[REVIEW]: TDEP: Temperature Dependent Effective Potentials #6150

editorialbot · 2023-12-14T18:55:55Z

Submitting author: @flokno (Florian Knoop)
Repository: https://github.com/tdep-developers/tdep
Branch with paper.md (empty if default branch): paper
Version: 24.01
Editor: @rkurchin
Reviewers: @ejmeitz, @corettialessandro
Archive: 10.5281/zenodo.10589895

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/cb141afb18fd37beb5c4fb8731ecaede"><img src="https://joss.theoj.org/papers/cb141afb18fd37beb5c4fb8731ecaede/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/cb141afb18fd37beb5c4fb8731ecaede/status.svg)](https://joss.theoj.org/papers/cb141afb18fd37beb5c4fb8731ecaede)

Reviewers and authors:

Please avoid lengthy details of difficulties in the review thread. Instead, please create a new issue in the target repository and link to those issues (especially acceptance-blockers) by leaving comments in the review thread below. (For completists: if the target issue tracker is also on GitHub, linking the review thread in the issue or vice versa will create corresponding breadcrumb trails in the link target.)

Reviewer instructions & questions

@ejmeitz, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review.
First of all you need to run this command in a separate comment to create the checklist:

@editorialbot generate my checklist

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @rkurchin know.

✨ Please start on your review when you are able, and be sure to complete your review in the next six weeks, at the very latest ✨

Checklists

📝 Checklist for @ejmeitz

📝 Checklist for @corettialessandro

The text was updated successfully, but these errors were encountered:

editorialbot · 2023-12-14T18:55:57Z

Hello humans, 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 · 2023-12-14T18:56:00Z

Software report:

github.com/AlDanial/cloc v 1.88  T=0.49 s (633.9 files/s, 318083.2 lines/s)
--------------------------------------------------------------------------------
Language                      files          blank        comment           code
--------------------------------------------------------------------------------
Fortran 90                      202           8351          34615          98672
Markdown                         52           2275              0           7650
make                             27            161             63           1301
TeX                               1             65              0            730
C++                               7             51            164            289
Bourne Shell                      2             31             93            276
Python                           10             99              2            205
Bourne Again Shell                6             77            124            156
YAML                              2              7              7             66
JavaScript                        1              2              0             18
--------------------------------------------------------------------------------
SUM:                            310          11119          35068         109363
--------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

editorialbot · 2023-12-14T18:56:03Z

Wordcount for paper.md is 2045

editorialbot · 2023-12-14T18:56:34Z

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

OK DOIs

- 10.48550/arxiv.2303.10621 is OK
- 10.1002/adma.202108352 is OK
- 10.1038/s41467-022-34755-y is OK
- 10.1038/s41524-022-00920-6 is OK
- 10.1002/adma.202107932 is OK
- 10.1103/physrevmaterials.6.033607 is OK
- 10.1088/1361-648x/ac066b is OK
- 10.1038/s41524-021-00523-7 is OK
- 10.1103/physrevb.103.184409 is OK
- 10.1016/j.cpc.2021.107945 is OK
- 10.1103/physrevlett.125.045701 is OK
- 10.1016/j.cpc.2020.107301 is OK
- 10.1002/adts.201800184 is OK
- 10.1038/s41467-019-09921-4 is OK
- 10.1103/physrevb.100.104304 is OK
- 10.1103/physrevb.98.085205 is OK
- 10.1073/pnas.1707745115 is OK
- 10.1103/physrevlett.121.226603 is OK
- 10.1088/1361-648x/aa680e is OK
- 10.1103/physrevlett.119.185901 is OK
- 10.1103/physrevb.95.014302 is OK
- 10.1103/physrevlett.117.276601 is OK
- 10.1103/physrevb.93.045202 is OK
- 10.1103/physrevlett.117.205502 is OK
- 10.1103/physrevb.91.214310 is OK
- 10.1103/physrevb.92.054301 is OK
- 10.1103/physrevb.91.054101 is OK
- 10.1103/physrevlett.112.058501 is OK
- 10.1088/0953-8984/26/22/225402 is OK
- 10.1103/physrevb.88.144301 is OK
- 10.1103/physrevb.87.104111 is OK
- 10.1103/physrevlett.111.177002 is OK
- 10.1103/physrevb.84.180301 is OK
- 10.1080/14786440408520576 is OK
- 10.1080/14786440408520575 is OK
- 10.1103/physrevb.77.144112 is OK
- 10.1103/physrevlett.100.095901 is OK
- 10.1063/1.2822891 is OK
- 10.1103/physrevlett.96.115504 is OK
- 10.1080/13642818608236861 is OK
- 10.1002/bip.360230610 is OK
- 10.1007/bf00654839 is OK
- 10.1007/bf00653877 is OK
- 10.1103/physreva.3.2074 is OK
- 10.1103/physrevb.1.572 is OK
- 10.1103/physrev.165.951 is OK
- 10.1103/physrevlett.17.89 is OK
- 10.1103/physrev.140.a1133 is OK
- 10.1103/physrev.136.b864 is OK
- 10.1080/00018736300101333 is OK
- 10.1080/14786435808243224 is OK
- 10.1007/bf01330055 is OK
- 10.1007/978-3-642-86703-3 is OK
- 10.1016/0031-8914(48)90032-9 is OK

