1) I don't quite understand your question about shifting the Fermi level, but it essentially corresponds to doping the device.
2) The specified temperature is the temperature that enters the Fermi distribution for the electrons in the electrodes. The default temperature is the average electrode temperature.
3) For the energy window, I think you simply need it to be wide enough to accommodate the temperature dependence. You set the energy window in the Transmission widget.
well, I mean 1).if I want to get conductance G in fig1 (△Ef=0.3eV ,T=500K), ATK will calculate conductance G using eq1(fig2) when EFL=0.3eV , TR=500K ,is that correct?
2). in this link: http://docs.quantumwise.com/tutorials/graphene_nanoribbon_device.html?highlight=linear%20response it says "At TL=TR=0TL=TR=0, the conductance is determined by the transmission coefficient at the Fermi Level, while for finite electrode temperatures, the conductance depends on the value of the transmission coefficient in an energy window around the Fermi level.", how do you define an energy window around the Fermi level for finite electrode temperatures?
by the way, is eq1 derived from eq2 (fig3) ?