Convergence issues with transiesta

Asked by Ebere Amadi on 2020-10-10

Hello,

I am having a bit of trouble getting my structures to converge with an applied bias. Zero-bias calculations work just fine, however when I apply a bias, the calculations do not converge. The convergence is also asymmetric, for instance 0.05V might converge for a structure while -0.05 V doesn't converge. I am using siesta v 4.0, and the mixing weight is currently 0.003. I've tried even lower mixing weights (0.0001) but that doesn't seem to work either. I was wondering if anyone had any tips for achieving convergence. I have also used DM files from converged bias points to try and get others to converge (for e.g. using 0.05 TSDE files in 0.1 V calculation), but it doesn't always work. I have also tried increasing the number of history steps (keyword: DM.NumberPulay) to 8, but that doesn't solve the issue either.

electrode:

LatticeConstant 1.00 Ang

%block LatticeVectors
     4.444170 7.697520 0.000000
     8.888330 0.000000 0.000000
     0.000000 0.000000 7.257293
%endblock LatticeVectors

# K-points

%block kgrid_Monkhorst_Pack
1 0 0 0.0
0 1 0 0.0
0 0 200 0.0
%endblock kgrid_Monkhorst_Pack

# ---------------------------------------------------------------------------
# Species and Atoms
# ---------------------------------------------------------------------------

NumberOfSpecies 1
NumberOfAtoms 27

%block ChemicalSpeciesLabel
  1 79 Au
%endblock ChemicalSpeciesLabel

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

AtomicCoordinatesFormat Ang

%block AtomicCoordinatesAndAtomicSpecies
      2.9627770 5.1316810 1.2095480 1
      1.4813890 2.5658410 1.2095480 1
      0.0000000 0.0000000 1.2095480 1
      5.9255550 5.1316810 1.2095480 1
      4.4441660 2.5658410 1.2095480 1
      2.9627770 0.0000000 1.2095480 1
      8.8883320 5.1316810 1.2095480 1
      7.4069440 2.5658410 1.2095480 1
      5.9255550 0.0000000 1.2095480 1
      4.4441660 5.9869610 3.6286460 1
      2.9627770 3.4211210 3.6286460 1
      1.4813890 0.8552800 3.6286460 1
      7.4069440 5.9869610 3.6286460 1
      5.9255550 3.4211210 3.6286460 1
      4.4441660 0.8552800 3.6286460 1
     10.3697200 5.9869610 3.6286460 1
      8.8883320 3.4211210 3.6286460 1
      7.4069440 0.8552800 3.6286460 1
      2.9627770 6.8422410 6.0477450 1
      1.4813890 4.2764010 6.0477450 1
     -0.0000000 1.7105600 6.0477450 1
      5.9255550 6.8422410 6.0477450 1
      4.4441660 4.2764010 6.0477450 1
      2.9627770 1.7105600 6.0477450 1
      8.8883320 6.8422410 6.0477450 1
      7.4069440 4.2764010 6.0477450 1
      5.9255550 1.7105600 6.0477450 1
%endblock AtomicCoordinatesAndAtomicSpecies

# Basis set variables
PAO.BasisType split
PAO.BasisSize DZP

# General variables

#NeglNonOverlapInt True
ElectronicTemperature 300 K
SolutionMethod diagon
MeshCutoff 200. Ry
xc.functional GGA # Exchange-correlation functional
xc.authors PBE
SpinPolarized false
          # Exchange-correlation version

# SCF variables

DM.MixSCF1 T
MaxSCFIterations 1000 # Maximum number of SCF iter
DM.MixH T
DM.MixingWeight 0.003 # New DM amount for next SCF cycle
DM.Tolerance 1.d-4 # Tolerance in maximum difference
DM.UseSaveDM true # to use continuation files
DM.NumberPulay 6

# MD variables

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

# Output variables

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

scattering region:

LatticeConstant 1.00 Ang

%block LatticeVectors
     4.444170 7.697520 0.000000
     8.888330 0.000000 0.000000
     0.000000 0.000000 107.124745
%endblock LatticeVectors

# ---------------------------------------------------------------------------
# Species and Atoms
# ---------------------------------------------------------------------------

NumberOfSpecies 4
NumberOfAtoms 174

%block ChemicalSpeciesLabel
  1 1 H
  2 6 C
  3 16 S
  4 79 Au
%endblock ChemicalSpeciesLabel