MISSING DOIs

- 10.1016/0021-9614(75)90071-3 may be a valid DOI for title: Thermodynamics of Crystals
- 10.1093/oso/9780192670083.001.0001 may be a valid DOI for title: Dynamical theory of crystal lattices

INVALID DOIs

- None

editorialbot · 2023-12-14T18:57:07Z

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

ejmeitz · 2023-12-15T02:42:52Z

Review checklist for @ejmeitz

Conflict of interest

I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

I confirm that I read and will adhere to the JOSS code of conduct.

General checks

Repository: Is the source code for this software available at the https://github.com/tdep-developers/tdep?
License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
Contribution and authorship: Has the submitting author (@flokno) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

Installation: Does installation proceed as outlined in the documentation?
Functionality: Have the functional claims of the software been confirmed?
Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
State of the field: Do the authors describe how this software compares to other commonly-used packages?
Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

rkurchin · 2024-01-02T15:02:33Z

@editorialbot add @corettialessandro as reviewer

(sorry, I somehow neglected to do this in pre review!)

editorialbot · 2024-01-02T15:02:35Z

@corettialessandro added to the reviewers list!

rkurchin · 2024-01-02T15:05:36Z

@ejmeitz, thanks for getting your review started! Feel free to leave any comments/feedback here, and/or in an issue on the project repo. If you open issues, please link back to this one for easy tracking.

@correttialessandro, let me know if you have any questions about getting your review started!

flokno · 2024-01-05T10:39:23Z

Dear @ejmeitz , thanks for starting the review!

Can you clarify the missing check on Functionality: Have the functional claims of the software been confirmed?: Is this a) with respect to the paper, or b) the online documentation incl. tutorials?

For a), we have cited a multitude of peer-reviewed papers that were prepared with TDEP, maybe this was not made clear enough?

For b), we have prepared an extensive set of online tutorials to introduce the core functionality of TDEP in depth. Is there anything else missing?

Another question, maybe also @rkurchin, for State of the field: Do the authors describe how this software compares to other commonly-used packages?: We have tried to clarify the conceptual similarity to the most common alternatives in the field (sscha, scp, qscaild) with references -- do you suggest to comment on the technical differences in these approaches? Some hints would be appreciated.

Thank you! And a happy new year to all!

ejmeitz · 2024-01-05T16:00:18Z

@flokno I just haven't gotten around to fully testing the package. Hopefully, I'll be done within the week and I'll add another comment with some feedback!

The second check I left empty as I was unsure if what was in the paper was enough. I think Rachel's response should help clarify that.

ejmeitz · 2024-01-05T18:28:38Z

@flokno is there a reason the holding codes are not shipped with the main branch of TDEP? I was hoping to just replace my old install from the TDEP development GitHub with this install, but the holding codes are gone. The build script still has the options for them. Is it safe to just copy the holding folder from my old install (I think it is since its a separate binary). I would like to use the remap_forceconstants code. If you think its not safe I will mess around with this later as the holding codes are not pertinent to the review.

