[PRE REVIEW]: PAPRECA: A parallel hybrid off-lattice kinetic Monte Carlo/molecular dynamics simulator

[editorialbot]

Submitting author: !--author-handle-->@sntioudis<!--end-author-handle-- (Stavros Ntioudis) Repository: https://github.com/sntioudis/papreca Branch with paper.md (empty if default branch): Version: v1.0.0 Editor: !--editor-->@srmnitc<!--end-editor-- Reviewers: @liamhuber, @jfaraudo Managing EiC: Kevin M. Moerman

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Author instructions

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

@sntioudis 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.

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.05 s (1491.6 files/s, 258735.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
C++                             20           2142           1597           2983
Markdown                        11            689              0           1213
C/C++ Header                    19            522            617            938
Python                           7            232            103            634
TeX                              1             32              0            377
CMake                            2             36             20            152
YAML                             3             24             13            113
Bourne Shell                     8             27             17             82
make                             2             29             19             52
-------------------------------------------------------------------------------
SUM:                            73           3733           2386           6544
-------------------------------------------------------------------------------

Commit count by author:

   106  Stavros Ntioudis
     5  James Ewen
     1  sntioudis

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 1317

✅ The paper includes a Statement of need section

[editorialbot]

License info:

🟡 License found: GNU General Public License v2.0 (Check here for OSI approval)

[editorialbot]

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

[Kevin-Mattheus-Moerman]

@editorialbot check references

[Kevin-Mattheus-Moerman]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.1016/j.commatsci.2023.112421 is OK
- 10.1016/j.cpc.2021.108171 is OK
- 10.1103/PhysRevB.75.205339 is OK
- 10.1021/acs.jctc.1c00921 is OK
- 10.1021/cr400234a is OK
- 10.1063/1.1369622 is OK
- 10.1063/1.2919546 is OK
- 10.1016/j.jcp.2015.12.001 is OK
- 10.1021/cs3005709 is OK
- 10.1007/978-3-319-44677-6_29 is OK
- 10.1039/C6NR01881E is OK
- 10.1016/j.triboint.2018.02.005 is OK
- 10.1063/1.461138 is OK
- 10.1016/0021-9991(76)90041-3 is OK
- 10.21105/joss.00247 is OK
- 10.21105/joss.01168 is OK
- 10.21105/joss.02307 is OK
- 10.21105/joss.02307 is OK
- 10.1088/1361-651X/accc4b is OK
- 10.1016/j.cpc.2014.04.017 is OK
- 10.3390/min10090825 is OK
- 10.1063/1.5046635 is OK
- 10.1088/0965-0393/22/5/055002 is OK
- 10.1063/1.1415500 is OK
- 10.3389/fchem.2019.00202 is OK

MISSING DOIs

- No DOI given, and none found for title: kmcos: Kinetic Monte Carlo of Systems
- No DOI given, and none found for title: Python-based Charge Dynamics (PyCD)
- No DOI given, and none found for title: VIS-A-VIS: agent-based simulator of viral infectio...
- No DOI given, and none found for title: MulSKIPS: A Kinetic Monte Carlo super-Lattice code
- No DOI given, and none found for title: Kimocs - Kinetic Monte Carlo for Surfaces
- No DOI given, and none found for title: KSOME: Kinetic Simulations of Microstructural Evol...
- No DOI given, and none found for title: kMCpy: Kinetic Monte Carlo Simulation using Python
- No DOI given, and none found for title: Morphokinetics

INVALID DOIs

- None

[sntioudis]

Thank you for opening this pre-review issue!

Here are some suggestions for reviewers:

• ptmerz
• shahmoradi
• corettialessandro
• masrul
• govarguz

[Kevin-Mattheus-Moerman]

@editorialbot invite @ppxasjsm as editor

[editorialbot]

Invitation to edit this submission sent!

[Kevin-Mattheus-Moerman]

@ppxasjsm you are off the hook, @srmnitc has offered to edit this one.

[Kevin-Mattheus-Moerman]

@editorialbot invite @srmnitc as editor

[editorialbot]

Invitation to edit this submission sent!

[srmnitc]

@editorialbot assign me as editor

[editorialbot]

Assigned! @srmnitc is now the editor

[srmnitc]

Hi @sntioudis , I will be the handling editor for this submission. The next step would be to find some reviewers for the submission. Meanwhile, feel free to ask me any questions here.

[srmnitc]

👋 @ptmerz @corettialessandro @liamhuber would any of you have time and be willing to review this submission for JOSS? As you might know, we carry out our checklist-driven reviews here in GitHub issues and follow these guidelines. Thanks for your time!

[liamhuber]

From the review guidelines I am inferring that I should actually take this thing for a spin. My first step was to check out the installation process, andthese were easy to find and docs overall look well organized and readable (kudos to the author team so far!)

