I have done molecular junction relaxation which includes 3 layers of electrodes attached to both sides of molecule using siesta in which I fixed the position of electrode atoms, after that I replaced these 3 layers of electrodes with electrode containing 6 layers for scattering region calculation. My question is what TSHS files should I include in scattering region (Transiesta) calculation which is TSHS files of electrode containing 6 layer or TSHS files of remaining three layer which are not included in molecular junction relaxation.
The length of the electrode unit cell should be sufficient to avoid interaction of non-adjacent cells (if you think of the electrode as a periodic sequence of the unit cells). That is it should be longer than the doubled cutoff radius for the orbitals. Also the atoms in the part of the structure corresponding to bulk electrodes should not be moved. If this is the case for 3 layers, then TSHS files for 3 layers should be used. If not, the electrode unit cell must be larger. However, there still needs to be a sufficient number of electrode layers at the contact that not belong to the bulk electrode part. They are needed to simulate the surface and guarantee that the electrode part actually behaves as bulk. So if a larger electrode cell is needed, it can be needed to add more electrode layers to the device structure.
Thankyou Irina for your explanation.
I am facing a problem related to DOS and PDOS after transiesta calculations. I have done Tbtrans calculations and want to locate HOMO - LUMO in PDOS, Transmission and DOS graphs. how can I do that is there any better way?