I am trying to compare the retarded Green's function of a simple 1D wire attached to two leads using two different methods:

(I)  Using  scattering wave function obtained from the Kwant software and using Eq. 25 in energy domain of  "Numerical simulations of time resolved quantum electronics (https://arxiv.org/abs/1307.6419) written by Kwant authors.

(II)  Direct computation of the retarded Green's function by inverting device Hamiltonian with self energies of the attached leads (again computed from the Kwant software): G^r(E) = [E+\i*\eta - H- \Sigma^r_{leads}]^{-1} for a relatively small system size (5 sites in the attached example). Here both H and \Sigma^r are computed from the Kwant software.

However, I find that these two results do not agree even in a simple 1D example when on-site potential is present in the few sites of device  or scattering region only. 

I have attached the Python script with this email.

Does anyone know the reason behind the discrepancy between the two methods?I would greatly appreciate any comments/suggestions on how we can resolve this error?

Thanks!