psi: initial Psi4 Mol extensions

[loriab]

Description

Molecule JSON exported from Psi4 has several extra fields already checked for self-consistency so that the Mol may henceforth be used without reconsulting a periodic table. This defines the fields of that main psi4mol extension. There are also two more extensions, one for EFP fragments and one for transmitting ZMat mol specifications.

Questions

• I tried to follow guidelines here. Properly there should have been a secondary repo. Here I just made an extensions folder. I'm sure that won't do for structuring a complex schema. I'll investigate further.
• The minimal required input fields for EFP are actually fragment_files, hint_types, geom_hints, and units. All other fields are valid after and EFP system has been populated by an EFP-reading program into a consistent, along-side "viz" representation. These alternate sets of "required" fields have not yet been programmatically imposed.

Status

• Ready to go

[dgasmith]

This is interesting as it is a formalization of the considered extensions. I would be interested in @ghutchis's (and others) thoughts on this.

[loriab]

This original molecule extension PR will be split.

• what remains in the PR is the bit that should be incorporated into moleucle_schema proper, which is 4 new optional keys
• from offline discussions it sounds like 9cf3dff#diff-fb40813be873a1ea003de289cb1f9373R6 and following line should be deleted. and the whole schema bumped from 1-->2. My opinion is that, while we shouldn't go overboard on segmenting the schema, having a few separate pieces doesn't hurt, especially when there are whole software projects that only deal with one piece (e.g., molviz and basissetexch)
• remaining pieces of original PR now missing in this PR are zmat and efp extensions. Are separate or combined extension PR(s) wanted for that?

[dgasmith]

I think we should get this in and not yet cut a new release until we have the multiple schema for molecule/input/output worked out.

[dgasmith]

Can you make an issue about z-mat and EFP and discuss the extensions there? I don't think we have a good framework of where to put these yet.