[PRE REVIEW]: FHI-vibes: Ab initio Vibrational Simulations

[whedon]

Submitting author: @flokno (Florian Knoop) Repository: https://gitlab.com/vibes-developers/vibes Version: v1.0.0 Editor: @jgostick Reviewers: @keipertk Managing EiC: Kevin M. Moerman

:warning: JOSS reduced service mode :warning:

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

Author instructions

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

The author's suggestion for the handling editor is @jgostick.

@flokno 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 @whedon is here to help you find and assign reviewers and start the main review. To find out what @whedon can do for you type:

@whedon commands

[whedon]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks.

:warning: JOSS reduced service mode :warning:

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

For a list of things I can do to help you, just type:

@whedon commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@whedon generate pdf

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.84  T=0.83 s (349.3 files/s, 41757.7 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                         227           5546           6376          15309
Markdown                        47           1265              0           3832
TeX                              1             28              0            304
SVG                              3              0              0            298
Fortran 90                       2             48             39            225
Jupyter Notebook                 2              0            837            145
YAML                             2             15              0            119
TOML                             1              9              0             67
JSON                             1              0              0             32
JavaScript                       1              0              0             24
make                             2              9              1             21
-------------------------------------------------------------------------------
SUM:                           289           6920           7253          20376
-------------------------------------------------------------------------------

Statistical information for the repository '2601' was gathered on 2020/08/26.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Flo-Think                       24           325            198            0.15
Florian Knoop                 1322        131784         112349           69.68
Florian Knoop (DRACO             1             2              2            0.00
Marcel                           2           334            186            0.15
Marcel Huelsberg                 2             3              3            0.00
Marcel Hülsberg                 11            56             24            0.02
Marcel Langer                    1             1              4            0.00
Thomas Purcell                 517         53595          49421           29.40
Tom Purcell                      2           885           1175            0.59

Below are the number of rows from each author that have survived and are still
intact in the current revision:

Author                     Rows      Stability          Age       % in comments
Florian Knoop             16463           12.5         10.7                9.09
Marcel                      161           48.2          5.3                9.94
Marcel Hülsberg              12           21.4         15.6                8.33
Marcel Langer                 1          100.0          7.9                0.00
Thomas Purcell            10521           19.6         10.5                5.97
Tom Purcell                  97           11.0         17.0                6.19

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[whedon]

Reference check summary:

OK DOIs

- 10.1088/1361-648X/aa680e is OK
- 10.1016/j.scriptamat.2015.07.021 is OK
- 10.1103/PhysRevB.91.094306 is OK
- 10.1016/j.cpc.2009.06.022 is OK
- 10.5334/jors.148 is OK
- 10.1109/MCSE.2011.37 is OK
- 10.1002/cpe.3505 is OK
- 10.1038/nmat3568 is OK
- 10.1103/PhysRevLett.78.4063 is OK
- 10.1103/PhysRevLett.118.175901 is OK
- 10.1002/adts.201800184 is OK
- 10.1002/anie.201812112 is OK
- 10.1021/acs.jpcc.5b11115 is OK
- 10.1038/nmat2090 is OK
- 10.1103/PhysRevLett.96.115504 is OK
- 10.1557/mrs.2018.208 is OK

MISSING DOIs

- https://doi.org/10.1016/j.jeurceramsoc.2007.12.023 may be missing for title: The influence of oxides on the performance of advanced gas turbines
- https://doi.org/10.1103/physrevb.79.064301 may be missing for title: Predicting phonon properties and thermal conductivity from anharmonic lattice dynamics calculations and molecular dynamics simulations

INVALID DOIs

- https://doi.org/10.1016/j.cpc.2018.09.020 is INVALID because of 'https://doi.org/' prefix

[Kevin-Mattheus-Moerman]

@jgostick @pibion @pdebuyl could one of you handle this submission?

