# voltage drop in the symmetrical junction

Dear siesta users and developers

I want get the voltage drop in a symmetrical junction. To do so, I used total potential under finite bias minus total potential under zero bias, and then, converted the grid file into a corresponding CUBE file.

However, after visualizing the CUBE file, I found that the zero potential point do not locate at the central point.

In my opinion, the zero point should locate at the geometric center, is that right? If I'm right, why it happens?

Zhikai

## Question information

Language:
English Edit question
Status:
For:
Siesta Edit question
Assignee:
No assignee Edit question
Last query:
2018-09-24
2018-09-24
 Nick Papior (nickpapior) said on 2018-09-24: #1

A symmetrical junction may mean a lot of things.

What do you mean by symmetric?

Also to plot the voltage drop you should plot the Hartree potential difference (electrostatic potential) and not the total potential. The total potential includes XC potential which isn't part of the voltage drop.

 zhikai (zhikaizhao) said on 2018-09-24: #2

Dear Papior

I mean the geometry is symmetrical, when I run transiesta calculation.

Follow you suggestion, I plot the Hartree electrostatic potential difference, and it's still not symmetrical.

zhikai

 Nick Papior (nickpapior) said on 2018-09-24: #3

1. We can't see what you see, is it far off, or only slightly off?
2. If there are errors in your calculation setup, then that propagates through to the results.
3. Which version are you using?

 zhikai (zhikaizhao) said on 2018-09-24: #4

Hello Nick,

I think it is far off. Here is the contour of the junction, https://pan.baidu.com/s/19V3BQgg7loTZ1JYybAp0iw

And my input fdf is right here, https://pan.baidu.com/s/19V3BQgg7loTZ1JYybAp0iw

I'm using the siesta-4.1-b2

zhikai

 zhikai (zhikaizhao) said on 2018-09-24: #5

sorry, my input fdf is right here, https://pan.baidu.com/s/13_5xSvVOPc6UBYlyCz996g

 Nick Papior (nickpapior) said on 2018-09-24: #6

I can't figure out your links, it's chinese and I have no idea what to press.

Secondly, 4.1-b3 is available. Please use that one.

 zhikai (zhikaizhao) said on 2018-09-24: #7

Hi Nick,

https://imgur.com/a/F8biguV

The input fdf is as follow

SolutionMethod transiesta

MullikenInSCF T
WriteMullikenPop 1

SaveTotalPotential T
SaveElectrostaticPotential T
SaveRho T
SaveDeltaRho T
SaveHS T

LatticeConstant 1.00 Ang

%block LatticeVectors
8.651275 0.000000 0.000000
0.000000 8.651275 0.000000
0.000000 0.000000 31.352171
%endblock LatticeVectors

NumberOfSpecies 4
NumberOfAtoms 102

%block ChemicalSpeciesLabel
1 1 H
2 6 C
3 7 N
4 79 Au
%endblock ChemicalSpeciesLabel

# ---------------------------------------------------------------------------
# Atomic Coordinates
# ---------------------------------------------------------------------------

