Siesta

about the transiesta/tbtrans in the system with hexagonal cells

Asked by xiaoboy

Dear all,
I am trying to calculate the current values in the system with hexagonal cell.
I am wondering whether my input files are correct.?
The input files for electrode and scattering region calculations could be found in attachments.
Note that the structures of scattering region are set up using different methods, while the calculated current values are quite different. What is wrong?
Best Wishes
Xiaoboy

1. input for electrode calculation

SystemName elec
SystemLabel elec
==================================================
==================================================
# SPECIES AND BASIS
# Number of species
NumberOfSpecies 5
%block ChemicalSpeciesLabel
  1 40 Zr
  2 6 C
  3 16 S
  4 7 N
  5 8 O
%endblock ChemicalSpeciesLabel
PAO.EnergyShift 100 meV
PAO.BasisType split

%block PAO.BasisSizes
Zr SZP
C SZP
S SZP
N SZP
O SZP
%endblock PAO.BasisSizes
LatticeConstant 1.0 Ang
==================================================
==================================================
# K-points
%block kgrid_Monkhorst_Pack
3 0 0 0.0
0 100 0 0.0
0 0 1 0.0
%endblock kgrid_Monkhorst_Pack
==================================================
==================================================
# UNIT CELL AND ATOMIC POSITIONS
# UNIT CELL
LatticeConstant 1.0 Ang
%block LatticeVectors
       10.3634004593 0.0000000000 0.0000000000
       -5.1797834960 8.9752662248 0.0000000000
       -0.2349093992 -0.0340890042 18.4590737621
%endblock LatticeVectors
# Atomic coordinates
NumberOfAtoms 45
AtomicCoordinatesFormat Ang
%block AtomicCoordinatesAndAtomicSpecies
    3.762081 0.503098 3.227586 2
    0.307568 0.503138 3.227630 2
    7.216527 0.503164 3.227640 2
   2.035321 1.500693 4.574973 1
   5.489832 1.500664 4.574923 1
   8.944292 1.500658 4.574945 1
    2.034869 1.499705 0.280263 3
    5.489327 1.499712 0.280259 3
    8.943788 1.499730 0.280255 3
    0.309622 2.498819 6.174441 3
    3.764081 2.498831 6.174431 3
    7.218512 2.498860 6.174478 3
   3.761731 2.497358 1.879399 1
   0.307266 2.497322 1.879379 1
   7.216189 2.497324 1.879404 1
   -1.419029 3.494895 3.227632 2
    2.035435 3.494884 3.227627 2
    5.489883 3.494896 3.227622 2
   0.308697 4.492436 4.574973 1
   3.763212 4.492440 4.574906 1
   7.217684 4.492420 4.574903 1
    0.308267 4.491486 0.280269 3
    3.762731 4.491463 0.280269 3
    7.217193 4.491489 0.280257 3
   -1.417025 5.490597 6.174465 3
    2.037442 5.490603 6.174470 3
    5.491944 5.490595 6.174436 3
  -1.419320 5.489085 1.879405 1
   2.035127 5.489100 1.879417 1
   5.489604 5.489092 1.879395 1
   -3.145639 6.486648 3.227630 2
    0.308855 6.486649 3.227639 2
    3.763298 6.486662 3.227640 2
  -1.417838 7.484186 4.574891 1
   2.036613 7.484214 4.574945 1
   5.491097 7.484179 4.574969 1
   -1.418325 7.483230 0.280269 3
    2.036146 7.483224 0.280262 3
    5.490607 7.483240 0.280264 3
   -3.143620 8.482359 6.174491 3
    0.310831 8.482360 6.174477 3
    3.765260 8.482400 6.174534 3
  -3.145921 8.480823 1.879400 1
   0.308568 8.480843 1.879389 1
   3.763001 8.480855 1.879410 1
%endblock AtomicCoordinatesAndAtomicSpecies
==================================================
MM.UnitsDistance Ang # what this program prints out DO NOT CHANGE
MM.UnitsEnergy eV # what this program prints out DO NOT CHANGE
MM.Grimme.S6 0.75 # Grimme-paper for PBE (correct for your functional)
MM.Grimme.D 20. # Grimme-paper (correct for your functional)
%block MM.Potentials
  1 1 Grimme 255.69 3.278 # Zr, 10.1002/jcc.20495
  1 2 Grimme 68.10 3.091 # Zr / C
  1 3 Grimme 121.49 3.322 # Zr / S
  1 4 Grimme 57.09 3.036 # Zr / N
  1 5 Grimme 43.07 2.981 # Zr / O
  2 2 Grimme 18.14 2.904 # C, 10.1002/jcc.20495
  2 3 Grimme 32.36 3.135 # C / S
  2 4 Grimme 15.21 2.849 # C / N
  2 5 Grimme 11.47 2.794 # C / O
  3 3 Grimme 57.73 3.366 # S, 10.1002/jcc.20495
  3 4 Grimme 27.13 3.080 # S / N
  3 5 Grimme 20.47 3.025 # S / O
  4 4 Grimme 12.75 2.794 # N, 10.1002/jcc.20495
  4 5 Grimme 9.62 2.739 # N / O
  5 5 Grimme 7.26 2.684 # O, 10.1002/jcc.20495
%endblock MM.Potentials
==================================================
# General variables
ElectronicTemperature 300 K
MeshCutoff 300. Ry
xc.functional GGA # Exchange-correlation functional
xc.authors PBE
SpinPolarized F
SolutionMethod Diagon
==================================================
==================================================
# SCF variables
DM.MixSCF1 T
MaxSCFIterations 300 # 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
#Write.TSHS.History .true.
WriteMullikenPop 1
WriteBands .false.
SaveRho .false.
SaveDeltaRho .false.
#veHS .true.
#SaveElectrostaticPotential True
SaveTotalPotential no
WriteCoorXmol .true.
#WriteMDXmol .true.
WriteMDhistory .false.
#WriteEigenvalues yes
==================================================
==================================================

2. input for scattering region calculation-A

SystemName scatt
SystemLabel scatt
==================================================
==================================================
# SPECIES AND BASIS
# Number of species
NumberOfSpecies 3
%block ChemicalSpeciesLabel
  1 40 Zr
  2 6 C
  3 16 S
%endblock ChemicalSpeciesLabel
PAO.EnergyShift 100 meV
PAO.BasisType split

%block PAO.BasisSizes
Zr SZP
C SZP
S SZP
%endblock PAO.BasisSizes
LatticeConstant 1.0 Ang
==================================================
==================================================
# K-points
%block kgrid_Monkhorst_Pack
3 0 0 0.0
0 1 0 0.0
0 0 1 0.0
%endblock kgrid_Monkhorst_Pack
==================================================
==================================================
# UNIT CELL AND ATOMIC POSITIONS
# UNIT CELL
LatticeConstant 1.0 Ang
%block LatticeVectors
       10.3634004593 0.0000000000 0.0000000000
       -5.1797834960 8.9752662248 0.0000000000
       -0.2349093992 -0.0340890042 18.4590737621
%endblock LatticeVectors
# Atomic coordinates
NumberOfAtoms 45
AtomicCoordinatesFormat Ang
%block AtomicCoordinatesAndAtomicSpecies
    3.762081 0.503098 3.227586 2
    0.307568 0.503138 3.227630 2
    7.216527 0.503164 3.227640 2
   2.035321 1.500693 4.574973 1
   5.489832 1.500664 4.574923 1
   8.944292 1.500658 4.574945 1
    2.034869 1.499705 0.280263 3
    5.489327 1.499712 0.280259 3
    8.943788 1.499730 0.280255 3
    0.309622 2.498819 6.174441 3
    3.764081 2.498831 6.174431 3
    7.218512 2.498860 6.174478 3
   3.761731 2.497358 1.879399 1
   0.307266 2.497322 1.879379 1
   7.216189 2.497324 1.879404 1
   -1.419029 3.494895 3.227632 2
    2.035435 3.494884 3.227627 2
    5.489883 3.494896 3.227622 2
   0.308697 4.492436 4.574973 1
   3.763212 4.492440 4.574906 1
   7.217684 4.492420 4.574903 1
    0.308267 4.491486 0.280269 3
    3.762731 4.491463 0.280269 3
    7.217193 4.491489 0.280257 3
   -1.417025 5.490597 6.174465 3
    2.037442 5.490603 6.174470 3
    5.491944 5.490595 6.174436 3
  -1.419320 5.489085 1.879405 1
   2.035127 5.489100 1.879417 1
   5.489604 5.489092 1.879395 1
   -3.145639 6.486648 3.227630 2
    0.308855 6.486649 3.227639 2
    3.763298 6.486662 3.227640 2
  -1.417838 7.484186 4.574891 1
   2.036613 7.484214 4.574945 1
   5.491097 7.484179 4.574969 1
   -1.418325 7.483230 0.280269 3
    2.036146 7.483224 0.280262 3
    5.490607 7.483240 0.280264 3
   -3.143620 8.482359 6.174491 3
    0.310831 8.482360 6.174477 3
    3.765260 8.482400 6.174534 3
  -3.145921 8.480823 1.879400 1
   0.308568 8.480843 1.879389 1
   3.763001 8.480855 1.879410 1
%endblock AtomicCoordinatesAndAtomicSpecies
==================================================

%block SuperCell
1 0 0
0 3 0
0 0 1
%endblock SuperCell
==================================================
==================================================
==================================================
# General variables
ElectronicTemperature 300 K
MeshCutoff 300. Ry
xc.functional GGA # Exchange-correlation functional
xc.authors PBE
SpinPolarized F
SolutionMethod transiesta
==================================================
==================================================
# SCF variables
DM.MixSCF1 T
MaxSCFIterations 500 # 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.
==================================================
MM.UnitsDistance Ang # what this program prints out DO NOT CHANGE
MM.UnitsEnergy eV # what this program prints out DO NOT CHANGE
MM.Grimme.S6 0.75 # Grimme-paper for PBE (correct for your functional)
MM.Grimme.D 20. # Grimme-paper (correct for your functional)
%block MM.Potentials
  1 1 Grimme 255.69 3.278 # Zr, 10.1002/jcc.20495
  1 2 Grimme 68.10 3.091 # Zr / C
  1 3 Grimme 121.49 3.322 # Zr / S
  1 4 Grimme 57.09 3.036 # Zr / N
  1 5 Grimme 43.07 2.981 # Zr / O
  2 2 Grimme 18.14 2.904 # C, 10.1002/jcc.20495
  2 3 Grimme 32.36 3.135 # C / S
  2 4 Grimme 15.21 2.849 # C / N
  2 5 Grimme 11.47 2.794 # C / O
  3 3 Grimme 57.73 3.366 # S, 10.1002/jcc.20495
  3 4 Grimme 27.13 3.080 # S / N
  3 5 Grimme 20.47 3.025 # S / O
  4 4 Grimme 12.75 2.794 # N, 10.1002/jcc.20495
  4 5 Grimme 9.62 2.739 # N / O
  5 5 Grimme 7.26 2.684 # O, 10.1002/jcc.20495
%endblock MM.Potentials
==================================================
# Output variables
WriteMullikenPop 1
WriteBands .false.
SaveRho .false.
SaveDeltaRho .false.
SaveHS .true.
SaveElectrostaticPotential True
SaveTotalPotential no
WriteCoorXmol .true.
WriteMDXmol .true.
WriteMDhistory .false.
WriteEigenvalues yes
==================================================
==================================================

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 cross-terms
TS.Elecs.GF.ReUse true
%block TS.Elecs
  Left
  Right
%endblock TS.Elecs

%block TS.Elec.Left
  HS ../elec.TSHS
  chem-pot Left
  semi-inf-dir -a2
  elec-pos begin 1
%endblock TS.Elec.Left

%block TS.Elec.Right
  HS ../elec.TSHS
  chem-pot Right
  semi-inf-dir +a2
  elec-pos end -1
%endblock TS.Elec.Right

TS.Contours.Eq.Pole 2.50000 eV
%block TS.Contour.c-Left
  part circle
   from -30.00000 eV + V/2 to -10. kT + V/2
    points 16
     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 -30.00000 eV - V/2 to -10. kT - V/2
    points 16
     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

# TBtrans options

%block TBT.k
  diag 1 20 1
%endblock

TBT.T.Eig 3
TBT.Elecs.Eta 0.0000136058 eV

%block TBT.Contours
  neq
%endblock TBT.Contours

%block TBT.Contour.neq
  part line
   from -10.00000 eV to 10.00000 eV
    delta 0.02000 eV
     method mid-rule
%endblock TBT.Contour.neq

# It is adviced to define a device region of
# particular interest

3. input for scattering region calculation-B

SystemName scatt
SystemLabel scatt
==================================================
==================================================
# SPECIES AND BASIS
# Number of species
NumberOfSpecies 3
%block ChemicalSpeciesLabel
  1 40 Zr
  2 6 C
  3 16 S
%endblock ChemicalSpeciesLabel
PAO.EnergyShift 100 meV
PAO.BasisType split

