I want to make a unit cell of NiO. We know that NiO is an antiferromagnetic material meaning the magnetic moments of the neighbouring Ni ions align in an alternating manner (one spin up and then down). So what should be the coordinates of the Ni and O ions, so that if I want to make a unit cell/supercell, the program can understand the location of spin up and down of Ni and the non-magnetic ion O?
Can you specify the editor / package you are using?
If you generate input for a quantum chemistry package, all you have are the positions of the atom nuclei forming an NaCl structure in this case, while the electrons don't know yet where they are and what spin they will get. If you run the program with a suitable method for magnetic properties (which means that basic DFT might not be enough), the electron distribution and spin densities should come out correctly after the calculation.