Siesta

transiesta not converged after long time parameter changing

Asked by Ziba Torkashvand

Hello everyone
I am using transiesta to calculate the transport properties of the following system:
An Armchair boron nitride nanoribbon and on the top of it two bulk nickel structures (boron nitride nickel interface as electrodes).
My input file for this system is as follow:

#TRANSSystemName scat
SystemLabel scat

NumberOfAtoms 156
NumberOfSpecies 4

%block ChemicalSpeciesLabel
  1 1 H
  2 5 B
  3 7 N
  4 28 Ni
%endblock ChemicalSpeciesLabel

PAO.BasisSize DZP
PAO.EnergyShift 0.05 Ry
PAO.SplitNorm 0.2

==================================================
==================================================
# K-points

%block kgrid_Monkhorst_Pack
   1 0 0 0.0
   0 1 0 0.0
   0 0 50 0.0
%endblock Kgrid_Monkhorst_Pack
==================================================
==================================================
# UNIT CELL AND ATOMIC POSITIONS

# UNIT CELL
LatticeConstant 1.00 Ang

%block LatticeVectors
       17.376571 0.000000 0.000000
        0.000000 12.968306 0.000000
        0.000000 0.000000 60.092144
%endblock LatticeVectors
AtomicCoordinatesFormat Ang

