Hai
Thanks for your reply.
It is clearly possible to project the hamiltonian to specific atoms in the representation using localized basis set.
By the way, let me ask two questions in relation to your reply.
In Fig. 10.1 of Page 197 in ATK manual 2008.10, MPSH of H2 molecule is drawn. Red lines are for isolated H2 molecule, while blue lines are for H2 in the two-probe geometry.
(1) If energy zero correspond to the average Fermi level of the electrode, are the energy level (Ei’) of the H2 molecule in the two probe geometry calculated using MPSH actually correspond to Ei-Ef(electrode)?
(2) If that is the case, should energy levels (=Ei) of isolated H2 molecule also to be drawn in comparison with those in the two probe geometry be shifted by the Fermi level of the electrode? Namely, should Ei’= Ei-Ef(electrode) be drawn instead of Ei ?