Addition of JDFTx code

[cote3804]

Summary

Adding support for JDFTx, an open source plane wave code that supports grand-canonical DFT and implements accurate solvation models.

Dependencies on other repositories

• Pymatgen
• Custodian

What we've done

• Written JDFTx input and output parsers in pymatgen/io
• Implemented base input set and generator plus three base input sets
• Implemented basic calculation input and output schema
• Written tests following CP2K and VASP format

Future Development

• Make JDFTx compliant with the adsorbate workflows
• Add more rich schemas and store custodian metadata in schemas

Developer Note

We are working with @mkhorton on this project. We are the developers behind the BEAST Database and have extensive experience using JDFTx for high-throughput workflows as well as direct collaboration with the developer of JDFTx.

[utf]

Hi @cote3804, this is fantastic. Thank you for contributing it.

Firstly, would you be able to send me an email? My address is aganose [at] imperial [dot] ac [dot] uk.

For the PR, here are some high level comments to start with:

• The best place for the IO functionality is pymatgen. Are you happy to submit a PR there once the input sets are completed? I'm happy for you to keep them in this PR while you work on finalising the workflows, as I realise this makes it easier for testing etc.
• You can rename the emmet folders to schemas inline with atomate2 convention.
• The READMEs and test files inside the atomate2/src directory aren't ideal. We can add a JDFTx page to the documentation (in docs) and the test files should go in tests (although currently it looks like most of these files will be in pymatgen anyway).
• To help conform with the atomate2 code style, can you install pre-commit and run it on all of your files. This gets called automatically as part of the GitHub CI and the tests won't pass until all style issues are resolved.

pip install pre-commit
pre-commit run -all

Once you're ready for me to look at the input sets and jobs/flows please let me know (currently they have a lot of VASP code still).

[cote3804]

Hi @utf,

I emailed [email protected] but didn't get a reply. Is that the correct email? Your faculty profile seems to show it as [email protected].

[cote3804]

Hi @utf

I think we're ready for you to look at the sets and jobs. You'll see that they're quite bare right now but functional. We haven't finished writing tests for the jobs, but @soge8904 is hard at work on that.

I tested the current scripts on NERSC's cluster and they are able to run JDFTx successfully starting from the set generators.