Hi,

So my final question is then. What is the unit cell? Doesn't a square lattice only have one site per unit cell? Or is it the number of interface sites?

The unit cell is whatever you define it to be with your choice of translational symmetry and sites that you add to the system. In the below example there are 3 sites in the unit cell of the system: lat = kwant.lattice.square(a=1) T = kwant.TranslationalSymmetry((-1, 0)) syst = kwant.Builder(T) syst[(lat(0, j) for j in range(3))] = 4 # the sites lat(x, y) are all mapped onto lat(0, y), # so the line below *overwrites* the onsites set above syst[(lat(1, j) for j in range(3))] = 6 I could have defined my translational symmetry to be something different, however. In the below example there are 6 sites in the unit cell of the system: lat = kwant.lattice.square(a=1) T = kwant.TranslationalSymmetry((-2, 0)) syst = kwant.Builder(T) syst[(lat(0, j) for j in range(3))] = 4 # because the symmetry vector is (-2, 0), the sites # in the line below are *distinct* from the sites above syst[(lat(1, j) for j in range(3))] = 6 Hope that clarifies, Joe