Transiesta procedure when relaxing the structure

Question

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:

1. Define the device region and completely relax it
2. Add one/two electrode layers, relax the structure but constraining the latter layers
3. Add another one/two layers and relax the whole structure constraing the latter added layers
4. Add the 'bulk' electrode with the converged amount of layers, relax the whole structure by constraining the bulk electrode and one/two connectivity layers.
5. 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!

Answer 1

The referred slides are just an example of how to fast get a relaxed geometry for complex geometries. Relaxing a geometry with 1000 constraints is slower than relaxing two geometries with 500 constraints (conceptually). So segmenting it for speeding up the process can in some cases be ideal.

It is definitely not a requirement to follow the procedure. Generally, relaxing all in one go is the most generic and accurate procedure, and sometimes (if your initial configuration is a good guess) isn't that much longer than the referenced procedure.

Typically the connectivity region should also be somewhat un-relaxed (same relative coordinates as the electrodes), but they can move a little. And it is thus recommended to have 1 or 2 layers with the same relative coordinates as the electrodes. But as everything, testing and knowing your electronic structure will let you bypass general recommendations. Testing is always a good idea.