basal plane electrode problem in the scattering region calculation

Asked by nayana devaraj on 2018-05-03

Hellow,
  I encounter the following error in the transiesta calculation for the scattering region.

ts: Using electrode: Left for Hartree correction
ts: Number of points used: 0
ts: Basal plane of electrode Left might be outside of unit cell.
ts: Please move structure so this point is inside unit cell (Ang):
ts: Point (Ang): 1.40108 0.29352 -0.15196
ts: You can use %block AtomicCoordinatesOrigin
ts: to easily move the entire structure.

The partitioning of the basal plane went wrong. No points are encapsulated.
Stopping Program from Node: 0

When i use something like
%block AtomicCoordinatesOrigin
0 0 -0.3000
%endblock AtomicCoordinatesOrigin
the error repeats with the same coordinates.

The unit cell and atomic positions I have used in the fdf file is the following one.
# UNIT CELL
LatticeConstant 1.00 Ang
%block LatticeVectors
        6.4800944328 0.0000000000 0.0000000000
        3.2397546226 5.6116284136 0.0000000000
        0.0671003143 0.1085815314 21.0425682725

%endblock LatticeVectors
# Atomic coordinates
NumberOfAtoms 68
AtomicCoordinatesFormat Ang
%block AtomicCoordinatesAndAtomicSpecies
     5.112454135 3.515927420 0.848693033 1
     1.409485878 0.307116574 0.846854638 1
     2.803578198 4.315530649 0.846902378 1
     6.967535515 5.115720693 0.848833272 1
     5.575636034 1.106961286 0.850097306 1
     3.259137901 1.909268718 0.851260373 1
     7.429142444 2.710101022 0.852619493 1
     2.798608710 0.566608299 2.823432118 1
     4.652972604 2.175442883 2.823783931 1
     2.333388624 2.980868539 2.824679768 1
     8.349258565 5.379164071 2.828240854 1
     4.186274271 4.577332776 2.829493521 1
     6.968212779 1.371824558 2.830029393 1
     6.500643842 3.775944610 2.831124340 1
     3.259232369 1.902967217 4.785325017 1
     5.582851351 1.093165878 4.817304242 1
     1.399543888 0.293162930 4.817446911 1
     2.794712396 4.314588549 4.816853344 1
     5.103331239 3.505233682 4.821580555 1
     6.969029798 5.117102142 4.822982476 1
     7.430755679 2.693319364 4.824651549 1
     4.665139732 2.139566083 6.757980818 1
     2.763758897 0.563696591 6.758577207 1
     2.350547580 2.996575167 6.765856158 1
     6.498558656 3.772204153 6.791396769 1
     4.170876697 4.550036557 6.812115474 1
     8.340410956 5.393832616 6.822402708 1
     6.986779687 1.364950895 6.824110975 1
     4.905726514 1.066903979 8.710430583 3
     1.712523840 0.930489981 8.711768851 3
     3.196033732 3.782392606 8.717059214 3
     6.509410837 3.787087993 8.895438997 3
     4.862708882 4.711614299 10.343254912 2
     8.128840767 4.776196708 10.346335940 2
     6.524284754 1.898615338 10.349514798 2
     3.276209351 1.927074099 10.377408353 2
     1.655662536 0.937035903 11.879056027 3
     3.227403013 3.831133361 11.898469073 3
     4.921765641 1.014842586 11.925075156 3
     6.524202114 3.780392881 12.075234656 3
     1.481584112 0.462207932 13.951835825 1
     2.901417224 4.395329414 13.956262019 1
     5.610682132 1.191346677 13.960461197 1
     5.208297760 3.633955046 13.973266935 1
     7.032151259 5.206461773 13.979356245 1
     7.473847042 2.837689380 13.997251667 1
     3.330282009 2.024580752 14.018300236 1
     8.427954634 5.477724319 15.938484810 1
     4.268049234 4.707169103 15.937781184 1
     7.015885128 1.487999506 15.940683484 1
     2.878094866 0.696398490 15.949954787 1
     4.713494650 2.292793692 15.950594447 1
     2.410778793 3.078725654 15.953969593 1
     6.567099203 3.898600797 15.957002333 1
     1.479490501 0.423885365 17.935111233 1
     7.494391816 2.824955823 17.935557741 1
     5.181475679 3.626689345 17.936293977 1
     2.867838104 4.427896914 17.936936145 1
     5.644764529 1.220746095 17.937720042 1
     7.033487549 5.228421605 17.938575430 1
     3.333497084 2.022260181 17.944027588 1
     4.259682848 4.692103264 19.911552001 1
     8.420995633 5.495657101 19.915220638 1
     2.404430689 3.090242127 19.915991993 1
     7.035996482 1.487778144 19.916828567 1
     2.869522178 0.684433088 19.917872091 1
     4.720483408 2.288607502 19.918313581 1
     6.571430737 3.889509256 19.923804621 1

%endblock AtomicCoordinatesAndAtomicSpecies

How to solve this problem?