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

AtomicCoordinatesFormat Ang

%block AtomicCoordinatesAndAtomicSpecies
      2.9627770 5.1316810 1.2095480 4
      1.4813890 2.5658410 1.2095480 4
      0.0000000 0.0000000 1.2095480 4
      5.9255550 5.1316810 1.2095480 4
      4.4441660 2.5658410 1.2095480 4
      2.9627770 0.0000000 1.2095480 4
      8.8883320 5.1316810 1.2095480 4
      7.4069440 2.5658410 1.2095480 4
      5.9255550 0.0000000 1.2095480 4
      4.4441660 5.9869610 3.6286460 4
      2.9627770 3.4211210 3.6286460 4
      1.4813890 0.8552800 3.6286460 4
      7.4069440 5.9869610 3.6286460 4
      5.9255550 3.4211210 3.6286460 4
      4.4441660 0.8552800 3.6286460 4
     10.3697200 5.9869610 3.6286460 4
      8.8883320 3.4211210 3.6286460 4
      7.4069440 0.8552800 3.6286460 4
      2.9627770 6.8422410 6.0477450 4
      1.4813890 4.2764010 6.0477450 4
     -0.0000000 1.7105600 6.0477450 4
      5.9255550 6.8422410 6.0477450 4
      4.4441660 4.2764010 6.0477450 4
      2.9627770 1.7105600 6.0477450 4
      8.8883320 6.8422410 6.0477450 4
      7.4069440 4.2764010 6.0477450 4
      5.9255550 1.7105600 6.0477450 4
      2.9627770 5.1316810 8.4668410 4
      1.4813890 2.5658410 8.4668410 4
      0.0000000 0.0000000 8.4668410 4
      5.9255550 5.1316810 8.4668410 4
      4.4441660 2.5658410 8.4668410 4
      2.9627770 0.0000000 8.4668410 4
      8.8883320 5.1316810 8.4668410 4
      7.4069440 2.5658410 8.4668410 4
      5.9255550 0.0000000 8.4668410 4
      4.4441660 5.9869610 10.8859400 4
      2.9627770 3.4211210 10.8859400 4
      1.4813890 0.8552800 10.8859400 4
      7.4069440 5.9869610 10.8859400 4
      5.9255550 3.4211210 10.8859400 4
      4.4441660 0.8552800 10.8859400 4
     10.3697200 5.9869610 10.8859400 4
      8.8883320 3.4211210 10.8859400 4
      7.4069440 0.8552800 10.8859400 4
      3.7034800 4.7040400 12.7615000 3
      3.7039250 4.7902420 14.5395900 2
      3.6928090 2.6334310 14.7209100 1
      3.7150410 6.9472050 14.7236800 1
      3.7101290 5.9945910 15.2530700 2
      3.6977040 3.5838820 15.2539200 2
      3.6976990 3.5838830 16.6449200 2
      3.7101340 5.9946380 16.6459700 2
      3.7150380 6.9472040 17.1753800 1
      3.6928050 2.6334300 17.1781400 1
      3.7039210 4.7901680 17.3593700 2
      3.7034800 4.7040210 19.1372800 3
      3.8889831 4.7210481 21.4297238 4
      3.8743031 6.6735380 23.5981938 4
      3.8952381 3.7921580 24.2392238 4
      3.8966871 5.6494780 26.4719238 4
      3.9027271 2.7682980 27.1131538 4
      3.9041481 4.7210480 29.2815538 4
      3.7031761 4.7062651 31.5727089 3
      3.8902961 4.8168931 33.3396789 2
      3.8791801 2.6600610 33.5209589 1
      3.9014111 6.9738350 33.5237289 1
      3.8840740 3.6105121 34.0539689 2
      3.8964891 6.0191651 34.0567689 2
      3.8840690 3.6105141 35.4449689 2
      3.8964621 6.0142490 35.4502289 2
      3.9013941 6.9710591 35.9739089 1
      3.8791760 2.6600600 35.9781889 1
      3.8892880 4.8125609 36.1665289 2
      3.7021780 4.7039439 37.9337689 3
      3.7133389 4.7049661 40.2337416 4
      3.6986589 6.6574560 42.4022116 4
      3.7195939 3.7760760 43.0432416 4
      3.7210429 5.6333960 45.2759416 4
      3.7270829 2.7522160 45.9171716 4
      3.7285039 4.7049660 48.0855716 4
      3.7031800 4.7062700 50.3767000 3
      3.8902999 4.8168980 52.1436700 2
      3.8791839 2.6600659 52.3249500 1
      3.9014150 6.9738399 52.3277200 1
      3.8840779 3.6105170 52.8579600 2
      3.8964930 6.0191700 52.8607600 2
