Overview

The system is made of semi-infinite left lead, a molecule, and semi-infinite right lead. L and R are in the equilibrium. The chemical potential at L is $\mu_L$ and $\mu_R$ at R. It is separated to L(semi-infinite left lead), C(molecule+lead=extended molecule) and R(semi-infinite right lead). Effects of L and R are taken into account of through the self-energy at C. It can be calculated via Green function at L or R connecting to C.

1. Green function at L or R. (surface Green function)
2. Green function at C
3. charge density at C
4. transfer matrix and conductance.