I am studying the magnetic properties of bulk ZnO, so I am doping it with transition metal elements in order to observe the magnetic spectrum. I replace a Zn atom with a transition metal element at different positions (first nearest neighbor, second nearest neighbor ...) at different concentrations. So the distance between atoms is very important in this study.
The problem is I don't know how to relax my structure because after the
vc-relax calculation all the atoms change the position and the transition element which I consider as the second-neighbor becomes the first-neighbor! I don't know exactly how can I optimize my structure?
In the attachment below, the Vanadium atom is chosen to be the second neighbor of the other vanadium atom (here I have dopped with two vanadium atoms) but after the vc-relax the position changes in a way that it becomes the first nearest neighbor! Does the optimization of cell parameters (i.e running test convergence on a and c parameters) is enough even if it is a supercell?