[PRE REVIEW]: DFTK: A Julian approach for simulating electrons in solids

[whedon]

Submitting author: @mfherbst (Michael F. Herbst) Repository: https://github.com/mfherbst/juliacon2020-proceedings-dftk.git Version: Editor: @crstnbr Reviewers: @MasonProtter, @jagot Managing EiC: Valentin Churavy

Author instructions

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

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

@mfherbst 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 JCON and may be suitable for this submission (please start at the bottom of the list).

Editor instructions

The JCON 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]

Failed to discover a Statement of need section in paper

[whedon]

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

OK DOIs

- None

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.84  T=0.02 s (95.8 files/s, 4597.1 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Markdown                         2              5              0             91
-------------------------------------------------------------------------------
SUM:                             2              5              0             91
-------------------------------------------------------------------------------

Statistical information for the repository 'e2ce2a5ae6db487c57efbb47' was
gathered on 2020/10/15.
No commited files with the specified extensions were found.

[whedon]

Failed to discover a valid open source license.

[whedon]

PDF failed to compile for issue #61 with the following error:

pandoc: /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-d14a699185fb/resources/jcon/latex.template: openBinaryFile: does not exist (No such file or directory) Looks like we failed to compile the PDF

[mfherbst]

@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

[mfherbst]

@whedon generate pdf

[whedon]

PDF failed to compile for issue #61 with the following error:

pandoc: /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-d14a699185fb/resources/jcon/latex.template: openBinaryFile: does not exist (No such file or directory) Looks like we failed to compile the PDF

[mfherbst]

Hmm I'm a bit surprised this fails, since it worked fine when I tested it at https://whedon.theoj.org/. Aim I missing something?

[vchuravy]

@whedon generate pdf

[whedon]

PDF failed to compile for issue #61 with the following error:

pandoc: /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-92346a0773a4/resources/jcon/latex.template: openBinaryFile: does not exist (No such file or directory) Looks like we failed to compile the PDF

[vchuravy]

@whedon assign @crstnbr as editor

[carstenbauer]

@whedon assign @crstnbr as editor

[whedon]

I'm sorry @crstnbr, I'm afraid I can't do that. That's something only editors are allowed to do.

[vchuravy]

@whedon assign @crstnbr as editor

[whedon]

OK, the editor is @crstnbr

[carstenbauer]

Hi @mfherbst, you're confusion about why this isn't working is understandable. Our website apparently contains outdated information which I only now am in the process of fixing.

Anyways, the issue is that in contrast to JOSS we are accepting LaTeX only submissions. So instead of a paper.md etc. you should have a paper.tex file. More specifically, check out our new author's guide. It points you to a template repository that shows you exactly how your repository/paper/ subfolder should look like. It should be rather straightforward to port your paper repo to this format.

Sorry for the inconvenience!

BTW: If you think there is something unclear in/to be added to the author's guide, I'd very much appreciate some feedback!

[mfherbst]

@crstnbr Thanks for letting me know. I was not aware of this at all, sorry about that. I changed the repo structure as shown in the docs. Hopefully it works now.

[mfherbst]

@whedon generate pdf

[whedon]

PDF failed to compile for issue #61 with the following error:

rm: cannot remove '*.aux': No such file or directory Latexmk: This is Latexmk, John Collins, 17 Jan. 2018, version: 4.55. Rule 'pdflatex': Rules & subrules not known to be previously run: pdflatex Rule 'pdflatex': The following rules & subrules became out-of-date: 'pdflatex'

Run number 1 of rule 'pdflatex'

---

Running 'pdflatex -recorder "paper.tex"'

===========Latexmk: Missing input file: 'dftk.pdf' from line 'LaTeX Warning: File dftk.pdf' not found on input line 82.' Latexmk: Missing input file: 'dftk.pdf' from line 'LaTeX Warning: Filedftk.pdf' not found on input line 82.' Latexmk: List of undefined refs and citations: Citation garrigue2021building' on page 1 undefined on input line 66 Citationscfanalysis' on page 1 undefined on input line 66 Citation scferror' on page 1 undefined on input line 66 Citationscferror' on page 1 undefined on input line 69 Citation scfprecondition' on page 1 undefined on input line 66 Citationscfprecondition' on page 1 undefined on input line 72 Reference `fig:logodftk' on page 1 undefined on input line 22 Latexmk: Summary of warnings: Latex failed to resolve 1 reference(s) Latex failed to resolve 8 citation(s) Rule 'pdflatex': File changes, etc: Changed files, or newly in use since previous run(s): 'paper.aux'

Run number 2 of rule 'pdflatex'

---

Running 'pdflatex -recorder "paper.tex"'

===========Latexmk: Missing input file: 'dftk.pdf' from line 'LaTeX Warning: File dftk.pdf' not found on input line 82.' Latexmk: Missing input file: 'dftk.pdf' from line 'LaTeX Warning: Filedftk.pdf' not found on input line 82.' Latexmk: List of undefined refs and citations: Citation garrigue2021building' on page 1 undefined on input line 66 Citationscfanalysis' on page 1 undefined on input line 66 Citation scferror' on page 1 undefined on input line 66 Citationscferror' on page 1 undefined on input line 69 Citation scfprecondition' on page 1 undefined on input line 66 Citationscfprecondition' on page 1 undefined on input line 72 Reference `fig:logodftk' on page 1 undefined on input line 22 Latexmk: Summary of warnings: Latex failed to resolve 1 reference(s) Latex failed to resolve 8 citation(s) Rule 'pdflatex': File changes, etc: Changed files, or newly in use since previous run(s): 'paper.out'