Thanks

Question information

Language:
English Edit question
Status:
Answered
For:
Siesta Edit question
Assignee:
No assignee Edit question
Last query:
2018-05-03
Last reply:
2018-05-06
Nick Papior (nickpapior) said : #1

Could you please add all required information to run the calculation.

nayana devaraj (devarajnayana) said : #2

Following is my fdf file.

SystemName Co_MoS2_Co
SystemLabel SR
==================================================
==================================================
# SPECIES AND BASIS
# Number of species
NumberOfSpecies 3
%block ChemicalSpeciesLabel
 1 27 Co
   2 42 Mo
   3 16 S
%endblock ChemicalSpeciesLabel
PAO.BasisSize DZP
PAO.EnergyShift 50 MeV
PAO.SplitNorm 0.15392
==================================================
==================================================
# K-points
%block kgrid_Monkhorst_Pack1
1 0 0 0.0
0 1 0 0.0
0 0 1 0.0
%endblock kgrid_Monkhorst_Pack
==================================================
==================================================
# UNIT CELL
LatticeConstant 1.00 Ang
%block LatticeVectors
        6.4800944328 0.0000000000 0.0000000000
        3.2397546226 5.6116284136 0.0000000000
        0.0671003143 0.1085815314 21.0425682725

%endblock LatticeVectors
# Atomic coordinates
NumberOfAtoms 68
AtomicCoordinatesFormat Ang
%block AtomicCoordinatesAndAtomicSpecies
     5.112454135 3.515927420 0.848693033 1
     1.409485878 0.307116574 0.846854638 1
     2.803578198 4.315530649 0.846902378 1
     6.967535515 5.115720693 0.848833272 1
     5.575636034 1.106961286 0.850097306 1
     3.259137901 1.909268718 0.851260373 1
     7.429142444 2.710101022 0.852619493 1
     2.798608710 0.566608299 2.823432118 1
     4.652972604 2.175442883 2.823783931 1
     2.333388624 2.980868539 2.824679768 1
     8.349258565 5.379164071 2.828240854 1
     4.186274271 4.577332776 2.829493521 1
     6.968212779 1.371824558 2.830029393 1
     6.500643842 3.775944610 2.831124340 1
     3.259232369 1.902967217 4.785325017 1
     5.582851351 1.093165878 4.817304242 1
     1.399543888 0.293162930 4.817446911 1
     2.794712396 4.314588549 4.816853344 1
     5.103331239 3.505233682 4.821580555 1
     6.969029798 5.117102142 4.822982476 1
     7.430755679 2.693319364 4.824651549 1
     4.665139732 2.139566083 6.757980818 1
     2.763758897 0.563696591 6.758577207 1
     2.350547580 2.996575167 6.765856158 1
     6.498558656 3.772204153 6.791396769 1
     4.170876697 4.550036557 6.812115474 1
     8.340410956 5.393832616 6.822402708 1
     6.986779687 1.364950895 6.824110975 1
     4.905726514 1.066903979 8.710430583 3
     1.712523840 0.930489981 8.711768851 3
     3.196033732 3.782392606 8.717059214 3
     6.509410837 3.787087993 8.895438997 3
     4.862708882 4.711614299 10.343254912 2
     8.128840767 4.776196708 10.346335940 2
     6.524284754 1.898615338 10.349514798 2
     3.276209351 1.927074099 10.377408353 2
     1.655662536 0.937035903 11.879056027 3
     3.227403013 3.831133361 11.898469073 3
     4.921765641 1.014842586 11.925075156 3
     6.524202114 3.780392881 12.075234656 3
     1.481584112 0.462207932 13.951835825 1
     2.901417224 4.395329414 13.956262019 1
     5.610682132 1.191346677 13.960461197 1
     5.208297760 3.633955046 13.973266935 1
     7.032151259 5.206461773 13.979356245 1
     7.473847042 2.837689380 13.997251667 1
     3.330282009 2.024580752 14.018300236 1
     8.427954634 5.477724319 15.938484810 1
     4.268049234 4.707169103 15.937781184 1
     7.015885128 1.487999506 15.940683484 1
     2.878094866 0.696398490 15.949954787 1
     4.713494650 2.292793692 15.950594447 1
     2.410778793 3.078725654 15.953969593 1
     6.567099203 3.898600797 15.957002333 1
     1.479490501 0.423885365 17.935111233 1
     7.494391816 2.824955823 17.935557741 1
     5.181475679 3.626689345 17.936293977 1
     2.867838104 4.427896914 17.936936145 1
     5.644764529 1.220746095 17.937720042 1
     7.033487549 5.228421605 17.938575430 1
     3.333497084 2.022260181 17.944027588 1
     4.259682848 4.692103264 19.911552001 1
     8.420995633 5.495657101 19.915220638 1
     2.404430689 3.090242127 19.915991993 1
     7.035996482 1.487778144 19.916828567 1
     2.869522178 0.684433088 19.917872091 1
     4.720483408 2.288607502 19.918313581 1
     6.571430737 3.889509256 19.923804621 1