[ooo[bot]]

:wave: Hey @Kevin-Mattheus-Moerman...

Letting you know, @pdebuyl is currently OOO until Monday, August 31st 2020. :heart:

[Kevin-Mattheus-Moerman]

@flokno can you check those missing DOIs :point_up:

[flokno]

Hi @Kevin-Mattheus-Moerman , I'll check, thanks for picking this up.

Since this is written in python and related to ASE and FHI-aims, a potential reviewer would be Adam Jackson ([at]ajjackson), who I cannot find on the list though.

[flokno]

@whedon commands

[whedon]

I'm sorry human, I don't understand that. You can see what commands I support by typing:

@whedon commands

[flokno]

@whedon commands

[whedon]

Here are some things you can ask me to do:

# List Whedon's capabilities
@whedon commands

# List of editor GitHub usernames
@whedon list editors

# List of reviewers together with programming language preferences and domain expertise
@whedon list reviewers

EDITORIAL TASKS

# Compile the paper
@whedon generate pdf

# Compile the paper from alternative branch
@whedon generate pdf from branch custom-branch-name

# Ask Whedon to check the references for missing DOIs
@whedon check references

# Ask Whedon to check repository statistics for the submitted software
@whedon check repository

[flokno]

@whedon generate pdf from branch joss

[whedon]

Attempting PDF compilation from custom branch joss. Reticulating splines etc...

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[flokno]

@whedon check references from branch joss

[whedon]

Attempting to check references... from custom branch joss

[whedon]

Reference check summary:

OK DOIs

- 10.1088/1361-648X/aa680e is OK
- 10.1016/j.scriptamat.2015.07.021 is OK
- 10.1103/PhysRevB.91.094306 is OK
- 10.1016/j.cpc.2009.06.022 is OK
- 10.1016/j.cpc.2018.09.020 is OK
- 10.5334/jors.148 is OK
- 10.1109/MCSE.2011.37 is OK
- 10.1002/cpe.3505 is OK
- 10.1038/nmat3568 is OK
- 10.1103/PhysRevLett.78.4063 is OK
- 10.1103/PhysRevLett.118.175901 is OK
- 10.1002/adts.201800184 is OK
- 10.1002/anie.201812112 is OK
- 10.1021/acs.jpcc.5b11115 is OK
- 10.1038/nmat2090 is OK
- 10.1016/j.jeurceramsoc.2007.12.023 is OK
- 10.1103/PhysRevLett.96.115504 is OK
- 10.1103/physrevb.79.064301 is OK
- 10.1557/mrs.2018.208 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[flokno]

@whedon check references

[whedon]

Reference check summary:

OK DOIs

- 10.1088/1361-648X/aa680e is OK
- 10.1016/j.scriptamat.2015.07.021 is OK
- 10.1103/PhysRevB.91.094306 is OK
- 10.1016/j.cpc.2009.06.022 is OK
- 10.1016/j.cpc.2018.09.020 is OK
- 10.5334/jors.148 is OK
- 10.1109/MCSE.2011.37 is OK
- 10.1002/cpe.3505 is OK
- 10.1038/nmat3568 is OK
- 10.1103/PhysRevLett.78.4063 is OK
- 10.1103/PhysRevLett.118.175901 is OK
- 10.1002/adts.201800184 is OK
- 10.1002/anie.201812112 is OK
- 10.1021/acs.jpcc.5b11115 is OK
- 10.1038/nmat2090 is OK
- 10.1016/j.jeurceramsoc.2007.12.023 is OK
- 10.1103/PhysRevLett.96.115504 is OK
- 10.1103/physrevb.79.064301 is OK
- 10.1557/mrs.2018.208 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[Kevin-Mattheus-Moerman]

@jgostick @pibion @pdebuyl could one of you handle this submission?

[Kevin-Mattheus-Moerman]

@jgostick @pibion @pdebuyl :wave: :point_up:

[jgostick]

There seems to be lots of capable MD reviewers on the list of volunteers, so this should be relatively easy to edit...