%block PAO.BasisSizes
Zr SZP
C SZP
S SZP
%endblock PAO.BasisSizes
LatticeConstant 1.0 Ang
==================================================
==================================================
# K-points
%block kgrid_Monkhorst_Pack
3 0 0 0.0
0 1 0 0.0
0 0 1 0.0
%endblock kgrid_Monkhorst_Pack
==================================================
==================================================
# UNIT CELL AND ATOMIC POSITIONS
# UNIT CELL
LatticeConstant 1.0 Ang
%block LatticeVectors
       10.3634004593 0.0000000000 0.0000000000
      -15.5393500113 26.9257978485 0.0000000000
       -0.2349093992 -0.0340890042 18.4590737621
%endblock LatticeVectors
# Atomic coordinates
NumberOfAtoms 135
AtomicCoordinatesFormat Ang
%block AtomicCoordinatesAndAtomicSpecies
3.762081 0.503098 3.227586 2
0.307568 0.503138 3.22763 2
7.216527 0.503164 3.22764 2
2.034869 1.499705 0.280263 3
5.489327 1.499712 0.280259 3
8.943788 1.49973 0.280255 3
8.944292 1.500658 4.574945 1
5.489832 1.500663 4.574923 1
2.035321 1.500693 4.574973 1
0.307267 2.497322 1.879379 1
7.216189 2.497324 1.879404 1
3.761731 2.497358 1.879399 1
0.309622 2.498819 6.174441 3
3.764081 2.498831 6.174431 3
7.218512 2.49886 6.174478 3
2.035435 3.494885 3.227627 2
-1.419029 3.494895 3.227632 2
5.489884 3.494896 3.227622 2
3.762731 4.491462 0.280269 3
0.308267 4.491486 0.280269 3
7.217193 4.491489 0.280257 3
7.217684 4.492419 4.574903 1
0.308697 4.492436 4.574973 1
3.763212 4.49244 4.574906 1
-1.41932 5.489085 1.879405 1
5.489604 5.489092 1.879395 1
2.035127 5.4891 1.879417 1
5.491944 5.490595 6.174436 3
-1.417025 5.490597 6.174465 3
2.037442 5.490603 6.17447 3
-3.145639 6.486648 3.22763 2
0.308855 6.486649 3.227639 2
3.763298 6.486662 3.22764 2
2.036146 7.483224 0.280262 3
-1.418324 7.483229 0.280269 3
5.490607 7.48324 0.280264 3
5.491097 7.484179 4.574969 1
-1.417838 7.484185 4.574891 1
2.036613 7.484213 4.574945 1
-3.145921 8.480822 1.8794 1
0.308568 8.480843 1.879389 1
3.763001 8.480855 1.87941 1
-3.14362 8.482359 6.174491 3
0.310832 8.482359 6.174477 3
3.76526 8.482399 6.174534 3
-1.417703 9.478364 3.227586 2
-4.872216 9.478404 3.22763 2
2.036743 9.47843 3.22764 2
-3.144914 10.474971 0.280263 3
0.309544 10.474978 0.280259 3
3.764005 10.474996 0.280255 3
3.764509 10.475923 4.574945 1
0.310049 10.475929 4.574923 1
-3.144462 10.475959 4.574973 1
-4.872517 11.472588 1.879379 1
2.036406 11.472589 1.879404 1
-1.418053 11.472624 1.879399 1
-4.870161 11.474085 6.174441 3
-1.415702 11.474097 6.174431 3
2.038729 11.474126 6.174478 3
-3.144349 12.47015 3.227627 2
-6.598812 12.470161 3.227632 2
0.3101 12.470162 3.227622 2
-1.417052 13.466729 0.280269 3
-4.871516 13.466751 0.280269 3
2.03741 13.466755 0.280257 3
2.037901 13.467686 4.574903 1
-4.871086 13.467702 4.574973 1
-1.416572 13.467707 4.574906 1
-6.599104 14.464351 1.879405 1
0.309821 14.464357 1.879395 1
-3.144656 14.464365 1.879417 1
0.312161 14.465861 6.174436 3
-6.596808 14.465862 6.174465 3
-3.142341 14.465869 6.17447 3
-8.325423 15.461914 3.22763 2
-4.870928 15.461914 3.227639 2
-1.416486 15.461929 3.22764 2
-3.143637 16.458489 0.280262 3
-6.598108 16.458495 0.280269 3
0.310824 16.458507 0.280264 3
0.311314 16.459444 4.574969 1
-6.597621 16.459451 4.574891 1
-3.14317 16.45948 4.574945 1
-8.325705 17.456088 1.8794 1
-4.871215 17.456109 1.879389 1
-1.416782 17.45612 1.87941 1
-8.323403 17.457625 6.174491 3
-4.868952 17.457625 6.174477 3
-1.414523 17.457665 6.174534 3
-6.597486 18.453629 3.227586 2
-10.051999 18.453669 3.22763 2
-3.14304 18.453695 3.22764 2
-8.324697 19.450236 0.280263 3
-4.87024 19.450244 0.280259 3
-1.415778 19.450262 0.280255 3
-1.415274 19.45119 4.574945 1
-4.869734 19.451195 4.574923 1
-8.324246 19.451225 4.574973 1
-10.0523 20.447853 1.879379 1
-3.143378 20.447856 1.879404 1
-6.597836 20.44789 1.879399 1
-10.049945 20.449352 6.174441 3
-6.595485 20.449363 6.174431 3
-3.141054 20.449392 6.174478 3
-8.324132 21.445417 3.227627 2
-11.778595 21.445426 3.227632 2
-4.869683 21.445428 3.227622 2
-6.596835 22.441994 0.280269 3
-10.051299 22.442017 0.280269 3
-3.142373 22.44202 0.280257 3
-3.141882 22.442951 4.574903 1
-10.050869 22.442967 4.574973 1
-6.596355 22.442972 4.574906 1
-11.778887 23.439616 1.879405 1
-4.869963 23.439624 1.879395 1
-8.32444 23.439632 1.879417 1
-4.867623 23.441128 6.174436 3
-11.776592 23.441129 6.174465 3
-8.322125 23.441136 6.17447 3
-13.505206 24.43718 3.22763 2
-10.050712 24.437181 3.227639 2
-6.596269 24.437194 3.22764 2
-8.323421 25.433756 0.280262 3
-11.777891 25.433761 0.280269 3
-4.868959 25.433772 0.280264 3
-4.86847 25.434711 4.574969 1
-11.777405 25.434718 4.574891 1
-8.322953 25.434745 4.574945 1
-13.505488 26.431354 1.8794 1
-10.050998 26.431375 1.879389 1
-6.596566 26.431387 1.87941 1
-13.503186 26.432891 6.174491 3
-10.048735 26.432891 6.174477 3
-6.594306 26.432931 6.174534 3
%endblock AtomicCoordinatesAndAtomicSpecies
==================================================

==================================================
# General variables
ElectronicTemperature 300 K
MeshCutoff 300. Ry
xc.functional GGA # Exchange-correlation functional
xc.authors PBE
SpinPolarized F
SolutionMethod transiesta
==================================================
==================================================
# SCF variables
DM.MixSCF1 T
MaxSCFIterations 500 # 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.
==================================================
MM.UnitsDistance Ang # what this program prints out DO NOT CHANGE
MM.UnitsEnergy eV # what this program prints out DO NOT CHANGE
MM.Grimme.S6 0.75 # Grimme-paper for PBE (correct for your functional)
MM.Grimme.D 20. # Grimme-paper (correct for your functional)
%block MM.Potentials
  1 1 Grimme 255.69 3.278 # Zr, 10.1002/jcc.20495
  1 2 Grimme 68.10 3.091 # Zr / C
  1 3 Grimme 121.49 3.322 # Zr / S
  1 4 Grimme 57.09 3.036 # Zr / N
  1 5 Grimme 43.07 2.981 # Zr / O
  2 2 Grimme 18.14 2.904 # C, 10.1002/jcc.20495
  2 3 Grimme 32.36 3.135 # C / S
  2 4 Grimme 15.21 2.849 # C / N
  2 5 Grimme 11.47 2.794 # C / O
  3 3 Grimme 57.73 3.366 # S, 10.1002/jcc.20495
  3 4 Grimme 27.13 3.080 # S / N
  3 5 Grimme 20.47 3.025 # S / O
  4 4 Grimme 12.75 2.794 # N, 10.1002/jcc.20495
  4 5 Grimme 9.62 2.739 # N / O
  5 5 Grimme 7.26 2.684 # O, 10.1002/jcc.20495
%endblock MM.Potentials
==================================================
# Output variables
WriteMullikenPop 1
WriteBands .false.
SaveRho .false.
SaveDeltaRho .false.
SaveHS .true.
SaveElectrostaticPotential True
SaveTotalPotential no
WriteCoorXmol .true.
WriteMDXmol .true.
WriteMDhistory .false.
WriteEigenvalues yes
==================================================
==================================================

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 cross-terms
TS.Elecs.GF.ReUse true
%block TS.Elecs
  Left
  Right
%endblock TS.Elecs

%block TS.Elec.Left
  HS ../elec.TSHS
  chem-pot Left
  semi-inf-dir -a2
  elec-pos begin 1
%endblock TS.Elec.Left

%block TS.Elec.Right
  HS ../elec.TSHS
  chem-pot Right
  semi-inf-dir +a2
  elec-pos end -1
%endblock TS.Elec.Right

TS.Contours.Eq.Pole 2.50000 eV
%block TS.Contour.c-Left
  part circle
   from -30.00000 eV + V/2 to -10. kT + V/2
    points 16
     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 -30.00000 eV - V/2 to -10. kT - V/2
    points 16
     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

# TBtrans options

%block TBT.k
  diag 1 20 1
%endblock

TBT.T.Eig 3
TBT.Elecs.Eta 0.0000136058 eV

%block TBT.Contours
  neq
%endblock TBT.Contours

%block TBT.Contour.neq
  part line
   from -10.00000 eV to 10.00000 eV
    delta 0.02000 eV
     method mid-rule
%endblock TBT.Contour.neq

# It is adviced to define a device region of
# particular interest

Question information

Language:
English Edit question
Status:
Solved
For:
Siesta Edit question
Assignee:
No assignee Edit question
Solved by:
Nick Papior
Solved:
Last query:
Last reply:
Revision history for this message
Nick Papior (nickpapior) said : 		#1

It isn't really clear from looking at this how the two are different. Could you please be more specific about the differences?

Revision history for this message
xiaoboy (xiaoboy) said : 		#2

In the case of input-A: the coordinates of scattering region is written by using unit cell, and the keyword of %block SuperCell is used to construct the supercell (1*3*1), while in the case of input-B, the coordinates of scattering region is written in the form of supercell (1*3*1). This is the only difference between two cases. The transport direction is a2, vdw interaction is considered in the simulation. As a result, the calculated current values in case A is about ten times lower than that of case B.

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

That indeed sounds weird. Did you check that the coordinates and lattice vectors are exactly the same?

Also, could you share the output of the two scattering region calculations?

Revision history for this message
xiaoboy (xiaoboy) said : 		#5

Output-B:
Siesta Version : siesta-psml-R1--709-594
Architecture : gfortran-mpi-example
Compiler version: GNU Fortran (GCC) 4.8.5 20150623 (Red Hat 4.8.5-28)
Compiler flags : mpif90 -O2 -fbacktrace
PP flags : -DCDF -DMPI -DMPI_TIMING -DF2003 -DSIESTA__DIAG_2STAGE
Libraries : libsiestaLAPACK.a libsiestaBLAS.a -L/home/student/siesta/new/siesta-bundle//install/install//lib -lnetcdff -lnetcdf /home/student/siesta/scalapack-2.1.0/libscalapack.a /home/student/siesta/BLACS/LIB/blacs_MPI-LINUX-0.a /home/student/siesta/BLACS/LIB/blacsCinit_MPI-LINUX-0.a /home/student/siesta/BLACS/LIB/blacsF77init_MPI-LINUX-0.a libsiestaLAPACK.a libsiestaBLAS.a
PARALLEL version
NetCDF support

* Running on 24 nodes in parallel
>> Start of run: 30-MAR-2021 10:26:23

                           ***********************
                           * WELCOME TO SIESTA *
                           ***********************

reinit: Reading from standard input
reinit: Dumped input in INPUT_TMP.02465
************************** Dump of input data file ****************************
SystemName scatt
SystemLabel scatt
==================================================
==================================================
# SPECIES AND BASIS
# Number of species
NumberOfSpecies 3
%block ChemicalSpeciesLabel
  1 40 Zr
  2 6 C
  3 16 S
%endblock ChemicalSpeciesLabel
PAO.EnergyShift 100 meV
PAO.BasisType split
%block PAO.BasisSizes
Zr SZP
C SZP
S SZP
%endblock PAO.BasisSizes
LatticeConstant 1.0 Ang
==================================================
==================================================
# K-points
%block kgrid_Monkhorst_Pack
3 0 0 0.0
0 1 0 0.0
0 0 1 0.0
%endblock kgrid_Monkhorst_Pack
==================================================
==================================================
# UNIT CELL AND ATOMIC POSITIONS
# UNIT CELL
LatticeConstant 1.0 Ang
%block LatticeVectors
       10.3634004593 0.0000000000 0.0000000000
      -15.5393500113 26.9257978485 0.0000000000
       -0.2349093992 -0.0340890042 18.4590737621
%endblock LatticeVectors
# Atomic coordinates
NumberOfAtoms 135
AtomicCoordinatesFormat Ang
%block AtomicCoordinatesAndAtomicSpecies
3.762081 0.503098 3.227586 2
0.307568 0.503138 3.22763 2
7.216527 0.503164 3.22764 2
2.034869 1.499705 0.280263 3
5.489327 1.499712 0.280259 3
8.943788 1.49973 0.280255 3
8.944292 1.500658 4.574945 1
5.489832 1.500663 4.574923 1
2.035321 1.500693 4.574973 1
0.307267 2.497322 1.879379 1
7.216189 2.497324 1.879404 1
3.761731 2.497358 1.879399 1
0.309622 2.498819 6.174441 3
3.764081 2.498831 6.174431 3
7.218512 2.49886 6.174478 3
2.035435 3.494885 3.227627 2
-1.419029 3.494895 3.227632 2
5.489884 3.494896 3.227622 2
3.762731 4.491462 0.280269 3
0.308267 4.491486 0.280269 3
7.217193 4.491489 0.280257 3
7.217684 4.492419 4.574903 1
0.308697 4.492436 4.574973 1
3.763212 4.49244 4.574906 1
-1.41932 5.489085 1.879405 1
5.489604 5.489092 1.879395 1
2.035127 5.4891 1.879417 1
5.491944 5.490595 6.174436 3
-1.417025 5.490597 6.174465 3
2.037442 5.490603 6.17447 3
-3.145639 6.486648 3.22763 2
0.308855 6.486649 3.227639 2
3.763298 6.486662 3.22764 2
2.036146 7.483224 0.280262 3
-1.418324 7.483229 0.280269 3
5.490607 7.48324 0.280264 3
5.491097 7.484179 4.574969 1
-1.417838 7.484185 4.574891 1
2.036613 7.484213 4.574945 1
-3.145921 8.480822 1.8794 1
0.308568 8.480843 1.879389 1
3.763001 8.480855 1.87941 1
-3.14362 8.482359 6.174491 3
0.310832 8.482359 6.174477 3
3.76526 8.482399 6.174534 3
-1.417703 9.478364 3.227586 2
-4.872216 9.478404 3.22763 2
2.036743 9.47843 3.22764 2
-3.144914 10.474971 0.280263 3
0.309544 10.474978 0.280259 3
3.764005 10.474996 0.280255 3
3.764509 10.475923 4.574945 1
0.310049 10.475929 4.574923 1
-3.144462 10.475959 4.574973 1
-4.872517 11.472588 1.879379 1
2.036406 11.472589 1.879404 1
-1.418053 11.472624 1.879399 1
-4.870161 11.474085 6.174441 3
-1.415702 11.474097 6.174431 3
2.038729 11.474126 6.174478 3
-3.144349 12.47015 3.227627 2
-6.598812 12.470161 3.227632 2
0.3101 12.470162 3.227622 2
-1.417052 13.466729 0.280269 3
-4.871516 13.466751 0.280269 3
2.03741 13.466755 0.280257 3
2.037901 13.467686 4.574903 1
-4.871086 13.467702 4.574973 1
-1.416572 13.467707 4.574906 1
-6.599104 14.464351 1.879405 1
0.309821 14.464357 1.879395 1
-3.144656 14.464365 1.879417 1
0.312161 14.465861 6.174436 3
-6.596808 14.465862 6.174465 3
-3.142341 14.465869 6.17447 3
-8.325423 15.461914 3.22763 2
-4.870928 15.461914 3.227639 2
-1.416486 15.461929 3.22764 2
-3.143637 16.458489 0.280262 3
-6.598108 16.458495 0.280269 3
0.310824 16.458507 0.280264 3
0.311314 16.459444 4.574969 1
-6.597621 16.459451 4.574891 1
-3.14317 16.45948 4.574945 1
-8.325705 17.456088 1.8794 1
-4.871215 17.456109 1.879389 1
-1.416782 17.45612 1.87941 1
-8.323403 17.457625 6.174491 3
-4.868952 17.457625 6.174477 3
-1.414523 17.457665 6.174534 3
-6.597486 18.453629 3.227586 2
-10.051999 18.453669 3.22763 2
-3.14304 18.453695 3.22764 2
-8.324697 19.450236 0.280263 3
-4.87024 19.450244 0.280259 3
-1.415778 19.450262 0.280255 3
-1.415274 19.45119 4.574945 1
-4.869734 19.451195 4.574923 1
-8.324246 19.451225 4.574973 1
-10.0523 20.447853 1.879379 1
-3.143378 20.447856 1.879404 1
-6.597836 20.44789 1.879399 1
-10.049945 20.449352 6.174441 3
-6.595485 20.449363 6.174431 3
-3.141054 20.449392 6.174478 3
-8.324132 21.445417 3.227627 2
-11.778595 21.445426 3.227632 2
-4.869683 21.445428 3.227622 2
-6.596835 22.441994 0.280269 3
-10.051299 22.442017 0.280269 3
-3.142373 22.44202 0.280257 3
-3.141882 22.442951 4.574903 1
-10.050869 22.442967 4.574973 1
-6.596355 22.442972 4.574906 1
-11.778887 23.439616 1.879405 1
-4.869963 23.439624 1.879395 1
-8.32444 23.439632 1.879417 1
-4.867623 23.441128 6.174436 3
-11.776592 23.441129 6.174465 3
-8.322125 23.441136 6.17447 3
-13.505206 24.43718 3.22763 2
-10.050712 24.437181 3.227639 2
-6.596269 24.437194 3.22764 2
-8.323421 25.433756 0.280262 3
-11.777891 25.433761 0.280269 3
-4.868959 25.433772 0.280264 3
-4.86847 25.434711 4.574969 1
-11.777405 25.434718 4.574891 1
-8.322953 25.434745 4.574945 1
-13.505488 26.431354 1.8794 1
-10.050998 26.431375 1.879389 1
-6.596566 26.431387 1.87941 1
-13.503186 26.432891 6.174491 3
-10.048735 26.432891 6.174477 3
-6.594306 26.432931 6.174534 3
%endblock AtomicCoordinatesAndAtomicSpecies
==================================================
==================================================
# General variables
ElectronicTemperature 300 K
MeshCutoff 300. Ry
xc.functional GGA # Exchange-correlation functional
xc.authors PBE
SpinPolarized F
SolutionMethod transiesta
==================================================
==================================================
# SCF variables
DM.MixSCF1 T
MaxSCFIterations 500 # 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.
==================================================
MM.UnitsDistance Ang # what this program prints out DO NOT CHANGE
MM.UnitsEnergy eV # what this program prints out DO NOT CHANGE
MM.Grimme.S6 0.75 # Grimme-paper for PBE (correct for your functional)
MM.Grimme.D 20. # Grimme-paper (correct for your functional)
%block MM.Potentials
  1 1 Grimme 255.69 3.278 # Zr, 10.1002/jcc.20495
  1 2 Grimme 68.10 3.091 # Zr / C
  1 3 Grimme 121.49 3.322 # Zr / S
  1 4 Grimme 57.09 3.036 # Zr / N
  1 5 Grimme 43.07 2.981 # Zr / O
  2 2 Grimme 18.14 2.904 # C, 10.1002/jcc.20495
  2 3 Grimme 32.36 3.135 # C / S
  2 4 Grimme 15.21 2.849 # C / N
  2 5 Grimme 11.47 2.794 # C / O
  3 3 Grimme 57.73 3.366 # S, 10.1002/jcc.20495
  3 4 Grimme 27.13 3.080 # S / N
  3 5 Grimme 20.47 3.025 # S / O
  4 4 Grimme 12.75 2.794 # N, 10.1002/jcc.20495
  4 5 Grimme 9.62 2.739 # N / O
  5 5 Grimme 7.26 2.684 # O, 10.1002/jcc.20495
%endblock MM.Potentials
==================================================
# Output variables
WriteMullikenPop 1
WriteBands .false.
SaveRho .false.
SaveDeltaRho .false.
SaveHS .true.
SaveElectrostaticPotential True
SaveTotalPotential no
WriteCoorXmol .true.
WriteMDXmol .true.
WriteMDhistory .false.
WriteEigenvalues yes
==================================================
==================================================
TS.Voltage 0.2 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 cross-terms
TS.Elecs.GF.ReUse true
%block TS.Elecs
  Left
  Right
%endblock TS.Elecs
%block TS.Elec.Left
  HS ../elec.TSHS
  chem-pot Left
  semi-inf-dir -a2
  elec-pos begin 1
%endblock TS.Elec.Left
%block TS.Elec.Right
  HS ../elec.TSHS
  chem-pot Right
  semi-inf-dir +a2
  elec-pos end -1
%endblock TS.Elec.Right
TS.Contours.Eq.Pole 2.50000 eV
%block TS.Contour.c-Left
  part circle
   from -30.2 eV + V/2 to -10. kT + V/2
    points 16
     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 -30.2 eV - V/2 to -10. kT - V/2
    points 16
     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
# TBtrans options
%block TBT.k
  diag 1 20 1
%endblock
TBT.T.Eig 3
TBT.Elecs.Eta 0.0000136058 eV
%block TBT.Contours
  neq
%endblock TBT.Contours
%block TBT.Contour.neq
  part line
   from -10.2 eV to 10.2 eV
    delta 0.02000 eV
     method mid-rule
%endblock TBT.Contour.neq
# It is adviced to define a device region of
# particular interest
************************** End of input data file *****************************