%endblock AtomicCoordinatesAndAtomicSpecies
==================================================
==================================================
# General variables
ElectronicTemperature 300 K # room temperature
MeshCutoff 300. Ry
xc.functional GGA # Exchange-correlation functional
xc.authors PBE
SpinPolarized .false.
SolutionMethod Transiesta
==================================================
==================================================
# SCF variables
DM.MixSCF1 T
MaxSCFIterations 400 # Maximum number of SCF iter
DM.MixingWeight 0.03 # 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 5
Diag.DivideAndConquer no
MixHamiltonian 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
Longoutput true
TBT.Projs.DOS.A true
TBT.DOS.A.All true #Calculate the DOS from the spectral function and do so with all electrodes

==================================================
==================================================
# Parallel variables
Diag.ParallelOverK yes
==================================================
==================================================
# Transiesta information
TS.Voltage 0.00000 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.Neglect.Principal true
TS.Elecs.GF.ReUse true
%block TS.Elecs
  Left
  Right
%endblock TS.Elecs
%block TS.Elec.Left
  TSHS ./Co_elec_left.TSHS
  chem-pot Left
  semi-inf-dir -a3
  elec-pos begin 1
%endblock TS.Elec.Left
%block TS.Elec.Right
  TSHS ./Co_elec_right.TSHS
  chem-pot Right
  semi-inf-dir +a3
  elec-pos end -1
%endblock TS.Elec.Right
TS.Contours.Eq.Pole 2.50000 eV
%block TS.Contour.c-Left
  part circle
   from -40.00000 eV + V/2 to -10. kT + V/2
    points 30
     method g-legendre
%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 -40.00000 eV - V/2 to -10. kT - V/2
    points 30
     method g-legendre
%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
TS.Elecs.Eta 0.0001 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
# TBtrans options
TBT.Elecs.Eta 0.0001 eV
%block TBT.Contours
  neq
%endblock TBT.Contours
%block TBT.Contour.neq
  part line
   from -1.0000 eV to 1.0000 eV
    delta 0.01000 eV
     method mid-rule
%endblock TBT.Contour.neq
TBT.T.Eig 3

Nick Papior (nickpapior) said : #3

Electrode input?

nayana devaraj (devarajnayana) said : #4

Following is the left electrode.

SystemName Co electrode
SystemLabel Co_elec_left

==================================================
==================================================
# SPECIES AND BASIS

# Number of species
NumberOfSpecies 1
NumberOfAtoms 28

%block ChemicalSpeciesLabel
  1 27 Co
%endblock ChemicalSpeciesLabel

PAO.BasisSize DZP
PAO.EnergyShift 50 MeV
PAO.SplitNorm 0.15392

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

%block kgrid_Monkhorst_Pack
1 0 0 0.0
0 1 0 0.0
0 0 20 0.0
%endblock kgrid_Monkhorst_Pack

==================================================
==================================================
# UNIT CELL AND ATOMIC POSITIONS

Atomic coordinates
 AtomicCoordinatesFormat Ang
%block AtomicCoordinatesAndAtomicSpecies
     5.112454135 3.515927420 0.848693033 1
     1.409485878 0.307116574 0.846854638 1
     2.803578198 4.315530649 0.846902378 1
     6.967535515 5.115720693 0.848833272 1
     5.575636034 1.106961286 0.850097306 1
     3.259137901 1.909268718 0.851260373 1
     7.429142444 2.710101022 0.852619493 1
     2.798608710 0.566608299 2.823432118 1
     4.652972604 2.175442883 2.823783931 1
     2.333388624 2.980868539 2.824679768 1
     8.349258565 5.379164071 2.828240854 1
     4.186274271 4.577332776 2.829493521 1
     6.968212779 1.371824558 2.830029393 1
     6.500643842 3.775944610 2.831124340 1
     3.259232369 1.902967217 4.785325017 1
     5.582851351 1.093165878 4.817304242 1
     1.399543888 0.293162930 4.817446911 1
     2.794712396 4.314588549 4.816853344 1
     5.103331239 3.505233682 4.821580555 1
     6.969029798 5.117102142 4.822982476 1
     7.430755679 2.693319364 4.824651549 1
     4.665139732 2.139566083 6.757980818 1
     2.763758897 0.563696591 6.758577207 1
     2.350547580 2.996575167 6.765856158 1
     6.498558656 3.772204153 6.791396769 1
     4.170876697 4.550036557 6.812115474 1
     8.340410956 5.393832616 6.822402708 1
     6.986779687 1.364950895 6.824110975 1

