Molecular junc with Ferro elec: transiesta convergence problem at 0 bias

Asked by Dongzhe Li on 2018-07-05

Dear Siesta developers and users,

I am new user for SIESTA package, and I have been trying to calculate the T(E) at 0 bias for benzene based molecule with ferromagnetic Ni electrodes. However, I got a terrible convergence problem, so I need your comments and suggestions.

What I have tried as follows:
1. played with DM.MixingWeight, I decreased it even to 0.0005, the scf part of siesta converges, but not the transiesta part...
2. increased the layer of electrodes to 6 (since it is ABC stacking) and used only 3 layers by using TS.NumUsedAtomsRight, otherwise the code gives me a warning, no effect on convergence.
3. increased the layer of scattering part until 9 layers on the left and another 9 on the right side, still not converge.
4. set TS.UpdateDMCROnly .true., does not really help too much.
5. tried also more simple basis such as SZ or DZ, even more terrible convergence.
6. tried also with different functionals LDA or GGA, no convergence.
7. decreased TS.BiasContour.Eta to 0.0001Ry, not really help, is it also related to the convergence?
8. Maybe one simple question, why at 0 bias, the Green's function should be iterated???

I attached my .fdf file for scattering part, any comments will be appreciated.

Dongzhe Li
Post-doc, Univ. Konstanz, Germany

#------------------------------------------------------
# FDF for Ni111 scat
#
SystemName Ni_scat # Descriptive name of the system
SystemLabel Ni_scat # Short name for naming files