reinit: -----------------------------------------------------------------------
reinit: System Name: scatt
reinit: -----------------------------------------------------------------------
reinit: System Label: scatt
reinit: -----------------------------------------------------------------------
Reading two-body potentials
Grimme - two-body potential between 1 and 1
Grimme - two-body potential between 1 and 2
Grimme - two-body potential between 1 and 3
Grimme - two-body potential between 1 and 4
Grimme - two-body potential between 1 and 5
Grimme - two-body potential between 2 and 2
Grimme - two-body potential between 2 and 3
Grimme - two-body potential between 2 and 4
Grimme - two-body potential between 2 and 5
Grimme - two-body potential between 3 and 3
Grimme - two-body potential between 3 and 4
Grimme - two-body potential between 3 and 5
Grimme - two-body potential between 4 and 4
Grimme - two-body potential between 4 and 5
Grimme - two-body potential between 5 and 5

initatom: Reading input for the pseudopotentials and atomic orbitals ----------
Species number: 1 Atomic number: 40 Label: Zr
Species number: 2 Atomic number: 6 Label: C
Species number: 3 Atomic number: 16 Label: S

Ground state valence configuration: 5s02 4d02

Reading pseudopotential from: Zr.psml

PSML file version: 1.1
Using libxc ids: 101 130
GGA--PBE XC_GGA_X_PBE--XC_GGA_C_PBE pb
 Using ATOM defaults for log grid...
PSML uuid: 855db780-be42-11e7-4bdf-8c7dadbbbec5
Dumping pseudopotential information in formatted form in Zr.psdump
Ground state valence configuration: 2s02 2p02

Reading pseudopotential from: C.psml

PSML file version: 1.1
Using libxc ids: 101 130
GGA--PBE XC_GGA_X_PBE--XC_GGA_C_PBE pb
 Using ATOM defaults for log grid...
PSML uuid: 297821e0-be41-11e7-6802-e1ff7dfff095
Dumping pseudopotential information in formatted form in C.psdump
Ground state valence configuration: 3s02 3p04

Reading pseudopotential from: S.psml

PSML file version: 1.1
Using libxc ids: 101 130
GGA--PBE XC_GGA_X_PBE--XC_GGA_C_PBE pb
 Using ATOM defaults for log grid...
PSML uuid: 909d2960-be41-11e7-50bc-670bf7fdfe34
Dumping pseudopotential information in formatted form in S.psdump
Semicore shell(s) with 8 electrons included in the valence for
Zr
resizes: Read basis size for species Zr = szp
resizes: Read basis size for species C = szp
resizes: Read basis size for species S = szp

Valence configuration for pseudopotential generation:
4s( 2.00) rc: 1.57
4p( 6.00) rc: 1.57
4d( 2.00) rc: 1.51
  -- Semicore analysis
For l=0, gen_n, nval_gs: 4 5
* There are 1 semicore shells
For l=1, gen_n, nval_gs: 4 5
* There are 1 semicore shells

Valence configuration for pseudopotential generation:
2s( 2.00) rc: 1.20
2p( 2.00) rc: 1.26

Valence configuration for pseudopotential generation:
3s( 2.00) rc: 1.45
3p( 4.00) rc: 1.45
3d( 0.00) rc: 1.62
For Zr, standard SIESTA heuristics set lmxkb to 3
 (one more than the basis l, including polarization orbitals).
Use PS.lmax or PS.KBprojectors blocks to override.
For C, standard SIESTA heuristics set lmxkb to 3
 (one more than the basis l, including polarization orbitals).
Use PS.lmax or PS.KBprojectors blocks to override.
For S, standard SIESTA heuristics set lmxkb to 3
 (one more than the basis l, including polarization orbitals).
Use PS.lmax or PS.KBprojectors blocks to override.
Pseudopotential only contains V_ls up to l=2 -- lmxkb reset.
Pseudopotential only contains V_ls up to l=1 -- lmxkb reset.
Pseudopotential only contains V_ls up to l=2 -- lmxkb reset.

<basis_specs>
===============================================================================
Zr Z= 40 Mass= 91.220 Charge= 0.17977+309
Lmxo=2 Lmxkb= 2 BasisType=split Semic=T
L=0 Nsemic=1 Cnfigmx=5
          n=1 nzeta=1 polorb=0 (4s)
            splnorm: 0.15000
               vcte: 0.0000
               rinn: 0.0000
               qcoe: 0.0000
               qyuk: 0.0000
               qwid: 0.10000E-01
                rcs: 0.0000
            lambdas: 1.0000
          n=2 nzeta=1 polorb=1 (5s) (to be polarized perturbatively)
            splnorm: 0.15000
               vcte: 0.0000
               rinn: 0.0000
               qcoe: 0.0000
               qyuk: 0.0000
               qwid: 0.10000E-01
                rcs: 0.0000
            lambdas: 1.0000
L=1 Nsemic=1 Cnfigmx=5
          n=1 nzeta=1 polorb=0 (4p)
            splnorm: 0.15000
               vcte: 0.0000
               rinn: 0.0000
               qcoe: 0.0000
               qyuk: 0.0000
               qwid: 0.10000E-01
                rcs: 0.0000
            lambdas: 1.0000
          n=2 nzeta=0 polorb=0 (5p) (empty shell -- could be pol. orbital)
L=2 Nsemic=0 Cnfigmx=4
          n=1 nzeta=1 polorb=0 (4d)
            splnorm: 0.15000
               vcte: 0.0000
               rinn: 0.0000
               qcoe: 0.0000
               qyuk: 0.0000
               qwid: 0.10000E-01
                rcs: 0.0000
            lambdas: 1.0000
-------------------------------------------------------------------------------
L=0 Nkbl=2 erefs: 0.17977+309 0.17977+309
L=1 Nkbl=2 erefs: 0.17977+309 0.17977+309
L=2 Nkbl=1 erefs: 0.17977+309
===============================================================================
</basis_specs>

atom: Called for Zr (Z = 40)

read_vps: Pseudopotential generation method:
read_vps: ONCVPSP-3.Hamann's oncvpsp
Total valence charge: 12.00000

read_vps: Pseudopotential includes a core correction:
read_vps: Pseudo-core for xc-correction

xc_check: Exchange-correlation functional:
xc_check: GGA Perdew, Burke & Ernzerhof 1996
Got Vlocal (oncv-fit) from psml data
Choosing vlocal chloc cutoff: 5.331374
qtot up to nchloc: 11.99992665
atom: Maximum radius forchloc: 5.33137
atom: Maximum radius for r*vlocal+2*Zval: 5.33137
Reading KB projs from Zr psml data
Using scalar-relativistic projectors in PSML file

PSML: Kleinman-Bylander projectors:
   l= 0 rc= 1.585788 Ekb= 21.243531
   l= 0 rc= 1.585788 Ekb= 1.797610
   l= 1 rc= 1.585788 Ekb= 11.699674
   l= 1 rc= 1.585788 Ekb= 1.500681
   l= 2 rc= 1.546633 Ekb= 3.062955
   l= 2 rc= 1.546633 Ekb= 1.006046

PSML: Total number of Kleinman-Bylander projectors: 18
atom: -------------------------------------------------------------------------

atom: SANKEY-TYPE ORBITALS:

SPLIT: Orbitals with angular momentum L= 0

SPLIT: Basis orbitals for state 4s

SPLIT: PAO cut-off radius determined from an
SPLIT: energy shift= 0.007350 Ry

   izeta = 1
                 lambda = 1.000000
                     rc = 3.274292
                 energy = -3.999476
                kinetic = 1.918062
    potential(screened) = -5.917538
       potential(ionic) = -18.717491

SPLIT: Basis orbitals for state 5s

SPLIT: PAO cut-off radius determined from an
SPLIT: energy shift= 0.007350 Ry

   izeta = 1
                 lambda = 1.000000
                     rc = 8.257427
                 energy = -0.327139
                kinetic = 0.683137
    potential(screened) = -1.010276
       potential(ionic) = -7.793053

SPLIT: Orbitals with angular momentum L= 1

SPLIT: Basis orbitals for state 4p

SPLIT: PAO cut-off radius determined from an
SPLIT: energy shift= 0.007350 Ry

   izeta = 1
                 lambda = 1.000000
                     rc = 3.804194
                 energy = -2.379844
                kinetic = 3.058785
    potential(screened) = -5.438629
       potential(ionic) = -17.714913

SPLIT: Orbitals with angular momentum L= 2

SPLIT: Basis orbitals for state 4d

SPLIT: PAO cut-off radius determined from an
SPLIT: energy shift= 0.007350 Ry

   izeta = 1
                 lambda = 1.000000
                     rc = 6.593677
                 energy = -0.257953
                kinetic = 2.827881
    potential(screened) = -3.085834
       potential(ionic) = -12.912185

POLgen: Perturbative polarization orbital with L= 1

POLgen: Polarization orbital for state 5s

   izeta = 1
                     rc = 8.257427
                 energy = -0.048652
                kinetic = 0.878892
    potential(screened) = -0.927544
       potential(ionic) = -7.141915
atom: Total number of Sankey-type orbitals: 13

atm_pop: Valence configuration (for local Pseudopot. screening):
 4s( 2.00) 5s( 2.00)
 4p( 6.00) 5p( 0.00)
 4d( 2.00)
Vna: chval, zval: 12.00000 12.00000

Vna: Cut-off radius for the neutral-atom potential: 8.257427
comcore: Pseudo-core radius Rcore= 2.647451

atom: _________________________________________________________________________

<basis_specs>
===============================================================================
C Z= 6 Mass= 12.010 Charge= 0.17977+309
Lmxo=2 Lmxkb= 1 BasisType=split Semic=F
L=0 Nsemic=0 Cnfigmx=2
          n=1 nzeta=1 polorb=0 (2s)
            splnorm: 0.15000
               vcte: 0.0000
               rinn: 0.0000
               qcoe: 0.0000
               qyuk: 0.0000
               qwid: 0.10000E-01
                rcs: 0.0000
            lambdas: 1.0000
L=1 Nsemic=0 Cnfigmx=2
          n=1 nzeta=1 polorb=1 (2p) (to be polarized perturbatively)
            splnorm: 0.15000
               vcte: 0.0000
               rinn: 0.0000
               qcoe: 0.0000
               qyuk: 0.0000
               qwid: 0.10000E-01
                rcs: 0.0000
            lambdas: 1.0000
L=2 Nsemic=0 Cnfigmx=3
          n=1 nzeta=0 polorb=0 (3d) (perturbative polarization orbital)
-------------------------------------------------------------------------------
L=0 Nkbl=1 erefs: 0.17977+309
L=1 Nkbl=1 erefs: 0.17977+309
===============================================================================
</basis_specs>

atom: Called for C (Z = 6)
read_vps: NOTE: Your pseudopotential does not have
read_vps: NOTE: L up to the canonical 2

read_vps: Pseudopotential generation method:
read_vps: ONCVPSP-3.Hamann's oncvpsp
Total valence charge: 4.00000

read_vps: Pseudopotential includes a core correction:
read_vps: Pseudo-core for xc-correction

xc_check: Exchange-correlation functional:
xc_check: GGA Perdew, Burke & Ernzerhof 1996
Got Vlocal (oncv-fit) from psml data
Choosing vlocal chloc cutoff: 4.139772
qtot up to nchloc: 3.99998844
atom: Maximum radius forchloc: 4.13977
atom: Maximum radius for r*vlocal+2*Zval: 4.13977
Reading KB projs from C psml data
Using scalar-relativistic projectors in PSML file

PSML: Kleinman-Bylander projectors:
   l= 0 rc= 1.231096 Ekb= 12.963096
   l= 0 rc= 1.231096 Ekb= 0.771007
   l= 1 rc= 1.294237 Ekb= -8.399923
   l= 1 rc= 1.294237 Ekb= -1.755033

