Add tests for the New Vasp input sets

[Zhuoying]

Summary

Major changes:

• Follow Standardise and update VASP input sets #3484, add tests and clean up test_sets.py

Todos

• Add more MD and NED-related tests
• Fix lints

Checklist

• Google format doc strings added. Check with ruff.
• Type annotations included. Check with mypy.
• Tests added for new features/fixes.
• If applicable, new classes/functions/modules have duecredit @due.dcite decorators to reference relevant papers by DOI (example)

Tip: Install pre-commit hooks to auto-check types and linting before every commit:

pip install -U pre-commit
pre-commit install

[Zhuoying]

Hi @utf, I have a quick question here: is there any particular reason for skipping ENCUT in INCAR (set as None) in MITMDSet and MPMDSet?

pymatgen/pymatgen/io/vasp/sets.py

Line 2409 in 7e0c8f4

"ENCUT": None,

pymatgen/pymatgen/io/vasp/sets.py

Line 2482 in 7e0c8f4

"ENCUT": None,

The default settings in MVLNPTMDSet look more reasonable to me if someone just wants to manually run an MD wo workflow and grab some snapshots from a single run.

pymatgen/pymatgen/io/vasp/sets.py

Line 2559 in 7e0c8f4

updates["ENCUT"] = max(enmax) * 1.5

[utf]

@Zhuoying, I didn't change the behaviour of the input sets. I just updated the implementation. E.g., for the two input sets you mentioned, see the old implementation where ENCUT was also removed from the input set.

• MITMDSet:

  pymatgen/pymatgen/io/vasp/sets.py

  Line 2602 in 36e289c

  self._config_dict["INCAR"].pop("ENCUT", None)

• MPMDSet:

  pymatgen/pymatgen/io/vasp/sets.py

  Line 2691 in 36e289c

  self._config_dict["INCAR"].pop("ENCUT", None)

I would highlight that the point of these tests is to ensure that the output of the new input set implementation is the same as the output of the old implementations.

[janosh]

thanks @Zhuoying! more tests are always appreciated! is this ready for review?

[Zhuoying]

@janosh Yeah, it is ready to review now. Pytest code coverage for pymatgen/io/vasp/sets.py improved from 93% to 95%.
The two failing checks are not related to this PR. Please let me know if you have any comments.
For other io.vasp modules (inputs, outputs, optics), I may submit new PRs for them later if needed.
Thanks.

Name                           Stmts   Miss  Cover
--------------------------------------------------
pymatgen/io/vasp/__init__.py       3      0   100%
pymatgen/io/vasp/help.py          35     35     0%
pymatgen/io/vasp/inputs.py      1071    109    90%
pymatgen/io/vasp/optics.py       186     18    90%
pymatgen/io/vasp/outputs.py     2350    211    91%
pymatgen/io/vasp/sets.py        1204     65    95%
--------------------------------------------------
TOTAL                           4849    438    91%

[janosh]

thanks a lot @Zhuoying! 👍 i feel safer already with this new test coverage (no joke) 😄

[janosh]

general hint: no need to check coverage files into version control.

[Zhuoying]

Thanks for the hint. I guess I did it unconsciously...

[JaGeo]

Yes, thanks a lot for these efforts!

[utf]

This is great, thanks very much @Zhuoying