%block AtomicCoordinatesAndAtomicSpecies
   12.50487396 5.18602407 0.35767997 4 1 Ni
    6.49340507 6.48459931 1.07304002 3 2 N
   10.52225628 6.48459931 1.07304002 4 3 Ni
    6.49340507 7.40080982 1.57776264 1 4 H
    6.49340507 5.18602407 1.78839996 2 5 B
    8.53963869 5.18602407 1.78839996 4 6 Ni
   12.50487396 6.48459931 2.50376001 4 7 Ni
    6.49340507 5.18602407 3.21911995 3 8 N
   10.52225628 5.18602407 3.21911995 4 9 Ni
    6.49340507 4.26981355 3.72384267 1 10 H
    6.49340507 6.48459931 3.93447999 2 11 B
    8.53963869 6.48459931 3.93447999 4 12 Ni
   12.50487396 5.18602407 4.64983994 4 13 Ni
    6.49340507 6.48459931 5.36519998 3 14 N
   10.52225628 6.48459931 5.36519998 4 15 Ni
    6.49340507 7.40080982 5.86992261 1 16 H
    6.49340507 5.18602407 6.08055993 2 17 B
    8.53963869 5.18602407 6.08055993 4 18 Ni
   12.50487396 6.48459931 6.79591997 4 19 Ni
    6.49340507 5.18602407 7.51127992 3 20 N
   10.52225628 5.18602407 7.51127992 4 21 Ni
    6.49340507 4.26981355 8.01600264 1 22 H
    6.49340507 6.48459931 8.22663996 2 23 B
    8.53963869 6.48459931 8.22663996 4 24 Ni
   12.50487396 5.18602407 8.94199991 4 25 Ni
    6.49340507 6.48459931 9.65735995 3 26 N
   10.52225628 6.48459931 9.65735995 4 27 Ni
    6.49340507 7.40080982 10.16208258 1 28 H
    6.49340507 5.18602407 10.37271990 2 29 B
    8.53963869 5.18602407 10.37271990 4 30 Ni
   12.50487396 6.48459931 11.08807994 4 31 Ni
    6.49340507 5.18602407 11.80343989 3 32 N
   10.52225628 5.18602407 11.80343989 4 33 Ni
    6.49340507 4.26981355 12.30816261 1 34 H
    6.49340507 6.48459931 12.51879993 2 35 B
    8.53963869 6.48459931 12.51879993 4 36 Ni
   12.50487396 5.18602407 13.23414632 4 37 Ni
    6.49340507 6.48459931 13.94950636 3 38 N
   10.52225628 6.48459931 13.94950636 4 39 Ni
    6.49340507 7.40080982 14.45422899 1 40 H
    6.49340507 5.18602407 14.66486631 2 41 B
    8.53963869 5.18602407 14.66486631 4 42 Ni
   12.50487396 6.48459931 15.38022635 4 43 Ni
    6.49340507 5.18602407 16.09558629 3 44 N
   10.52225628 5.18602407 16.09558629 4 45 Ni
    6.49340507 4.26981355 16.60030902 1 46 H
    6.49340507 6.48459931 16.81094634 2 47 B
    8.53963869 6.48459931 16.81094634 4 48 Ni
   12.50487396 5.18602407 17.52630628 4 49 Ni
    6.49340507 6.48459931 18.24166633 3 50 N
   10.52225628 6.48459931 18.24166633 4 51 Ni
    6.49340507 7.40080982 18.74638895 1 52 H
    6.49340507 5.18602407 18.95702627 2 53 B
    8.53963869 5.18602407 18.95702627 4 54 Ni
   12.50487396 6.48459931 19.67238632 4 55 Ni
    6.49340507 5.18602407 20.38774626 3 56 N
   10.52225628 5.18602407 20.38774626 4 57 Ni
    6.49340507 4.26981355 20.89246899 1 58 H
    6.49340507 6.48459931 21.10310631 2 59 B
    8.53963869 6.48459931 21.10310631 4 60 Ni
   12.50487396 5.18602407 21.81846625 4 61 Ni
    6.49340507 6.48459931 22.53382630 3 62 N
   10.52225628 6.48459931 22.53382630 4 63 Ni
    6.49340507 7.40080982 23.03854892 1 64 H
    6.49340507 5.18602407 23.24918624 2 65 B
    8.53963869 5.18602407 23.24918624 4 66 Ni
   12.50487396 6.48459931 23.96454628 4 67 Ni
    6.49340507 5.18602407 24.67990623 3 68 N
   10.52225628 5.18602407 24.67990623 4 69 Ni
    8.53963869 6.48459931 25.39526627 4 70 Ni
    6.49340507 4.26981355 25.18462895 1 71 H
    6.49340507 6.48459931 25.39526627 2 72 B
    6.49340507 6.33956805 26.81516814 3 73 N
    6.49340507 7.14320232 27.52938363 1 74 H
    6.49340507 5.12496389 27.58235961 2 75 B
    6.49340507 5.28625479 28.94693407 3 76 N
    6.49340507 4.51188497 29.66565381 1 77 H
    6.49340507 6.53615425 29.71339269 2 78 B
    6.49340507 6.38733293 31.09719972 3 79 N
