Addition of JDFTx code by cote3804 · Pull Request #955 · materialsproject/atomate2

cote3804 · 2024-08-13T16:27:53Z

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

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 · 2024-08-14T08:29:57Z

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 · 2024-08-16T16:00:28Z

Hi @utf,

I emailed aganose@imperial.ac.uk but didn't get a reply. Is that the correct email? Your faculty profile seems to show it as a.ganose@imperial.ac.uk.

… of the out file path, as well as some typing updates

…ergence data

… individual JEiter

…lyzing an irrelevant out file slice

…ttings of different minimization stuff

…t of redundancy here now with the jstrucs but I'm keeping it becuase I'm not 100% sure what the existing code is doing yet

file and run jdftx. It returns a jobflow Response. Unittest_BaseJdftxMaker.py is a unit test that was used to test BaseJdftxMaker and passed.

…thod (previously assumed nbands was set to only the number of electrons in the calculation)

cote3804 · 2025-04-25T12:01:21Z

Hi @utf
This PR should now be ready to merge. All of the JDFTx related tests should pass. There is one cp2k test that's failing, however this is also the case for the main branch.

utf · 2025-06-19T17:36:28Z

Hi @cote3804, apologies for the delay responding on this. Overall, I think it looks great. I'd just note that in most cases, we have now moved the input sets into pymatgen directly. Would you be OK to submit a PR to transition them over?

The only other thing is the jdftxcov.xml file which I think can be removed and added to the gitignore.

Once those changes are made I'm happy to merge it.

cote3804 · 2025-06-19T18:15:23Z

Hi @utf

I'm happy to make both of those changes. Do you think it makes sense to merge the changes before moving the sets to pymatgen for the sake of having the JDFTx code working when the publication goes live? I'll still open the PR here and in pymatgen to move the sets.

Updated dependencies in pyproject.toml

Moved JDFTx set over to Pymatgen

Moved sets to pymatgen

cote3804 · 2025-08-13T18:13:54Z

Hi @utf,

Sorry for the long pause on this from my end. I deleted the jdftxcov.xml file and didn't include it in the gitignore because I don't think it's necessary.

I moved our base input set over to Pymatgen and tried to follow the VASP style as faithfully as I could. There was very little code I changed. The PR is active at materialsproject/pymatgen#4479

esoteric-ephemera · 2026-03-05T20:46:37Z

Thanks @cote3804 and sorry for the delay on this! I'd like to get this merged soon. Have made some small changes (outdated type annotations, removed some possible unintentional cp2k modifications, and supporting gzipped test data)

esoteric-ephemera · 2026-03-05T21:08:07Z

Looks like the BaseJdftxSet.yaml file wasn't packaged with pymatgen at the time of the last release. Given the major reorg of pymatgen, to unblock this PR, I'm leaning towards temporarily reinstating that yaml file

JaGeo · 2026-03-05T21:10:01Z

Looks like the BaseJdftxSet.yaml file wasn't packaged with pymatgen at the time of the last release. Given the major reorg of pymatgen, to unblock this PR, I'm leaning towards temporarily reinstating that yaml file

Agreed!

cote3804 · 2026-03-06T12:47:41Z

Thanks for the help in pushing this along @esoteric-ephemera!
Just for reference, the JDFTx yaml build issue is merged in pymatgen-core in this PR

soge8904 and others added 28 commits September 5, 2024 13:18

implementing run.py

d526340

Updating out_to_log functions to take that "text" list of str instead…

d3174e1

… of the out file path, as well as some typing updates

Collection of class objects for (relatively) flexible storing of conv…

eb650bc

…ergence data

Updated testing

d534eb5

Organization + typing

da2eae7

Moving JEiters test to test_JEiters.py

8326192

taking a leap of faith on forces units

ac838ea

Staging to pour one out for JAtoms

8a1f8cf

Restructuring for convergence info to only be held be JEiters, not an…

f3d53cd

… individual JEiter

Restructuring for convergence info to only be held by JEiters, not an…

984dd33

… individual JEiter

Can't think of anything else to test for this suite of classes

201b202

Adding to eventually replace read_file to remove io time spent on ana…

24ed025

…lyzing an irrelevant out file slice

Adding JStructures class super to List to be a list of JStructure

736ab92

Fixing super init

63fe282

typo

9e78597

new files to use for testing

33e6299

This might be overkill but creating class series for storing input se…

f4769d7

…ttings of different minimization stuff

Set the generic settings types upon init

63a8a43

Functionalizing existing operations within "from_file" - there's a lo…

e007c92

…t of redundancy here now with the jstrucs but I'm keeping it becuase I'm not 100% sure what the existing code is doing yet

Commenting this out for now - need to talk to Cooper to discuss

1d5f207

Made changes to base.py to get it to write input

bcf9ae9

file and run jdftx. It returns a jobflow Response. Unittest_BaseJdftxMaker.py is a unit test that was used to test BaseJdftxMaker and passed.

Docustrings for JStructures suite

c7cd7b4

test checks for GC optimizations

a8000a9

Comment on deprecation

698e5d0

Updated docustrings (got the format wrong) + changed _set_Nbands's me…

2f5e4dd

…thod (previously assumed nbands was set to only the number of electrons in the calculation)

docustrings

7f9b156

Consistent indentation

a1e9a67

No longer using the old out_to_log functions

85baae9

cote3804 and others added 2 commits April 24, 2025 22:00

pre-commit fix for Self importing

d8a0ffa

Merge branch 'materialsproject:main' into test_pass

c4f1269

Merge branch 'main' into main

fe8fd70

cote3804 added 2 commits August 13, 2025 08:46

Merge branch 'main' into toml_change

0ec9bdd

Merge pull request #31 from cote3804/toml_change

a49e375

Updated dependencies in pyproject.toml

cote3804 closed this Aug 13, 2025

cote3804 deleted the toml_change branch August 13, 2025 12:52

cote3804 restored the toml_change branch August 13, 2025 12:54

cote3804 reopened this Aug 13, 2025

Moved JDFTx set over to Pymatgen

7a35619

cote3804 mentioned this pull request Aug 13, 2025

Move JDFTx sets from atomate2 to pymatgen materialsproject/pymatgen#4479

Merged

cote3804 added 2 commits August 13, 2025 14:10

Merge pull request #32 from cote3804/pymatgen_sets

62d93e6

Moved JDFTx set over to Pymatgen

Merge pull request #33 from cote3804/main

45af7c4

Moved sets to pymatgen

cote3804 and others added 7 commits February 28, 2026 11:29

Merged materials project changes

f9b73a7

emmet update, pymatgen import fix, and pyproject dependency update

ae31381

Merge branch 'main' into toml_change

6a6d48c

Merge remote-tracking branch 'upstream/main' into toml_change

d827064

replace legacy type annotations and cp2k changes

5664210

gzip jdftx test data + suppport that in tests

8b56dd0

precommit / mypy

fbfd164

temporarily reinstate base jdftx set pending pmg reorg

f16b124

Merge remote-tracking branch 'upstream/main' into toml_change

7179e7c

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Addition of JDFTx code#955

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Summary

Dependencies on other repositories

What we've done

Future Development

Developer Note

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utf commented Aug 14, 2024

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cote3804 commented Aug 13, 2024 •

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