Hi Camilla, The scattering matrix contains the transmission/reflection amplitudes of propagating modes. Those are in general superpositions of all the orbitals present in the system. This is why the probability to scattering from orbital 1 in one lead to orbital 2 in another lead isn't defined, since it will change depending on e.g. distance from the scattering region. Hope that clarifies things, Anton On Fri, Nov 25, 2016 at 2:48 AM, Camilla Espedal <camilla.espedal@ntnu.no> wrote:

Hi again,

This question is sort of related to one of mye previous questions (https://www.mail-archive.com/kwant-discuss@kwant-project.org/msg01029.html) but I am writing it as a new one. The questions relates to the sites in the lead unit cell and the scattering matrix.

Say I have a system (simple 2D wire), where I have 3 sites in my unit cell (3 orbitals). I then make a system at an energy which is so low that I only have one propagating mode in the system. If I then run

smatrix.lead_info[0]

it returns a 2x3 matrix (which corresponds to left/right going and number of orbitals). If I then run

smatrix.submatrix(0,0)

I only get one element, which orbital does this element “belong” to, or how does it relate to these orbitals? Is the scattering matrix the same for all orbitals? Is the probability of scattering from say orbital 1 in one lead to orbital 2 in another the same as from orbital 1 to orbital 1?

Hope my question makes sens.

Best regards,

Camilla