[PRE REVIEW]: RNMC: kinetic Monte Carlo implementations for complex reaction networks

[editorialbot]

Submitting author: @espottesmith (Evan Spotte-Smith)
Repository: https://github.com/BlauGroup/RNMC
Branch with paper.md (empty if default branch):
Version: v1.0.0
Editor: @mbarzegary
Reviewers: @Anshuman5, @ptmerz, @lorenzo-rovigatti
Managing EiC: Kevin M. Moerman

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/7d071341934be452863d5523edb17413"><img src="https://joss.theoj.org/papers/7d071341934be452863d5523edb17413/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/7d071341934be452863d5523edb17413/status.svg)](https://joss.theoj.org/papers/7d071341934be452863d5523edb17413)

Author instructions

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

@espottesmith 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]

⚠️ An error happened when generating the pdf.

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.33 s (251.2 files/s, 40303.4 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
C++                             26           1091            558           4470
C/C++ Header                    27            618            354           2236
Jupyter Notebook                 5              0           1178           1479
SVG                              1              0              0            308
make                             4             86             85            162
Markdown                         3             31              0            147
TeX                              1             11              0            114
Ruby                             1             28             12            106
Bourne Shell                     2             23              2             71
Nix                              2              8              4             63
YAML                             2              1              4             33
JSON                             9              0              0             32
-------------------------------------------------------------------------------
SUM:                            83           1897           2197           9221
-------------------------------------------------------------------------------

Commit count by author:

   229	Laura Zichi
   174	Daniel Barter
    28	Evan Walter Clark Spotte-Smith
    28	lzichi
    14	Evan Walter Clark Spotte-Smith, PhD

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 962

✅ The paper includes a Statement of need section

[editorialbot]

License info:

🟡 License found: Other (Check here for OSI approval)

[espottesmith]

Possible reviewers:

• Anshuman Kumar
• @lorenzo-rovigatti
• @ptmerz
• @corettialessandro

[espottesmith]

@editorialbot generate pdf

[editorialbot]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[editorialbot]

Five most similar historical JOSS papers:

PAPRECA: A parallel hybrid off-lattice kinetic Monte Carlo/molecular dynamics simulator
Submitting author: @sntioudis
Handling editor: @srmnitc (Active)
Reviewers: @liamhuber, @jfaraudo
Similarity score: 0.8010

Excimontec v1.0: An Open-Source Software Tool for Kinetic Monte Carlo Simulations of Organic Electronic Devices
Submitting author: @MikeHeiber
Handling editor: @pdebuyl (Active)
Reviewers: @mdavezac, @Luthaf
Similarity score: 0.7552

Monte Carlo / Dynamic Code (MC/DC): An accelerated Python package for fully transient neutron transport and rapid methods development
Submitting author: @jpmorgan98
Handling editor: @kellyrowland (Active)
Reviewers: @lewisfish, @szabo137
Similarity score: 0.7497

lattice_mc: A Python Lattice-Gas Monte Carlo Module
Submitting author: @bjmorgan
Handling editor: @labarba (Retired)
Reviewers: @asmit3
Similarity score: 0.7472

kinisi: Bayesian analysis of mass transport from molecular dynamics simulations
Submitting author: @arm61
Handling editor: @zhubonan (Active)
Reviewers: @hmacdope, @dengzeyu
Similarity score: 0.7255

⚠️ 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.

[mbarzegary]

@editorialbot assign me as editor

[editorialbot]

Assigned! @mbarzegary is now the editor

[mbarzegary]

Hi @Anshuman5, @lorenzo-rovigatti, @ptmerz, @corettialessandro 👋
Considering your field of expertise as well as your experience with JOSS, would any of you be willing to review this submission? As you know, we carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

Paper: https://raw.githubusercontent.com/openjournals/joss-papers/joss.07159/joss.07159/10.21105.joss.07159.pdf
Software: https://github.com/BlauGroup/RNMC

[Anshuman5]

@mbarzegary Yes, I can review this.

[ptmerz]

@mbarzegary Yes, I can review this.

[lorenzo-rovigatti]

Hi! Sorry for the late reply. I can also review this one.

[corettialessandro]

Hi, for me it would be a bit complicated right now. Also, maybe you do not need me at this point ;)

[mbarzegary]

@Anshuman5, @lorenzo-rovigatti, @ptmerz, @corettialessandro thank you guys for your replies.

[mbarzegary]

@editorialbot add @Anshuman5 as reviewer

[editorialbot]

@Anshuman5 added to the reviewers list!

[mbarzegary]

@editorialbot add @ptmerz as reviewer

[editorialbot]

@ptmerz added to the reviewers list!

[mbarzegary]

@editorialbot add @lorenzo-rovigatti as reviewer

[editorialbot]

@lorenzo-rovigatti added to the reviewers list!

[mbarzegary]

@editorialbot start review

[editorialbot]

OK, I've started the review over in #7244.