[PRE REVIEW]: GLUE Code: A framework handling communication and interfaces between scales

[editorialbot]

Submitting author: !--author-handle-->@apachalieva<!--end-author-handle-- (Aleksandra Pachalieva) Repository: https://github.com/lanl/GLUE Branch with paper.md (empty if default branch): manuscript Version: v1.0.0 Editor: !--editor-->@danielskatz<!--end-editor-- Reviewers: @govarguz, @keipertk Managing EiC: Arfon Smith

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/a200507cb0091621b80baa85ee59186c"><img src="https://joss.theoj.org/papers/a200507cb0091621b80baa85ee59186c/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/a200507cb0091621b80baa85ee59186c/status.svg)](https://joss.theoj.org/papers/a200507cb0091621b80baa85ee59186c)

Author instructions

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

@apachalieva if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). In addition, this list of people have already agreed to review for JOSS and may be suitable for this submission (please start at the bottom of the list).

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]

Checking the BibTeX entries failed with the following error:

No paper file path

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.06 s (818.1 files/s, 124788.7 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          13            710           1106           2180
C/C++ Header                     4             87            482            577
JSON                             9              0              0            508
C                                5             68             61            474
C++                              2             45             25            256
Fortran 90                       3             42             93            198
YAML                             2              5              6             70
CMake                            3             14              7             53
Markdown                         4             30              0             40
Bourne Shell                     2              0              0             32
-------------------------------------------------------------------------------
SUM:                            47           1001           1780           4388
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

[editorialbot]

Failed to discover a Statement of need section in paper

[editorialbot]

:warning: An error happened when generating the pdf. Paper file not found.

[arfon]

@editorialbot set manuscript as branch

[editorialbot]

Done! branch is now manuscript

[editorialbot]

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

[danielskatz]

@editorialbot assign me as editor

[editorialbot]

Assigned! @danielskatz is now the editor

[danielskatz]

👋 @apachalieva - I'll be the editor for your submission.

Please provide some suggestions for potential reviewers by mentioning them here in this thread (without tagging them with an @). In addition, this list of people have already agreed to review for JOSS and may be suitable for this submission (please start at the bottom of the list).

[apachalieva]

Hi, @danielskatz! We think that govarguz and Raffaello Potestio (raffaello.potestio@unitn.it) will be suitable reviewers for our submission.

[danielskatz]

Thanks @apachalieva - Given that we need 2 reviewers, a few more suggestions would also be welcome.

[danielskatz]

👋 @govarguz - Would you be willing to review this JOSS submission?

[danielskatz]

👋 @potestiolab - would you be willing to review this submission for JOSS?

JOSS is a free, open-source, community driven and developer-friendly online journal (no publisher is seeking to raise revenue from the volunteer labor of researchers!).

The review process at JOSS is unique: it takes place in a GitHub issue, is open, and author-reviewer-editor conversations are encouraged.

JOSS reviews involve downloading and installing the software, and inspecting the repository and submitted paper for key elements. See https://joss.readthedocs.io/en/latest/review_criteria.html

Editors and reviewers post comments on the Review issue, and authors respond to the comments and improve their submission until acceptance (or withdrawal, if they feel unable to satisfy the review).

If you are not able to review this submission for JOSS, can you recommend someone from your lab/team to help out?

[apachalieva]

Hi, @danielskatz - these are some more reviewers I think would be suitable: jeffhammond, corettialessandro, and KEIPERTK.

Thanks!

[apachalieva]

@editorialbot commands

[editorialbot]

Hello @apachalieva, here are the things you can ask me to do:

# List all available commands
@editorialbot commands

# Get a list of all editors's GitHub handles
@editorialbot list editors

# Check the references of the paper for missing DOIs
@editorialbot check references

# Perform checks on the repository
@editorialbot check repository

# Adds a checklist for the reviewer using this command
@editorialbot generate my checklist

# Set a value for branch
@editorialbot set joss-paper as branch

# Generates the pdf paper
@editorialbot generate pdf

# Generates a LaTeX preprint file
@editorialbot generate preprint

# Get a link to the complete list of reviewers
@editorialbot list reviewers

[apachalieva]

@editorialbot check references

[editorialbot]

