Hi, I just stated using Kwant but maybe I can help. You can retrieve the S matrix using `kwant.smatrix(syst, energy)`, which contains the transmission matrix of the system. Then, for a given input wavefunction, you can compute the transmitted one with a simple matrix multiplication. I did something similar for optical waveguides here: https://github.com/wavefrontshaping/WFS.net/blob/master/Kwant_disordered_wav... Hope it helps,