Add support for vaspout.h5, improvements to potcar handling

[esoteric-ephemera]

Summary

The vaspout.h5 file appears to be a replacement for / supplement to the vasprun.xml file, and has been available in certain VASP versions >= 6. This PR aims to add support for parsing this file.

However the vaspout.h5 file appears to be still in development. For example, no electronic self-consistency info is included in it as of 11 April, 2024, but there is a PR on VASP's py4vasp GH to add OSZICAR info to vaspout.h5

Major changes:

• Add support for parsing vaspout.h5 through pymatgen.io.vasp.outputs.Vaspout. This subclasses Vasprun in the spirit that the two should contain roughly the same information now.
• Add .from_str method to pymatgen.io.vasp.inputs.Potcar (needed because vaspout.h5 stores the complete potcar as a str)
  • To avoid issues of copyright, there's a kwarg, store_potcar, to enable/disable storing the full POTCAR or its just spec
• The structure at each ionic_step now has site_properties with the s, p, d,...-resolved and tot charge / magnetization, if applicable. This is the same format as Outcar.charge and Outcar.magnetization, but added as a site property at each ionic step instead of a top-level attr for only the final structure

Some related changes for VASP I/O

• Add spec attr to PotcarSingle and Potcar. This standardizes the POTCAR spec attr added to vasprun.xml and vaspout.h5 objects
• Add from_spec method to Potcar, which attempts to generate a POTCAR with a consistent functional just from the spec. Note that multiple matches are possible, this only takes the first consistent match.

Todos

• Some information currently contained in vasprun.xml appears not to be available in vaspout.h5. That might change in the near future, or I may be mistaken
• Support for selective dynamics (if applicable)
• Various TODO's sprinkled through current code
• Tests

[janosh]

there's going to be a new pmg release soon to close #3744. do we want to get this in before that? let us know if others can help with this PR

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[esoteric-ephemera]

This isn't super urgent for release. What I'd like to do is ensure that this works across a wider variety of vaspout's, and make sure that all fields currently included in the vaspout are being mapped correctly to the PMG object

Rn, it doesn't seems like vaspout.h5 has the same level of detail as vasprun.xml so figuring out a way to handle that would also be good

[Shibu778]

Following features can be included to extract information from one-shot band-structure calculation.

[Shibu778]

You can add following parameter and attributes to the class.

1. dos_kpoints_opt
2. eigenvalues_kpoints_opt
3. projectors_kpoints_opt
   It will be useful in case of one-shot calculation of bandstructure. Particularly, it is useful while doing HSE calculations (ref), which requires adding the kpoints with fake weights for hartree-fock calculations(ref). One-shot calculations reduces the two step calculations to one-step with two kpoints file, i.e., KPOINTS and KPOINTS_OPT.

[esoteric-ephemera]

Yeah I'll get on this next, will also bring the PR up to date with #3509

[mkhorton]

Thanks for this PR @esoteric-ephemera. Do you happen to know if magnetic moments are now stored in the vaspout.h5?

Previously these were not available in the vasprun.xml, although perhaps they have since been added and we haven't noticed. I do see a MAGDIPOLOUT key.

[esoteric-ephemera]

Hi @mkhorton, yes both the magnetic moments and charges are stored in vaspout.h5, and thankfully to normal floating point precision

I need to revisit this PR soon - will try to this week or next

[mkhorton]

Saw this is stale, that's no problem but wondered if you were expecting any updates to this. I saw VASP 6.5 is out with some further hdf5 support.

More generally, given there is now first-party support for parsing from the VASP developers in py4vasp, do you have any new thoughts on how this should fit in with pymatgen? Should development of parsing continue to be done in parallel, or are there scenarios where having a dep on py4vasp might make sense?

[esoteric-ephemera]

Sorry @mkhorton, I'll try to get this synced up tomorrow to merge. The only thing I wanted to add was KPOINTS_OPT parsing, which I think I have enough test files for

In general, I don't think we can nor want to chase VASP's support for their own schemas but that's a discussion worth having with the p4vasp team

[esoteric-ephemera]

Hey @mkhorton @shyuep - I think this is ready for review. Some features are missing to bring Vaspout to full parity with Vasprun. That might be due to the schema of Vaspout being not fixed yet (there are already code blocks that support older / newer versions of Vaspout schemas) or something I missed

Either way, I think it's best we have a template to add to / modify as Vaspout is developed

[shyuep]

Thanks. I will merge and release. I think we can do the usual approach of release first then iterate as necessary. It is a format still in flux but no reason why we cannot support it now first.