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

OK DOIs

- None

MISSING DOIs

- 10.1103/physreve.102.023310 may be a valid DOI for title: Multiscale simulation of plasma flows using active learning
- 10.1063/1.1724389 may be a valid DOI for title: Transport coefficients determined using the shielded Coulomb potential
- 10.1103/physrevlett.112.135001 may be a valid DOI for title: First observations of nonhydrodynamic mix at the fuel-shell interface in shock-driven inertial confinement implosions
- 10.2172/10176421 may be a valid DOI for title: Fast parallel algorithms for short-range molecular dynamics
- 10.1007/10968987_3 may be a valid DOI for title: Slurm: Simple Linux utility for resource management
- 10.1145/2834899.2834908 may be a valid DOI for title: Database assisted distribution to improve fault tolerance for multiphysics applications
- 10.1177/1094342009106189 may be a valid DOI for title: Fault tolerance in petascale/exascale systems: Current knowledge, challenges and research opportunities
- 10.1063/1.5031206 may be a valid DOI for title: Adaptive resolution molecular dynamics technique: Down to the essential
- 10.1021/ct400566j may be a valid DOI for title: Multiscale simulation of liquid water using a four-to-one mapping for coarse-graining

INVALID DOIs

- None

[apachalieva]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.1103/physreve.102.023310 is OK
- 10.1063/1.1724389 is OK
- 10.1063/1.4921935 is OK
- 10.1103/physrevlett.112.135001 is OK
- 10.1103/PhysRevLett.118.185003 is OK
- 10.1063/1.872643 is OK
- 10.1145/1362622.1362700 is OK
- 10.2172/10176421 is OK
- 10.1007/10968987_3 is OK
- 10.48550/arXiv.1202.1056 is OK
- 10.1145/2834899.2834908 is OK
- 10.1177/1094342009106189 is OK
- 10.1063/1.5031206 is OK
- 10.1021/ct400566j is OK
- 10.48550/ARXIV.2209.09811 is OK
- 10.1038/s41598-020-69661-0 is OK

MISSING DOIs

- None

INVALID DOIs

- 10.5555/3454287.3455008 is INVALID
- 10.5555/1953048.2078195 is INVALID
- 10.5555/324493.325074 is INVALID

[danielskatz]

👋 @jeffhammond, @corettialessandro, and @KEIPERTK - would two of you be willing to review this submission for JOSS?

[danielskatz]

👋 @apachalieva - note that the reference check looks at all references in your .bib file. If you are not using some of them in your paper, you can remove them from this file, then not worry about if they have DOIs. On the other hand, if the references associated with the invalid DOIs are needed in your paper, you will need to fix the invalid DOIs.

[govarguz]

Hi, @danielskatz! I can review this submission!

[danielskatz]

Thanks @govarguz - I'll add you to the system, but we won't start the review until we find one more reviewer as well

[danielskatz]

@editorialbot add @govarguz as reviewer

[editorialbot]

@govarguz added to the reviewers list!

[editorialbot]

Checking the BibTeX entries failed with the following error:

Failed to parse BibTeX on value "url" (NAME) [#<BibTeX::Bibliography data=[10]>, "@", #<BibTeX::Entry >, {:title=>["Py{T}orch: {A}n Imperative Style, High-Performance Deep Learning Library"], :author=>["Paszke, Adam and Gross, Sam and Massa, Francisco and Lerer, Adam and Bradbury, James and Chanan, Gregory and Killeen, Trevor and Lin, Zeming and Gimelshein, Natalia and Antiga, Luca and Desmaison, Alban and Kopf, Andreas and Yang, Edward and DeVito, Zachary and Raison, Martin and Tejani, Alykhan and Chilamkurthy, Sasank and Steiner, Benoit and Fang, Lu and Bai, Junjie and Chintala, Soumith"], :booktitle=>["Advances in Neural Information Processing Systems 32"], :pages=>["8024--8035"], :year=>["2019"], :publisher=>["Curran Associates, Inc."], :doi=>["https://dl.acm.org/doi/10.5555/3454287.3455008"]}]

[apachalieva]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.1103/physreve.102.023310 is OK
- 10.1063/1.1724389 is OK
- 10.1063/1.4921935 is OK
- 10.1103/physrevlett.112.135001 is OK
- 10.1103/PhysRevLett.118.185003 is OK
- 10.1063/1.872643 is OK
- 10.1145/1362622.1362700 is OK
- 10.2172/10176421 is OK
- 10.1007/10968987_3 is OK
- 10.48550/arXiv.1202.1056 is OK
- 10.1145/2834899.2834908 is OK
- 10.1177/1094342009106189 is OK
- 10.1063/1.5031206 is OK
- 10.1021/ct400566j is OK
- 10.48550/ARXIV.2209.09811 is OK
- 10.1038/s41598-020-69661-0 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[keipertk]

Sure I can review this submission

[danielskatz]

Thanks @keipertk - I'll add you, and start the review

[danielskatz]

@editorialbot add @keipertk as reviewer

[editorialbot]

@keipertk added to the reviewers list!

[danielskatz]

@editorialbot start review

[editorialbot]

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/4822.