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I have a problem with a Transiesta calculation, I could not get the transmission (TBT calculation) as well DOS and current. I perform the I-V for graphene nanoribbons (electrode containing 20 atom , and al device 140 atoms). Just to validate at first the calculation for 0 voltage. So For the Transiesta calculation, the running gives me a not-perfect electrode (as you see in Figure). I refer to the Siesta 4.1 b4 manual and I add the command:

TS.Elecs.Neglect.Principal

also this:

 TBT.Elecs.Coord.EPS 0.02 Ang
 TS.Elecs.Coord.EPS 0.02 Ang

at now it doesnt work and it still give me :

Electrode connectivity is not perfect, refer to the manual for achieving a perfect electrode.

enter image description here

Stopping Program from Node:    0

enter image description here

Thank you

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    $\begingroup$ +1. Welcome to our new community, and thank you so much for contributing your question here! We hope to see much more of you in the future!!! How did you find this site? Also, your image is not displaying. Please try to fix that! $\endgroup$ Jul 22, 2022 at 23:22
  • $\begingroup$ The electrode coordinate check is probably because you relaxed the electrode coordinates as well. Try and relax a minimal GNR, then tile/expand/repeat this structure to your desired electrode size and device size, then run those calculations. I can't see the error that tbtrans gives you, so I can't be of more help than this (for now). Please add the final details ;) $\endgroup$
    – nickpapior
    Jul 23, 2022 at 5:41
  • $\begingroup$ @Nike Dattani Thank ypu for uou response i fixe the picture and i found this web site due to Mr. Nickpapior advice $\endgroup$
    – Hananab
    Jul 25, 2022 at 13:36
  • $\begingroup$ @nickpapior thank you, please check the picture that I add with the last is given by TBT.out calculation (all my calculations are done including the electrode calculation , also Scattering cal. except this TBT ) $\endgroup$
    – Hananab
    Jul 25, 2022 at 13:39
  • $\begingroup$ Could you please be more specific with some more details? Your question is very hard to follow given the scattered details. Could you please put the pictures in the post so it is easier to follow your line of thought? $\endgroup$
    – nickpapior
    Jul 28, 2022 at 12:53

1 Answer 1

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I will quote the manual. :)

It is extremely important that the electrodes only interact with one neighboring supercell due to the self-energy calculation 1, TranSiesta will print out a block as this (<> is the electrode name):

<> principal cell is perfect!

if the electrode is correctly setup and it only interacts with its neighboring supercell.
In case the electrode is erroneously setup, something similar to the following will be shown in the output file.

<> principal cell is extending out with 96 elements:
Atom 1 connects with atom 3
Orbital 8 connects with orbital 26
Hamiltonian value: |H(8,6587)|@R=-2 =  0.651E-13 eV
Overlap          :  S(8,6587)|@R=-2 =   0.00    

It is imperative that you have a perfect electrode as otherwise nonphysical results will occur. This means that you need to add more layers in your electrode calculation (and hence also in your scattering region). An example is an ABC stacking electrode. If the above error is shown one has to create an electrode with ABCABC stacking in order to retain periodicity.
By default TranSiesta will die if there are connections beyond the principal cell. One may control whether this is allowed or not by using TS.Elecs.Neglect.Principal

To expand on this.

The self-energy calculation has these restrictions on the connectivity along the semi-infinite direction. There are no restrictions on the transverse directions.
In fact, TranSiesta/TBtrans can get much better performance if one can utilize Bloch's theorem (see the Bloch keyword in the electrode block). It only requires the ordering of the electrode region to be set in a specific manner.

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