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initially, after optimization of the pristine molecule, I attached a few layers of electrodes to either side of the molecule to make a scattering region after optimization the electrodes will be re-arranged according to the molecule.

my question is after the optimization of the scattering region how do I add new layers of electrodes to the optimized scattering region electrodes? should I replace these few layers of the electrode with new layers or do I have to add new electrode layers to it in order to maintain the potential of the electrode and molecule?

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It depends on what you want to achieve.

In TranSiesta there are 1 + number of electrodes calculations.

  • The electrodes are so-called "pristine electrodes", or "bulk electrodes" and constitute the electronic structure that is used for the self-energies etc.
  • then the device calculation which makes use of the pristine electrodes

The basic principle of NEGF calculations is that the potential at the electrode regions in the device calculation corresponds with the bulk potential of the pure electrode calculations. If this is not obeyed you'll get wrong results.

Basically you should increase the number of layers towards the electrodes until convergence (electrostaticly) has been reached. This is not simple to test, but a good indication is that your properties of interest does not change when you add more electrode layers.

Lastly, the electrode layers (in the device region) that correspond to the bulk electrodes should have exactly the same relative coordinates as the pristine electrode calculation.

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  • $\begingroup$ Dear Sir, I didn't get the last statement(the electrode layers (in the device region) that correspond to the bulk electrodes should have exactly the same coordinates as the pristine electrode calculation.) of your explanation can you please explain it more elaboratively sir? $\endgroup$ Jun 15, 2023 at 9:06
  • $\begingroup$ what means a pristine electrode calculation. $\endgroup$ Jun 15, 2023 at 9:07
  • $\begingroup$ see updated comments $\endgroup$
    – nickpapior
    Jun 15, 2023 at 9:34

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