We describe the ab initio nonequilibrium Green’s function method for electron-transport calculations in nanoscale devices based on the “efficient molecular-orbital approach.” This is implemented in the density-functional theory code SIESTA with the additional option of including effects originating from electron-phonon coupling. We also derive simple expressions for the conductance and the inelastic electron tunneling spectrum (IETS) based on the rigorous lowest-order expansion formalism. In order to illustrate our method, we have performed calculations of inelastic transport in a linear gold atomic wire and a benzene-dithiol molecule both sandwiched between gold electrodes. In the latter case the leads have been constrained to maintain an overall $D_{2h}$ symmetry, as typical of both high- and low-conductance systems. The shapes of the IETS, the effect of the temperature, and of the symmetry of the IETS signals are analyzed in details.

• Received 30 July 2008

DOI:https://doi.org/10.1103/PhysRevB.78.235420