PSML: Total number of Kleinman-Bylander projectors: 8
atom: -------------------------------------------------------------------------

atom: SANKEY-TYPE ORBITALS:

SPLIT: Orbitals with angular momentum L= 0

SPLIT: Basis orbitals for state 2s

SPLIT: PAO cut-off radius determined from an
SPLIT: energy shift= 0.007350 Ry

   izeta = 1
                 lambda = 1.000000
                     rc = 4.632753
                 energy = -1.003181
                kinetic = 0.940934
    potential(screened) = -1.944115
       potential(ionic) = -5.493150

SPLIT: Orbitals with angular momentum L= 1

SPLIT: Basis orbitals for state 2p

SPLIT: PAO cut-off radius determined from an
SPLIT: energy shift= 0.007350 Ry

   izeta = 1
                 lambda = 1.000000
                     rc = 5.658549
                 energy = -0.380902
                kinetic = 2.464200
    potential(screened) = -2.845101
       potential(ionic) = -6.254437

** Using vlocal for PAOs with L= 2

POLgen: Perturbative polarization orbital with L= 2

POLgen: Polarization orbital for state 2p

   izeta = 1
                     rc = 5.658549
                 energy = 1.108070
                kinetic = 2.284008
    potential(screened) = -1.175938
       potential(ionic) = -3.987008
atom: Total number of Sankey-type orbitals: 9

atm_pop: Valence configuration (for local Pseudopot. screening):
 2s( 2.00)
 2p( 2.00)
 3d( 0.00)
Vna: chval, zval: 4.00000 4.00000

Vna: Cut-off radius for the neutral-atom potential: 5.658549
comcore: Pseudo-core radius Rcore= 1.682861

atom: _________________________________________________________________________

<basis_specs>
===============================================================================
S Z= 16 Mass= 32.070 Charge= 0.17977+309
Lmxo=2 Lmxkb= 2 BasisType=split Semic=F
L=0 Nsemic=0 Cnfigmx=3
          n=1 nzeta=1 polorb=0 (3s)
            splnorm: 0.15000
               vcte: 0.0000
               rinn: 0.0000
               qcoe: 0.0000
               qyuk: 0.0000
               qwid: 0.10000E-01
                rcs: 0.0000
            lambdas: 1.0000
L=1 Nsemic=0 Cnfigmx=3
          n=1 nzeta=1 polorb=1 (3p) (to be polarized perturbatively)
            splnorm: 0.15000
               vcte: 0.0000
               rinn: 0.0000
               qcoe: 0.0000
               qyuk: 0.0000
               qwid: 0.10000E-01
                rcs: 0.0000
            lambdas: 1.0000
L=2 Nsemic=0 Cnfigmx=3
          n=1 nzeta=0 polorb=0 (3d) (perturbative polarization orbital)
-------------------------------------------------------------------------------
L=0 Nkbl=1 erefs: 0.17977+309
L=1 Nkbl=1 erefs: 0.17977+309
L=2 Nkbl=1 erefs: 0.17977+309
===============================================================================
</basis_specs>

atom: Called for S (Z = 16)

read_vps: Pseudopotential generation method:
read_vps: ONCVPSP-3.Hamann's oncvpsp
Total valence charge: 6.00000

read_vps: Pseudopotential includes a core correction:
read_vps: Pseudo-core for xc-correction

xc_check: Exchange-correlation functional:
xc_check: GGA Perdew, Burke & Ernzerhof 1996
Got Vlocal (oncv-fit) from psml data
Choosing vlocal chloc cutoff: 5.418845
qtot up to nchloc: 6.00010210
atom: Maximum radius forchloc: 5.41884
atom: Maximum radius for r*vlocal+2*Zval: 5.41884
Reading KB projs from S psml data
Using scalar-relativistic projectors in PSML file

PSML: Kleinman-Bylander projectors:
   l= 0 rc= 1.476695 Ekb= 13.527902
   l= 0 rc= 1.476695 Ekb= 1.148216
   l= 1 rc= 1.476695 Ekb= 6.454160
   l= 1 rc= 1.476695 Ekb= 1.774658
   l= 2 rc= 1.652547 Ekb= -7.095324
   l= 2 rc= 1.652547 Ekb= -1.973049

PSML: Total number of Kleinman-Bylander projectors: 18
atom: -------------------------------------------------------------------------

atom: SANKEY-TYPE ORBITALS:

SPLIT: Orbitals with angular momentum L= 0

SPLIT: Basis orbitals for state 3s

SPLIT: PAO cut-off radius determined from an
SPLIT: energy shift= 0.007350 Ry

   izeta = 1
                 lambda = 1.000000
                     rc = 4.606082
                 energy = -1.261269
                kinetic = 0.950516
    potential(screened) = -2.211786
       potential(ionic) = -7.154616

SPLIT: Orbitals with angular momentum L= 1

SPLIT: Basis orbitals for state 3p

SPLIT: PAO cut-off radius determined from an
SPLIT: energy shift= 0.007350 Ry

   izeta = 1
                 lambda = 1.000000
                     rc = 5.768340
                 energy = -0.508268
                kinetic = 1.446482
    potential(screened) = -1.954751
       potential(ionic) = -6.542013

POLgen: Perturbative polarization orbital with L= 2

POLgen: Polarization orbital for state 3p

   izeta = 1
                     rc = 5.768340
                 energy = 0.654686
                kinetic = 2.019286
    potential(screened) = -1.364600
       potential(ionic) = -5.498501
atom: Total number of Sankey-type orbitals: 9

atm_pop: Valence configuration (for local Pseudopot. screening):
 3s( 2.00)
 3p( 4.00)
 3d( 0.00)
Vna: chval, zval: 6.00000 6.00000

Vna: Cut-off radius for the neutral-atom potential: 5.768340
comcore: Pseudo-core radius Rcore= 2.203046

atom: _________________________________________________________________________

prinput: Basis input
* WARNING: This information might be incomplete!!!
----------------------------------------------------------

PAO.BasisType split

%block ChemicalSpeciesLabel
    1 40 Zr # Species index, atomic number, species label
    2 6 C # Species index, atomic number, species label
    3 16 S # Species index, atomic number, species label
%endblock ChemicalSpeciesLabel

%block PAO.Basis # Define Basis set
# WARNING: This information might be incomplete!!!
Zr 4 # Species label, number of l-shells
 n=4 0 1 # n, l, Nzeta
   3.274
   1.000
 n=5 0 1 P 1 # n, l, Nzeta, Polarization, NzetaPol
   8.257
   1.000
 n=4 1 1 # n, l, Nzeta
   3.804
   1.000
 n=4 2 1 # n, l, Nzeta
   6.594
   1.000
C 2 # Species label, number of l-shells
 n=2 0 1 # n, l, Nzeta
   4.633
   1.000
 n=2 1 1 P 1 # n, l, Nzeta, Polarization, NzetaPol
   5.659
   1.000
S 2 # Species label, number of l-shells
 n=3 0 1 # n, l, Nzeta
   4.606
   1.000
 n=3 1 1 P 1 # n, l, Nzeta, Polarization, NzetaPol
   5.768
   1.000
%endblock PAO.Basis

prinput: ----------------------------------------------------------------------

 CH_OVERLAP: Z1= 11.997475338769984 ZVAL1= 12.000000000000000
 CH_OVERLAP: Z2= 11.997475338769984 ZVAL2= 12.000000000000000
 CH_OVERLAP: Z1= 3.9934911538047020 ZVAL1= 4.0000000000000000
 CH_OVERLAP: Z2= 3.9934911538047020 ZVAL2= 4.0000000000000000
 CH_OVERLAP: Z1= 3.9934911538047020 ZVAL1= 4.0000000000000000
 CH_OVERLAP: Z2= 11.997475338769984 ZVAL2= 12.000000000000000
 CH_OVERLAP: Z1= 5.9893992321624037 ZVAL1= 6.0000000000000000
 CH_OVERLAP: Z2= 5.9893992321624037 ZVAL2= 6.0000000000000000
 CH_OVERLAP: Z1= 5.9893992321624037 ZVAL1= 6.0000000000000000
 CH_OVERLAP: Z2= 3.9934911538047020 ZVAL2= 4.0000000000000000
 CH_OVERLAP: Z1= 5.9893992321624037 ZVAL1= 6.0000000000000000
 CH_OVERLAP: Z2= 11.997475338769984 ZVAL2= 12.000000000000000
Dumping basis to NetCDF file Zr.ion.nc
Dumping basis to NetCDF file C.ion.nc
Dumping basis to NetCDF file S.ion.nc
coor: Atomic-coordinates input format = Cartesian coordinates
coor: (in Angstroms)

siesta: Atomic coordinates (Bohr) and species
siesta: 7.10931 0.95072 6.09926 2 1
siesta: 0.58122 0.95079 6.09934 2 2
siesta: 13.63727 0.95084 6.09936 2 3
siesta: 3.84535 2.83403 0.52962 3 4
siesta: 10.37333 2.83405 0.52961 3 5
siesta: 16.90132 2.83408 0.52961 3 6
siesta: 16.90227 2.83583 8.64540 1 7
siesta: 10.37428 2.83584 8.64535 1 8
siesta: 3.84620 2.83590 8.64545 1 9
siesta: 0.58065 4.71926 3.55151 1 10
siesta: 13.63663 4.71926 3.55156 1 11
siesta: 7.10864 4.71932 3.55155 1 12
siesta: 0.58510 4.72209 11.66801 3 13
siesta: 7.11309 4.72211 11.66799 3 14
siesta: 13.64102 4.72216 11.66808 3 15
siesta: 3.84642 6.60438 6.09933 2 16
siesta: -2.68158 6.60440 6.09934 2 17
siesta: 10.37438 6.60440 6.09932 2 18
siesta: 7.11053 8.48764 0.52963 3 19
siesta: 0.58254 8.48768 0.52963 3 20
siesta: 13.63852 8.48769 0.52961 3 21
siesta: 13.63945 8.48944 8.64532 1 22
siesta: 0.58335 8.48948 8.64545 1 23
siesta: 7.11144 8.48948 8.64532 1 24
siesta: -2.68213 10.37287 3.55156 1 25
siesta: 10.37385 10.37288 3.55154 1 26
siesta: 3.84583 10.37290 3.55158 1 27
siesta: 10.37827 10.37572 11.66800 3 28
siesta: -2.67779 10.37573 11.66805 3 29
siesta: 3.85021 10.37574 11.66806 3 30
siesta: -5.94440 12.25799 6.09934 2 31
siesta: 0.58365 12.25799 6.09936 2 32
siesta: 7.11161 12.25802 6.09936 2 33
siesta: 3.84776 14.14125 0.52962 3 34
siesta: -2.68024 14.14126 0.52963 3 35
siesta: 10.37575 14.14128 0.52962 3 36
siesta: 10.37667 14.14305 8.64544 1 37
siesta: -2.67933 14.14307 8.64529 1 38
siesta: 3.84864 14.14312 8.64540 1 39
siesta: -5.94493 16.02644 3.55155 1 40
siesta: 0.58311 16.02648 3.55153 1 41
siesta: 7.11104 16.02650 3.55157 1 42
siesta: -5.94058 16.02934 11.66810 3 43
siesta: 0.58739 16.02934 11.66808 3 44
siesta: 7.11531 16.02942 11.66818 3 45
siesta: -2.67907 17.91152 6.09926 2 46
siesta: -9.20716 17.91159 6.09934 2 47
siesta: 3.84889 17.91164 6.09936 2 48
siesta: -5.94303 19.79483 0.52962 3 49
siesta: 0.58495 19.79485 0.52961 3 50
siesta: 7.11294 19.79488 0.52961 3 51
siesta: 7.11389 19.79663 8.64540 1 52
siesta: 0.58591 19.79664 8.64535 1 53
siesta: -5.94217 19.79670 8.64545 1 54
siesta: -9.20773 21.68006 3.55151 1 55
siesta: 3.84825 21.68006 3.55156 1 56
siesta: -2.67973 21.68013 3.55155 1 57
siesta: -9.20327 21.68289 11.66801 3 58
siesta: -2.67529 21.68291 11.66799 3 59
siesta: 3.85264 21.68296 11.66808 3 60
siesta: -5.94196 23.56518 6.09933 2 61
siesta: -12.46995 23.56520 6.09934 2 62
siesta: 0.58600 23.56520 6.09932 2 63
siesta: -2.67784 25.44844 0.52963 3 64
siesta: -9.20583 25.44848 0.52963 3 65
siesta: 3.85015 25.44849 0.52961 3 66
siesta: 3.85108 25.45025 8.64532 1 67
siesta: -9.20502 25.45028 8.64545 1 68
siesta: -2.67693 25.45029 8.64532 1 69
siesta: -12.47050 27.33367 3.55156 1 70
siesta: 0.58548 27.33368 3.55154 1 71
siesta: -5.94254 27.33370 3.55158 1 72
siesta: 0.58990 27.33653 11.66800 3 73
siesta: -12.46617 27.33653 11.66805 3 74
siesta: -5.93817 27.33654 11.66806 3 75
siesta: -15.73278 29.21879 6.09934 2 76
siesta: -9.20472 29.21879 6.09936 2 77
siesta: -2.67677 29.21882 6.09936 2 78
siesta: -5.94062 31.10205 0.52962 3 79
siesta: -12.46862 31.10206 0.52963 3 80
siesta: 0.58737 31.10208 0.52962 3 81
siesta: 0.58830 31.10385 8.64544 1 82
siesta: -12.46770 31.10387 8.64529 1 83
siesta: -5.93973 31.10392 8.64540 1 84
siesta: -15.73331 32.98724 3.55155 1 85
siesta: -9.20527 32.98728 3.55153 1 86
siesta: -2.67733 32.98730 3.55157 1 87
siesta: -15.72896 32.99014 11.66810 3 88
siesta: -9.20099 32.99014 11.66808 3 89
siesta: -2.67306 32.99022 11.66818 3 90
siesta: -12.46745 34.87232 6.09926 2 91
siesta: -18.99553 34.87239 6.09934 2 92
siesta: -5.93949 34.87244 6.09936 2 93
siesta: -15.73140 36.75563 0.52962 3 94
siesta: -9.20342 36.75565 0.52961 3 95
siesta: -2.67543 36.75568 0.52961 3 96
siesta: -2.67448 36.75744 8.64540 1 97
siesta: -9.20247 36.75745 8.64535 1 98
siesta: -15.73055 36.75750 8.64545 1 99
siesta: -18.99610 38.64086 3.55151 1 100
siesta: -5.94013 38.64086 3.55156 1 101
siesta: -12.46811 38.64093 3.55155 1 102
siesta: -18.99165 38.64369 11.66801 3 103
siesta: -12.46367 38.64371 11.66799 3 104
siesta: -5.93573 38.64377 11.66808 3 105
siesta: -15.73034 40.52598 6.09933 2 106
siesta: -22.25833 40.52600 6.09934 2 107
siesta: -9.20237 40.52600 6.09932 2 108
siesta: -12.46622 42.40924 0.52963 3 109
siesta: -18.99421 42.40928 0.52963 3 110
siesta: -5.93823 42.40929 0.52961 3 111
siesta: -5.93730 42.41105 8.64532 1 112
siesta: -18.99340 42.41108 8.64545 1 113
siesta: -12.46531 42.41109 8.64532 1 114
siesta: -22.25888 44.29447 3.55156 1 115
siesta: -9.20290 44.29449 3.55154 1 116
siesta: -15.73092 44.29450 3.55158 1 117
siesta: -9.19848 44.29733 11.66800 3 118
siesta: -22.25454 44.29733 11.66805 3 119
siesta: -15.72654 44.29734 11.66806 3 120
siesta: -25.52115 46.17960 6.09934 2 121
siesta: -18.99310 46.17960 6.09936 2 122
siesta: -12.46515 46.17962 6.09936 2 123
siesta: -15.72899 48.06285 0.52962 3 124
siesta: -22.25700 48.06286 0.52963 3 125
siesta: -9.20100 48.06288 0.52962 3 126
siesta: -9.20008 48.06466 8.64544 1 127
siesta: -22.25608 48.06467 8.64529 1 128
siesta: -15.72811 48.06472 8.64540 1 129
siesta: -25.52168 49.94804 3.55155 1 130
siesta: -18.99364 49.94808 3.55153 1 131
siesta: -12.46571 49.94810 3.55157 1 132
siesta: -25.51733 49.95094 11.66810 3 133
siesta: -18.98936 49.95094 11.66808 3 134
siesta: -12.46144 49.95102 11.66818 3 135

