Yes I am wondering this as well, and I suppose the other thing is, what will ATK assume about periodicity of the system, I saw other posts that said it is assumed to be periodic in X and Y, but that cannot be the case, for example with Graphene, since it is only periodic in Z ... so then how does it know which directions are to be periodic? since I use the graphene builder tools, I am not sure since you do not directly set the unit cells, etc .. but I would guess it has to do with how you setup the unit cell is that correct? So then maybe to be periodic in Y but not X, you have to leave some space in the X directions maybe? Also Yang, when you run a TransmissionSpectrum, you can specify the kpoints parameter to use .. for example:
transmission_spectrum = TransmissionSpectrum(
configuration = device_configuration,
energies = transSpecEnergies,
kpoints = MonkhorstPackGrid(1,1),
energy_zero_parameter = AverageFermiLevel,
infinitesimal = 1e-06*eV,
self_energy_calculator = KrylovSelfEnergy(),
)