# Write electrode Hamiltonian
TS.SaveHS .true.
TS.SaveLead .true.

# Atomic coordinates
NumberOfAtoms 219
AtomicCoordinatesFormat Ang
%block AtomicCoordinatesAndAtomicSpecies
  0.000000000 0.000000000 0.000000000 1
  2.491695000 0.000000000 0.000000000 1
  4.983392000 0.000000000 0.000000000 1
  1.245848000 2.157872000 0.000000000 1
  3.737544000 2.157872000 0.000000000 1
  6.229240000 2.157872000 0.000000000 1
  2.491695000 4.315744000 0.000000000 1
  4.983392000 4.315744000 0.000000000 1
  7.475087000 4.315744000 0.000000000 1
  7.475100000 0.000000000 0.000000000 1
  8.720948000 2.157872000 0.000000000 1
  9.966795000 4.315744000 0.000000000 1
  3.737550000 6.473626000 0.000000000 1
  6.229245000 6.473626000 0.000000000 1
  8.720942000 6.473626000 0.000000000 1
 11.212650000 6.473626000 0.000000000 1
  1.245848000 0.719290000 2.034461000 1
  3.737544000 0.719290000 2.034461000 1
  6.229240000 0.719290000 2.034461000 1
  2.491695000 2.877163000 2.034461000 1
  4.983392000 2.877163000 2.034461000 1
  7.475087000 2.877163000 2.034461000 1
  3.737544000 5.035034000 2.034461000 1
  6.229240000 5.035034000 2.034461000 1
  8.720935000 5.035034000 2.034461000 1
  8.720948000 0.719290000 2.034461000 1
  9.966795000 2.877163000 2.034461000 1
 11.212644000 5.035034000 2.034461000 1
  4.983398000 7.192917000 2.034461000 1
  7.475094000 7.192917000 2.034461000 1
  9.966790000 7.192917000 2.034461000 1
 12.458498000 7.192917000 2.034461000 1
 -0.000000000 1.438581000 4.068923000 1
  2.491695000 1.438581000 4.068923000 1
  4.983392000 1.438581000 4.068923000 1
  1.245848000 3.596453000 4.068923000 1
  3.737544000 3.596453000 4.068923000 1
  6.229240000 3.596453000 4.068923000 1
  2.491695000 5.754325000 4.068923000 1
  4.983392000 5.754325000 4.068923000 1
  7.475087000 5.754325000 4.068923000 1
  7.475100000 1.438581000 4.068923000 1
  8.720948000 3.596453000 4.068923000 1
  9.966795000 5.754325000 4.068923000 1
  3.737550000 7.912207000 4.068923000 1
  6.229245000 7.912207000 4.068923000 1
  8.720942000 7.912207000 4.068923000 1
 11.212650000 7.912207000 4.068923000 1
  0.000000000 0.000000000 6.103383000 1
  2.491695000 0.000000000 6.103383000 1
  4.983392000 0.000000000 6.103383000 1
  1.245848000 2.157872000 6.103383000 1
  3.737544000 2.157872000 6.103383000 1
  6.229240000 2.157872000 6.103383000 1
  2.491695000 4.315744000 6.103383000 1
  4.983392000 4.315744000 6.103383000 1
  7.475087000 4.315744000 6.103383000 1
  7.475100000 0.000000000 6.103383000 1
  8.720948000 2.157872000 6.103383000 1
  9.966795000 4.315744000 6.103383000 1
  3.737550000 6.473626000 6.103383000 1
  6.229245000 6.473626000 6.103383000 1
  8.720942000 6.473626000 6.103383000 1
 11.212650000 6.473626000 6.103383000 1
       1.245244750 0.717377809 8.008069339 1
       3.734060152 0.718720186 7.993526122 1
       6.234514964 0.718522425 7.993526915 1
       2.489701980 2.873709295 7.994884287 1
       4.983980916 2.878634065 7.991943219 1
       7.476970800 2.874258014 7.995757602 1
       3.740569015 5.039588297 7.996217305 1
       6.226946087 5.039481340 7.996318039 1
       8.718722539 5.032941171 8.002567308 1
       8.722866488 0.717215195 8.008197876 1
       9.966909281 2.881355557 8.009696101 1
      11.216003634 5.033205921 8.002549110 1
       4.984010628 7.187415682 8.011958345 1
       7.480859550 7.190901997 8.009327824 1
       9.967580597 7.195773513 8.003605288 1
      12.454301278 7.190531703 8.009737871 1
       0.001032951 1.437839851 9.920059196 1
       2.483290782 1.433000128 9.913427343 1
       4.985812555 1.384003729 9.885893879 1
       1.246667541 3.589611970 9.922437528 1
       3.689004227 3.627787648 9.893236719 1
       6.276896612 3.630273099 9.895098876 1
       2.499100499 5.758069706 9.923055326 1
       4.983702602 5.750571003 9.933553325 1
       7.469297810 5.758703673 9.921922917 1
       7.484000889 1.434026521 9.914525545 1
       8.720147799 3.589641126 9.922433268 1
       9.967551426 5.754535996 9.907542233 1
       3.739648996 7.910184101 9.920473851 1
       6.229334997 7.910193526 9.919784574 1
       8.715819106 7.918546940 9.924254144 1
      11.220281751 7.918051502 9.924369501 1
       3.809329951 2.183392993 11.679165058 1
       6.159290057 2.189598093 11.682072868 1
       4.977720327 4.197371352 11.713662018 1
       4.971061809 2.740986700 13.592276376 1
       4.765872713 0.911300141 22.888142477 2
       5.014894294 3.848074400 19.666915814 3
       5.020925725 4.126972159 18.312739001 3
       5.098102998 4.660182425 20.394254048 2
       5.110974211 5.168030573 17.995446072 2
       4.910543673 3.103320456 17.363487237 3
       4.807727440 1.790921769 17.833950058 3
       4.800472138 1.519843950 19.186506015 3
       4.727742169 0.967763837 17.116761088 2
       4.709022324 0.486507556 19.529321795 2
       4.901221703 2.542302028 20.142909796 3
       4.850857609 3.422273108 15.611437052 4
       4.885496222 2.258327504 21.575930728 3
       4.766343118 0.979274459 21.890372731 5
       4.969508239 3.116075188 22.485230183 5
       4.991595992 5.199727370 15.547092870 3
       5.947028503 5.538252030 15.974485819 2
       4.967780038 5.426242956 14.468147082 2
       4.143207871 5.685107873 16.052054513 2
       4.962588064 2.974730040 24.377227346 1
       4.958785183 1.570022239 26.233101525 1
       3.792997558 3.583752987 26.274004087 1
       6.132220507 3.577621504 26.269902161 1
      -0.004314585 0.002677468 28.053108409 1
       2.495122457 0.000957977 28.033697293 1
       4.978989017 0.006940563 28.020903777 1
       1.245233839 2.167128961 28.035027851 1
       3.687665360 2.135765018 28.065848872 1
       6.267683737 2.131102783 28.057507960 1
       2.478319889 4.323246597 28.045860719 1
       4.976742781 4.372715850 28.079360078 1
       7.474889028 4.319274307 28.036464668 1
       7.464820981 -0.001087623 28.035106705 1
       8.714915236 2.166407839 28.035250597 1
       9.963184484 4.318705654 28.038455400 1
       3.727331908 6.468542595 28.033516717 1
       6.231791750 6.469169854 28.032892911 1
       8.718494488 6.477568088 28.037608308 1
      11.207105276 6.477181571 28.038520458 1
       1.247126365 0.721770448 29.954647276 1
       3.739206179 0.716018983 29.958599235 1
       6.223275128 0.716481973 29.956809008 1
       2.486856753 2.881180748 29.963161387 1
       4.982863888 2.876949846 29.967120673 1
       7.474234075 2.881226345 29.958844108 1
       3.729738875 5.037697285 29.965628943 1
       6.233718914 5.036951359 29.963535198 1
       8.718944716 5.036866732 29.946976231 1
       8.714827344 0.722249110 29.955168330 1
       9.964878640 2.873996234 29.945469762 1
      11.209041732 5.037492056 29.950074822 1
       4.981608710 7.190486946 29.953482661 1
       7.469337642 7.195726605 29.945541878 1
       9.964664443 7.198838579 29.944440918 1
      12.460754282 7.195194614 29.946123390 1
      -0.000000000 1.438581000 31.851977178 1
       2.491695000 1.438581000 31.851977178 1
       4.983392000 1.438581000 31.851977178 1
       1.245848000 3.596453000 31.851977178 1
       3.737544000 3.596453000 31.851977178 1
       6.229240000 3.596453000 31.851977178 1
       2.491695000 5.754325000 31.851977178 1
       4.983392000 5.754325000 31.851977178 1
       7.475087000 5.754325000 31.851977178 1
       7.475100000 1.438581000 31.851977178 1
       8.720948000 3.596453000 31.851977178 1
       9.966795000 5.754325000 31.851977178 1
       3.737550000 7.912207000 31.851977178 1
       6.229245000 7.912207000 31.851977178 1
       8.720942000 7.912207000 31.851977178 1
      11.212650000 7.912207000 31.851977178 1
     0.000000000 0.000000000 33.886438178 1
     2.491695000 0.000000000 33.886438178 1
     4.983392000 0.000000000 33.886438178 1
     1.245848000 2.157872000 33.886438178 1
     3.737544000 2.157872000 33.886438178 1
     6.229240000 2.157872000 33.886438178 1
     2.491695000 4.315744000 33.886438178 1
     4.983392000 4.315744000 33.886438178 1
     7.475087000 4.315744000 33.886438178 1
     7.475100000 0.000000000 33.886438178 1
     8.720948000 2.157872000 33.886438178 1
     9.966795000 4.315744000 33.886438178 1
     3.737550000 6.473626000 33.886438178 1
     6.229245000 6.473626000 33.886438178 1
     8.720942000 6.473626000 33.886438178 1
    11.212650000 6.473626000 33.886438178 1
     1.245848000 0.719290000 35.920899178 1
     3.737544000 0.719290000 35.920899178 1
     6.229240000 0.719290000 35.920899178 1
     2.491695000 2.877163000 35.920899178 1
     4.983392000 2.877163000 35.920899178 1
     7.475087000 2.877163000 35.920899178 1
     3.737544000 5.035034000 35.920899178 1
     6.229240000 5.035034000 35.920899178 1
     8.720935000 5.035034000 35.920899178 1
     8.720948000 0.719290000 35.920899178 1
     9.966795000 2.877163000 35.920899178 1
    11.212644000 5.035034000 35.920899178 1
     4.983398000 7.192917000 35.920899178 1
     7.475094000 7.192917000 35.920899178 1
     9.966790000 7.192917000 35.920899178 1
    12.458498000 7.192917000 35.920899178 1
    -0.000000000 1.438581000 37.955361178 1
     2.491695000 1.438581000 37.955361178 1
     4.983392000 1.438581000 37.955361178 1
     1.245848000 3.596453000 37.955361178 1
     3.737544000 3.596453000 37.955361178 1
     6.229240000 3.596453000 37.955361178 1
     2.491695000 5.754325000 37.955361178 1
     4.983392000 5.754325000 37.955361178 1
     7.475087000 5.754325000 37.955361178 1
     7.475100000 1.438581000 37.955361178 1
     8.720948000 3.596453000 37.955361178 1
     9.966795000 5.754325000 37.955361178 1
     3.737550000 7.912207000 37.955361178 1
     6.229245000 7.912207000 37.955361178 1
     8.720942000 7.912207000 37.955361178 1
    11.212650000 7.912207000 37.955361178 1
%endblock AtomicCoordinatesAndAtomicSpecies

# UNIT CELL
LatticeConstant 1.0 Ang
%block LatticeVectors
    9.96680 0.00000 0.0000000000
    4.98340 8.63150 0.0000000000
    0.00000 0.00000 39.989822178
%endblock LatticeVectors

# K-points

%block kgrid_Monkhorst_Pack
6 0 0 0.0
0 6 0 0.0
0 0 01 0.5
%endblock kgrid_Monkhorst_Pack

# Chemical species

NumberOfSpecies 5
%block ChemicalSpeciesLabel
  1 28 Ni
  2 1 H
  3 6 C
  4 16 S
  5 8 O
%endblock ChemicalSpeciesLabel

# Basis set variables
PAO.BasisType split
PAO.BasisSize DZP
PAO.EnergyShift 50 meV

# Transiesta information
SolutionMethod Transiesta

# General variables
#NeglNonOverlapInt True
#ElectronicTemperature 25 meV
MeshCutoff 200. Ry
xc.functional LDA # Exchange-correlation functional
xc.authors CA
SpinPolarized .true.