siesta: System type = slab

initatomlists: Number of atoms, orbitals, and projectors: 135 1431 2160

coxmol: Writing XMOL coordinates into file scatt.xyz

siesta: ******************** Simulation parameters ****************************
siesta:
siesta: The following are some of the parameters of the simulation.
siesta: A complete list of the parameters used, including default values,
siesta: can be found in file out.fdf
siesta:
redata: Spin configuration = none
redata: Number of spin components = 1
redata: Time-Reversal Symmetry = T
redata: Spin-spiral = F
redata: Long output = F
redata: Number of Atomic Species = 3
redata: Charge density info will appear in .RHO file
redata: Write Mulliken Pop. = Atomic and Orbital charges
redata: Matel table size (NRTAB) = 1024
redata: Mesh Cutoff = 300.0000 Ry
redata: Net charge of the system = 0.0000 |e|
redata: Min. number of SCF Iter = 0
redata: Max. number of SCF Iter = 500
redata: SCF convergence failure will abort job
redata: SCF mix quantity = Hamiltonian
redata: Mix DM or H after convergence = F
redata: Recompute H after scf cycle = F
redata: Mix DM in first SCF step = T
redata: Write Pulay info on disk = F
redata: New DM Mixing Weight = 0.0300
redata: New DM Occupancy tolerance = 0.000000000001
redata: No kicks to SCF
redata: DM Mixing Weight for Kicks = 0.5000
redata: Require Harris convergence for SCF = F
redata: Harris energy tolerance for SCF = 0.000100 eV
redata: Require DM convergence for SCF = T
redata: DM tolerance for SCF = 0.000100
redata: Require EDM convergence for SCF = F
redata: EDM tolerance for SCF = 0.001000 eV
redata: Require H convergence for SCF = T
redata: Hamiltonian tolerance for SCF = 0.001000 eV
redata: Require (free) Energy convergence for SCF = F
redata: (free) Energy tolerance for SCF = 0.000100 eV
redata: Using Saved Data (generic) = F
redata: Use continuation files for DM = T
redata: Neglect nonoverlap interactions = F
redata: Method of Calculation = Transiesta
redata: Fix the spin of the system = F
redata: Max. number of TDED Iter = 1
redata: Number of TDED substeps = 3
redata: Dynamics option = Single-point calculation
mix.SCF: Pulay mixing = Pulay
mix.SCF: Variant = stable
mix.SCF: History steps = 5
mix.SCF: Linear mixing weight = 0.030000
mix.SCF: Mixing weight = 0.030000
mix.SCF: SVD condition = 0.1000E-07
redata: ***********************************************************************

%block SCF.Mixers
  Pulay
%endblock SCF.Mixers

%block SCF.Mixer.Pulay
  # Mixing method
  method pulay
  variant stable

  # Mixing options
  weight 0.0300
  weight.linear 0.0300
  history 5
%endblock SCF.Mixer.Pulay

DM_history_depth set to one: no extrapolation allowed by default for geometry relaxation
Size of DM history Fstack: 1
Total number of electrons: 1080.000000
Total ionic charge: 1080.000000

* ProcessorY, Blocksize: 4 24

* Orbital distribution balance (max,min): 72 48

 Kpoints in: 2 . Kpoints trimmed: 2

siesta: k-grid: Number of k-points = 2
siesta: k-points from Monkhorst-Pack grid
siesta: k-cutoff (effective) = 9.230 Ang
siesta: k-point supercell and displacements
siesta: k-grid: 3 0 0 0.000
siesta: k-grid: 0 1 0 0.000
siesta: k-grid: 0 0 1 0.000

diag: Algorithm = Expert
diag: Parallel over k = T
diag: Use parallel 2D distribution = T
diag: Parallel block-size = 24
diag: Parallel distribution = 4 x 6
diag: Used triangular part = Lower
diag: Absolute tolerance = 0.100E-15
diag: Orthogonalization factor = 0.100E-05
diag: Memory factor = 1.0000

superc: Internal auxiliary supercell: 3 x 3 x 1 = 9
superc: Number of atoms, orbitals, and projectors: 1215 12879 19440

 Kpoints in: 2 . Kpoints trimmed: 2

siesta: transiesta k-grid: Number of k-points = 2
siesta: transiesta k-points from Monkhorst-Pack grid
siesta: transiesta k-cutoff (effective) = 9.230 Ang
siesta: transiesta k-point supercell and displacements
siesta: k-grid: 3 0 0 0.000
siesta: k-grid: 0 1 0 0.000
siesta: k-grid: 0 0 1 0.000

ts: **************************************************************
ts: Voltage = 0.2000 Volts
ts: Save H and S matrices = T
ts: Electronic temperature = 299.997806 K
ts: Transport along unit-cell vector = A2
ts: Transport along Cartesian vector = Y
ts: Fixing Hartree potential at electrode-plane = Left
ts: Fix Hartree potential fraction = 1.0000
ts: Hartree potential offset = 0.000000 eV
ts: Solution method = BTD
ts: BTD pivoting method = atom+Left
ts: BTD creation algorithm = speed
ts: BTD spectral function algorithm = propagation
ts: SCF.TS DM tolerance = 0.100E-03
ts: SCF.TS Hamiltonian tolerance = 0.001000 eV
ts: Initialize DM by = diagon
ts: Initial DM for electrodes = this
ts: Hartree potential as linear ramp
ts: Hartree potential ramp across central region
ts: Thermal non-equilibrium in distributions = F
ts: Non-equilibrium contour weight method = orb-orb
ts: Non-equilibrium contour weight k-method = Correlated k-points
ts: Will not correct charge fluctuations
ts: TS.SCF mixing options same as SCF
ts: >> Electrodes <<
ts: >> Left
ts: Electrode cell pivoting: E1, E2, E3 = A1, A2, A3
ts: GF file = scatt.TSGFLeft
ts: Reuse existing GF-file = T
ts: Electrode TSHS file = ../elec.TSHS
ts: # atoms used in electrode = 45
ts: Electrode Bloch unity [E1 x E2 x E3] = 1 x 1 x 1
ts: Position in geometry = 1 -- 45
ts: Semi-infinite direction for electrode = negative wrt. E2
ts: Chemical shift = 0.100000 eV
ts: Electronic temperature = 299.997806 K
ts: Bulk values in electrode = T
ts: Cross-terms are updated
ts: Hamiltonian E-C Ef fractional shift = 0.0000
ts: Electrode self-energy imaginary Eta = 0.1000E-03 eV
ts: Electrode self-energy accuracy = 0.1000E-13 eV
ts: Electrode inter-layer distance (semi-inf) = 1.1436 Ang
ts: >> Right
ts: Electrode cell pivoting: E1, E2, E3 = A1, A2, A3
ts: GF file = scatt.TSGFRight
ts: Reuse existing GF-file = T
ts: Electrode TSHS file = ../elec.TSHS
ts: # atoms used in electrode = 45
ts: Electrode Bloch unity [E1 x E2 x E3] = 1 x 1 x 1
ts: Position in geometry = 91 -- 135
ts: Semi-infinite direction for electrode = positive wrt. E2
ts: Chemical shift = -0.100000 eV
ts: Electronic temperature = 299.997806 K
ts: Bulk values in electrode = T
ts: Cross-terms are updated
ts: Hamiltonian E-C Ef fractional shift = 0.0000
ts: Electrode self-energy imaginary Eta = 0.1000E-03 eV
ts: Electrode self-energy accuracy = 0.1000E-13 eV
ts: Electrode inter-layer distance (semi-inf) = 1.1436 Ang
ts: ----------------- Contour -----------------
ts: >> Residual contour <<
ts: Pole chemical potential = 0.1000 eV
ts: Chemical potential temperature = 299.9978 K
ts: Number of poles = 16
ts: Top energy point = 2.5989 eV
ts: Pole chemical potential = -0.1000 eV
ts: Chemical potential temperature = 299.9978 K
ts: Number of poles = 16
ts: Top energy point = 2.5989 eV
ts: >> Equilibrium contour <<
ts: Contour name = TS.Contour.c-Left
ts: circle contour E_min = -30.1000 eV
ts: circle contour E_max = -0.1585 eV
ts: circle contour points = 16
ts: circle contour method = Gauss-Legendre
ts: Contour name = TS.Contour.t-Left
ts: tail contour E_min = -0.1585 eV
ts: tail contour E_max = Infinity
ts: tail contour points = 11
ts: tail contour method = Gauss-Fermi (0kT)
ts: Contour name = TS.Contour.c-Right
ts: circle contour E_min = -30.3000 eV
ts: circle contour E_max = -0.3585 eV
ts: circle contour points = 16
ts: circle contour method = Gauss-Legendre
ts: Contour name = TS.Contour.t-Right
ts: tail contour E_min = -0.3585 eV
ts: tail contour E_max = Infinity
ts: tail contour points = 11
ts: tail contour method = Gauss-Fermi (0kT)
ts: >> non-Equilibrium contour <<
ts: Device Green function imaginary Eta = 0.000 eV
ts: Fermi-function cut-off = 5.000 kT
ts: Contour name = TS.Contour.nEq.neq
ts: line contour E_min = -0.2293 eV
ts: line contour E_max = 0.2293 eV
ts: line contour points = 46
ts: line contour method = Mid-rule
ts: **************************************************************

************************ Begin: TS CHECKS AND WARNINGS ************************
Without loosing performance you can increase the equilibrium integration precision.
You can add 10 more energy points in the equilibrium contours, for FREE!
This is 5 more energy points per chemical potential.
Without loosing performance you can increase the non-equilibrium integration precision.
You can add 2 more energy points in the non-equilibrium contours, for FREE!
************************ End: TS CHECKS AND WARNINGS **************************

>>> TranSiesta block information for FDF-file START <<<

%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
%block TS.Contour.c-Left
  part circle
   from -30.2 eV + V/2 to -10. kT + V/2
      points 16
        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 -30.2 eV - V/2 to -10. kT - V/2
      points 16
        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
%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

>>> TranSiesta block information for FDF-file END <<<

transiesta: Regions of atoms:
   ## (45): Elec.Left
     [ 1 -- 45 ]
   ## (45): Elec.Right
     [ 91 -- 135 ]
   -- (45): Device
     [ 46 -- 90 ]

  <sparsity:../elec.TSHS
    nrows_g=477 nrows=477 sparsity=1.3782 nnzs=313587, refcount: 3>
  <sparsity:(TM [--, 0,--] of: ../elec.TSHS)
    nrows_g=477 nrows=477 sparsity=.9440 nnzs=214785, refcount: 3>
  <sparsity:(TM [--,-1,--] of: ../elec.TSHS)
    nrows_g=477 nrows=477 sparsity=.2171 nnzs=49401, refcount: 3>
 Left principal cell is perfect!

Calculating all surface Green functions for: Left
 Fermi level shift in electrode (chemical potential) : 0.10000 eV
 Atoms available / used atoms : 45 / 45
 Orbitals available / used orbitals: 477 / 477
 Total self-energy calculations: 264
 Saving surface Green functions in: scatt.TSGFLeft
 Estimated file size: 930.447 MB
 Lopez Sancho, Lopez Sancho & Rubio recursive surface self-energy calculation...
 Lopez Sancho, Lopez Sancho & Rubio: Mean/std iterations: 9.0379 / 6.3918
 Lopez Sancho, Lopez Sancho & Rubio: Min/Max iterations : 4 / 18
Done creating 'scatt.TSGFLeft'.

  <sparsity:../elec.TSHS
    nrows_g=477 nrows=477 sparsity=1.3782 nnzs=313587, refcount: 3>
  <sparsity:(TM [--, 0,--] of: ../elec.TSHS)
    nrows_g=477 nrows=477 sparsity=.9440 nnzs=214785, refcount: 3>
  <sparsity:(TM [--, 1,--] of: ../elec.TSHS)
    nrows_g=477 nrows=477 sparsity=.2171 nnzs=49401, refcount: 3>
 Right principal cell is perfect!

Calculating all surface Green functions for: Right
 Fermi level shift in electrode (chemical potential) : -0.10000 eV
 Atoms available / used atoms : 45 / 45
 Orbitals available / used orbitals: 477 / 477
 Total self-energy calculations: 264
 Saving surface Green functions in: scatt.TSGFRight
 Estimated file size: 930.447 MB
 Lopez Sancho, Lopez Sancho & Rubio recursive surface self-energy calculation...
 Lopez Sancho, Lopez Sancho & Rubio: Mean/std iterations: 9.1477 / 6.5143
 Lopez Sancho, Lopez Sancho & Rubio: Min/Max iterations : 4 / 18
Done creating 'scatt.TSGFRight'.

                     ====================================
                        Single-point calculation
                     ====================================

superc: Internal auxiliary supercell: 3 x 3 x 1 = 9
superc: Number of atoms, orbitals, and projectors: 1215 12879 19440

outcell: Unit cell vectors (Ang):
       10.363400 0.000000 0.000000
      -15.539350 26.925798 0.000000
       -0.234909 -0.034089 18.459074

outcell: Cell vector modules (Ang) : 10.363400 31.088100 18.460600
outcell: Cell angles (23,13,12) (deg): 89.7272 90.7291 119.9900
outcell: Cell volume (Ang**3) : 5150.8721
<dSpData1D:S at geom step 0
  <sparsity:sparsity for geom step 0
    nrows_g=1431 nrows=72 sparsity=.0234 nnzs=47933, refcount: 7>
  <dData1D:(new from dSpData1D) n=47933, refcount: 1>
refcount: 1>
new_DM -- step: 1
Initializing Density Matrix...

