A technique is to perform a supercell calculation where in the calculation is performed over several cells instead of a single unit cell. The desired change is made to a single cell within this larger structure. This does make your change periodic, but if the supercell is large enough, then the change can be made essentially local. This method has been used to generate electronic structures for substitutional series like FeSi$_{(1-x)}$Ge$_x$ and $\text{X}_x\text{W}_{(1-x)}\text{O}_3$ (X=Nb,V,Re) (link). So, a small structural change is not out of the question. I know wien2k and quantum espresso have a scripts for generating supercell, but I don't know what other major packages do. VASP does not seem to.
As to how big a supercell to make, I don't know. I have not actively looked for one, but I have not found a resource giving such guidance. I'd suggest starting as small as possible, possibly $2\times2\times1$ or $2\times2\times2$, and increasing the size until the effect seems localized to the interior of the supercell. Obviously, this will put a strain on your computing power, so the smaller the better.
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