Edit: It seems to have built fine just copying the holding folder from tdep-devel to tdep.

rkurchin · 2024-01-05T19:54:00Z

@flokno, regarding your question about the paper, what you have now looks fine to me – frankly, your paper is already on the longer side for JOSS papers, which tend to be quite brief!

ejmeitz · 2024-01-07T19:13:58Z

@flokno Everything looks functional except an issue with the LAMMPS output format. I opened an issue in the main branch:
#35. Once that's resolved I'll check that last box.

flokno · 2024-01-08T08:23:23Z

@flokno is there a reason the holding codes are not shipped with the main branch of TDEP? I was hoping to just replace my old install from the TDEP development GitHub with this install, but the holding codes are gone. The build script still has the options for them. Is it safe to just copy the holding folder from my old install (I think it is since its a separate binary). I would like to use the remap_forceconstants code. If you think its not safe I will mess around with this later as the holding codes are not pertinent to the review.

Edit: It seems to have built fine just copying the holding folder from tdep-devel to tdep.

@ejmeitz indeed, the codes in holding (and also staging) are more experimental, less well tested, and potentially (though not necessarily) buggy. Also, those features are not needed to use TDEP for the usual use cases as documented. For the public release, we therefore decided to include the mature features only, and add updated versions of codes like remap_forceconstants upon popular request. Please feel free to open an issue an request this feature to be added to the public repo (*).

(*): remapping is internally done anyways, so usually remap_forceconstants is not explicitly needed for any of the default features of TDEP.

ejmeitz · 2024-01-10T14:01:32Z

@flokno thanks for dealing with the LAMMPS stuff. I checked off the last box on my review!

I do have a question about the remap_forceconstant still. TDEP gives the force constants for a unit cell of the material; however, my calculations require the full force constant matrix for a supercell. Olle had told me to use remap_forceconstant for this. Is there still a way to get the supercell forceconstants from TDEP or will I have to write my own script? (can move to the discussion board on TDEP if needed)

flokno · 2024-01-10T14:36:48Z

@flokno thanks for dealing with the LAMMPS stuff. I checked off the last box on my review!

I do have a question about the remap_forceconstant still. TDEP gives the force constants for a unit cell of the material; however, my calculations require the full force constant matrix for a supercell. Olle had told me to use remap_forceconstant for this. Is there still a way to get the supercell forceconstants from TDEP or will I have to write my own script? (can move to the discussion board on TDEP if needed)

Ok I understand. For the time being you can just use the code in tdep-devel, the code base is basically the same. If you think it should be added to the public repo, please request the feature per issue.

Thank you for the review and the feedback!

@rkurchin and @corettialessandro , any more comments?

corettialessandro · 2024-01-12T16:31:13Z

Review checklist for @corettialessandro

Conflict of interest

I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

I confirm that I read and will adhere to the JOSS code of conduct.

General checks

Repository: Is the source code for this software available at the https://github.com/tdep-developers/tdep?
License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
Contribution and authorship: Has the submitting author (@flokno) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

Installation: Does installation proceed as outlined in the documentation?
Functionality: Have the functional claims of the software been confirmed?
Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
State of the field: Do the authors describe how this software compares to other commonly-used packages?
Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

corettialessandro · 2024-01-17T11:18:58Z

I am still checking some functionalities via the tutorials, I should be done for the end of the week.

In the meantime, in the file important_settings.conda the default PATH is still the one from one of the authors. You should maybe think about changing it to something more neutral like path/to/your/conda/environment/ or something like that.

Running the test suite goes without issues, it only yields a warning that I was not able to address:

atomic_distribution/test_atomic_distribution.py::test_hdf5
  <frozen importlib._bootstrap>:241: RuntimeWarning: numpy.ndarray size changed, may indicate binary incompatibility. Expected 16 from C header, got 96 from PyObject

-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html

If it is something that also others are experiencing, maybe you could mention it in the README in the tests folder.