%endblock AtomicCoordinatesAndAtomicSpecies

==================================================
LatticeConstant 1.00 Ang

%block LatticeVectors
        6.4800944328 0.0000000000 0.0000000000
        3.2397546226 5.6116284136 0.0000000000
        0.0671003143 0.1085815314 7.974877368

%endblock LatticeVectors=================================================
# General variables

ElectronicTemperature 100 K
MeshCutoff 300. Ry
xc.functional GGA # Exchange-correlation functional
xc.authors PBE
SpinPolarized .false.
SolutionMethod Diagon

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

DM.MixSCF1 T
MaxSCFIterations 200 # Maximum number of SCF iter
DM.MixingWeight 0.03 # 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 5
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 .true.
WriteEigenvalues yes
longoutput .true.
==================================================
==================================================

Right electrode is given below.

SystemName Co electrode
SystemLabel Co_elec_right

==================================================
==================================================
# SPECIES AND BASIS

# Number of species
NumberOfSpecies 1
NumberOfAtoms 28

%block ChemicalSpeciesLabel
  1 27 Co
%endblock ChemicalSpeciesLabel

PAO.BasisSize DZP
PAO.EnergyShift 50 MeV
PAO.SplitNorm 0.15392

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

%block kgrid_Monkhorst_Pack
1 0 0 0.0
0 1 0 0.0
0 0 20 0.0
%endblock kgrid_Monkhorst_Pack

==================================================
==================================================
# UNIT CELL AND ATOMIC POSITIONS

Atomic coordinates
 AtomicCoordinatesFormat Ang
%block AtomicCoordinatesAndAtomicSpecies
     1.481584112 0.462207932 13.951835825 1
     2.901417224 4.395329414 13.956262019 1
     5.610682132 1.191346677 13.960461197 1
     5.208297760 3.633955046 13.973266935 1
     7.032151259 5.206461773 13.979356245 1
     7.473847042 2.837689380 13.997251667 1
     3.330282009 2.024580752 14.018300236 1
     8.427954634 5.477724319 15.938484810 1
     4.268049234 4.707169103 15.937781184 1
     7.015885128 1.487999506 15.940683484 1
     2.878094866 0.696398490 15.949954787 1
     4.713494650 2.292793692 15.950594447 1
     2.410778793 3.078725654 15.953969593 1
     6.567099203 3.898600797 15.957002333 1
     1.479490501 0.423885365 17.935111233 1
     7.494391816 2.824955823 17.935557741 1
     5.181475679 3.626689345 17.936293977 1
     2.867838104 4.427896914 17.936936145 1
     5.644764529 1.220746095 17.937720042 1
     7.033487549 5.228421605 17.938575430 1
     3.333497084 2.022260181 17.944027588 1
     4.259682848 4.692103264 19.911552001 1
     8.420995633 5.495657101 19.915220638 1
     2.404430689 3.090242127 19.915991993 1
     7.035996482 1.487778144 19.916828567 1
     2.869522178 0.684433088 19.917872091 1
     4.720483408 2.288607502 19.918313581 1
     6.571430737 3.889509256 19.923804621 1

%endblock AtomicCoordinatesAndAtomicSpecies

==================================================
LatticeConstant 1.00 Ang

%block LatticeVectors
        6.4800944328 0.0000000000 0.0000000000
        3.2397546226 5.6116284136 0.0000000000
        0.0671003143 0.1085815314 7.951745829

%endblock LatticeVectors=================================================
# General variables

ElectronicTemperature 100 K
MeshCutoff 300. Ry
xc.functional GGA # Exchange-correlation functional
xc.authors PBE
SpinPolarized .false.
SolutionMethod Diagon

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

DM.MixSCF1 T
MaxSCFIterations 200 # Maximum number of SCF iter
DM.MixingWeight 0.03 # 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 5
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 .true.
WriteEigenvalues yes
longoutput .true.
==================================================
==================================================

Nick Papior (nickpapior) said : #5

1) it seems like what you really want to simulate is a system with the transport lattice vector being orthogonal to your other two lattice vectors. I would HIGHLY recommend you to ensure this!

2) If you add this block to your device input, it should run.
%block AtomicCoordinatesOrigin
  0.00093 0.00151 0.29194
%endblock
However, I think you are doing the calculation unexpectedly. You should really try and solve the above problem.

Can you help with this problem?

Provide an answer of your own, or ask nayana devaraj for more information if necessary.

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