2015-08-18 19:27 GMT+00:00 leoqmc . <[email protected]>:
> Dear Nick and transiesta users,
>
> I am interested in transport calculations in single-molecule two-probe
> systems[Au(111)-Molecule-Au(111)]. I searched in the list for the following
> questions, but I think that these questions were not explicitly solved for
> a beginner. Please help me.
>
> 1) Charge: The Molecule is charged(charge +2). Not make sense uses the
> option (NetCharge 2.0) in the transiesta calculation, since that the charge
> will be screened. I'm right?
>
No that will most likely not work, currently this is not an easy task.
>
> 2) Setup for the electrodes:
> a) The third lattice's vector (z-direction) should have length minimal
> possible, namely it should be enough for the atoms+basis functions. I'm
> right?
>
In your case, make the z-direction periodic.
> b) The lattice's vectors in x,y direction should include large vacuum
> (~20 Angstroms). I'm right?
>
No, not necessarily, here you can also impose periodicity. Please look at
the examples in the test directory, an example of gold, gold-chain, gold is
shown. That could be the basis for your further geometry creation. See
example ts_au_100, both the repetition and non-repeated structure.
> c) Usually you use how many units ("N") of the electrodes (N * ABC)?
>
In your 111 direction I would think a single ABC stacking should be enough.
This depends on your basis range, you need to check this your-self.
>
> 3) Setup for complete device (Electrodes + Molecule):
>
> a) My electrodes are equal. In this case it is mandatory to include
> vacuum in the z direction, such that the device is not affected by their
> image in the calculation of siesta prior to the calculation of transiesta?
>
Please re-read 2a. If electrodes are the same, having a periodic setup is
far better than the alternative. Again refer to the example as suggested in
2b.
>
> Thanks in advance.
>
> Leone Carmo Garcia
>
--
Kind regards Nick