%block DM.InitSpin
1 1.
2 0.
3 0.
4 0.
5 0.
%endblock DM.InitSpin

# SCF variables
DM.MixSCF1 T
MaxSCFIterations 1000 # Maximum number of SCF iter
DM.MixH T
DM.MixingWeight 0.001 # New DM amount for next SCF cycle, modify until 0.003
DM.Tolerance 1.d-4 # Tolerance in maximum difference
DM.UseSaveDM true # to use continuation files
DM.NumberPulay 10
##DM.NumberKick 20
##DM.KickMixingWeight 1.000

# 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 .false.
SaveRho .false.
SaveDeltaRho .false.
SaveHS .true.
SaveElectrostaticPotential .false.
SaveTotalPotential .false.
WriteCoorXmol .true.
WriteMDXmol .true.
WriteMDhistory .false.
WriteEigenvalues .true.

# GENGF OPTIONS
TS.UpdateDMCROnly .true. # updates only the DM of the C
TS.ComplexContour.Emin -4.0 Ry
TS.ComplexContour.NPoles 10
TS.ComplexContour.NCircle 29
TS.ComplexContour.NLine 11
TS.MixH .true.

# BIAS OPTIONS
TS.BiasContour.Eta 0.000001 Ry
TS.biasContour.NumPoints 11

# TS OPTIONS
TS.Voltage 0.0 eV

# TBT OPTIONS
TS.TBT.Emin -3 eV
TS.TBT.Emax +3 eV
TS.TBT.NPoints 601
TS.TBT.NEigen 3
TS.TBT.Eta 0.000001 Ry

# LEFT ELECTRODE
TS.HSFileLeft ../elec/Ni_elec.TSHS
TS.NumUsedAtomsLeft 48

# RIGHT ELECTRODE
TS.HSFileRight ../elec/Ni_elec.TSHS
TS.NumUsedAtomsRight 48

%block TBT.k
6 0 0 0.
0 6 0 0.
0 0 1 0.5
%endblock
##-----------------------

Question information

Language:
English Edit question
Status:
Answered
For:
Siesta Edit question
Assignee:
No assignee Edit question
Last query:
2018-07-26
Last reply:
2018-07-29
Nick Papior (nickpapior) said : #1

1) Does it oscillate? You are performing a spin calculation which is very troublesome to converge.
2) What warning, this should not result in a warning. Could you please share an example output
3) This together with 2) should not complain.
4) It is defaulted to .true., try setting it to false (I don't suspect this will change the convergence behaviour however.)
5) Ok.
6) Ok.
7) This flag only influences bias calculations, and if difficulties arise in convergences one can increase this value.
8) Because you are attaching semi-infinite leads, this is very different from a siesta (fully periodic) calculation.

There is no guarantee that transiesta will converge, but you may need a bit more fiddling with parameters. Also, it may be because there are two spin-states that oscillates. Such instances are hard to go by. Sometimes a simple linear mixing may be better in those cases.

Lastly, unless you use a subset of the electrode atoms I would not advice to use these flags: TS.NumUsedAtomsRight. They are error-prone if used incorrectly.

Dongzhe Li (dongzhe) said : #2

Dear Nick,

Thanks for your comments.

1. Even for the siesta part, I am not able to converge to 1e-04, as you can see below, dDmax is almost constant to 0.008 until more than 400 iterations...

