Yes, it's certainly possible, you just need to apply a periodic transformation to the coordinates in the Builder "Coordinate Tools>Transform by Expression". Or, you can install the attached prototype plugin, it will do it for you a little bit easier. However, I think it's important to realize that the structure in the referenced article is large (20,000 atoms) and also is obtained as a result of (not as input to) a calculation, viz. an MD simulation. Which, of course, you could carry out in ATK using the Brenner potential, which certainly should be able to handle 20,000 atoms.