      3.8840729 3.6105190 54.2489600 2
      3.8964659 6.0142539 54.2542200 2
      3.9013980 6.9710639 54.7779000 1
      3.8791799 2.6600648 54.7821800 1
      3.8892919 4.8125658 54.9705200 2
      3.7021819 4.7039488 56.7377600 3
      3.7133427 4.7049706 59.0377327 4
      3.6986628 6.6574606 61.2062027 4
      3.7195977 3.7760806 61.8472327 4
      3.7210468 5.6334005 64.0799327 4
      3.7270867 2.7522205 64.7211627 4
      3.7285077 4.7049705 66.8895627 4
      3.7030836 4.7062749 69.1894218 3
      3.8902035 4.8169029 70.9563918 2
      3.8790875 2.6600708 71.1376718 1
      3.9013185 6.9738449 71.1404418 1
      3.8839815 3.6105219 71.6706818 2
      3.8963965 6.0191750 71.6734818 2
      3.8839764 3.6105239 73.0616818 2
      3.8963695 6.0142589 73.0669418 2
      3.9013015 6.9710689 73.5906218 1
      3.8790834 2.6600698 73.5949018 1
      3.8891955 4.8125707 73.7832418 2
      3.7020854 4.7039537 75.5504818 3
      3.7132463 4.7049759 77.8504545 4
      3.6985663 6.6574658 80.0189245 4
      3.7195013 3.7760858 80.6599545 4
      3.7209503 5.6334057 82.8926545 4
      3.7269903 2.7522258 83.5338845 4
      3.7284113 4.7049757 85.7022845 4
      3.7030837 4.7062749 88.0021446 3
      3.8902036 4.8169029 89.7691146 2
      3.8790876 2.6600708 89.9503946 1
      3.9013186 6.9738448 89.9531647 1
      3.8839816 3.6105219 90.4834046 2
      3.8963966 6.0191749 90.4862047 2
      3.8839766 3.6105239 91.8744046 2
      3.8963697 6.0142588 91.8796646 2
      3.9013017 6.9710688 92.4033447 1
      3.8790836 2.6600697 92.4076246 1
      3.8891956 4.8125707 92.5959647 2
      3.7020856 4.7039536 94.3632047 3
      7.4055535 0.8551924 96.2388045 4
      8.8869416 3.4210334 96.2388046 4
      4.4427755 0.8551925 96.2388046 4
      5.9241646 3.4210335 96.2388046 4
     10.3683357 5.9868733 96.2388046 4
      1.4799985 0.8551927 96.2388046 4
      7.4055537 5.9868734 96.2388046 4
      2.9613866 3.4210336 96.2388047 4
      4.4427757 5.9868736 96.2388047 4
      5.9241645 -0.0000876 98.6578946 4
      7.4055536 2.5657533 98.6578946 4
     -0.0013905 -0.0000873 98.6578946 4
      2.9613865 -0.0000874 98.6578946 4
      1.4799986 2.5657536 98.6578947 4
      8.8869418 5.1315933 98.6578947 4
      4.4427756 2.5657535 98.6578947 4
      2.9613867 5.1315936 98.6578947 4
      5.9241647 5.1315934 98.6578947 4
     -0.0013904 1.7104726 101.0769945 4
      5.9241646 1.7104723 101.0769945 4
      2.9613866 1.7104725 101.0769945 4
      1.4799987 4.2763136 101.0769945 4
      7.4055537 4.2763133 101.0769946 4
      4.4427757 4.2763134 101.0769946 4
      2.9613868 6.8421535 101.0769946 4
      8.8869418 6.8421532 101.0769946 4
      5.9241648 6.8421534 101.0769946 4
      1.4799985 0.8551925 103.4960944 4
      7.4055535 0.8551922 103.4960945 4
      4.4427756 0.8551924 103.4960945 4
      2.9613866 3.4210334 103.4960945 4
      8.8869417 3.4210332 103.4960945 4
      5.9241647 3.4210333 103.4960946 4
      4.4427758 5.9868734 103.4960946 4
     10.3683358 5.9868731 103.4960946 4
      7.4055538 5.9868732 103.4960946 4
     -0.0013905 -0.0000875 105.9151944 4
      2.9613865 -0.0000877 105.9151945 4
      1.4799986 2.5657534 105.9151945 4
      4.4427756 2.5657533 105.9151946 4
      2.9613867 5.1315934 105.9151946 4
      5.9241645 -0.0000878 105.9151947 4
      5.9241648 5.1315932 105.9151947 4
      7.4055537 2.5657531 105.9151948 4
      8.8869418 5.1315931 105.9151948 4
%endblock AtomicCoordinatesAndAtomicSpecies

