As the title says, I'm interested in performing Transiesta calculations with a device region that needs to be optimized. I read the slides reported here: https://departments.icmab.es/leem/SIESTA_MATERIAL/Docs/Tutorials/tlv14/slides12.pdf
However, I was wondering about the specific procedure regarding the connectivity atoms between the device region and the electrodes. In my case, I don't have a molecule but rather a bulk material presenting defects in the device region. This material is the same as used in the electrode, but without the defects. So should the procedure be:
- Define the device region and completely relax it
- Add one/two electrode layers, relax the structure but constraining the latter layers
- Add another one/two layers and relax the whole structure constraing the latter added layers
- Add the 'bulk' electrode with the converged amount of layers, relax the whole structure by constraining the bulk electrode and one/two connectivity layers.
- Proceed with the transport calculations.
I'm still unsure about step 4 and whether I should relax the connectivity layers.
Moreover, since in my case the structure is a simple graphene monolayer with an atomic defect in the device region, I was wondering if I should actually do this step by step or go directly to step 4 (and thus construct the whole scattering region and relax the structure by freezing the electrodes+connectivity atoms) would be sufficient. Thanks for your help!