

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

[prashjha]

@editorialbot generate pdf

[prashjha]

Hi @kyleniemeyer, missing dois are fixed. Thank you!

[editorialbot]

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

[editorialbot]

Five most similar historical JOSS papers:

NLMech: Implementation of finite difference/meshfree discretization of nonlocal fracture models Submitting author: @diehlpk Handling editor: @Kevin-Mattheus-Moerman (Active) Reviewers: @vijaysm, @chennachaos Similarity score: 0.6784

Stokesian Dynamics in Python Submitting author: @Pecnut Handling editor: @philipcardiff (Active) Reviewers: @rajeshrinet, @szwiep Similarity score: 0.6487

cRacklet: a spectral boundary integral method library for interfacial rupture simulation Submitting author: @tiburoch Handling editor: @diehlpk (Active) Reviewers: @srmnitc, @kylebeggs Similarity score: 0.6469

Tamaas: a library for elastic-plastic contact of periodic rough surfaces Submitting author: @prs513rosewood Handling editor: @Kevin-Mattheus-Moerman (Active) Reviewers: @likask, @agshvarts, @srmnitc, @chennachaos Similarity score: 0.6464

Akantu: an HPC finite-element library for contact and dynamic fracture simulations Submitting author: @nrichart Handling editor: @diehlpk (Active) Reviewers: @vijaysm, @chennachaos Similarity score: 0.6393

⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before considering asking the reviewers of these papers to review again for JOSS.

[matthewfeickert]

@editorialbot assign @matthewfeickert as editor

[editorialbot]

Assigned! @matthewfeickert is now the editor

[matthewfeickert]

(I'm currently traveling for a work conference so I will be delayed a few days on finding reviewers.)

[prashjha]

Hi @matthewfeickert, no worries. I look forward to working with you on this. If you need any suggestions for potential reviewers, please let me know.

[prashjha]

@editorialbot generate pdf

[editorialbot]

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

[editorialbot]

Five most similar historical JOSS papers:

NLMech: Implementation of finite difference/meshfree discretization of nonlocal fracture models Submitting author: @diehlpk Handling editor: @Kevin-Mattheus-Moerman (Active) Reviewers: @vijaysm, @chennachaos Similarity score: 0.6850

cRacklet: a spectral boundary integral method library for interfacial rupture simulation Submitting author: @tiburoch Handling editor: @diehlpk (Active) Reviewers: @srmnitc, @kylebeggs Similarity score: 0.6560

Tamaas: a library for elastic-plastic contact of periodic rough surfaces Submitting author: @prs513rosewood Handling editor: @Kevin-Mattheus-Moerman (Active) Reviewers: @likask, @agshvarts, @srmnitc, @chennachaos Similarity score: 0.6547

$hp\mathrm{3D}$: A Scalable MPI/OpenMP $hp$-Adaptive Finite Element Software Library for Complex Multiphysics Applications Submitting author: @stefanhenneking Handling editor: @jedbrown (Active) Reviewers: @peterrum, @likask Similarity score: 0.6520

Stokesian Dynamics in Python Submitting author: @Pecnut Handling editor: @philipcardiff (Active) Reviewers: @rajeshrinet, @szwiep Similarity score: 0.6519

⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before considering asking the reviewers of these papers to review again for JOSS.

[prashjha]

Hello @matthewfeickert, please could you start looking for reviewers? It has been 3 weeks already!

[matthewfeickert]

Hello @matthewfeickert, please could you start looking for reviewers?

I have been and will follow up again.

It has been 3 weeks already!

I did mention I am currently traveling. If your timeline is accelerated and you feel I am not fast enough for you feel free to request another editor.

[matthewfeickert]

@editorialbot add @divijghose as reviewer

[editorialbot]

@divijghose added to the reviewers list!

[matthewfeickert]

@editorialbot add @nrichart as reviewer

[editorialbot]

@nrichart added to the reviewers list!

[matthewfeickert]

We now have the minimum two reviewers required, so I'll go ahead and start the review. Additional reviewers are very welcome so if other potential reviewers I contacted would be interested in helping I can add you to the review after it has started.

[matthewfeickert]

@editorialbot start review

[editorialbot]

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/7525.