Add electronic structure methods for Species

[rkingsbury]

Summary

Replacing #3851 , this PR implements electronic_structure, full_electronic_structure, and valence methods for Species.

Major changes:

• Electronic configurations of ions is added to periodic_table.json. Instead of a single string, the ["Electronic structure"] key for each element is now a dict keyed by oxidation state, so the elemental electronic structures are found in ["Electronic structure"]["0"]. Those of ions corresponding to the common oxidation states are added accordingly, e.g. under ["Electronic structure"]["2"]. This parallels the way ionic_radii are stored. The data themselves are taken from the NIST ASD database listed in the docstrings of the respective methods.
• I removed the word "(tentative") from the electron config of Lr (0) because the one listed is shown in the NIST database (presumably last time the .json file was updated, Lr was not as well understood as it is now).
• Update electronic_structure in Element to accommodate the new data format
• Implement electronic_structure, full_electronic_structure, and valence methods for Species
• Added unit tests, including a comprehensive test covering all Element and common_oxidation_states which ensures the total number of electrons between the Element and Species (based on the full_electronic_structure is consistent with the oxidation state.
• Updated docstrings with references and slightly more explanatory text for all methods.

Note

the NIST database only contains electronic structures of cations. I was unable to find a similar resource for anions, however all of the negative "common oxidation states" could be achieved by filling p orbitals of the corresponding ground state element (e.g., ground state is p2, -4 anion is p6). I took this approach for all negative oxidation states (which are relatively few in comparison to the positive ones) because I feel confident it is correct. However, I welcome suggestions if anyone knows where to find hard data to confirm this.

[rkingsbury]

@shyuep can I have your thoughts on this implementation? I think all that remains to finish the PR is entering data for the rest of the common oxidation states, but before I spend time on that I want to make sure this looks workable to you. Thanks!

[rkingsbury]

@shyuep can I have your thoughts on this implementation? I think all that remains to finish the PR is entering data for the rest of the common oxidation states, but before I spend time on that I want to make sure this looks workable to you. Thanks!

@shyuep friendly reminder about this - once I get your blessing on the approach I've taken, I'll populate the remaining data.

[rkingsbury]

Also just a note that the pre-commit tests are currently unhappy about some spellings in aflow_prototypes

src/pymatgen/analysis/aflow_prototypes.json:1: cristalline ==> crystalline
src/pymatgen/analysis/aflow_prototypes.json:1: Ond ==> One, And
src/pymatgen/analysis/aflow_prototypes.json:1: Bever ==> Never
src/pymatgen/analysis/aflow_prototypes.json:1: CaCl ==> calc
src/pymatgen/analysis/aflow_prototypes.json:1: Parth ==> Path
src/pymatgen/analysis/aflow_prototypes.json:1: cristalline ==> crystalline
src/pymatgen/analysis/aflow_prototypes.json:1: CaF ==> calf
src/pymatgen/analysis/aflow_prototypes.json:1: Sclar ==> Scalar
src/pymatgen/analysis/aflow_prototypes.json:1: Zink ==> Zinc
src/pymatgen/analysis/aflow_prototypes.json:1: Pease ==> Peace, Piece, Please, Lease

[shyuep]

Seems ok to me. Ignore the spelling issues.

[rkingsbury]

@shyuep @mkhorton this is ready for review / merge!

[shyuep]

Merged. Thanks!