Finally, I would remove the self-link from the webpage of the manual. I understand that it is arising from the markdown README of GitHub, but it gives the impression that there is yet another page for the manual, and the link redirects to the same page. I would simply remove the section Manual from the webpage.

@rkurchin these are not serious problems that prevent publication, should I still open issues about them?

flokno · 2024-01-17T12:57:49Z

Hi @corettialessandro ,

ok for the path, addressed in tdep-developers/tdep@a2680cf
The warning is about your python environment, this typically occurs when a different numpy version was used when building the environment vs. when running the application. I think it's a good idea to mention those in the readme, done in tdep-developers/tdep@ea40439
I will see if there is a good solution for the link to the manual.

Thanks!

corettialessandro · 2024-01-19T19:18:00Z

Hi @flokno,

Everything fine here, this repository is really impressive!
Nothing really important to say, I checked all the boxes in the review list.

Minor points:

The routine extract_forceconstants can be run with the option --polar only if an input file infile.lotosplitting is present in the folder. If this is not the case the error message is really cryptic. I guess it should be easy to make it more informative. I also imagine that this could be the case for other routines (if it is not even better). In future versions some improvements in handling of errors would benefit user and developers.
In the tutorial page for sTDEP with DFT forces there are some typos in the README. It is not important in the text, but it could become tedious when the routines are misspelled (e.g. generature_structure or `extract_forceconsant). Take a look at that when you have time.

flokno · 2024-01-19T19:58:19Z

Thanks @corettialessandro !

You're right with the error messages. I'll see if I get around this.

If you remember which typos you stumbled over, I'd appreciate if you open an issue with the respective line(s). Thanks again!

flokno · 2024-01-30T10:09:53Z

@rkurchin thanks for the reminder, here goes:

Version tag: https://github.com/tdep-developers/tdep/releases/tag/24.01
DOI: https://doi.org/10.5281/zenodo.10589895

Please let me know if this looks good. Thanks!

rkurchin · 2024-01-30T16:24:44Z

@editorialbot set 24.01 as version

editorialbot · 2024-01-30T16:24:46Z

Done! version is now 24.01

rkurchin · 2024-01-30T16:26:13Z

@flokno great, can you just make sure the title of the archive matches the title of this submission please?

flokno · 2024-01-30T16:29:24Z

@rkurchin done: https://zenodo.org/records/10589895

rkurchin · 2024-01-30T17:36:48Z

@editorialbot set 10.5281/zenodo.10589895 as archive

editorialbot · 2024-01-30T17:36:50Z

Done! archive is now 10.5281/zenodo.10589895

rkurchin · 2024-01-30T17:37:19Z

@editorialbot recommend-accept

editorialbot · 2024-01-30T17:37:22Z

Attempting dry run of processing paper acceptance...

editorialbot · 2024-01-30T17:39:02Z

👋 @openjournals/pe-eics, this paper is ready to be accepted and published.

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#4964, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