   scf: 275 -192579.9351 -192579.9348 -192581.7623 0.00827 -8.2955
   scf: 276 -192579.9326 -192579.9337 -192581.7613 0.00832 -8.2955
   scf: 277 -192579.9341 -192579.9339 -192581.7614 0.00832 -8.2955
   scf: 278 -192579.9341 -192579.9340 -192581.7615 0.00832 -8.2955
   scf: 279 -192579.9342 -192579.9341 -192581.7616 0.00832 -8.2955
   scf: 280 -192579.9351 -192579.9346 -192581.7620 0.00831 -8.2955
   scf: 281 -192579.9340 -192579.9343 -192581.7618 0.00842 -8.2956
   scf: 282 -192579.9366 -192579.9354 -192581.7628 0.00827 -8.2955
   scf: 283 -192579.9327 -192579.9341 -192581.7615 0.00828 -8.2955
   scf: 284 -192579.9357 -192579.9349 -192581.7623 0.00831 -8.2955
   scf: 285 -192579.9376 -192579.9362 -192581.7635 0.00822 -8.2954
   scf: 286 -192579.9414 -192579.9388 -192581.7660 0.00844 -8.2954
   scf: 287 -192581.2867 -192581.2916 -192583.1190 0.84717 -8.2955
   scf: 288 -192581.2963 -192581.2939 -192583.1212 0.84711 -8.2955
   scf: 289 -192579.9374 -192579.9366 -192581.7639 0.00819 -8.2955
   scf: 290 -192579.9363 -192579.9365 -192581.7636 0.00817 -8.2955
   scf: 291 -192579.9344 -192579.9353 -192581.7627 0.00831 -8.2955
   scf: 292 -192579.9317 -192579.9335 -192581.7610 0.00818 -8.2955
   scf: 293 -192579.9348 -192579.9341 -192581.7616 0.00822 -8.2955
   scf: 294 -192579.9350 -192579.9346 -192581.7620 0.00815 -8.2955
   scf: 295 -192586.5100 -192586.5101 -192588.3376 1.49403 -8.2955
   scf: 296 -192586.5113 -192586.5107 -192588.3381 1.49400 -8.2954
   scf: 297 -192579.9376 -192579.9363 -192581.7637 0.00814 -8.2954
   scf: 298 -192579.9328 -192579.9346 -192581.7620 0.00827 -8.2955
   scf: 299 -192579.9342 -192579.9344 -192581.7618 0.00814 -8.2955
   scf: 300 -192579.9384 -192579.9364 -192581.7637 0.00818 -8.2955
   scf: 301 -192579.9389 -192579.9377 -192581.7648 0.00818 -8.2955
   scf: 302 -192579.9212 -192579.9293 -192581.7572 0.00832 -8.2955
   scf: 303 -192579.9400 -192579.9345 -192581.7618 0.00823 -8.2955
   scf: 304 -192579.9260 -192579.9302 -192581.7578 0.00814 -8.2957
   scf: 305 -192579.9320 -192579.9311 -192581.7587 0.00821 -8.2956
   scf: 306 -192579.9315 -192579.9313 -192581.7589 0.00814 -8.2956
   scf: 307 -192579.9317 -192579.9315 -192581.7590 0.00811 -8.2956
   scf: 308 -192579.9301 -192579.9308 -192581.7584 0.00815 -8.2956
   scf: 309 -192579.9310 -192579.9309 -192581.7584 0.00816 -8.2956
   scf: 310 -192579.9333 -192579.9321 -192581.7596 0.00810 -8.2956
   scf: 311 -192579.9300 -192579.9311 -192581.7586 0.00814 -8.2956
   scf: 312 -192579.9312 -192579.9311 -192581.7586 0.00809 -8.2956
   scf: 313 -192579.9345 -192579.9328 -192581.7602 0.00812 -8.2956
   scf: 314 -192579.9336 -192579.9332 -192581.7606 0.00814 -8.2956
   scf: 315 -192579.9332 -192579.9332 -192581.7605 0.00813 -8.2956
   scf: 316 -192579.9296 -192579.9314 -192581.7589 0.00812 -8.2956
   scf: 317 -192579.9318 -192579.9316 -192581.7591 0.00812 -8.2957
   scf: 318 -192579.9330 -192579.9323 -192581.7598 0.00814 -8.2956
   scf: 319 -192579.9313 -192579.9318 -192581.7593 0.00811 -8.2957
   scf: 320 -192579.9323 -192579.9321 -192581.7595 0.00810 -8.2957
   scf: 321 -192579.9315 -192579.9318 -192581.7593 0.00810 -8.2957
   scf: 322 -192579.9320 -192579.9319 -192581.7594 0.00809 -8.2957
   scf: 323 -192579.9320 -192579.9319 -192581.7594 0.00810 -8.2957
   scf: 324 -192579.9320 -192579.9320 -192581.7594 0.00813 -8.2957
   scf: 325 -192579.9303 -192579.9311 -192581.7586 0.00815 -8.2957
   scf: 326 -192579.9321 -192579.9316 -192581.7591 0.00806 -8.2957
   scf: 327 -192579.9328 -192579.9322 -192581.7596 0.00811 -8.2957
   scf: 328 -192579.9371 -192579.9346 -192581.7618 0.00810 -8.2956
   scf: 329 -192579.9316 -192579.9331 -192581.7605 0.00813 -8.2957
   scf: 330 -192579.9404 -192579.9367 -192581.7638 0.00805 -8.2956
   scf: 331 -192579.9365 -192579.9366 -192581.7637 0.00803 -8.2957
   scf: 332 -192579.9368 -192579.9367 -192581.7638 0.00803 -8.2957
   scf: 333 -192579.9357 -192579.9362 -192581.7633 0.00804 -8.2957
   scf: 334 -192579.9364 -192579.9363 -192581.7634 0.00807 -8.2957
   scf: 335 -192579.9267 -192579.9315 -192581.7589 0.00807 -8.2957
   scf: 336 -192579.9308 -192579.9311 -192581.7585 0.00802 -8.2958
   scf: 337 -192579.9337 -192579.9324 -192581.7597 0.00817 -8.2957
   scf: 338 -192581.3702 -192581.3699 -192583.1971 0.38870 -8.2958
   scf: 339 -192581.3700 -192581.3700 -192583.1971 0.38867 -8.2958
   scf: 340 -192579.9324 -192579.9325 -192581.7597 0.00805 -8.2958
   scf: 341 -192579.9342 -192579.9334 -192581.7606 0.00810 -8.2957
   scf: 342 -192579.9331 -192579.9333 -192581.7605 0.00810 -8.2957
   scf: 343 -192579.9325 -192579.9329 -192581.7602 0.00812 -8.2957
   scf: 344 -192579.9361 -192579.9345 -192581.7617 0.00810 -8.2956
   scf: 345 -192579.9258 -192579.9302 -192581.7576 0.00819 -8.2958
   scf: 346 -192579.9284 -192579.9293 -192581.7568 0.00820 -8.2958
   scf: 347 -192579.9352 -192579.9322 -192581.7595 0.00814 -8.2958
   scf: 348 -192579.9299 -192579.9311 -192581.7584 0.00814 -8.2958
   scf: 349 -192579.9281 -192579.9296 -192581.7570 0.00810 -8.2958
   scf: 350 -192579.9299 -192579.9297 -192581.7572 0.00821 -8.2958
   scf: 351 -192579.9331 -192579.9314 -192581.7587 0.00816 -8.2958
