Kwant is kind of general in terms of the type of tight-binding models it can simulate. On one hand you can start from a discrete model in terms of atoms and orbitals, but you can also take a continuous model and get a tight-binding model by discretizing it (see here http://kwant-project.org/doc/1.0/tutorial/tutorial1.html).
The sites in a Kwant system are therefore not necessarily atoms; they could represent discretization points. Out of the box Kwant does not contain any physical "models", concretely this means that you have to provide all of the onsites/hoppings yourself depending on what model you want to simulate; this includes deciding on what your tight-binding model physically "means" (discretization of a continuous model vs. atoms/atomic orbitals).
Hope that clarifies,
On 13 September 2015 at 20:10, siddheshwar chopra firstname.lastname@example.org wrote:
Dear All, I have never performed the conductance calculations earlier, and have just read the Kwant manual. I quite understood the defining of left,right leads and the scattering region. But I could not find anywhere how to add the atomic number details of the atoms used in leads, and the scattering region. Could somebody help me in this? The conductivity would depend on the lattice type, atom type etc. right?