Hi,

>
> I have a matrix giving me the complex wave function at each site. How
> do I know which mode (m/n) do the amplitudes correspond to?

Where did you get this matrix from? Is this the wavefunction of a mode
in a lead, from 'kwant.modes', or of a scattering wavefunction, from
'kwant.wave_function'? Bear in mind that a mode wavefunction and a
scattering wavefunction are defined in different places: a mode
wavefunction is defined in the lead only (i.e. over a single unit cell,
and you use Bloch's theorem to get the wavefunction in neighboring unit
cells), whereas the scattering wavefunction may only be queried in the
scattering region itself (even though it extends infinitely far into the
leads, Kwant does not allow you to query the amplitude of a scattering
wavefunction on sites the leads).

> Also, I am not aware of the method to get wavenumbers k_m. Could you
> kindly help me out with that as well?
>
You can get the wavenumbers by calling 'kwant.modes' on a lead and
querying the propagating modes. This contains the wavefunctions for the
modes of the provided lead, as well as the wavenumbers and velocities.

Happy Kwanting,

Joe

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