   scf: 352 -192579.9259 -192579.9286 -192581.7561 0.00814 -8.2958
   scf: 353 -192579.9279 -192579.9283 -192581.7557 0.00813 -8.2959
   scf: 354 -192579.9318 -192579.9300 -192581.7575 0.00828 -8.2957
   scf: 355 -192579.9272 -192579.9286 -192581.7562 0.00807 -8.2958
   scf: 356 -192579.9304 -192579.9295 -192581.7570 0.00798 -8.2956
   scf: 357 -192579.9298 -192579.9296 -192581.7572 0.00798 -8.2956
   scf: 358 -192579.9283 -192579.9290 -192581.7565 0.00800 -8.2957
   scf: 359 -192579.9289 -192579.9290 -192581.7565 0.00800 -8.2957
   scf: 360 -192579.9305 -192579.9298 -192581.7572 0.00798 -8.2957
   scf: 361 -192579.9322 -192579.9310 -192581.7584 0.00798 -8.2957
   scf: 362 -192579.9300 -192579.9305 -192581.7579 0.00796 -8.2957
   scf: 363 -192579.9304 -192579.9304 -192581.7579 0.00797 -8.2957
   scf: 364 -192579.9239 -192579.9271 -192581.7547 0.00793 -8.2956
   scf: 365 -192579.9273 -192579.9272 -192581.7548 0.00795 -8.2956
   scf: 366 -192579.9260 -192579.9266 -192581.7543 0.00798 -8.2957
   scf: 367 -192579.9272 -192579.9269 -192581.7547 0.00815 -8.2955
   scf: 368 -192579.9258 -192579.9263 -192581.7542 0.00813 -8.2955
   scf: 369 -192579.9279 -192579.9271 -192581.7548 0.00812 -8.2955
   scf: 370 -192579.9274 -192579.9272 -192581.7549 0.00810 -8.2955
   scf: 371 -192579.9282 -192579.9277 -192581.7554 0.00813 -8.2955
   scf: 372 -192579.9268 -192579.9273 -192581.7549 0.00807 -8.2956
   scf: 373 -192579.9300 -192579.9286 -192581.7562 0.00802 -8.2956
   scf: 374 -192579.9217 -192579.9251 -192581.7529 0.00804 -8.2956
   scf: 375 -192579.9338 -192579.9294 -192581.7569 0.00814 -8.2955
   scf: 376 -192579.9211 -192579.9253 -192581.7530 0.00802 -8.2958
   scf: 377 -192579.9258 -192579.9255 -192581.7532 0.00804 -8.2958
   scf: 378 -192579.9266 -192579.9260 -192581.7538 0.00817 -8.2957
   scf: 379 -192579.9287 -192579.9274 -192581.7552 0.00819 -8.2955
   scf: 380 -192579.9213 -192579.9243 -192581.7522 0.00805 -8.2957
   scf: 381 -192579.9336 -192579.9289 -192581.7563 0.00809 -8.2956
   scf: 382 -192579.9320 -192579.9304 -192581.7579 0.00806 -8.2955
   scf: 383 -192579.9157 -192579.9230 -192581.7509 0.00817 -8.2957
   scf: 384 -192579.9279 -192579.9254 -192581.7532 0.00800 -8.2957
   scf: 385 -192579.9346 -192579.9300 -192581.7575 0.00815 -8.2955
   scf: 386 -192579.9272 -192579.9286 -192581.7561 0.00796 -8.2956
   scf: 387 -192579.9116 -192579.9200 -192581.7481 0.00795 -8.2958
   scf: 388 -192579.9448 -192579.9322 -192581.7595 0.00817 -8.2955
   scf: 389 -192579.9207 -192579.9264 -192581.7540 0.00809 -8.2955
   scf: 390 -192579.9078 -192579.9168 -192581.7449 0.00788 -8.2957
   scf: 391 -192579.9111 -192579.9139 -192581.7421 0.00783 -8.2959
   scf: 392 -192579.9116 -192579.9128 -192581.7411 0.00790 -8.2959
   scf: 393 -192579.9172 -192579.9150 -192581.7433 0.00791 -8.2957
   scf: 394 -192579.9127 -192579.9138 -192581.7422 0.00789 -8.2958
   scf: 395 -192579.9159 -192579.9149 -192581.7432 0.00786 -8.2958
   scf: 396 -192579.9129 -192579.9138 -192581.7422 0.00787 -8.2958
   scf: 397 -192579.9216 -192579.9176 -192581.7460 0.00799 -8.2955
   scf: 398 -192579.9133 -192579.9154 -192581.7437 0.00793 -8.2957
   scf: 399 -192579.9128 -192579.9141 -192581.7426 0.00794 -8.2956
   scf: 400 -192579.9211 -192579.9175 -192581.7458 0.00799 -8.2956
   scf: 401 -192579.9181 -192579.9178 -192581.7461 0.00798 -8.2956
   scf: 402 -192579.9171 -192579.9175 -192581.7458 0.00804 -8.2955
   scf: 403 -192579.9205 -192579.9190 -192581.7473 0.00809 -8.2956
   scf: 404 -192579.9203 -192579.9196 -192581.7477 0.00809 -8.2955
   scf: 405 -192579.9197 -192579.9197 -192581.7478 0.00811 -8.2955
   scf: 406 -192579.9160 -192579.9178 -192581.7460 0.00798 -8.2956
   scf: 407 -192579.9183 -192579.9180 -192581.7462 0.00802 -8.2955
   scf: 408 -192579.9224 -192579.9202 -192581.7483 0.00804 -8.2955
   scf: 409 -192579.9292 -192579.9245 -192581.7524 0.00818 -8.2953
   scf: 410 -192579.9138 -192579.9189 -192581.7469 0.00801 -8.2957
   scf: 411 -192579.9135 -192579.9162 -192581.7445 0.00804 -8.2956
   scf: 412 -192579.9242 -192579.9202 -192581.7483 0.00804 -8.2954
   scf: 413 -192579.9180 -192579.9190 -192581.7471 0.00794 -8.2955
   scf: 414 -192579.9269 -192579.9229 -192581.7508 0.00800 -8.2955
   scf: 415 -192579.9303 -192579.9266 -192581.7542 0.00793 -8.2955
   scf: 416 -192579.9083 -192579.9157 -192581.7438 1.96627 -8.2954
   scf: 417 -192579.9158 -192579.9157 -192581.7439 1.96625 -8.2955
   scf: 418 -192579.9194 -192579.9191 -192581.7471 0.00791 -8.2955
   scf: 419 -192579.9268 -192579.9230 -192581.7508 0.00796 -8.2954
   scf: 420 -192579.9265 -192579.9247 -192581.7523 0.00796 -8.2954
   scf: 421 -192579.9257 -192579.9252 -192581.7526 0.00794 -8.2955
   scf: 422 -192579.9241 -192579.9246 -192581.7521 0.00797 -8.2955
   scf: 423 -192579.9261 -192579.9253 -192581.7529 0.00796 -8.2953
   scf: 424 -192579.9193 -192579.9223 -192581.7500 0.00797 -8.2955
   scf: 425 -192579.9239 -192579.9231 -192581.7508 0.00799 -8.2954
   scf: 426 -192579.9201 -192579.9216 -192581.7494 0.00797 -8.2955
   scf: 427 -192579.9237 -192579.9226 -192581.7503 0.00798 -8.2955
   scf: 428 -192579.9284 -192579.9255 -192581.7531 0.00800 -8.2955