@whedon assign @jgostick as editor

[jgostick]

@whedon assign @jgostick as editor

[whedon]

OK, the editor is @jgostick

[flokno]

Hi @jgostick thanks for picking this up, I suggest ajjackson and marshallmcdonnell as potential reviewers.

[jgostick]

Hello @keipertk ...you've listed yourself as a potential reviewer for molecular dynamics software, but according to the JOSS statistics, have not done one yet. Would you be interested and available to do review this submission?

[keipertk]

Yes sure

[jgostick]

@keipertk, thanks for the positive and expedient reply! I need to find a second reviewer, then I will start the official review in a new issue...stay posted.

[jgostick]

Hello @tonigi, you are listed as a potential volunteer reviewer for JOSS, and according to our spreadsheet of statistics, haven't had the pleasure of doing one yet. Would you be interested/available to review this submission?

[tonigi]

Hm... I'm more on the biomolecular side, so not a perfect match, but can still do a technical review if necessary.

[jgostick]

@tonigi, No probs, I'll keep looking, but may circle back to you if I can't find anyone.

[jgostick]

Hi @pszi1ard, would you be interested/available in reviewing this submission? You're listed as an volunteer with expertise in the area, and have not done a review yet, so this is your chance ;-)

[jgostick]

I'm going to start this review, then add the second reviewer when I get a positive response.

[jgostick]

@whedon commands

[whedon]

Here are some things you can ask me to do:

# List all of Whedon's capabilities
@whedon commands

# Assign a GitHub user as the sole reviewer of this submission
@whedon assign @username as reviewer

# Add a GitHub user to the reviewers of this submission
@whedon add @username as reviewer

# Re-invite a reviewer (if they can't update checklists)
@whedon re-invite @username as reviewer

# Remove a GitHub user from the reviewers of this submission
@whedon remove @username as reviewer

# List of editor GitHub usernames
@whedon list editors

# List of reviewers together with programming language preferences and domain expertise
@whedon list reviewers

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# Set the software archive DOI at the top of the issue e.g.
@whedon set 10.0000/zenodo.00000 as archive

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@whedon set v1.0.1 as version

# Open the review issue
@whedon start review

EDITORIAL TASKS

# All commands can be run on a non-default branch, to do this pass a custom 
# branch name by following the command with `from branch custom-branch-name`.
# For example:

# Compile the paper
@whedon generate pdf

# Compile the paper from alternative branch
@whedon generate pdf from branch custom-branch-name

# Remind an author or reviewer to return to a review after a
# certain period of time (supported units days and weeks)
@whedon remind @reviewer in 2 weeks

# Ask Whedon to do a dry run of accepting the paper and depositing with Crossref
@whedon accept

# Ask Whedon to check the references for missing DOIs
@whedon check references

# Ask Whedon to check repository statistics for the submitted software
@whedon check repository

EiC TASKS

# Invite an editor to edit a submission (sending them an email)
@whedon invite @editor as editor

# Reject a paper
@whedon reject

# Withdraw a paper
@whedon withdraw

# Ask Whedon to actually accept the paper and deposit with Crossref
@whedon accept deposit=true

[jgostick]

@whedon start review

[whedon]

It looks like you don't have an editor and reviewer assigned yet so I can't start the review. Try one or more of these commands:

# Change editorial assignment
@whedon assign @username as editor

# Assign a GitHub user as the sole reviewer of this submission
@whedon assign @username as reviewer

# Add a GitHub user to the reviewers of this submission
@whedon add @username as reviewer

[jgostick]

@whedon assign @keipertk as reviewer

[whedon]

OK, @keipertk is now a reviewer

[jgostick]

@whedon assign @jgostick as editor

[whedon]

OK, the editor is @jgostick

[jgostick]

@whedon start review

[whedon]

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/2671.