editorialbot · 2024-01-30T17:39:11Z

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

OK DOIs

- 10.1063/5.0174255 is OK
- 10.1002/adma.202108352 is OK
- 10.1038/s41467-022-34755-y is OK
- 10.1038/s41524-022-00920-6 is OK
- 10.1002/adma.202107932 is OK
- 10.1103/physrevmaterials.6.033607 is OK
- 10.1088/1361-648x/ac066b is OK
- 10.1038/s41524-021-00523-7 is OK
- 10.1103/physrevb.103.184409 is OK
- 10.1016/j.cpc.2021.107945 is OK
- 10.1103/physrevlett.125.045701 is OK
- 10.1016/j.cpc.2020.107301 is OK
- 10.1002/adts.201800184 is OK
- 10.1038/s41467-019-09921-4 is OK
- 10.1103/physrevb.100.104304 is OK
- 10.1103/physrevb.98.085205 is OK
- 10.1073/pnas.1707745115 is OK
- 10.1103/physrevlett.121.226603 is OK
- 10.1088/1361-648x/aa680e is OK
- 10.1103/physrevlett.119.185901 is OK
- 10.1103/physrevb.95.014302 is OK
- 10.1103/physrevlett.117.276601 is OK
- 10.1103/physrevb.93.045202 is OK
- 10.1103/physrevlett.117.205502 is OK
- 10.1103/physrevb.91.214310 is OK
- 10.1103/physrevb.92.054301 is OK
- 10.1103/physrevb.91.054101 is OK
- 10.1103/physrevlett.112.058501 is OK
- 10.1088/0953-8984/26/22/225402 is OK
- 10.1103/physrevb.88.144301 is OK
- 10.1103/physrevb.87.104111 is OK
- 10.1103/physrevlett.111.177002 is OK
- 10.1103/physrevb.84.180301 is OK
- 10.1080/14786440408520576 is OK
- 10.1080/14786440408520575 is OK
- 10.1103/physrevb.77.144112 is OK
- 10.1103/physrevlett.100.095901 is OK
- 10.1063/1.2822891 is OK
- 10.1103/physrevlett.96.115504 is OK
- 10.1080/13642818608236861 is OK
- 10.1002/bip.360230610 is OK
- 10.1007/bf00654839 is OK
- 10.1007/bf00653877 is OK
- 10.1103/physreva.3.2074 is OK
- 10.1103/physrevb.1.572 is OK
- 10.1103/physrev.165.951 is OK
- 10.1103/physrevlett.17.89 is OK
- 10.1103/physrev.140.a1133 is OK
- 10.1103/physrev.136.b864 is OK
- 10.1080/00018736300101333 is OK
- 10.1080/14786435808243224 is OK
- 10.1007/bf01330055 is OK
- 10.1093/oso/9780192670083.001.0001 is OK
- 10.1007/978-3-642-86703-3 is OK
- 10.1016/0031-8914(48)90032-9 is OK

MISSING DOIs

- 10.1016/0021-9614(75)90071-3 may be a valid DOI for title: Thermodynamics of Crystals

INVALID DOIs

- None

flokno · 2024-01-30T17:55:57Z

@rkurchin can you please double check your own link? I get a 404, I am unsure whether this might be normal before publishing. Everything else looks good.

rkurchin · 2024-01-30T22:43:13Z

Huh! @openjournals/pe-eics, I'm not even sure what that's supposed to link to and my PDF reader isn't even succeeding in copying the link so I can check what's broken...any insights?

kyleniemeyer · 2024-01-31T00:04:04Z

It works for me - clicking on @rkurchin's name takes me to https://rkurchin.github.io

flokno · 2024-01-31T08:46:09Z

Ok it works for me when using Adobe Acrobat, but it does not work using Firefox or Preview (mac).

In Firefox at least, the link points to: https://raw.githubusercontent.com/openjournals/joss-papers/joss.06150/joss.06150/rkurchin.github.io

Should we move on and hope for the best?

Edit: I checked recently published JOSS papers and the respective links seem to work.

flokno · 2024-01-31T19:01:55Z

@rkurchin @kyleniemeyer just ?

rkurchin · 2024-01-31T20:23:03Z

Yeah, @kyleniemeyer I'd say let's just go ahead here...seems to be some weird PDF-side thing most likely, I'm not too worried; I'm pretty Google-able if people want to find me 🤪

kyleniemeyer · 2024-02-01T01:25:05Z

OK, looks good to me!

kyleniemeyer · 2024-02-01T01:25:08Z

@editorialbot accept

editorialbot · 2024-02-01T01:25:10Z

Doing it live! Attempting automated processing of paper acceptance...

editorialbot · 2024-02-01T01:31:49Z

Ensure proper citation by uploading a plain text CITATION.cff file to the default branch of your repository.

If using GitHub, a Cite this repository menu will appear in the About section, containing both APA and BibTeX formats. When exported to Zotero using a browser plugin, Zotero will automatically create an entry using the information contained in the .cff file.

