I am calculating a real system, with 32 orbitals per unit cell. Moreover, I
need to use supercells so that I can simulate periodical boundary conditions. For example, I want to scatter along x direction. Also, I want z direction to be finite and y direction to be periodical. Since kwant does not allow hoppings beyond nearest unit cell in leads, I have to make a supercell that contains all unit cells in y direction!
Ok, I think we've got mixed in our nomenclature somewhere. My basic question still stands, though. Have you tried doing as Anton and I suggested and just putting a single "slice" of one of the leads as a central region, and seeing how long it takes to compute whatever you are interested in? This solution is the easiest, and my guess is that the cost will not be inhibitive.