   scf: 429 -192578.0419 -192578.0446 -192579.8723 1.95022 -8.2955
   scf: 430 -192578.0446 -192578.0446 -192579.8723 1.95022 -8.2955
   scf: 431 -192597.2621 -192597.2623 -192599.0900 0.40226 -8.2955
   scf: 432 -192597.2621 -192597.2622 -192599.0899 0.40226 -8.2955
   scf: 433 -192579.9216 -192579.9217 -192581.7495 0.00802 -8.2955
   scf: 434 -192579.9263 -192579.9239 -192581.7512 0.00790 -8.2956
   scf: 435 -192579.9246 -192579.9243 -192581.7516 0.00789 -8.2955
   scf: 436 -192579.9186 -192579.9213 -192581.7490 0.00804 -8.2954
   scf: 437 -192579.9220 -192579.9217 -192581.7493 0.00804 -8.2954
   scf: 438 -192579.9224 -192579.9220 -192581.7497 0.00803 -8.2954
   scf: 439 -192579.9228 -192579.9224 -192581.7500 0.00802 -8.2954
   scf: 440 -192618.0529 -192618.0526 -192619.8802 0.39812 -8.2954
   scf: 441 -192618.1506 -192618.1023 -192619.9298 0.38595 -8.2954
   scf: 442 -192579.9265 -192579.9248 -192581.7522 0.00792 -8.2955
   scf: 443 -192579.9194 -192579.9211 -192581.7487 0.00809 -8.2942
   scf: 444 -192579.9204 -192579.9207 -192581.7484 0.00811 -8.2942
   scf: 445 -192579.9289 -192579.9244 -192581.7517 0.00831 -8.2932
   scf: 446 -192579.9266 -192579.9255 -192581.7528 0.00828 -8.2932
   scf: 447 -192579.9253 -192579.9254 -192581.7527 0.00830 -8.2932
   scf: 448 -192579.9292 -192579.9273 -192581.7545 0.00833 -8.2930
   scf: 449 -192579.9292 -192579.9282 -192581.7554 0.00834 -8.2929
   scf: 450 -192579.9290 -192579.9286 -192581.7556 0.00828 -8.2928
   scf: 451 -192579.9344 -192579.9315 -192581.7583 0.00825 -8.2928
   scf: 452 -192579.9289 -192579.9302 -192581.7570 0.00825 -8.2929
   scf: 453 -192579.9261 -192579.9282 -192581.7551 0.00827 -8.2928
   scf: 454 -192579.9292 -192579.9287 -192581.7556 0.00824 -8.2929
   scf: 455 -192579.9287 -192579.9287 -192581.7556 0.00823 -8.2929
   scf: 456 -192579.9286 -192579.9286 -192581.7556 0.00823 -8.2930
   scf: 457 -192579.9298 -192579.9291 -192581.7561 0.00831 -8.2927
   scf: 458 -192579.9292 -192579.9292 -192581.7561 0.00829 -8.2927
   scf: 459 -192579.9298 -192579.9295 -192581.7564 0.00829 -8.2927
   scf: 460 -192579.9294 -192579.9295 -192581.7564 0.00828 -8.2927
   scf: 461 -192585.6103 -192585.6086 -192587.4355 1.96811 -8.2927
   scf: 462 -192585.6179 -192585.6132 -192587.4402 1.96804 -8.2928
   scf: 463 -192579.9296 -192579.9293 -192581.7562 0.00825 -8.2927
   scf: 464 -192579.9302 -192579.9298 -192581.7566 0.00829 -8.2927
   scf: 465 -192579.9275 -192579.9286 -192581.7556 0.00827 -8.2927
   scf: 466 -192579.9313 -192579.9299 -192581.7568 0.00828 -8.2928
   scf: 467 -192579.9294 -192579.9296 -192581.7565 0.00828 -8.2928
   scf: 468 -192579.9243 -192579.9270 -192581.7541 0.00814 -8.2930
   scf: 469 -192579.9266 -192579.9268 -192581.7539 0.00813 -8.2930
   scf: 470 -192579.9226 -192579.9247 -192581.7520 0.00809 -8.2932
   scf: 471 -192579.9221 -192579.9234 -192581.7508 0.00815 -8.2932
   scf: 472 -192579.9232 -192579.9232 -192581.7507 0.00831 -8.2930
   scf: 473 -192580.7374 -192580.7398 -192582.5674 1.95524 -8.2928
   scf: 474 -192580.7385 -192580.7391 -192582.5667 1.95526 -8.2928
   scf: 475 -192581.2057 -192581.2023 -192583.0295 1.95195 -8.2928
   scf: 476 -192581.2027 -192581.2025 -192583.0297 1.95195 -8.2928
   scf: 477 -192581.2065 -192581.2045 -192583.0316 1.95196 -8.2927
   scf: 478 -192581.1990 -192581.2017 -192583.0290 1.95191 -8.2928
   scf: 479 -192581.1938 -192581.1977 -192583.0253 1.95202 -8.2930
   scf: 480 -192581.2019 -192581.1998 -192583.0272 1.95201 -8.2930
   scf: 481 -192600.6396 -192591.0609 -192592.8881 1.87647 -8.2929
   scf: 482 -192571.0138 -192581.1790 -192583.0062 1.95242 -8.2931
   scf: 483 -192581.2167 -192581.1977 -192583.0249 1.95220 -8.2928
   scf: 484 -192581.1624 -192581.1800 -192583.0076 1.95219 -8.2928
   scf: 485 -192675.0341 -192649.2126 -192650.9122 2.06827 -8.3118
   scf: 486 -192642.7341 -192646.2090 -192647.8852 2.22139 -8.3060
   scf: 487 -192634.0691 -192642.0780 -192643.7579 2.45136 -8.2977
   scf: 488 -192639.0742 -192640.8117 -192642.5282 2.53074 -8.3118
   scf: 489 -192641.2719 -192640.8701 -192642.5995 2.49113 -8.3040
   scf: 490 -192643.5969 -192642.1331 -192643.8912 2.43581 -8.3069
   scf: 491 -192643.7399 -192643.1267 -192644.8434 2.11566 -8.2773
   scf: 492 -192648.8831 -192642.8789 -192644.5401 2.17624 -8.3466
   scf: 493 -192645.9035 -192644.4305 -192646.1136 2.07743 -8.2931
   scf: 494 -192589.6530 -192629.0755 -192630.6584 2.51887 -8.3419
   scf: 495 -192419.5126 -192540.0906 -192541.5149 4.49348 -8.3808
   scf: 496 -192513.0551 -192534.5928 -192535.8643 4.82052 -8.3490
   scf: 497 -192639.6105 -192607.5506 -192609.0074 2.66699 -8.2232
   scf: 498 -192617.3503 -192614.9702 -192616.4017 2.68943 -8.2537
   scf: 499 -192672.7833 -192650.4057 -192651.8955 1.58340 -8.2567
   scf: 500 -192663.9943 -192659.1550 -192660.6837 1.10035 -8.2491
   scf: 501 -192658.7581 -192658.9892 -192660.5295 1.05315 -8.2441
   scf: 502 -192621.9925 -192645.7767 -192647.1845 1.84430 -8.3363
   scf: 503 -192672.4798 -192663.0617 -192664.5765 1.07734 -8.3191
   scf: 504 -192671.8961 -192669.8910 -192671.4129 0.88886 -8.2743
   scf: 505 -192607.3489 -192647.9800 -192649.4616 2.06981 -8.2447

