At this time, I don't know how to contain two or more ions in a first principles calculation. Could you give me some examples, such as INCAR file of VASP or input file for Abinit?
In addition, as Uttam Pal said, if the electron density of atom is fixed in our calculation, is this calculation reasonable? In other words, which do we fix in the calculation of a supercell containing ion? the charge of special atom or the charge of supercell?
Just use the NELECT tag in the INCAR file of VASP (https://cms.mpi.univie.ac.at/vasp/vasp/NELECT.html). You have to just mention the total number of valance electrons in the system. If there are two positively charged atoms, there will be two less electrons in the system. Let VASP calculate where the holes will be. You cannot pin point that.