Add properties to Structure and Molecule

[gpetretto]

Closes #2884.

This PR implements a properties attribute for Structure and Molecule. I also modified the Poscar object to store the predictor_corrector_preamble in the structure properties.

[janosh]

Thanks @gpetretto for taking this on! Looks promising. 👍

I think we need better file IO support before merging. Right now, the properties are written to JSON

json_str = struct_with_props.to(fmt="json")
assert '"test_property": 42' in json_str

but they're not read back in Structure.from_str, i.e. this fails:

struct = Structure.from_str(json_str, fmt="json")
assert struct.properties == props

As I mentioned in #2884 (comment) it would be nice to retain properties when reading and writing to as many file formats as possible. JSON at least is easy to do.

[janosh]

@arosen93 @utf Would you mind taking a look at this to ensure it addresses your use cases?

[Andrew-S-Rosen]

At a very quick glance, this seems reasonable. Once merged, I will need to update the ASE atoms adapter to ensure this is handled nicely. But that's for me to deal with.

[janosh]

Thanks @gpetretto! 👍

[Andrew-S-Rosen]

@gpetretto: Any thoughts about (de)serialization with the new .properties flag? In principle, a user can define .properties such that it contains data that is not jsonable or that makes the following fail. Is this something where we put the onus on the user, or should we be incorporating some sort of check?

d = jsanitize(structure, strict=True, enum_values=True)
MontyDecoder().process_decoded(d)

[janosh]

Good question! Not obvious what's the best solution here. We could issue a silenceable runtime warning when users set non-JSONable properties.

[gpetretto]

This is a good point. I actually did not think much about this kind of problems since in my view properties is somewhat equivalent to the site_properties, which suffer from the same limitation.
In general, adding non serializable properties could still be a valid use case, as long as the structure in not serialized. So, I would not strictly prevent a user from doing that. In any case one would get an error when trying to dump the structure to a file.