# K-points

%block kgrid_Monkhorst_Pack
1 0 0 0.0
0 1 0 0.0
0 0 1 0.0
%endblock kgrid_Monkhorst_Pack

# Chemical species

NumberOfSpecies 4
%block ChemicalSpeciesLabel
  1 79 Au
  2 6 C
  3 1 H
  4 16 S
%endblock ChemicalSpeciesLabel

# Basis set variables
PAO.BasisType split
PAO.BasisSize DZP

# General variables

#NeglNonOverlapInt True
ElectronicTemperature 300 K
SolutionMethod transiesta
MeshCutoff 200. Ry
xc.functional GGA # Exchange-correlation functional
xc.authors PBE
SpinPolarized false
          # Exchange-correlation version

# SCF variables

DM.MixSCF1 T
MaxSCFIterations 10000 # Maximum number of SCF iter
DM.MixH T
DM.MixingWeight 0.003 # New DM amount for next SCF cycle
DM.Tolerance 1.d-4 # Tolerance in maximum difference
DM.UseSaveDM true # to use continuation files
DM.NumberPulay 6

# MD variables

MD.FinalTimeStep 1
MD.TypeOfRun CG
MD.NumCGsteps 000
#%block GeometryConstraints
#position from 1 to 36
#position from 41 to 85
#%endblock GeometryConstraints
MD.UseSaveXV .true.

# Output variables

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

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

TS.TBT.Emin -3.0 eV
TS.TBT.Emax 3.0 eV
TS.TBT.NPoints 3001

TS.TBT.NEigen 5

# Bias voltage
TS.Voltage 0.05 eV
TS.biasContour.NumPoints 50

# Transiesta: electrode definition:
# LEFT ELECTRODE

TS.HSFileLeft ./left-Elec-Au.TSHS
TS.ReplicateA1Left 1
TS.ReplicateA2Left 1
TS.NumUsedAtomsLeft 27
TS.BufferAtomsLeft 0

# RIGHT ELECTRODE
TS.HSFileRight ./right-Elec-Au.TSHS
TS.ReplicateA1Right 1
TS.ReplicateA2Right 1
TS.NumUsedAtomsRight 27
TS.BufferAtomsRight 0

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

Write.Denchar true
WFS.Write.For.Bands true
Denchar.TypeOfRun 3D
Denchar.PlotCharge true

# END OF VNL EXPORT
# ---------------------------------------------------------------------------
# ---------------------------------------------------------------------------

Question information

Language:
English Edit question
Status:
Solved
For:
Siesta Edit question
Assignee:
No assignee Edit question
Solved by:
Nick Papior
Solved:
2020-10-14
Last query:
2020-10-14
Last reply:
2020-10-14
Nick Papior (nickpapior) said : #1

I would advice you to use some k-points.

Ebere Amadi (aybee) said : #2

Thank you for your reply Nick,

I do have some k points set up for the electrodes, but not as many for the scattering region, because I was of the opinion that any value that is set gets truncated to 1 k-point. Were you referring to the kx and ky points in the electrodes?

Thanks,
Ebere.

Best Nick Papior (nickpapior) said : #3

Only the k-points along the transport direction (semi-infinite direction) gets truncated. Please carefully try to understand why this is so ;)

Ebere Amadi (aybee) said : #4

Oh, that makes sense. Thanks so much, Nick! :)