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I am having a doubt regarding electrode setup in scattering region calculation (transiesta) firstly, I have done molecular junction relaxation using using 3 layers of electrodes attached to both the sides of molecule. and after that I removed this 3 layers of electrodes and replaced it with 6 layers of electrode for scattering region calculation. My doubt is should I include .tshs files of electrode containing 6 layers or .tshs containing remaining 3 layer except layers used in junction relaxation.

I am currently using remaining layers .tshs files except those layers invovled in junction relaxation is it ok or I need to change.

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As far as I know, if the 3-layer electrode is enough to ensure the interaction with only one neighboring supercell along the transport direction, you can safely use the latter including the .TSHS file of the corresponding electrode size. The latter should be exactly the same coordinates as in the normal siesta run.

When constructing the device+electrodes model, thus including the molecule, you should add some layers of the electrode that relax (and thus connect the molecule to the bulk electrode) and they shouldn't be included in the first electrode calculation (and thus the .TSHS file that you're using).

Please, refer to the Siesta manual from pg. 135 for more insights about the electrode set-up.

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  • $\begingroup$ I am unable to understand what represnts a neighbouring supercell, is it a cell which contains molecule or something else, can you explain me a little please. $\endgroup$ Commented Jan 30, 2023 at 12:53
  • $\begingroup$ A neighboring cell is a cell with which the primary unit cell interacts. Since it's related to the calculation of the self-energy, it has to contain ONLY the bulk electrode. Note that when this is the case, siesta prints 'Left/Right cell is perfect' in the output. Otherwise, it will die by default $\endgroup$
    – Laura
    Commented Jan 30, 2023 at 14:21
  • $\begingroup$ Thankyou I got it. $\endgroup$ Commented Jan 30, 2023 at 14:39
  • $\begingroup$ Note that I have updated the answer with the reference to the Siesta manual! :) $\endgroup$
    – Laura
    Commented Jan 30, 2023 at 14:54
  • $\begingroup$ SIESTA chat room: chat.stackexchange.com/rooms/136776/siesta $\endgroup$ Commented Jan 30, 2023 at 15:20

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