2. If I use 3 layers of ABC stacking for my electrodes calculations, then for the scattering calculations, I got a warning. I used 12 k-points in the z direction for the electrode calculations. If I use 6 layers of ABCABC, and use only 3 layers by using TS.NumUsedAtomsleft (Right), then no warning. However, it is not related anyway with convergence.

----------------------------------------------------------------------------------------------------------
 WARNING: Connections across 2 unit cells or more in the transport direction.
 WARNING: This is inadvisable.
 WARNING: Please increase the electrode size in the transport direction.
 WARNING: Will proceed without further notice.
 WARNING: Connections across 2 unit cells or more in the transport direction.
 WARNING: This is inadvisable.
 WARNING: Please increase the electrode size in the transport direction.
 WARNING: Will proceed without further notice.

3. If I use non-magnetic lead such as Au or Ag, I do not have any convergence problems. I even tried to make the system simpler, remove the molecule and create the Ni atomic contact, but even with this simple system, the siesta part does not converge. If I use Plane-wave code (quantum espresso), super easy to converge (less than 30 iterations).

#------------------------------------------------------
# FDF for Ni111 scat
#
SystemName Ni111 # Descriptive name of the system
SystemLabel Ni111 # Short name for naming files

# Atomic coordinates
NumberOfAtoms 121
AtomicCoordinatesFormat Ang
%block AtomicCoordinatesAndAtomicSpecies
    0.000000000 0.000000000 0.000000000 1
    2.492000000 0.000000000 0.000000000 1
    4.984000000 0.000000000 0.000000000 1
    7.476000000 0.000000000 0.000000000 1
    1.246000000 -2.158140000 0.000000000 1
    3.738000000 -2.158140000 0.000000000 1
    6.230000000 -2.158140000 0.000000000 1
    8.722000000 -2.158140000 0.000000000 1
    2.492000000 -4.316270000 0.000000000 1
    4.984000000 -4.316270000 0.000000000 1
    7.476000000 -4.316270000 0.000000000 1
    9.968000000 -4.316270000 0.000000000 1
    3.738000000 -6.474410000 0.000000000 1
    6.230000000 -6.474410000 0.000000000 1
    8.722000000 -6.474410000 0.000000000 1
   11.214000000 -6.474410000 0.000000000 1
   -0.000000000 1.438760000 2.034670000 1
    2.492000000 1.438760000 2.034670000 1
    4.984000000 1.438760000 2.034670000 1
    7.476000000 1.438760000 2.034670000 1
    1.246000000 -0.719378000 2.034670000 1
    3.738000000 -0.719378000 2.034670000 1
    6.230000000 -0.719378000 2.034670000 1
    8.722000000 -0.719378000 2.034670000 1
    2.492000000 -2.877510000 2.034670000 1
    4.984000000 -2.877510000 2.034670000 1
    7.476000000 -2.877510000 2.034670000 1
    9.968000000 -2.877510000 2.034670000 1
    3.738000000 -5.035650000 2.034670000 1
    6.230000000 -5.035650000 2.034670000 1
    8.722000000 -5.035650000 2.034670000 1
   11.214000000 -5.035650000 2.034670000 1
   -1.248825172 0.719766193 4.110968422 1
    1.245291600 0.716965517 4.104095704 1
    3.739428955 0.719667556 4.111166240 1
    6.228991905 0.719055824 4.111011412 1
   -0.001597089 -1.439860938 4.106721432 1
    2.492533252 -1.439649828 4.107753319 1
    4.984073415 -1.439298528 4.103941653 1
    7.474667419 -1.439438050 4.103242512 1
    1.245464251 -3.598805697 4.111234934 1
    3.737405613 -3.597474697 4.102014391 1
    6.229144339 -3.597163059 4.075271754 1
    8.721052469 -3.597310485 4.101497985 1
    2.491333372 -5.754607645 4.110884362 1
    4.982897036 -5.756455643 4.099486009 1
    7.475343193 -5.756728746 4.099799620 1
    9.966235183 -5.754305463 4.111900729 1
    0.000236100 -0.002832195 6.164086078 1
    2.490295651 -0.002311078 6.164434751 1
    4.981255848 0.002500666 6.164215074 1
    7.478679390 0.002275412 6.163559933 1
    1.245336730 -2.155834943 6.164422048 1
    3.723947660 -2.151031533 6.151212399 1
    6.229579914 -2.125964092 6.138132210 1
    8.736669763 -2.150331945 6.148356255 1
    2.487405139 -4.314786955 6.163594011 1
    4.953093301 -4.338519668 6.130572661 1
    7.507063529 -4.338996159 6.129442278 1
    9.971456602 -4.314527767 6.164495454 1
    3.736020616 -6.480392300 6.163608745 1
    6.229333791 -6.500722035 6.139210763 1
    8.722804579 -6.479947083 6.164934938 1
   11.213703852 -6.474612861 6.156600152 1
    5.036761774 -2.928655154 8.029855291 1
    7.428743201 -2.926930292 8.026460019 1
    6.230950748 -5.007408809 8.014728052 1
    6.243504466 -3.655649910 9.990258435 1
      6.276264310 -3.638129818 12.097267205 1
     -0.000000000 1.438760000 22.141900000 1
      2.492000000 1.438760000 22.141900000 1
      4.984000000 1.438760000 22.141900000 1
      7.476000000 1.438760000 22.141900000 1
      1.246000000 -0.719380000 22.141900000 1
      3.738000000 -0.719380000 22.141900000 1
      6.230000000 -0.719380000 22.141900000 1
      8.722000000 -0.719380000 22.141900000 1
      2.492000000 -2.877510000 22.141900000 1
      4.984000000 -2.877510000 22.141900000 1
      7.476000000 -2.877510000 22.141900000 1
      9.968000000 -2.877510000 22.141900000 1
      3.738000000 -5.035650000 22.141900000 1
      6.230000000 -5.035650000 22.141900000 1
      8.722000000 -5.035650000 22.141900000 1
     11.214000000 -5.035650000 22.141900000 1
     -1.247591251 0.719253524 20.066306890 1
      1.246695693 0.716751190 20.072521184 1
      3.740338445 0.718510244 20.066534324 1
      6.230398270 0.718382426 20.066489708 1
      0.002019465 -1.439600947 20.072552132 1
      2.494042233 -1.440919865 20.069534414 1
      4.985614208 -1.440061943 20.074754545 1
      7.476369660 -1.439467557 20.077120414 1
      1.247386326 -3.600456905 20.066490114 1
      3.739577958 -3.598912918 20.074528514 1
      6.230750643 -3.598335040 20.102492000 1
      8.723609357 -3.598564013 20.078282055 1
      2.493361199 -5.755630130 20.065767306 1
      4.984305669 -5.756915341 20.076024450 1
      7.476861930 -5.757318462 20.077611791 1
      9.967589892 -5.755620159 20.065671502 1
      0.002814276 -0.002981154 18.013299837 1
      2.491715959 -0.003590277 18.012816604 1
      4.981591828 0.001236230 18.013765191 1
      7.480172783 0.001684207 18.014100838 1
      1.248783299 -2.157432608 18.013706385 1
      3.726307824 -2.152132744 18.026039274 1
      6.234075865 -2.124293305 18.045207821 1
      8.743094727 -2.148111432 18.036206743 1
      2.489586680 -4.317073364 18.012978473 1
      4.956137506 -4.338165184 18.044634846 1
      7.511802400 -4.336801088 18.050882143 1
      9.974059828 -4.316352727 18.013744527 1
      3.737652807 -6.481070580 18.012784325 1
      6.230913469 -6.499133680 18.035256565 1
      8.723277778 -6.481269415 18.013190093 1
     11.215082211 -6.476239900 18.020964208 1
      5.053741492 -2.917176346 16.149595882 1
      7.447326077 -2.911446625 16.161719253 1
      6.247494143 -4.996215364 16.165051584 1
      6.276264310 -3.638129818 14.197267205 1
%endblock AtomicCoordinatesAndAtomicSpecies