    6.49340507 7.19704752 31.78224228 1 80 H
    6.49340507 5.16903884 31.87070887 2 81 B
    6.49340507 5.34746647 33.24168120 3 82 N
    6.49340507 4.56238555 33.95170042 1 83 H
    6.49340507 6.57768805 34.00988808 2 84 B
   12.50487396 5.18602407 34.69494615 4 85 Ni
    6.49340507 6.48459931 35.41030620 3 86 N
   10.52225628 6.48459931 35.41030620 4 87 Ni
    6.49340507 7.40080982 35.91502882 1 88 H
    6.49340507 5.18602407 36.12566614 2 89 B
    8.53963869 5.18602407 36.12566614 4 90 Ni
   12.50487396 6.48459931 36.84102619 4 91 Ni
    6.49340507 5.18602407 37.55638613 3 92 N
   10.52225628 5.18602407 37.55638613 4 93 Ni
    6.49340507 4.26981355 38.06110886 1 94 H
    6.49340507 6.48459931 38.27174618 2 95 B
    8.53963869 6.48459931 38.27174618 4 96 Ni
   12.50487396 5.18602407 38.98710612 4 97 Ni
    6.49340507 6.48459931 39.70246616 3 98 N
   10.52225628 6.48459931 39.70246616 4 99 Ni
    6.49340507 7.40080982 40.20718879 1 100 H
    6.49340507 5.18602407 40.41782611 2 101 B
    8.53963869 5.18602407 40.41782611 4 102 Ni
   12.50487396 6.48459931 41.13318615 4 103 Ni
    6.49340507 5.18602407 41.84854610 3 104 N
   10.52225628 5.18602407 41.84854610 4 105 Ni
    6.49340507 4.26981355 42.35326882 1 106 H
    6.49340507 6.48459931 42.56390614 2 107 B
    8.53963869 6.48459931 42.56390614 4 108 Ni
   12.50487396 5.18602407 43.27926609 4 109 Ni
    6.49340507 6.48459931 43.99462613 3 110 N
   10.52225628 6.48459931 43.99462613 4 111 Ni
    6.49340507 7.40080982 44.49934886 1 112 H
    6.49340507 5.18602407 44.70998608 2 113 B
    8.53963869 5.18602407 44.70998608 4 114 Ni
   12.50487396 6.48459931 45.42534612 4 115 Ni
    6.49340507 5.18602407 46.14070607 3 116 N
   10.52225628 5.18602407 46.14070607 4 117 Ni
    6.49340507 4.26981355 46.64542879 1 118 H
    6.49340507 6.48459931 46.85606611 2 119 B
    8.53963869 6.48459931 46.85606611 4 120 Ni
   12.50487396 5.18602407 47.57142289 4 121 Ni
    6.49340507 6.48459931 48.28678293 3 122 N
   10.52225628 6.48459931 48.28678293 4 123 Ni
    6.49340507 7.40080982 48.79150556 1 124 H
    6.49340507 5.18602407 49.00214288 2 125 B
    8.53963869 5.18602407 49.00214288 4 126 Ni
   12.50487396 6.48459931 49.71750292 4 127 Ni
    6.49340507 5.18602407 50.43286287 3 128 N
   10.52225628 5.18602407 50.43286287 4 129 Ni
    6.49340507 4.26981355 50.93758559 1 130 H
    6.49340507 6.48459931 51.14822291 2 131 B
    8.53963869 6.48459931 51.14822291 4 132 Ni
   12.50487396 5.18602407 51.86358286 4 133 Ni
    6.49340507 6.48459931 52.57894290 3 134 N
   10.52225628 6.48459931 52.57894290 4 135 Ni
    6.49340507 7.40080982 53.08366552 1 136 H
    6.49340507 5.18602407 53.29430284 2 137 B
    8.53963869 5.18602407 53.29430284 4 138 Ni
   12.50487396 6.48459931 54.00966289 4 139 Ni
    6.49340507 5.18602407 54.72502283 3 140 N
   10.52225628 5.18602407 54.72502283 4 141 Ni
    6.49340507 4.26981355 55.22974556 1 142 H
    6.49340507 6.48459931 55.44038288 2 143 B
    8.53963869 6.48459931 55.44038288 4 144 Ni
   12.50487396 5.18602407 56.15574282 4 145 Ni
    6.49340507 6.48459931 56.87110287 3 146 N
   10.52225628 6.48459931 56.87110287 4 147 Ni
    6.49340507 7.40080982 57.37582549 1 148 H
    6.49340507 5.18602407 57.58646281 2 149 B
    8.53963869 5.18602407 57.58646281 4 150 Ni
   12.50487396 6.48459931 58.30182286 4 151 Ni
    6.49340507 5.18602407 59.01718280 3 152 N
   10.52225628 5.18602407 59.01718280 4 153 Ni
    6.49340507 4.26981355 59.52190553 1 154 H
    6.49340507 6.48459931 59.73254285 2 155 B
    8.53963869 6.48459931 59.73254285 4 156 Ni
%endblock AtomicCoordinatesAndAtomicSpecies