Attempting to read DM, EDM from TSDE file... Succeeded...
DM from file:
<dSpData2D:IO-TSDE: scatt.TSDE
  <sparsity:IO-TSDE: scatt.TSDE
    nrows_g=1431 nrows=72 sparsity=.0234 nnzs=47933, refcount: 2>
  <dData2D:(new from dSpData2D) n=47933 m=1, refcount: 1>
refcount: 1>

transiesta: Starting immediately

                     ***************************
                     * WELCOME TO TRANSIESTA *
                     ***************************

No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 137 207
New grid distribution: 1
           1 1: 48 1: 36 1: 17
           2 1: 48 1: 36 18: 34
           3 1: 48 1: 36 35: 51
           4 1: 48 1: 36 52: 68
           5 1: 48 1: 36 69: 84
           6 1: 48 1: 36 85: 100
           7 1: 48 37: 72 1: 17
           8 1: 48 37: 72 18: 34
           9 1: 48 37: 72 35: 51
          10 1: 48 37: 72 52: 68
          11 1: 48 37: 72 69: 84
          12 1: 48 37: 72 85: 100
          13 1: 48 73: 108 1: 17
          14 1: 48 73: 108 18: 34
          15 1: 48 73: 108 35: 51
          16 1: 48 73: 108 52: 68
          17 1: 48 73: 108 69: 84
          18 1: 48 73: 108 85: 100
          19 1: 48 109: 144 1: 17
          20 1: 48 109: 144 18: 34
          21 1: 48 109: 144 35: 51
          22 1: 48 109: 144 52: 68
          23 1: 48 109: 144 69: 84
          24 1: 48 109: 144 85: 100

InitMesh: MESH = 96 x 288 x 200 = 5529600
InitMesh: (bp) = 48 x 144 x 100 = 691200
InitMesh: Mesh cutoff (required, used) = 300.000 316.192 Ry
ExtMesh (bp) on 0 = 144 x 132 x 113 = 2147904
New grid distribution: 2
           1 1: 48 109: 144 1: 9
           2 1: 48 73: 108 20: 24
           3 1: 24 1: 36 25: 100
           4 1: 24 73: 108 10: 19
           5 1: 48 73: 108 1: 9
           6 1: 48 109: 144 20: 24
           7 1: 48 37: 72 20: 24
           8 1: 24 37: 72 25: 100
           9 25: 48 37: 72 25: 100
          10 1: 48 37: 72 1: 9
          11 1: 24 1: 36 10: 19
          12 1: 48 1: 36 20: 24
          13 25: 48 1: 36 25: 100
          14 1: 48 1: 36 1: 9
          15 25: 48 1: 36 10: 19
          16 1: 24 37: 72 10: 19
          17 1: 24 73: 108 25: 100
          18 1: 24 109: 144 10: 19
          19 25: 48 109: 144 10: 19
          20 1: 24 109: 144 25: 100
          21 25: 48 73: 108 25: 100
          22 25: 48 109: 144 25: 100
          23 25: 48 37: 72 10: 19
          24 25: 48 73: 108 10: 19
New grid distribution: 3
           1 1: 48 109: 144 1: 11
           2 1: 48 1: 36 1: 11
           3 1: 24 73: 108 12: 32
           4 25: 48 1: 36 43: 100
           5 1: 24 1: 36 43: 100
           6 1: 48 73: 108 33: 43
           7 1: 48 1: 36 32: 42
           8 1: 48 109: 144 33: 42
           9 1: 48 73: 108 1: 11
          10 1: 24 37: 72 43: 100
          11 1: 48 37: 72 32: 42
          12 1: 24 1: 36 12: 31
          13 25: 48 37: 72 43: 100
          14 25: 48 109: 144 12: 32
          15 1: 24 37: 72 12: 31
          16 1: 24 73: 108 44: 100
          17 25: 48 109: 144 43: 100
          18 25: 48 73: 108 44: 100
          19 25: 48 37: 72 12: 31
          20 1: 24 109: 144 12: 32
          21 1: 48 37: 72 1: 11
          22 1: 24 109: 144 43: 100
          23 25: 48 73: 108 12: 32
          24 25: 48 1: 36 12: 31
Setting up quadratic distribution...
ExtMesh (bp) on 0 = 144 x 132 x 105 = 1995840
PhiOnMesh: Number of (b)points on node 0 = 15552
PhiOnMesh: nlist on node 0 = 1299162

ts: Using electrode: Left for Hartree correction
ts: Grid fraction plane 0.00051
ts: Grid point plane (Ang): -0.00796 0.01380 0.00000

ts-voltage: Ramp 0.100 eV to -0.100 eV placed between cell coordinates (Ang):
  { -4.964 8.601 0.000 } to { -10.521 18.231 0.000 }
ts-Vha: 0.54604E+00 eV

transiesta: created local update sparsity pattern:
  <sparsity:(M of: T T T sparsity for geom step 0)
    nrows_g=1431 nrows=72 sparsity=.0089 nnzs=18298, refcount: 1>

transiesta: update sparsity pattern same as H and S.

transiesta: Determining an optimal tri-matrix using: atom+Left
transiesta: Established a near-optimal partition for the tri-diagonal matrix.
BTD partitions (5):
  [ 121, [370] * 2, 411, 159 ]
transiesta: Matrix elements in % of full matrix: 62.54739 %

transiesta: mem of electrodes (static): 20.83MB
transiesta: mem of global update arrays (static): 32.72MB
transiesta: mem of master node sparse arrays: 0.84MB
transiesta: mem of tri-diagonal matrices: 39.09MB
transiesta: Total memory usage: 93.63MB

transiesta: Charge distribution, target = 1080.00000
Total charge [Q] : 1079.60171
Device [D] : 366.50780
Left [E1] : 353.55387
Left / device [C1] : 1.14764
Right [E2] : 353.55387
Right / device [C2] : -1.60760
Other [O] : 6.44613

ts-err-D: ij( 620, 620), M = 1.2461 , ew = 0.45541E-1, em = 0.53373E-1. avg_m = -.38012E-05
ts-err-E: ij( 611, 611), M = -2.2991 , ew = -.10967E-2, em = -.12855E-2. avg_m = -.76465E-07
ts-w-q: qP1 qP2
ts-w-q: 182.899 182.484
ts-q: D E1 C1 E2 C2 dQ
ts-q: 365.892 353.554 1.123 353.554 -1.672 -1.103E+0
ts-Vha: 0.11661E+01 eV

siesta: Program's energy decomposition (eV):
siesta: Ebs = -21828.995123
siesta: Eions = 151352.356254
siesta: Ena = 36831.577039
siesta: Ekin = 31694.495273
siesta: Enl = 8053.682223
siesta: Eso = 0.000000
siesta: Eldau = 0.000000
siesta: DEna = 5020.398855
siesta: DUscf = 819.292141
siesta: DUext = 0.000000
siesta: Enegf = 0.041427
siesta: Exc = -20247.348293
siesta: eta*DQ = 0.000000
siesta: Emadel = 0.000000
siesta: Emeta = 0.000000
siesta: Emolmec = -39.083037
siesta: Ekinion = 0.000000
siesta: Eharris = -89212.511753
siesta: Etot = -89219.300625
siesta: FreeEng = -89219.300625

        iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV)
ts-scf: 1 -89212.511753 -89219.300625 -89219.300625 0.104018 -6.158508 4.106153
timer: Routine,Calls,Time,% = TS 1 59.434 8.00
ts-err-D: ij( 824, 824), M = 1.4903 , ew = 0.13219E-1, em = 0.13220E-1. avg_m = -.83741E-06
ts-err-E: ij( 824, 824), M = -3.3499 , ew = -.15697E-2, em = -.15697E-2. avg_m = 0.11389E-06
ts-w-q: qP1 qP2
ts-w-q: 196.533 196.443
ts-q: D E1 C1 E2 C2 dQ
ts-q: 390.536 353.554 3.631 353.554 -1.278 2.644E+1
ts-Vha: -0.24273E+02 eV
ts-scf: 2 -86392.184692 -88574.942035 -88574.942035 0.888150 -6.158508103.399640
ts-err-D: ij( 620, 620), M = 1.3496 , ew = 0.25840E-1, em = 0.45901E-1. avg_m = -.57099E-05
ts-err-E: ij( 620, 620), M = -2.4220 , ew = -.14775E-2, em = -.26246E-2. avg_m = 0.28632E-07
ts-w-q: qP1 qP2
ts-w-q: 183.617 183.151
ts-q: D E1 C1 E2 C2 dQ
ts-q: 367.205 353.554 1.335 353.554 -1.733 3.610E-1
ts-Vha: -0.14262E+00 eV
ts-scf: 3 -89125.412476 -89228.753472 -89228.753472 0.782219 -6.158508 3.629814
ts-err-D: ij( 611, 611), M = 1.2891 , ew = 0.38564E-1, em = 0.51701E-1. avg_m = -.57565E-05
ts-err-E: ij( 611, 611), M = -2.3486 , ew = -.15107E-2, em = -.20253E-2. avg_m = 0.12944E-07
ts-w-q: qP1 qP2
ts-w-q: 183.204 182.793
ts-q: D E1 C1 E2 C2 dQ
ts-q: 366.427 353.554 1.224 353.554 -1.684 -4.787E-1
ts-Vha: 0.61923E+00 eV
ts-scf: 4 -89219.350913 -89224.979679 -89224.979679 0.073412 -6.158508 0.633465
ts-err-D: ij( 620, 620), M = 1.3041 , ew = 0.35740E-1, em = 0.50998E-1. avg_m = -.57891E-05
ts-err-E: ij( 620, 620), M = -2.3640 , ew = -.15825E-2, em = -.22581E-2. avg_m = 0.23000E-07
ts-w-q: qP1 qP2
ts-w-q: 183.308 182.882
ts-q: D E1 C1 E2 C2 dQ
ts-q: 366.613 353.554 1.244 353.554 -1.676 -2.650E-1
ts-Vha: 0.43113E+00 eV
ts-scf: 5 -89227.738799 -89226.364826 -89226.364826 0.020884 -6.158508 0.576775
ts-err-D: ij( 620, 620), M = 1.2946 , ew = 0.37561E-1, em = 0.51697E-1. avg_m = -.51843E-05
ts-err-E: ij( 620, 620), M = -2.3510 , ew = -.15625E-2, em = -.21506E-2. avg_m = -.47627E-08
ts-w-q: qP1 qP2
ts-w-q: 183.237 182.783
ts-q: D E1 C1 E2 C2 dQ
ts-q: 366.455 353.554 1.207 353.554 -1.655 -4.391E-1
ts-Vha: 0.59070E+00 eV
ts-scf: 6 -89223.878885 -89225.189655 -89225.189655 0.011135 -6.158508 0.226902
ts-err-D: ij( 611, 611), M = 1.3032 , ew = 0.35831E-1, em = 0.50917E-1. avg_m = -.56887E-05
ts-err-E: ij( 611, 611), M = -2.3621 , ew = -.15783E-2, em = -.22428E-2. avg_m = 0.22851E-07
ts-w-q: qP1 qP2
ts-w-q: 183.294 182.874
ts-q: D E1 C1 E2 C2 dQ
ts-q: 366.590 353.554 1.219 353.554 -1.651 -2.879E-1
ts-Vha: 0.45488E+00 eV
ts-scf: 7 -89227.355785 -89226.258038 -89226.258038 0.009920 -6.158508 0.415339
ts-err-D: ij( 620, 620), M = 1.2992 , ew = 0.36614E-1, em = 0.51144E-1. avg_m = -.63955E-05
ts-err-E: ij( 620, 620), M = -2.3577 , ew = -.15484E-2, em = -.21629E-2. avg_m = 0.20823E-06
ts-w-q: qP1 qP2
ts-w-q: 183.251 182.838
ts-q: D E1 C1 E2 C2 dQ
ts-q: 366.526 353.554 1.195 353.554 -1.645 -3.711E-1
ts-Vha: 0.52640E+00 eV
ts-scf: 8 -89224.638843 -89225.473197 -89225.473197 0.007120 -6.158508 0.089492
ts-err-D: ij( 620, 620), M = 1.2993 , ew = 0.36824E-1, em = 0.51373E-1. avg_m = -.54182E-05
ts-err-E: ij( 620, 620), M = -2.3578 , ew = -.15796E-2, em = -.22036E-2. avg_m = 0.41599E-07
ts-w-q: qP1 qP2
ts-w-q: 183.248 182.800
ts-q: D E1 C1 E2 C2 dQ
ts-q: 366.495 353.554 1.192 353.554 -1.648 -4.068E-1
ts-Vha: 0.55877E+00 eV
ts-scf: 9 -89225.013016 -89225.252667 -89225.252667 0.005146 -6.158508 0.044953
ts-err-D: ij( 620, 620), M = 1.3008 , ew = 0.36738E-1, em = 0.51296E-1. avg_m = -.52364E-05
ts-err-E: ij( 620, 620), M = -2.3613 , ew = -.15965E-2, em = -.22291E-2. avg_m = 0.13307E-07
ts-w-q: qP1 qP2
ts-w-q: 183.245 182.793
ts-q: D E1 C1 E2 C2 dQ
ts-q: 366.494 353.554 1.178 353.554 -1.643 -4.167E-1
ts-Vha: 0.56552E+00 eV
ts-scf: 10 -89224.941363 -89225.099539 -89225.099539 0.001557 -6.158508 0.058643
ts-err-D: ij( 620, 620), M = 1.3013 , ew = 0.36583E-1, em = 0.51156E-1. avg_m = -.56466E-05
ts-err-E: ij( 620, 620), M = -2.3623 , ew = -.15855E-2, em = -.22171E-2. avg_m = 0.85904E-07
ts-w-q: qP1 qP2
ts-w-q: 183.247 182.809
ts-q: D E1 C1 E2 C2 dQ
ts-q: 366.510 353.554 1.178 353.554 -1.642 -4.002E-1
ts-Vha: 0.55010E+00 eV
ts-scf: 11 -89225.249619 -89225.170744 -89225.170744 0.004534 -6.158508 0.026938
ts-err-D: ij( 620, 620), M = 1.3017 , ew = 0.36634E-1, em = 0.51181E-1. avg_m = -.53812E-05
ts-err-E: ij( 620, 620), M = -2.3636 , ew = -.15971E-2, em = -.22313E-2. avg_m = 0.39477E-07
ts-w-q: qP1 qP2
ts-w-q: 183.247 182.801
ts-q: D E1 C1 E2 C2 dQ
ts-q: 366.505 353.554 1.176 353.554 -1.641 -4.063E-1
ts-Vha: 0.55572E+00 eV
ts-scf: 12 -89225.129471 -89225.151401 -89225.151401 0.004305 -6.158508 0.029699
ts-err-D: ij( 620, 620), M = 1.3033 , ew = 0.36521E-1, em = 0.51021E-1. avg_m = -.53561E-05
ts-err-E: ij( 620, 620), M = -2.3683 , ew = -.16089E-2, em = -.22477E-2. avg_m = 0.37698E-07
ts-w-q: qP1 qP2
ts-w-q: 183.250 182.806
ts-q: D E1 C1 E2 C2 dQ
ts-q: 366.515 353.554 1.173 353.554 -1.640 -3.985E-1
ts-Vha: 0.54821E+00 eV
ts-scf: 13 -89225.213202 -89225.180166 -89225.180166 0.001676 -6.158508 0.014839
ts-err-D: ij( 620, 620), M = 1.3041 , ew = 0.36515E-1, em = 0.50969E-1. avg_m = -.52342E-05
ts-err-E: ij( 620, 620), M = -2.3708 , ew = -.16197E-2, em = -.22609E-2. avg_m = 0.18906E-07
ts-w-q: qP1 qP2
ts-w-q: 183.250 182.803
ts-q: D E1 C1 E2 C2 dQ
ts-q: 366.514 353.554 1.170 353.554 -1.639 -4.007E-1
ts-Vha: 0.55007E+00 eV
ts-scf: 14 -89225.116930 -89225.148996 -89225.148996 0.001039 -6.158508 0.007513
ts-err-D: ij( 620, 620), M = 1.3051 , ew = 0.36522E-1, em = 0.50901E-1. avg_m = -.51320E-05
ts-err-E: ij( 620, 620), M = -2.3739 , ew = -.16341E-2, em = -.22774E-2. avg_m = 0.57295E-08
ts-w-q: qP1 qP2
ts-w-q: 183.250 182.801
ts-q: D E1 C1 E2 C2 dQ
ts-q: 366.513 353.554 1.169 353.554 -1.639 -4.038E-1
ts-Vha: 0.55302E+00 eV
ts-scf: 15 -89225.064260 -89225.107428 -89225.107428 0.001329 -6.158508 0.013971
ts-err-D: ij( 620, 620), M = 1.3054 , ew = 0.36506E-1, em = 0.50866E-1. avg_m = -.51252E-05
ts-err-E: ij( 620, 620), M = -2.3750 , ew = -.16373E-2, em = -.22814E-2. avg_m = 0.56929E-08
ts-w-q: qP1 qP2
ts-w-q: 183.251 182.802
ts-q: D E1 C1 E2 C2 dQ
ts-q: 366.514 353.554 1.169 353.554 -1.639 -4.027E-1
ts-Vha: 0.55199E+00 eV
ts-scf: 16 -89225.120279 -89225.113556 -89225.113556 0.000345 -6.158508 0.009809
ts-err-D: ij( 620, 620), M = 1.3058 , ew = 0.36480E-1, em = 0.50822E-1. avg_m = -.51228E-05
ts-err-E: ij( 620, 620), M = -2.3762 , ew = -.16404E-2, em = -.22853E-2. avg_m = 0.64177E-08
ts-w-q: qP1 qP2
ts-w-q: 183.251 182.803
ts-q: D E1 C1 E2 C2 dQ
ts-q: 366.515 353.554 1.169 353.554 -1.639 -4.009E-1
ts-Vha: 0.55039E+00 eV
ts-scf: 17 -89225.132697 -89225.122673 -89225.122673 0.000423 -6.158508 0.004596
ts-err-D: ij( 620, 620), M = 1.3060 , ew = 0.36478E-1, em = 0.50811E-1. avg_m = -.51157E-05
ts-err-E: ij( 620, 620), M = -2.3767 , ew = -.16420E-2, em = -.22871E-2. avg_m = 0.59351E-08
ts-w-q: qP1 qP2
ts-w-q: 183.251 182.803
ts-q: D E1 C1 E2 C2 dQ
ts-q: 366.515 353.554 1.169 353.554 -1.639 -4.012E-1
ts-Vha: 0.55067E+00 eV
ts-scf: 18 -89225.122130 -89225.122482 -89225.122482 0.000134 -6.158508 0.004444
ts-err-D: ij( 620, 620), M = 1.3063 , ew = 0.36462E-1, em = 0.50781E-1. avg_m = -.51117E-05
ts-err-E: ij( 620, 620), M = -2.3775 , ew = -.16442E-2, em = -.22898E-2. avg_m = 0.61509E-08
ts-w-q: qP1 qP2
ts-w-q: 183.252 182.803
ts-q: D E1 C1 E2 C2 dQ
ts-q: 366.515 353.554 1.169 353.554 -1.639 -4.006E-1
ts-Vha: 0.55011E+00 eV
ts-scf: 19 -89225.128432 -89225.125298 -89225.125298 0.000296 -6.158508 0.003646
ts-err-D: ij( 620, 620), M = 1.3068 , ew = 0.36442E-1, em = 0.50736E-1. avg_m = -.50964E-05
ts-err-E: ij( 620, 620), M = -2.3790 , ew = -.16486E-2, em = -.22952E-2. avg_m = 0.52175E-08
ts-w-q: qP1 qP2
ts-w-q: 183.252 182.803
ts-q: D E1 C1 E2 C2 dQ
ts-q: 366.515 353.554 1.169 353.554 -1.638 -4.008E-1
ts-Vha: 0.55026E+00 eV
ts-scf: 20 -89225.110802 -89225.118095 -89225.118095 0.000474 -6.158508 0.002821
ts-err-D: ij( 620, 620), M = 1.3069 , ew = 0.36436E-1, em = 0.50722E-1. avg_m = -.50903E-05
ts-err-E: ij( 620, 620), M = -2.3795 , ew = -.16499E-2, em = -.22968E-2. avg_m = 0.47926E-08
ts-w-q: qP1 qP2
ts-w-q: 183.252 182.803
ts-q: D E1 C1 E2 C2 dQ
ts-q: 366.515 353.554 1.168 353.554 -1.638 -4.008E-1
ts-Vha: 0.55030E+00 eV
ts-scf: 21 -89225.112024 -89225.115072 -89225.115072 0.000141 -6.158508 0.002579
ts-err-D: ij( 620, 620), M = 1.3070 , ew = 0.36428E-1, em = 0.50705E-1. avg_m = -.50848E-05
ts-err-E: ij( 620, 620), M = -2.3800 , ew = -.16513E-2, em = -.22985E-2. avg_m = 0.45127E-08
ts-w-q: qP1 qP2
ts-w-q: 183.252 182.803
ts-q: D E1 C1 E2 C2 dQ
ts-q: 366.515 353.554 1.168 353.554 -1.638 -4.008E-1
ts-Vha: 0.55020E+00 eV
ts-scf: 22 -89225.111153 -89225.113089 -89225.113089 0.000156 -6.158508 0.002274
ts-err-D: ij( 620, 620), M = 1.3070 , ew = 0.36426E-1, em = 0.50702E-1. avg_m = -.50862E-05
ts-err-E: ij( 620, 620), M = -2.3800 , ew = -.16512E-2, em = -.22983E-2. avg_m = 0.47987E-08
ts-w-q: qP1 qP2
ts-w-q: 183.252 182.803
ts-q: D E1 C1 E2 C2 dQ
ts-q: 366.515 353.554 1.169 353.554 -1.639 -4.009E-1
ts-Vha: 0.55034E+00 eV
ts-scf: 23 -89225.110815 -89225.111996 -89225.111996 0.000109 -6.158508 0.001699
ts-err-D: ij( 620, 620), M = 1.3070 , ew = 0.36426E-1, em = 0.50705E-1. avg_m = -.50911E-05
ts-err-E: ij( 620, 620), M = -2.3798 , ew = -.16504E-2, em = -.22974E-2. avg_m = 0.53733E-08
ts-w-q: qP1 qP2
ts-w-q: 183.252 182.803
ts-q: D E1 C1 E2 C2 dQ
ts-q: 366.515 353.554 1.169 353.554 -1.639 -4.008E-1
ts-Vha: 0.55021E+00 eV
ts-scf: 24 -89225.117371 -89225.114651 -89225.114651 0.000063 -6.158508 0.001391
ts-err-D: ij( 620, 620), M = 1.3070 , ew = 0.36427E-1, em = 0.50705E-1. avg_m = -.50906E-05
ts-err-E: ij( 620, 620), M = -2.3799 , ew = -.16505E-2, em = -.22975E-2. avg_m = 0.53119E-08
ts-w-q: qP1 qP2
ts-w-q: 183.252 182.803
ts-q: D E1 C1 E2 C2 dQ
ts-q: 366.515 353.554 1.169 353.554 -1.639 -4.008E-1
ts-Vha: 0.55025E+00 eV
ts-scf: 25 -89225.113955 -89225.114312 -89225.114312 0.000009 -6.158508 0.001331
ts-err-D: ij( 620, 620), M = 1.3069 , ew = 0.36429E-1, em = 0.50709E-1. avg_m = -.50921E-05
ts-err-E: ij( 620, 620), M = -2.3798 , ew = -.16502E-2, em = -.22971E-2. avg_m = 0.54542E-08
ts-w-q: qP1 qP2
ts-w-q: 183.252 182.803
ts-q: D E1 C1 E2 C2 dQ
ts-q: 366.515 353.554 1.169 353.554 -1.639 -4.008E-1
ts-Vha: 0.55024E+00 eV
ts-scf: 26 -89225.116653 -89225.115475 -89225.115475 0.000038 -6.158508 0.001119
ts-err-D: ij( 620, 620), M = 1.3069 , ew = 0.36431E-1, em = 0.50713E-1. avg_m = -.50934E-05
ts-err-E: ij( 620, 620), M = -2.3796 , ew = -.16499E-2, em = -.22966E-2. avg_m = 0.55669E-08
ts-w-q: qP1 qP2
ts-w-q: 183.252 182.803
ts-q: D E1 C1 E2 C2 dQ
ts-q: 366.515 353.554 1.169 353.554 -1.639 -4.007E-1
ts-Vha: 0.55022E+00 eV
ts-scf: 27 -89225.117775 -89225.116613 -89225.116613 0.000042 -6.158508 0.000940