Run number 3 of rule 'pdflatex'

---

Running 'pdflatex -recorder "paper.tex"'

===========Latexmk: Missing input file: 'dftk.pdf' from line 'LaTeX Warning: File dftk.pdf' not found on input line 82.' Latexmk: Missing input file: 'dftk.pdf' from line 'LaTeX Warning: Filedftk.pdf' not found on input line 82.' Latexmk: List of undefined refs and citations: Citation garrigue2021building' on page 1 undefined on input line 66 Citationscfanalysis' on page 1 undefined on input line 66 Citation scferror' on page 1 undefined on input line 66 Citationscferror' on page 1 undefined on input line 69 Citation scfprecondition' on page 1 undefined on input line 66 Citationscfprecondition' on page 1 undefined on input line 72 Reference `fig:logodftk' on page 1 undefined on input line 22 Latexmk: Summary of warnings: Latex failed to resolve 1 reference(s) Latex failed to resolve 8 citation(s) Failure to make 'paper.pdf' Collected error summary (may duplicate other messages): pdflatex: Command for 'pdflatex' gave return code 1 Refer to 'paper.log' for details Looks like we failed to compile the PDF

[mfherbst]

@whedon generate pdf

[whedon]

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

[mfherbst]

Hooray :smile:. Let me know if/when there is something else to be done on my end @crstnbr.

[carstenbauer]

@whedon check references

[whedon]

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

OK DOIs

- 10.1039/d0fd00048e is OK
- 10.1088/1361-648x/abcbdb is OK

MISSING DOIs

- None

INVALID DOIs

- None

[carstenbauer]

@mfherbst Great to see that compilation worked this time!

Typically our standard for the "extended abstract" papers is one page excluding references. Do you think it is possible to slightly extend the current paper in a meaningful way to meet this criterium?

Also it would be great if you could suggest potential referees. Physics + Julia background would be ideal but is no strict requirement. Please don't ping the potential referees directly but just send me the plain GitHub handles/names or similar.

[mfherbst]

@crstnbr Sure I can extend the paper a little to meet that criterion, but I can't guarantee I get to it within the next two weeks as my schedule is pretty heavy.

Regarding referees in the intersection of quantum physics and Julia, how about: davpoolechem, haampie, jagot, jgreener64, PhilipVinc.

[carstenbauer]

Sure I can extend the paper a little to meet that criterion, but I can't guarantee I get to it within the next two weeks as my schedule is pretty heavy.

That's perfectly fine, just let whedon recompile the article proof once you've made the changes.

[carstenbauer]

@whedon add @MasonProtter as reviewer

[whedon]

OK, @MasonProtter is now a reviewer

[mfherbst]

@crstnbr @MasonProtter Ready for review on our end!

[mfherbst]

@whedon generate pdf

[whedon]

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

[mfherbst]

Ups one second too quick ... git push was not done.

[mfherbst]

@whedon generate pdf

[whedon]

PDF failed to compile for issue #61 with the following error:

rm: cannot remove '*.aux': No such file or directory Latexmk: This is Latexmk, John Collins, 17 Jan. 2018, version: 4.55. Rule 'pdflatex': Rules & subrules not known to be previously run: pdflatex Rule 'pdflatex': The following rules & subrules became out-of-date: 'pdflatex'

Run number 1 of rule 'pdflatex'

---

Running 'pdflatex -recorder "paper.tex"'

===========Latexmk: Missing input file: 'lipsum.sty' from line '! LaTeX Error: File lipsum.sty' not found.' Latexmk: Missing input file: 'lipsum.sty' from line '! LaTeX Error: Filelipsum.sty' not found.' Failure to make 'paper.pdf' Collected error summary (may duplicate other messages): pdflatex: Command for 'pdflatex' gave return code 1 Refer to 'paper.log' for details Looks like we failed to compile the PDF

[mfherbst]

@whedon generate pdf

[whedon]

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

[mfherbst]

@whedon generate pdf

[whedon]

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

[mfherbst]

@whedon check references

[whedon]

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

OK DOIs

- 10.1039/d0fd00048e is OK
- 10.1088/1361-648x/abcbdb is OK
- 10.1038/natrevmats.2015.4 is OK
- 10.1038/ncomms11962 is OK
- 10.1021/jacs.7b02120 is OK
- 10.1038/nmat1752 is OK
- 10.1063/1.3148892 is OK
- 10.1021/acscentsci.8b00229 is OK
- 10.1063/1.5144261 is OK
- 10.1063/5.0005082 is OK
- 10.1103/PhysRevB.54.1703 is OK
- 10.1103/PhysRevLett.77.3865 is OK
- 10.1088/1361-648x/aa680e is OK
- 10.1016/j.commatsci.2012.10.028 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[mfherbst]

Interesting ... so whedon sees the new version, because it extracts all the new references, but the PDF it builds is still the version I submitted a few weeks ago. @crstnbr any idea why?

[mfherbst]

What now it got updated ... ok anyway: the PDFs linked by whedon now point to the version we want to submit.

[carstenbauer]

I will move things to review stage once I've added a second reviewer.

[carstenbauer]

@whedon add @jagot as reviewer

[whedon]

OK, @jagot is now a reviewer

[carstenbauer]

@whedon start review