QuantumATK V-2023.12-SP1 version released on Mar 11, 2024
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Regarding to the k, it also stands for the kinetic momentum of electrons. Sure, the electron states with kz[tex]\neq[/tex] 0 also have contribution to the electron transport.
For the transmission calculation you only specify k-points in the x and y directions, The k-points in the transport direction are selected through the energy, i.e. T(E0, kx,ky) gives the transmission of all states with energy, E(kx,ky,kz) = E0