Dear Adel:
Thanks for your reply and the code. I have read it through (also the linked
thread). I am aware that the green's function is not the total one.
What I am doing is obtain the total one by inverse the whole Hamiltonian matrix
plus the self-energy. Then select the part that connected to the leads, and
compare it with the one kwant calculated. I found they don't match.
I have added the some comments on my code to clarify my question
```
lat = kwant.lattice.square()
def make_system(r=20, t=-1):
def circle(pos):
x, y = pos
return x**2 + y**2 < r**2
syst = kwant.Builder()
syst[lat.shape(circle, (0, 0))] = 0
syst[lat.neighbors()] = t
syst.eradicate_dangling()
def lead_shape(pos):
return -15 < pos[0] < 15
lead = kwant.Builder( kwant.TranslationalSymmetry((0, 1)))
lead[lat.shape(lead_shape, (0, 0))] = 0
lead[lat.neighbors()] = -t
syst.attach_lead(lead)
return syst
syst = make_system()
fsyst = syst.finalized()
kwant.plot(fsyst)
greens_function=kwant.greens_function(fsyst)
Hc = fsyst.hamiltonian_submatrix(sparse=False)
# the index of the sites IN SYSTEM which connected to lead
index = fsyst.lead_interfaces[0]
# add the self energy to the original matrix
Hc[np.ix_(index, index)] += greens_function.lead_info[0]
# inverse it, to get the total Green's function of the whole system
Gr = np.linalg.inv(-Hc)
# Should be a zero matrix! The first term is the green's function of the
selected sites.
Gr[np.ix_(index, index)]-greens_function.submatrix(0, 0)
```
I am also very interested in your last comment, about how to get the whole
green's function of the system (include the bulk sites). I hope you can provide
me some links, thank you very much.
