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_waveguide.ipynb

Hope it helps,

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