I got to here:

The current version of PAPRECA (1.0) runs only on LINUX-based systems. Cross-platform compatibility will be available in future versions. At the moment, non-LINUX users can run PAPRECA on a virtual machine (e.g., VirtualBox or Windows Subsystem for Linux).

@sntioudis what are the odds this is an overly-restrictive statement? I'm running OSX on my laptop, so I have ready access to unix but not linux. My other machine runs Windows. If you think there's a chance unix will cut it, I'll give it a go and see what happens.

If linux is a hard requirement, and assuming one of the other people tagged is able to review, I'll recuse myself by reason of laziness. As long as I'm not critically required, I'd prefer to avoid setting up a VM or dual partition on my windows machine before even starting the review.

[sntioudis]

Hi @liamhuber, thank you for taking the time to review the PAPRECA documentation pages!

@sntioudis what are the odds this is an overly-restrictive statement? I'm running OSX on my laptop, so I have ready access to unix but not linux. My other machine runs Windows. If you think there's a chance unix will cut it, I'll give it a go and see what happens.

Unfortunately, we have no access to macOS and therefore, we did not test PAPRECA on such a system. PAPRECA was only tested on Linux and this is why this overly restrictive statement is present in the documentation: "The current version of PAPRECA (1.0) runs only on LINUX-based systems. Cross-platform compatibility will be available in future versions. At the moment, non-LINUX users can run PAPRECA on a virtual machine (e.g., VirtualBox or Windows Subsystem for Linux)."

That being said, there is a chance that PAPRECA can be installed on macOS but there is no way for us to check if it is running properly. Also, as we have no access to macOS we will not be able to support you and make the necessary changes if any issues manifest during the review.

I'd prefer to avoid setting up a VM or dual partition on my windows machine before even starting the review.

Finally, I just wanted to mention that if you are a Windows user there is not really a need to set up a virtual machine or a partition in order to run PAPRECA. You can use the Windows subsystem for Linux (WSL) which gives you a Linux terminal on Windows. Installing WSL can be as easy as running a single command from your PowerShell.

[srmnitc]

From the review guidelines I am inferring that I should actually take this thing for a spin. My first step was to check out the installation process, andthese were easy to find and docs overall look well organized and readable (kudos to the author team so far!)

I got to here:

The current version of PAPRECA (1.0) runs only on LINUX-based systems. Cross-platform compatibility will be available in future versions. At the moment, non-LINUX users can run PAPRECA on a virtual machine (e.g., VirtualBox or Windows Subsystem for Linux).

@sntioudis what are the odds this is an overly-restrictive statement? I'm running OSX on my laptop, so I have ready access to unix but not linux. My other machine runs Windows. If you think there's a chance unix will cut it, I'll give it a go and see what happens.

If linux is a hard requirement, and assuming one of the other people tagged is able to review, I'll recuse myself by reason of laziness. As long as I'm not critically required, I'd prefer to avoid setting up a VM or dual partition on my windows machine before even starting the review.

@liamhuber If you would still like to go ahead with a review, let us know. For the review itself, I will start a separate issue. We will start the review once we have found two reviewers. At the moment, a confirmation from you would be enough :)

[corettialessandro]

Hi @srmnitc! I am sorry, but I am really busy the following months and I would not be able to provide a good review in due time.

Thanks for the invitation anyway :)

[liamhuber]

@sntioudis thanks for the WSL tip! @srmnitc, go ahead and ~invite~ tag/assign me, I'll start working on it next week.

[srmnitc]

@editorialbot add @liamhuber as reviewer

[editorialbot]

@liamhuber added to the reviewers list!

[srmnitc]

👋 @ptmerz @corettialessandro @liamhuber would any of you have time and be willing to review this submission for JOSS? As you might know, we carry out our checklist-driven reviews here in GitHub issues and follow these guidelines. Thanks for your time!

@sntioudis thanks for the WSL tip! @srmnitc, go ahead and ~invite~ tag/assign me, I'll start working on it next week.

Thanks a lot @liamhuber, once I find one more reviewer I will start review issue and close this one.

[srmnitc]

👋 @jfaraudo @shahmoradi would any of you have time and be willing to review this submission for JOSS? As you might know, we carry out our checklist-driven reviews here in GitHub issues and follow these guidelines. Thanks for your time!

[shahmoradi]

@srmnitc Thank you for your invitation. Unfortunately, my schedule for May is completely taken and I am afraid I will not be able to provide timely feedback.

[ptmerz]

@srmnitc, I can help reviewing!

[jfaraudo]

@srmnitc Yes, I can help with this.

[srmnitc]

@jfaraudo thank you so much!

[srmnitc]

@editorialbot add @jfaraudo as reviewer

[editorialbot]

@jfaraudo added to the reviewers list!

[srmnitc]

@editorialbot start review

[editorialbot]

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/6714.