AtomicCoordinatesFormat Ang

%block AtomicCoordinatesAndAtomicSpecies
2.1628171 2.1628171 1.0195875 4
5.0465754 2.1628171 1.0195875 4
7.9303336 2.1628171 1.0195875 4
2.1628171 5.0465754 1.0195875 4
5.0465754 5.0465754 1.0195875 4
7.9303336 5.0465754 1.0195875 4
2.1628171 7.9303336 1.0195875 4
5.0465754 7.9303336 1.0195875 4
7.9303336 7.9303336 1.0195875 4
0.7209380 0.7209380 3.0587125 4
3.6046962 0.7209380 3.0587125 4
6.4884545 0.7209380 3.0587125 4
0.7209380 3.6046962 3.0587125 4
3.6046962 3.6046962 3.0587125 4
6.4884545 3.6046962 3.0587125 4
0.7209380 6.4884545 3.0587125 4
3.6046962 6.4884545 3.0587125 4
6.4884545 6.4884545 3.0587125 4
2.1628171 2.1628171 5.0978375 4
5.0465754 2.1628171 5.0978375 4
7.9303336 2.1628171 5.0978375 4
2.1628171 5.0465754 5.0978375 4
5.0465754 5.0465754 5.0978375 4
7.9303336 5.0465754 5.0978375 4
2.1628171 7.9303336 5.0978375 4
5.0465754 7.9303336 5.0978375 4
7.9303336 7.9303336 5.0978375 4
0.7209380 0.7209380 7.1369625 4
3.6046962 0.7209380 7.1369625 4
6.4884545 0.7209380 7.1369625 4
0.7209380 3.6046962 7.1369625 4
3.6046962 3.6046962 7.1369625 4
6.4884545 3.6046962 7.1369625 4
0.7209380 6.4884545 7.1369625 4
3.6046962 6.4884545 7.1369625 4
6.4884545 6.4884545 7.1369625 4
5.0465754 5.0465754 9.1760875 4
6.0458305673 2.7627493622 10.1953017345 1
5.4871668716 3.3573943082 10.7812028018 3
7.9684359137 4.2528021578 11.0846581479 1
4.5743985035 2.9549574563 10.8815451196 1
7.4718999832 4.1158963811 12.0253124044 2
6.1112498477 3.6511021095 12.0384848384 2
9.1260837772 4.7255062553 13.1841058627 1
8.1096682615 4.3826095734 13.193383357 2
4.4282249143 3.1478840893 13.2192861217 1
5.4430704936 3.4989101373 13.2088747973 2
7.4491425446 4.2089222931 14.459879228 2
6.0883303725 3.7696674789 14.4616747131 2
9.1194515202 4.7588807626 15.6761523856 1
8.097066646 4.4302392629 15.6761270824 2
5.4333993866 3.5708372115 15.6760488508 2
4.4134210836 3.2362312179 15.6760144819 1
7.4490755454 4.2089247501 16.8923215875 2
6.0882570191 3.7696658503 16.8904446747 2
9.1259442522 4.7255054914 18.168198549 1
8.1095320282 4.3825985433 18.158867101 2
5.4429257662 3.498894723 18.1432189777 2
4.428084864 3.1478574598 18.1327409505 1
7.4716911773 4.1158879192 19.3268924732 2
6.1110306698 3.6510888795 19.3136398375 2
7.9681559812 4.2527983498 20.2675819508 1
4.5739973171 2.9552255503 20.470521181 1
5.4868943832 3.3573686661 20.5709057107 3
6.0453938245 2.7624397636 21.1566763802 1
5.0465800 5.0465800 22.1760834 4
0.7209427 0.7209427 24.2152084 4
3.6047009 0.7209427 24.2152084 4
6.4884591 0.7209427 24.2152084 4
0.7209427 3.6047009 24.2152084 4
3.6047009 3.6047009 24.2152084 4
6.4884591 3.6047009 24.2152084 4
0.7209427 6.4884591 24.2152084 4
3.6047009 6.4884591 24.2152084 4
6.4884591 6.4884591 24.2152084 4
2.1628218 2.1628218 26.2543334 4
5.0465800 2.1628218 26.2543334 4
7.9303382 2.1628218 26.2543334 4
2.1628218 5.0465800 26.2543334 4
5.0465800 5.0465800 26.2543334 4
7.9303382 5.0465800 26.2543334 4
2.1628218 7.9303382 26.2543334 4
5.0465800 7.9303382 26.2543334 4
7.9303382 7.9303382 26.2543334 4
0.7209427 0.7209427 28.2934584 4
3.6047009 0.7209427 28.2934584 4
6.4884591 0.7209427 28.2934584 4
0.7209427 3.6047009 28.2934584 4
3.6047009 3.6047009 28.2934584 4
6.4884591 3.6047009 28.2934584 4
0.7209427 6.4884591 28.2934584 4
3.6047009 6.4884591 28.2934584 4
6.4884591 6.4884591 28.2934584 4
2.1628218 2.1628218 30.3325834 4
5.0465800 2.1628218 30.3325834 4
7.9303382 2.1628218 30.3325834 4
2.1628218 5.0465800 30.3325834 4
5.0465800 5.0465800 30.3325834 4
7.9303382 5.0465800 30.3325834 4
2.1628218 7.9303382 30.3325834 4
5.0465800 7.9303382 30.3325834 4
7.9303382 7.9303382 30.3325834 4
%endblock AtomicCoordinatesAndAtomicSpecies

%block PAO.BasisSizes
C DZP
H DZP
N DZP
Au SZP
%endblock PAO.BasisSizes

%block kgrid_Monkhorst_Pack
2 0 0 0.
0 2 0 0.
0 0 2 0.
%endblock kgrid_Monkhorst_Pack

XC.functional GGA
XC.authors PBE
MeshCutoff 230.000000 Ry
MinSCFIterations 3
MaxSCFIterations 300
DM.Tolerance 1.d-4
DM.Require.Energy.Convergence F
NeglNonOverlapInt F
DM.UseSaveDM T
DM.MixingWeight 0.01
DM.NumberPulay 5
ElectronicTemperature 77 K

#
# Transiesta options
#

TS.Voltage 0.5 eV # the voltage is here

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

%block TS.Elec.Left
TSHS ../../left_elec/elec_left_au_100.TSHS
chemical-potential Left
semi-inf-direction -a3
electrode-position 1
%endblock TS.Elec.Left

%block TS.Elec.Right
TSHS ../../right_elec/elec_right_au_100.TSHS
chemical-potential Right
semi-inf-direction +a3
electrode-position end -1
%endblock TS.Elec.Right

%block TS.ChemPots
Left
Right
%endblock TS.ChemPots
%block TS.ChemPot.Left
mu V/2
contour.eq
begin
c-left
t-left
end
%endblock

%block TS.ChemPot.Right
mu -V/2
contour.eq
begin
c-right
t-right
end
%endblock

%block TS.Contour.c-left
part circle
from - 3. Ry + V/2 to -10 kT + V/2
points 33
method g-legendre
%endblock TS.Contour.c-left
%block TS.Contour.c-right
part circle
from - 3. Ry - V/2 to -10 kT - V/2
points 33
method g-legendre
%endblock TS.Contour.c-right

%block TS.Contour.t-left
part tail
from prev to inf
points 9
method g-fermi
%endblock TS.Contour.t-left
%block TS.Contour.t-right
part tail
from prev to inf
points 9
method g-fermi
%endblock TS.Contour.t-right

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

zhikai

 Nick Papior (nickpapior) said on 2018-09-24: #8

1) Even though your system is symmetric it does not mean that you will get a linear potential drop. Probably you will get two step potentials.
2) From the image it seems clear that your calculation setup is wrong.
a) If your electrode is comprising 2 layers, then the electrode is too short. In this case transiesta would even die because of this.
b) (I guess this is your calculation). Your electrode is comprising 4 layers, however, there is no extended electrode region to screen off the defect with the device.