Transiesta geometry optimization

Question

Reading the transiesta manual, I understand that it would be sufficient to optimize the structure within siesta and then use the result for a transiesta run.

However, I have also read that it would be necessary to re-run the optimization with transiesta if the forces obtained from the calculation at zero bias are particularly large. On the other hand, the forces shouldn't be trusted near the electrodes. So, what could be a threshold for forces in a transiesta run? Should one consider, for the latter, only the force on atoms far enough from the electrodes?

Answer 1

Generally it would be sufficient to optimize the geometry in siesta since that geometry will likely be the same geometry as for V=0. The reason should be straightforwardly understood if one thinks about the requirements of the electrodes, hint the electrodes needs to behave like a bulk electrode in the device region.

Generally one should constrain the atoms close to the electrodes since various options in transiesta invalidates the force calculations on the atoms closest to the electrodes. This shouldn't be confused with actual physical properties (unless one does not have true bulk properties of the electrode region in the device).

IFF you experience small forces in the Siesta run and relatively large forces in the V=0 calculation far from the electrode interface, then my first guess would be that your electrodes in the device region does not behave like bulk electrodes, and hence your system is erroneously setup.

Like all things, giving a number for tolerance is very difficult as it depends on the chemistry etc..