SCF Convergence by DM+H criterion
max |DM_out - DM_in| : 0.0000417929
max |H_out - H_in| (eV) : 0.0009401396
SCF cycle converged after 27 iterations

Using DM_out to compute the final energy and forces
No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 137 207
ts-Vha: 0.55022E+00 eV

MM-Stress (kbar): 9.02 9.03 3.65 0.01 0.00 0.00

siesta: E_KS(eV) = -89225.1166

siesta: E_KS - E_eggbox = -89225.1166

siesta: Atomic forces (eV/Ang):
----------------------------------------
   Tot -0.060129 0.119866 -0.092391
----------------------------------------
   Max 6.840307
   Res 1.467494 sqrt( Sum f_i^2 / 3N )
----------------------------------------
   Max 6.840307 constrained

Stress-tensor-Voigt (kbar): 7.56 29.96 -14.16 0.14 -7.98 0.25
(Free)E + p*V (eV/cell) -89250.1597
Target enthalpy (eV/cell) -89225.1166

mulliken: Atomic and Orbital Populations:

Species: Zr
Atom Qatom Qorb
               4s 5s 4py 4pz 4px 4dxy 4dyz 4dz2
               4dxz 4dx2-y2 5Ppy 5Ppz 5Ppx
   7 11.300 1.986 0.440 1.985 1.988 1.985 0.472 0.556 0.401
              0.556 0.472 0.136 0.188 0.136
   8 11.300 1.986 0.440 1.985 1.988 1.985 0.472 0.556 0.401
              0.556 0.472 0.136 0.188 0.136
   9 11.300 1.986 0.440 1.985 1.988 1.985 0.472 0.556 0.401
              0.556 0.472 0.136 0.188 0.136
  10 11.300 1.986 0.440 1.985 1.988 1.985 0.472 0.556 0.401
              0.556 0.472 0.136 0.188 0.136
  11 11.300 1.986 0.440 1.985 1.988 1.985 0.472 0.556 0.401
              0.556 0.472 0.136 0.188 0.136
  12 11.300 1.986 0.440 1.985 1.988 1.985 0.472 0.556 0.401
              0.556 0.472 0.136 0.188 0.136
  22 11.299 1.986 0.440 1.985 1.988 1.985 0.472 0.556 0.401
              0.556 0.472 0.135 0.188 0.136
  23 11.299 1.986 0.440 1.985 1.988 1.985 0.472 0.556 0.401
              0.556 0.472 0.135 0.188 0.136
  24 11.299 1.986 0.440 1.985 1.988 1.985 0.472 0.556 0.401
              0.556 0.472 0.135 0.188 0.136
  25 11.295 1.986 0.439 1.985 1.988 1.985 0.472 0.556 0.401
              0.556 0.472 0.133 0.188 0.136
  26 11.295 1.986 0.439 1.985 1.988 1.985 0.472 0.556 0.401
              0.556 0.472 0.133 0.188 0.136
  27 11.295 1.986 0.439 1.985 1.988 1.985 0.472 0.556 0.401
              0.556 0.472 0.133 0.188 0.136
  37 10.944 1.966 0.389 1.977 1.990 1.979 0.460 0.553 0.396
              0.553 0.458 -0.015 0.176 0.063
  38 10.944 1.966 0.389 1.977 1.990 1.979 0.460 0.553 0.396
              0.553 0.458 -0.015 0.176 0.063
  39 10.944 1.966 0.389 1.977 1.990 1.979 0.460 0.553 0.396
              0.553 0.458 -0.015 0.176 0.063
  40 10.889 1.952 0.387 1.984 1.990 1.985 0.447 0.539 0.384
              0.558 0.462 0.010 0.126 0.066
  41 10.889 1.952 0.387 1.984 1.990 1.985 0.447 0.539 0.384
              0.558 0.462 0.010 0.126 0.066
  42 10.889 1.952 0.387 1.984 1.990 1.985 0.447 0.539 0.384
              0.558 0.462 0.010 0.126 0.066
  52 12.585 0.004 1.079 -0.002 -0.004 -0.002 2.075 2.056 2.092
              2.052 2.069 0.496 0.373 0.294
  53 12.585 0.004 1.079 -0.002 -0.004 -0.002 2.075 2.056 2.092
              2.052 2.069 0.496 0.373 0.294
  54 12.585 0.004 1.079 -0.002 -0.004 -0.002 2.075 2.056 2.092
              2.052 2.069 0.496 0.373 0.294
  55 12.359 0.006 1.056 -0.002 -0.002 -0.000 2.074 2.049 2.089
              2.051 2.069 0.382 0.313 0.275
  56 12.359 0.006 1.056 -0.002 -0.002 -0.000 2.074 2.049 2.089
              2.051 2.069 0.382 0.313 0.275
  57 12.359 0.006 1.056 -0.002 -0.002 -0.000 2.074 2.049 2.089
              2.051 2.069 0.382 0.313 0.275
  67 12.068 0.007 1.035 0.000 -0.002 0.000 2.066 2.047 2.085
              2.047 2.067 0.197 0.290 0.228
  68 12.069 0.007 1.035 0.000 -0.002 0.000 2.066 2.047 2.085
              2.047 2.067 0.197 0.290 0.228
  69 12.069 0.007 1.035 0.000 -0.002 0.000 2.066 2.047 2.085
              2.047 2.067 0.197 0.290 0.228
  70 12.068 0.007 1.034 0.000 -0.002 -0.000 2.066 2.047 2.086
              2.047 2.067 0.202 0.286 0.227
  71 12.068 0.007 1.034 0.000 -0.002 -0.000 2.066 2.047 2.086
              2.047 2.067 0.202 0.286 0.227
  72 12.068 0.007 1.034 0.000 -0.002 -0.000 2.066 2.047 2.086
              2.047 2.067 0.202 0.286 0.227
  82 12.391 0.006 1.061 -0.001 -0.001 -0.001 2.076 2.048 2.091
              2.051 2.069 0.424 0.308 0.261
  83 12.391 0.006 1.061 -0.001 -0.001 -0.001 2.076 2.048 2.091
              2.051 2.069 0.424 0.308 0.261
  84 12.391 0.006 1.061 -0.001 -0.001 -0.001 2.076 2.048 2.091
              2.051 2.069 0.424 0.308 0.261
  85 12.659 0.005 1.106 -0.001 -0.002 -0.000 2.077 2.053 2.094
              2.049 2.070 0.517 0.396 0.295
  86 12.659 0.005 1.106 -0.001 -0.002 -0.000 2.077 2.053 2.094
              2.049 2.070 0.517 0.396 0.295
  87 12.659 0.005 1.106 -0.001 -0.002 -0.000 2.077 2.053 2.094
              2.049 2.070 0.517 0.396 0.295
  97 10.814 1.958 0.354 1.969 1.978 1.977 0.459 0.546 0.403
              0.549 0.459 -0.022 0.117 0.068
  98 10.814 1.958 0.354 1.969 1.978 1.977 0.459 0.546 0.403
              0.549 0.459 -0.022 0.117 0.068
  99 10.814 1.958 0.354 1.969 1.978 1.977 0.459 0.546 0.403
              0.549 0.459 -0.022 0.117 0.068
 100 10.906 1.970 0.375 1.967 1.988 1.979 0.467 0.547 0.401
              0.554 0.461 -0.043 0.172 0.069
 101 10.906 1.970 0.375 1.967 1.988 1.979 0.467 0.547 0.401
              0.554 0.461 -0.043 0.172 0.069
 102 10.906 1.970 0.375 1.967 1.988 1.979 0.467 0.547 0.401
              0.554 0.461 -0.043 0.172 0.069
 112 11.298 1.986 0.439 1.985 1.988 1.985 0.472 0.556 0.401
              0.556 0.472 0.135 0.188 0.136
 113 11.298 1.986 0.439 1.985 1.988 1.985 0.472 0.556 0.401
              0.556 0.472 0.135 0.188 0.136
 114 11.298 1.986 0.439 1.985 1.988 1.985 0.472 0.556 0.401
              0.556 0.472 0.135 0.188 0.136
 115 11.298 1.986 0.439 1.985 1.988 1.985 0.472 0.556 0.401
              0.556 0.472 0.135 0.188 0.136
 116 11.298 1.986 0.439 1.985 1.988 1.985 0.472 0.556 0.401
              0.556 0.472 0.135 0.188 0.136
 117 11.298 1.986 0.439 1.985 1.988 1.985 0.472 0.556 0.401
              0.556 0.472 0.135 0.188 0.136
 127 11.300 1.986 0.440 1.985 1.988 1.985 0.472 0.556 0.401
              0.556 0.472 0.136 0.188 0.136
 128 11.300 1.986 0.440 1.985 1.988 1.985 0.472 0.556 0.401
              0.556 0.472 0.136 0.188 0.136
 129 11.300 1.986 0.440 1.985 1.988 1.985 0.472 0.556 0.401
              0.556 0.472 0.136 0.188 0.136
 130 11.300 1.986 0.440 1.985 1.988 1.985 0.472 0.556 0.401
              0.556 0.472 0.136 0.188 0.136
 131 11.300 1.986 0.440 1.985 1.988 1.985 0.472 0.556 0.401
              0.556 0.472 0.136 0.188 0.136
 132 11.300 1.986 0.440 1.985 1.988 1.985 0.472 0.556 0.401
              0.556 0.472 0.136 0.188 0.136

