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Good day, I trust you are doing well. I am trying to calculate transport properties for a 3D structure stacked between two gold electrodes along the c-axis. The 3D structure and the electrodes should be periodic along the ab plane. I have successfully obtained the .TSHS files for my electrodes, and set up my input as follows (all.fdf file excluded for security reasons).

In particular I have a semi-inf-direction = ab plane, which produced an error telling me to fix a plane when using this tag and I have opted for TS.Hartree.Fix = C, but replacing C with +AC, -AB, etc. for example then also produces the error:

Electrode: Left uses real-space SE, but the GF file is not present! In-core self-energy calculations is currently not implemented Please use sisl to create the TBTGF file.

So SIESTA is looking for a TBTGF file for the electrodes, but I have no idea how to generate them with SIESTA or sisl. Could you please provide assistance?

TS.Voltage 0 eV
%block TS.ChemPots
  Left
  Right
%endblock TS.ChemPots

%block TS.ChemPot.Left
  mu V/2
  contour.eq
    begin
      C-Left
      T-Left
    end
%endblock TS.ChemPot.Left
%block TS.ChemPot.Right
  mu -V/2
  contour.eq
    begin
      C-Right
      T-Right
    end
%endblock TS.ChemPot.Right

TS.Contours.Eq.Pole 2.5 eV
%block TS.Contour.C-Left
  part circle
   from -40. eV + V/2 to -10 kT + V/2
     points 25
      method g-legendre
       opt right
%endblock TS.Contour.C-Left
%block TS.Contour.T-Left
  part tail
   from prev to inf
     points 10
      method g-fermi
%endblock TS.Contour.T-Left
%block TS.Contour.C-Right
  part circle
   from -40. eV -V/2 to -10 kT -V/2
     points 25
      method g-legendre
       opt right
%endblock TS.Contour.C-Right
%block TS.Contour.T-Right
  part tail
   from prev to inf
     points 10
      method g-fermi
%endblock TS.Contour.T-Right

%block TS.Contours.nEq
  neq-1
%endblock TS.Contours.nEq
%block TS.Contour.nEq.neq-1
  part line
   from -|V|/2 - 5 kT to |V|/2 + 5 kT
     delta 0.01 eV
      method mid-rule
%endblock TS.Contour.nEq.neq-1

TS.Hartree.Fix C

%block TS.Elecs
  Left
  Right
%endblock TS.Elecs

%block TS.Elec.Left
  HS elecleft.TSHS
  chemical-potential Left
  semi-inf-direction ab
  electrode-position 1
  used-atoms 36
%endblock TS.Elec.Left
%block TS.Elec.Right
  HS elecright.TSHS
  chemical-potential Right
  semi-inf-direction ab
  electrode-position begin 37
  used-atoms 36
%endblock TS.Elec.Right

%include all.fdf

Edit: The electrodes and the central structure are periodic in the A and B direction, with a large vacuum above these structures along the C direction.

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    $\begingroup$ +1, Welcome to the forum. $\endgroup$ Commented Feb 27 at 12:03

1 Answer 1

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I don't know how setting the semi infinite direction to a plane works, but I think this is not what you want judging by how you describe your system.

The semi infinite direction is the direction in which your electrode extends infinitely, and it seems like one of your electrodes should extend on the -c direction and the other one on the +c direction.

When you change that, you should remove the TS.Hartree.Fix as well.

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  • $\begingroup$ When changing it to +c and -c and removing TS.Hartree.Fix, I now get an error of: Electrode Left has no transfer matrix. The self-energy cannot be calculated with a zero transfer matrix! Elec: transfer matrix has 0 elements. The self-energy cannot be calculated. Please check your electrode electronic structure. $\endgroup$ Commented Feb 29 at 10:49
  • $\begingroup$ Try replacing "c" with "a3" $\endgroup$
    – Pol Febrer
    Commented Mar 1 at 11:21
  • $\begingroup$ @LenardCarroll seems like you should update your question with a better description of the periodicity of your electrodes + device region. :) $\endgroup$
    – nickpapior
    Commented Mar 1 at 14:25
  • $\begingroup$ I tried with a3, but the same error persists. I have also updated the question to describe the system's periodicity. $\endgroup$ Commented Mar 2 at 14:10
  • $\begingroup$ @LenardCarroll perhaps you should show an image of the full device, with markings of the electrodes etc. One thing is periodicity, another thing is how it connects to the device region (which is where the decision on real-space self-energies vs. 1D self-energies comes into play). $\endgroup$
    – nickpapior
    Commented Mar 4 at 14:04

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