feat: support returning of ions and bare elements in `get_chemical_symbols`

[cadenmyers13]

Problem

Currently, Structure.get_chemical_symbols() only returns bare chemical species and does not offer support for returning ions.

Proposed solution

Add an optional input to atom_bare_symbol to return ions. Default is to return bare symbol. We might want to update the function name to better represent this behavior. Its been deprecated so this would just involve changing the atom_bare_symbol to something like parse_atom_symbols.