# UNIT CELL
LatticeConstant 1.0 Ang
%block LatticeVectors
    9.96680 0.00000 0.0000000000
   -4.98340 8.63150 0.0000000000
    0.00000 0.00000 24.176570000
%endblock LatticeVectors

# K-points

%block kgrid_Monkhorst_Pack
4 0 0 0.0
0 4 0 0.0
0 0 01 0.5
%endblock kgrid_Monkhorst_Pack

# Chemical species

NumberOfSpecies 1
%block ChemicalSpeciesLabel
  1 28 Ni
%endblock ChemicalSpeciesLabel

# Basis set variables
PAO.BasisType split
PAO.BasisSize DZP
PAO.EnergyShift 50 meV

# Transiesta information
SolutionMethod diagon

# General variables
#NeglNonOverlapInt True
##ElectronicTemperature 25 meV
MeshCutoff 200. Ry
xc.functional LDA # Exchange-correlation functional
xc.authors CA
SpinPolarized .true.

%block DM.InitSpin
1 1.0
%endblock DM.InitSpin

# SCF variables
DM.MixSCF1 T
MaxSCFIterations 1000 # Maximum number of SCF iter
DM.MixingWeight 0.003 # New DM amount for next SCF cycle, modify until 0.003
DM.Tolerance 1.d-4 # Tolerance in maximum difference
DM.UseSaveDM true # to use continuation files
DM.NumberPulay 8
##DM.NumberKick 20
##DM.KickMixingWeight 1.000

# 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 .false.
SaveRho .false.
SaveDeltaRho .false.
SaveHS .true.
SaveElectrostaticPotential .false.
SaveTotalPotential .false.
WriteCoorXmol .true.
WriteMDXmol .true.
WriteMDhistory .false.
WriteEigenvalues .true.
-----------------------------------------------------

4. I used the pseudopotentials from:
https://departments.icmab.es/leem/siesta/Databases/Pseudopotentials/periodictable-intro.html

Should I play with basis parameters or pseudopotentials? Any comments will be appreciated.
Best regards,
Dongzhe

Univ. Konstanz, Germany

Nick Papior (nickpapior) said : #3

1) This just shows how difficult a system it is. You could try and restart the calculation with linear mixing. Sometimes a linear mixing helps close to convergence.

2) I would suggest you to use at least 50 k-points in your electrode transport direction. Also the reason why you don't get a warning for ABCABC is a mistake. You should probably use ABCABC and then use CABC for the left electrode and ABCA for the right electrode (i.e. you should introduce the B layer as buffer region. However, this has no influence on the convergence in the Siesta part.

3) Why is this geometry different than your initial geometry? This one is not suited for transiesta.

4) Probably yes, you should play with the pseudo's. This is beyond my expertise so wont be able to help you.

Dongzhe Li (dongzhe) said : #4

Dear Nick,

Thanks a lot for your answer.

I found my problem, it was related to the initial spin moment, I mis-understood the "DM.InitSpin" flag, I thought that 1,2,3,... are the species but they are actually the number of atoms. As a consequence, I performed the spin-polarized calculations starting from almost zero-polarization, very far away from the final numerical solution... I re-did the calculation with reasonable starting magnetism, the calculation converges quickly (less than 100 and 50 iterations for siesta and transiesta parts, respectively).

I still cannot understand your comment about the Warning:
----------------------------------------------------------------------------------------------------------
 WARNING: Connections across 2 unit cells or more in the transport direction.
 WARNING: This is inadvisable.
 WARNING: Please increase the electrode size in the transport direction.
 WARNING: Will proceed without further notice.
-----------------------------------------------------------------------------------------------------------

In the manual 3.8 at page 112:
"Here, it will almost always give this warning. However,
one can overcome this by making the electrode to an ABCABC stacking of 6 atoms, and use
TS.NumUsedAtomsLeft/Right equal to 4, or 3 (this will still have a little error, however,
the surface Green’s function has been calculated using the full ABCABC stacking which holds
more information)"

1) I used ABCABC 6 layers for my bulk electrode calculations and use only 3 layers using the flag "TS.NumUsedAtomsLeft/Right", it is not correct??? Anyway in this case, there is no warning.

2) Why you suggest to use at least 50 k-points in z??? If I compare 12 k-poins and 50 k-points for the Mulliken charges, almost no difference actually.

3) One more question about the spin moment of Ni for bulk electrodes, I found the spin moment of about 0.72uB from siesta, but it is about 0.65 uB from Quantum-Espresso (QE). If I try bcc-Fe bulk, it is about 2.6uB and 2.2uB by siesta and QE, respectively. It seems like the siesta underestimates the spin-moment, do you have a comment on this?

Best regards,
Dongzhe

Univ. Konstanz, Germany

Nick Papior (nickpapior) said : #5

1) Like I wrote, the fact that you don't get a warning for ABCABC and num-used atoms 3 is a mistake. You should probably use 4 layers as a check. The thing you quote explicitly states this.

2) Because the electrode calculation is a one-time calculation and you want this to represent a truly bulk part. Generally we recommend 100 points, but 50 would probably suffice. I think 12 is a little too low.

3) Spin-moments etc. are sensitive to basis-sets.

Can you help with this problem?

Provide an answer of your own, or ask Dongzhe Li for more information if necessary.

To post a message you must log in.