# General variables

ElectronicTemperature 300 K
MeshCutoff 300. Ry
xc.functional GGA
xc.authors PBE
SpinPolarized .false.
SolutionMethod Transiesta

==================================================
==================================================
# SCF variables

DM.MixSCF1 T
MaxSCFIterations 4000
DM.MixingWeight 0.0001
DM.OccupancyTolerance 0.1000000000E-11
DM.NumberKick 0
DM.KickMixingWeight 0.0050000000
DM.Tolerance 1.d-4
SCF.Mix density
SCF.DM.Converge .true.
SCF.H.Converge .true.
SCF.H.Tolerance 1.d-3 eV

DM.UseSaveDM .true.
UseSaveData .true.
DM.NumberPulay 12
Diag.DivideAndConquer no
Diag.ParallelOverK yes

==================================================
==================================================
# MD variables

MD.FinalTimeStep 1
MD.TypeOfRun CG
MD.NumCGsteps 000
MD.UseSaveXV .true.

==================================================
==================================================
# Output variables

WriteMullikenPop 1
WriteBands .true.
SaveRho .true.
SaveDeltaRho .true.
SaveHS .true.
SaveElectrostaticPotential True
SaveTotalPotential no
WriteCoorXmol .true.
WriteMDXmol .true.
WriteMDhistory .false.
WriteEigenvalues yes

==================================================
==================================================

# Transiesta information

TS.biasContour.NumPoints 10
TS.Voltage 0.000000 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.Elecs.Bulk true
TS.Elecs.DM.Update none
TS.Elecs.GF.ReUse true

%block TS.Elecs
left
right
%endblock TS.Elecs

%block TS.Elec.Left
  HS elecl.TSHS
  chem-pot Left
  semi-inf-dir -a3
  elec-pos begin 25
  used-atoms 24
%endblock TS.Elec.Left

%block TS.Elec.Right
  HS elecr.TSHS
  chem-pot Right
  semi-inf-dir +a3
  elec-pos end -25
  used-atoms 24
%endblock TS.Elec.Right

%block TS.Atoms.Buffer
atom [ 1 -- 24 ]
atom [ 133 -- 156 ]
%endblock

TS.Contours.Eq.Pole 2.50000 eV
TS.Contours.Eq.Pole.N 16

TS.HS.Save true
TS.DE.Save true

%block TS.Contour.c-Left
  part circle
   from -40.00000 eV + V/2 to -10. kT + V/2
    points 54
     method g-legendre
%endblock TS.Contour.c-Left

%block TS.Contour.t-Left
  part tail
   from prev to inf
    points 11
     method g-fermi
%endblock TS.Contour.t-Left

%block TS.Contour.c-Right
  part circle
   from -40.00000 eV - V/2 to -10. kT - V/2
    points 54
     method g-legendre
%endblock TS.Contour.c-Right

%block TS.Contour.t-Right
  part tail
   from prev to inf
    points 11
     method g-fermi
%endblock TS.Contour.t-Right

TS.Elecs.Eta 0.0001000000 eV

%block TS.Contours.nEq
  neq
%endblock TS.Contours.nEq

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

I have used 100 points along the transport direction for electrode calculation.
I have changed DM.NumberPulay from 8 to 12 and DM.MixingWeight from 0.0001 to 0.001 by 0.0001 steps and almost for all of them siesta DM will converge but there is no evidence of convergengence for transiesta calculations.
Unfortunately, for all of my calculations the amount of dQ is so large (at least E+0).
Now, I included 4 layers of electrodes to each side of the scattering region so, I wonder if I should include more layers?
Any suggestions would be appreciated.

Question information

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Revision history for this message
Nick Papior (nickpapior) said : 		#1

Hi

1) Are these structures semiconductors? If so I wouldn't start doing transiesta calculation on them (transiesta relies on metallic electrodes)
2) You use buffer atoms, why? They are not needed for periodic setups. Typically they are only needed for different electrode configurations and/or number of electrodes different from 2.

/ Nick

Revision history for this message
Ziba Torkashvand (ziba) said : 		#2

Thank you Nick for your reply
Actually, in my concept, the bulk nickel electrodes are positioning on the top of nanoribbon so this structure seems to be inevitable but, do you think changing B and N atoms in electrode areas to C can help?
I have also tried the same structure without buffer atoms but there were no differences.

Revision history for this message
Nick Papior (nickpapior) said : 		#3

I don't understand what you mean in your first paragraph. Again, if your electrodes are semi-conductors/insulators, the calculation won't work. Check the bandstructures of the electrodes if in doubt.

I would suggest you to not use buffer atoms and rely on the periodicity of the cell to have the electrodes next to each other.

Revision history for this message
Launchpad Janitor (janitor) said : 		#4

This question was expired because it remained in the 'Needs information' state without activity for the last 15 days.