Abinit DFPT

[emarazzi]

Hi everyone,

Together with @VicTrqt and @gpetretto, we updated and extended the previous ABINIT DFPT PR.

We went through several rounds of internal revisions.

Looking forward to your feedback.

Summary of Changes

1. Core Workflow Enhancements

• New DFPT (Density Functional Perturbation Theory) Workflows:

  • Added a DfptFlowMaker class in src/atomate2/abinit/flows/dfpt_base.py to generate workflows for DFPT calculations.
    • Added SHGFlowMaker and PhononFlowMaker classes in src/atomate2/abinit/flows/dfpt_core.py to generate workflows for second-harmonic generation and phonon calculations.

• Updated Workflows:

  • Updated RelaxFlowMaker in src/atomate2/abinit/flows/core.py.
  • Updated BandStructureMaker in src/atomate2/abinit/flows/core.py.

---

2. File Handling Improvements

• Added del_gzip_files Job to delete and gzip files from previous jobs/flows, with configurable exclusions/inclusions, when appended at the end of a flow.

3. Binary File Storage

• Added AbinitStoredFile class in src/atomate2/abinit/schemas/outfiles.py to store raw ABINIT output files (e.g., out_DDB, out_POT, out_WFK) as binary or string data in a serializable format in the additional Store.

---

Dependencies

• New: abinit (for perturbation generation in CI).
• Updated: abipy >= 1.0.0.

[Copilot]

Copilot wasn't able to review this pull request because it exceeds the maximum number of files (300). Try reducing the number of changed files and requesting a review from Copilot again.

[esoteric-ephemera]

Thanks @emarazzi, @VicTrqt, and @davidwaroquiers!

To make the review a bit easier, could you:

• Gzip the PSPs (you'll need to make sure the tests decompress them prior to running but this is done elsewhere in CI)
• Prune some of the test data (seeing a lot of tmpdir and .empty.gz directories/files which may not be needed?)