Remove unnecesary isotope conversion in core.periodic_table.get_el_sp

[DanielYang59]

To close #4171.

This isotope conversion may not be working as we expected as the name of an isotope Element/Species is the "isotope name" (e.g. "D" for Element.D and Species("D") instead of "H"):

pymatgen/src/pymatgen/core/periodic_table.py

Line 1649 in 31f1e1f

return Element(obj.name) if isinstance(obj, Element) else Species(str(obj))

pymatgen/src/pymatgen/core/periodic_table.py

Lines 1105 to 1106 in 31f1e1f

	def __str__(self) -> str:
	output = self.name if hasattr(self, "name") else self.symbol

from pymatgen.core.periodic_table import Element, Species, get_el_sp


print(get_el_sp(Element.D).name)  # D
print(get_el_sp(Element.D) == Element.D)  # True

print(get_el_sp(Species("D")).name)  # D
print(get_el_sp(Species("D")) == Species("D"))  # True

print(get_el_sp(Species("D", 1)).name)  # D
print(get_el_sp(Species("D", 1)) == Species("D", 1))  # True

---

Meanwhile the isotope characteristic removing in Composition.add_charges_from_oxi_state_guesses is not done by this but Composition.get_el_amt_dict, full analysis in #4171 (reply in thread).

This could also be confirmed by all unit tests passing including:

pymatgen/tests/core/test_composition.py

Lines 845 to 856 in 31f1e1f

	def test_isotopes(self):
	composition = Composition({"D": 2, "O": 1})
	assert "Deuterium" in [elem.long_name for elem in composition.elements]
	# adding oxidation state removes Deuterium characteristic
	composition = composition.add_charges_from_oxi_state_guesses()
	assert "Deuterium" not in [elem.long_name for elem in composition.elements]
	# however the user can explicitly add an oxidation state to deuterium
	composition = Composition({"D+": 2, "O": 1})
	assert composition.elements[0].oxi_state == 1
	assert "Deuterium" in [elem.long_name for elem in composition.elements]

credit to @esoteric-ephemera for providing the context and the helpful discussion as always, and @benrich37 @mkhorton for bringing up the topic

[DanielYang59]

@esoteric-ephemera Do we have further concerns on this change here? If not I might mark as ready?

[mkhorton]

If you mark as ready I'm happy to merge @DanielYang59, thank you!

[esoteric-ephemera]

Good to go from my side, not sure these lines are needed anymore. Thanks for checking!

[DanielYang59]

No problem guys, happy holiday :)