You can copy the contents for your CITATION.cff file here:

CITATION.cff

cff-version: "1.2.0"
authors:
- family-names: Knoop
  given-names: Florian
  orcid: "https://orcid.org/0000-0002-7132-039X"
- family-names: Shulumba
  given-names: Nina
  orcid: "https://orcid.org/0000-0002-2374-7487"
- family-names: Castellano
  given-names: Aloïs
  orcid: "https://orcid.org/0000-0002-8783-490X"
- family-names: Batista
  given-names: J. P. Alvarinhas
  orcid: "https://orcid.org/0000-0002-3314-249X"
- family-names: Farris
  given-names: Roberta
  orcid: "https://orcid.org/0000-0001-6710-0100"
- family-names: Verstraete
  given-names: Matthieu J.
  orcid: "https://orcid.org/0000-0001-6921-5163"
- family-names: Heine
  given-names: Matthew
  orcid: "https://orcid.org/0000-0002-4882-6712"
- family-names: Broido
  given-names: David
  orcid: "https://orcid.org/0000-0003-0182-4450"
- family-names: Kim
  given-names: Dennis S.
  orcid: "https://orcid.org/0000-0002-5707-2609"
- family-names: Klarbring
  given-names: Johan
  orcid: "https://orcid.org/0000-0002-6223-5812"
- family-names: Abrikosov
  given-names: Igor A.
  orcid: "https://orcid.org/0000-0001-7551-4717"
- family-names: Simak
  given-names: Sergei I.
  orcid: "https://orcid.org/0000-0002-1320-389X"
- family-names: Hellman
  given-names: Olle
  orcid: "https://orcid.org/0000-0002-3453-2975"
doi: 10.5281/zenodo.10589895
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Knoop
    given-names: Florian
    orcid: "https://orcid.org/0000-0002-7132-039X"
  - family-names: Shulumba
    given-names: Nina
    orcid: "https://orcid.org/0000-0002-2374-7487"
  - family-names: Castellano
    given-names: Aloïs
    orcid: "https://orcid.org/0000-0002-8783-490X"
  - family-names: Batista
    given-names: J. P. Alvarinhas
    orcid: "https://orcid.org/0000-0002-3314-249X"
  - family-names: Farris
    given-names: Roberta
    orcid: "https://orcid.org/0000-0001-6710-0100"
  - family-names: Verstraete
    given-names: Matthieu J.
    orcid: "https://orcid.org/0000-0001-6921-5163"
  - family-names: Heine
    given-names: Matthew
    orcid: "https://orcid.org/0000-0002-4882-6712"
  - family-names: Broido
    given-names: David
    orcid: "https://orcid.org/0000-0003-0182-4450"
  - family-names: Kim
    given-names: Dennis S.
    orcid: "https://orcid.org/0000-0002-5707-2609"
  - family-names: Klarbring
    given-names: Johan
    orcid: "https://orcid.org/0000-0002-6223-5812"
  - family-names: Abrikosov
    given-names: Igor A.
    orcid: "https://orcid.org/0000-0001-7551-4717"
  - family-names: Simak
    given-names: Sergei I.
    orcid: "https://orcid.org/0000-0002-1320-389X"
  - family-names: Hellman
    given-names: Olle
    orcid: "https://orcid.org/0000-0002-3453-2975"
  date-published: 2024-02-01
  doi: 10.21105/joss.06150
  issn: 2475-9066
  issue: 94
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 6150
  title: "TDEP: Temperature Dependent Effective Potentials"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.06150"
  volume: 9
title: "TDEP: Temperature Dependent Effective Potentials"

If the repository is not hosted on GitHub, a .cff file can still be uploaded to set your preferred citation. Users will be able to manually copy and paste the citation.

Find more information on .cff files here and here.

editorialbot · 2024-02-01T01:31:53Z

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot · 2024-02-01T01:31:54Z

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.06150 joss-papers#4974
Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.06150
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

kyleniemeyer · 2024-02-01T01:34:23Z

Congratulations @flokno on your article's publication in JOSS! Please consider signing up as a reviewer if you haven't already.

Many thanks to @ejmeitz and @corettialessandro for reviewing this, and @rkurchin for editing.

editorialbot · 2024-02-01T01:34:41Z

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

If you would like to include a link to your paper from your README use the following code snippets:

Markdown:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.06150/status.svg)](https://doi.org/10.21105/joss.06150)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.06150">
  <img src="https://joss.theoj.org/papers/10.21105/joss.06150/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.06150/status.svg
   :target: https://doi.org/10.21105/joss.06150

This is how it will look in your documentation:

We need your help!

The Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:

Volunteering to review for us sometime in the future. You can add your name to the reviewer list here: https://reviewers.joss.theoj.org/join
Making a small donation to support our running costs here: https://numfocus.org/donate-to-joss

flokno · 2024-02-01T06:37:22Z

Thanks a lot everyone! 🙌

editorialbot added Makefile review Shell TeX Track: 3 (PE) Physics and Engineering labels Dec 14, 2023

editorialbot assigned rkurchin Dec 14, 2023

editorialbot mentioned this issue Dec 14, 2023

[PRE REVIEW]: TDEP: Temperature Dependent Effective Potenials #6039

Closed

editorialbot added the Fortran label Dec 14, 2023

editorialbot added the recommend-accept Papers recommended for acceptance in JOSS. label Jan 30, 2024

editorialbot added accepted published Papers published in JOSS labels Feb 1, 2024

kyleniemeyer closed this as completed Feb 1, 2024

[REVIEW]: TDEP: Temperature Dependent Effective Potentials #6150

[REVIEW]: TDEP: Temperature Dependent Effective Potentials #6150

Comments

editorialbot commented Dec 14, 2023 • edited

Status

Reviewer instructions & questions

Checklists

editorialbot commented Dec 14, 2023

editorialbot commented Dec 14, 2023

editorialbot commented Dec 14, 2023

editorialbot commented Dec 14, 2023

editorialbot commented Dec 14, 2023

ejmeitz commented Dec 15, 2023 • edited

Review checklist for @ejmeitz

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

rkurchin commented Jan 2, 2024

editorialbot commented Jan 2, 2024

rkurchin commented Jan 2, 2024

flokno commented Jan 5, 2024

ejmeitz commented Jan 5, 2024

ejmeitz commented Jan 5, 2024 • edited

rkurchin commented Jan 5, 2024

ejmeitz commented Jan 7, 2024 • edited

flokno commented Jan 8, 2024

ejmeitz commented Jan 10, 2024 • edited

flokno commented Jan 10, 2024

corettialessandro commented Jan 12, 2024 • edited

Review checklist for @corettialessandro

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

corettialessandro commented Jan 17, 2024

flokno commented Jan 17, 2024

corettialessandro commented Jan 19, 2024

flokno commented Jan 19, 2024 • edited

flokno commented Jan 30, 2024

rkurchin commented Jan 30, 2024

editorialbot commented Jan 30, 2024

rkurchin commented Jan 30, 2024

flokno commented Jan 30, 2024

rkurchin commented Jan 30, 2024

editorialbot commented Jan 30, 2024

rkurchin commented Jan 30, 2024

editorialbot commented Jan 30, 2024

editorialbot commented Jan 30, 2024

editorialbot commented Jan 30, 2024

flokno commented Jan 30, 2024

rkurchin commented Jan 30, 2024

kyleniemeyer commented Jan 31, 2024

flokno commented Jan 31, 2024 • edited

flokno commented Jan 31, 2024

rkurchin commented Jan 31, 2024

kyleniemeyer commented Feb 1, 2024

kyleniemeyer commented Feb 1, 2024

editorialbot commented Feb 1, 2024

editorialbot commented Feb 1, 2024

editorialbot commented Feb 1, 2024

editorialbot commented Feb 1, 2024

kyleniemeyer commented Feb 1, 2024

editorialbot commented Feb 1, 2024

flokno commented Feb 1, 2024

editorialbot commented Dec 14, 2023 •

edited

ejmeitz commented Dec 15, 2023 •

edited

ejmeitz commented Jan 5, 2024 •

edited

ejmeitz commented Jan 7, 2024 •

edited

ejmeitz commented Jan 10, 2024 •

edited

corettialessandro commented Jan 12, 2024 •

edited

flokno commented Jan 19, 2024 •

edited

flokno commented Jan 31, 2024 •

edited