Whether an atom is an "ion" or not in a compound is not something you decide beforehand. Actually real ions only exist in isolation and can be handled in DFT by changing the charge. If the atom is bound to other atoms, there is a charge redistribution that may deprive or enrich the atomic site with electronic charge, and this is what is considered the "charge state". You can simulate a crystal cell that has a certain amount of excess (positive or negative) charge in total, but where this charge is localized should generally be determined by the simulation itself.