Species: C
Atom Qatom Qorb
               2s 2py 2pz 2px 2Pdxy 2Pdyz 2Pdz2 2Pdxz
               2Pdx2-y2
   1 4.760 1.490 1.039 1.102 1.039 0.018 0.018 0.018 0.018
              0.018
   2 4.760 1.490 1.039 1.102 1.039 0.018 0.018 0.018 0.018
              0.018
   3 4.760 1.490 1.039 1.102 1.039 0.018 0.018 0.018 0.018
              0.018
  16 4.760 1.490 1.039 1.102 1.039 0.018 0.018 0.018 0.018
              0.018
  17 4.760 1.490 1.039 1.102 1.039 0.018 0.018 0.018 0.018
              0.018
  18 4.760 1.490 1.039 1.102 1.039 0.018 0.018 0.018 0.018
              0.018
  31 4.766 1.491 1.043 1.102 1.039 0.018 0.019 0.018 0.018
              0.018
  32 4.766 1.491 1.043 1.102 1.039 0.018 0.019 0.018 0.018
              0.018
  33 4.766 1.491 1.043 1.102 1.039 0.018 0.019 0.018 0.018
              0.018
  46 4.388 1.495 1.010 0.976 0.994 -0.018 -0.009 -0.025 -0.012
             -0.022
  47 4.388 1.495 1.010 0.976 0.994 -0.018 -0.009 -0.025 -0.012
             -0.022
  48 4.388 1.495 1.010 0.976 0.994 -0.018 -0.009 -0.025 -0.012
             -0.022
  61 3.904 1.551 0.870 0.886 0.892 -0.064 -0.050 -0.067 -0.050
             -0.064
  62 3.904 1.551 0.870 0.886 0.892 -0.064 -0.050 -0.067 -0.050
             -0.064
  63 3.904 1.551 0.870 0.886 0.892 -0.064 -0.050 -0.067 -0.050
             -0.064
  76 3.898 1.549 0.858 0.893 0.892 -0.064 -0.049 -0.067 -0.050
             -0.064
  77 3.898 1.549 0.858 0.893 0.892 -0.064 -0.049 -0.067 -0.050
             -0.064
  78 3.898 1.549 0.858 0.893 0.892 -0.064 -0.049 -0.067 -0.050
             -0.064
  91 4.433 1.420 0.982 1.120 1.054 -0.029 -0.018 -0.039 -0.024
             -0.033
  92 4.433 1.420 0.982 1.120 1.054 -0.029 -0.018 -0.039 -0.024
             -0.033
  93 4.433 1.420 0.982 1.120 1.054 -0.029 -0.018 -0.039 -0.024
             -0.033
 106 4.765 1.491 1.040 1.102 1.039 0.018 0.019 0.019 0.018
              0.018
 107 4.765 1.491 1.040 1.102 1.039 0.018 0.019 0.019 0.018
              0.018
 108 4.765 1.491 1.040 1.102 1.039 0.018 0.019 0.019 0.018
              0.018
 121 4.760 1.490 1.039 1.102 1.039 0.018 0.018 0.018 0.018
              0.018
 122 4.760 1.490 1.039 1.102 1.039 0.018 0.018 0.018 0.018
              0.018
 123 4.760 1.490 1.039 1.102 1.039 0.018 0.018 0.018 0.018
              0.018

Species: S
Atom Qatom Qorb
               3s 3py 3pz 3px 3Pdxy 3Pdyz 3Pdz2 3Pdxz
               3Pdx2-y2
   4 6.320 1.828 1.431 1.503 1.431 0.021 0.028 0.028 0.028
              0.021
   5 6.320 1.828 1.431 1.503 1.431 0.021 0.028 0.028 0.028
              0.021
   6 6.320 1.828 1.431 1.503 1.431 0.021 0.028 0.028 0.028
              0.021
  13 6.320 1.829 1.431 1.503 1.431 0.021 0.028 0.028 0.028
              0.021
  14 6.320 1.829 1.431 1.503 1.431 0.021 0.028 0.028 0.028
              0.021
  15 6.320 1.829 1.431 1.503 1.431 0.021 0.028 0.028 0.028
              0.021
  19 6.320 1.828 1.431 1.503 1.431 0.021 0.028 0.028 0.028
              0.021
  20 6.320 1.828 1.431 1.503 1.431 0.021 0.028 0.028 0.028
              0.021
  21 6.320 1.828 1.431 1.503 1.431 0.021 0.028 0.028 0.028
              0.021
  28 6.321 1.829 1.431 1.503 1.431 0.021 0.028 0.028 0.028
              0.021
  29 6.321 1.829 1.431 1.503 1.431 0.021 0.028 0.028 0.028
              0.021
  30 6.321 1.829 1.431 1.503 1.431 0.021 0.028 0.028 0.028
              0.021
  34 6.334 1.829 1.439 1.506 1.433 0.021 0.029 0.028 0.028
              0.021
  35 6.334 1.829 1.439 1.506 1.433 0.021 0.029 0.028 0.028
              0.021
  36 6.334 1.829 1.439 1.506 1.433 0.021 0.029 0.028 0.028
              0.021
  43 6.193 1.814 1.408 1.512 1.402 -0.001 0.019 0.009 0.018
              0.011
  44 6.193 1.814 1.408 1.512 1.402 -0.001 0.019 0.009 0.018
              0.011
  45 6.193 1.814 1.408 1.512 1.402 -0.001 0.019 0.009 0.018
              0.011
  49 6.091 1.823 1.463 1.486 1.306 0.000 0.012 -0.002 0.012
             -0.008
  50 6.091 1.823 1.463 1.486 1.306 0.000 0.012 -0.002 0.012
             -0.008
  51 6.091 1.823 1.463 1.486 1.306 0.000 0.012 -0.002 0.012
             -0.008
  58 5.890 1.833 1.347 1.458 1.296 -0.016 0.004 -0.018 0.003
             -0.017
  59 5.890 1.833 1.347 1.458 1.296 -0.016 0.004 -0.018 0.003
             -0.017
  60 5.890 1.833 1.347 1.458 1.296 -0.016 0.004 -0.018 0.003
             -0.017
  64 5.906 1.827 1.256 1.469 1.397 -0.016 0.004 -0.019 0.003
             -0.014
  65 5.906 1.827 1.256 1.470 1.397 -0.016 0.004 -0.019 0.003
             -0.014
  66 5.906 1.827 1.256 1.469 1.397 -0.016 0.004 -0.019 0.003
             -0.014
  73 5.908 1.827 1.267 1.470 1.384 -0.016 0.005 -0.018 0.003
             -0.014
  74 5.908 1.827 1.267 1.470 1.384 -0.016 0.005 -0.018 0.003
             -0.014
  75 5.908 1.827 1.267 1.470 1.384 -0.016 0.005 -0.018 0.003
             -0.014
  79 5.891 1.831 1.337 1.443 1.322 -0.015 0.004 -0.018 0.004
             -0.017
  80 5.891 1.831 1.337 1.443 1.322 -0.015 0.004 -0.018 0.004
             -0.017
  81 5.891 1.831 1.337 1.443 1.322 -0.015 0.004 -0.018 0.004
             -0.017
  88 6.087 1.825 1.462 1.484 1.306 -0.000 0.011 -0.003 0.011
             -0.008
  89 6.087 1.825 1.462 1.484 1.306 -0.000 0.011 -0.003 0.011
             -0.008
  90 6.087 1.825 1.462 1.484 1.306 -0.000 0.011 -0.003 0.011
             -0.008
  94 6.172 1.819 1.400 1.497 1.399 -0.000 0.018 0.009 0.018
              0.012
  95 6.172 1.819 1.400 1.497 1.399 -0.000 0.018 0.009 0.018
              0.012
  96 6.172 1.819 1.400 1.497 1.399 -0.000 0.018 0.009 0.018
              0.012
 103 6.325 1.829 1.434 1.504 1.431 0.021 0.029 0.028 0.028
              0.021
 104 6.325 1.829 1.434 1.504 1.431 0.021 0.029 0.028 0.028
              0.021
 105 6.325 1.829 1.434 1.504 1.431 0.021 0.029 0.028 0.028
              0.021
 109 6.321 1.829 1.431 1.503 1.431 0.021 0.028 0.028 0.028
              0.021
 110 6.321 1.829 1.431 1.503 1.431 0.021 0.028 0.028 0.028
              0.021
 111 6.321 1.829 1.431 1.503 1.431 0.021 0.028 0.028 0.028
              0.021
 118 6.320 1.829 1.431 1.503 1.431 0.021 0.028 0.028 0.028
              0.021
 119 6.320 1.829 1.431 1.503 1.431 0.021 0.028 0.028 0.028
              0.021
 120 6.320 1.829 1.431 1.503 1.431 0.021 0.028 0.028 0.028
              0.021
 124 6.320 1.828 1.431 1.503 1.431 0.021 0.028 0.028 0.028
              0.021
 125 6.320 1.828 1.431 1.503 1.431 0.021 0.028 0.028 0.028
              0.021
 126 6.320 1.828 1.431 1.503 1.431 0.021 0.028 0.028 0.028
              0.021
 133 6.320 1.829 1.431 1.503 1.431 0.021 0.028 0.028 0.028
              0.021
 134 6.320 1.829 1.431 1.503 1.431 0.021 0.028 0.028 0.028
              0.021
 135 6.320 1.829 1.431 1.503 1.431 0.021 0.028 0.028 0.028
              0.021

mulliken: Qtot = 1079.599

coxmol: Writing XMOL coordinates into file scatt.xyz

siesta: Program's energy decomposition (eV):
siesta: Ebs = -20857.736369
siesta: Eions = 151352.356254
siesta: Ena = 36831.577039
siesta: Ekin = 31721.159604
siesta: Enl = 8053.112286
siesta: Eso = 0.000000
siesta: Eldau = 0.000000
siesta: DEna = 5000.891658
siesta: DUscf = 817.362136
siesta: DUext = 0.000000
siesta: Enegf = 0.044848
siesta: Exc = -20257.824894
siesta: eta*DQ = 0.000000
siesta: Emadel = 0.000000
siesta: Emeta = 0.000000
siesta: Emolmec = -39.083037
siesta: Ekinion = 0.000000
siesta: Eharris = -89225.117775
siesta: Etot = -89225.116613
siesta: FreeEng = -89225.116613

siesta: Final energy (eV):
siesta: Band Struct. = -20857.736369
siesta: Kinetic = 31721.159604
siesta: Hartree = 232322.986080
siesta: Eldau = 0.000000
siesta: Eso = 0.000000
siesta: Ext. field = 0.000000
siesta: Enegf = 0.044848
siesta: Exch.-corr. = -20257.824894
siesta: Ion-electron = -499616.889822
siesta: Ion-ion = 166644.490607
siesta: Ekinion = 0.000000
siesta: Total = -89225.116613
siesta: Fermi = -6.158508

siesta: Atomic forces (eV/Ang):
siesta: 1 -0.004418 -0.098051 0.003761
siesta: 2 -0.004191 -0.098190 0.003541
siesta: 3 -0.004518 -0.098702 0.003336
siesta: 4 -0.000210 -0.001783 -1.233276
siesta: 5 -0.000247 -0.001738 -1.233245
siesta: 6 -0.000281 -0.001831 -1.233257
siesta: 7 0.002963 0.011119 -1.639236
siesta: 8 0.003083 0.010759 -1.639095
siesta: 9 0.003370 0.010613 -1.639467
siesta: 10 -0.011875 -0.016867 1.630053
siesta: 11 -0.011871 -0.016833 1.629898
siesta: 12 -0.012079 -0.017392 1.629914
siesta: 13 0.007849 0.035727 1.221390
siesta: 14 0.008051 0.035762 1.221152
siesta: 15 0.008271 0.035403 1.220878
siesta: 16 -0.004172 0.071915 0.021702
siesta: 17 -0.004123 0.071836 0.021648
siesta: 18 -0.004042 0.071873 0.021620
siesta: 19 -0.000292 0.029084 -1.200034
siesta: 20 -0.000202 0.028957 -1.200019
siesta: 21 -0.000178 0.028902 -1.199914
siesta: 22 0.003014 -0.265081 -1.614852
siesta: 23 0.003169 -0.264933 -1.614989
siesta: 24 0.002976 -0.265055 -1.614715
siesta: 25 -0.012364 -0.398519 1.474544
siesta: 26 -0.012352 -0.398385 1.474581
siesta: 27 -0.012506 -0.398860 1.474672
siesta: 28 0.008068 0.170960 1.122273
siesta: 29 0.008078 0.171088 1.121997
siesta: 30 0.008355 0.170912 1.121928
siesta: 31 -0.001742 -0.116606 0.034178
siesta: 32 -0.001884 -0.116657 0.034150
siesta: 33 -0.001780 -0.116679 0.034205
siesta: 34 0.007841 0.223899 -0.876916
siesta: 35 0.007833 0.223875 -0.876894
siesta: 36 0.007710 0.223877 -0.876876
siesta: 37 -0.000179 2.114681 -1.173543
siesta: 38 0.000001 2.114079 -1.173179
siesta: 39 -0.000095 2.114231 -1.173055
siesta: 40 -0.005588 2.031245 1.501576
siesta: 41 -0.005543 2.031517 1.501352
siesta: 42 -0.005131 2.031453 1.501592
siesta: 43 0.046828 2.075814 -0.886534
siesta: 44 0.046609 2.076028 -0.886813
siesta: 45 0.047201 2.075409 -0.886744
siesta: 46 0.004261 -1.985173 -0.622577
siesta: 47 0.005282 -1.986037 -0.623149
siesta: 48 0.004841 -1.986649 -0.623637
siesta: 49 -0.002309 -0.965654 -2.003798
siesta: 50 -0.002590 -0.965490 -2.003723
siesta: 51 -0.002549 -0.965735 -2.003946
siesta: 52 0.033263 -3.194011 -0.642749
siesta: 53 0.033205 -3.194400 -0.642909
siesta: 54 0.034843 -3.195307 -0.645339
siesta: 55 0.042333 0.476640 3.176975
siesta: 56 0.042561 0.476845 3.176088
siesta: 57 0.042865 0.476367 3.176611
siesta: 58 -0.103184 -0.116961 2.322009
siesta: 59 -0.101974 -0.117052 2.321042
siesta: 60 -0.101936 -0.117208 2.320642
siesta: 61 -0.055256 0.391231 0.158522
siesta: 62 -0.054395 0.390492 0.157974
siesta: 63 -0.054181 0.390857 0.158286
siesta: 64 0.008941 -0.088275 -2.136829
siesta: 65 0.009349 -0.088884 -2.136861
siesta: 66 0.009363 -0.089037 -2.136445
siesta: 67 0.045555 0.013622 -3.066280
siesta: 68 0.047220 0.013960 -3.068070
siesta: 69 0.044960 0.014160 -3.065795
siesta: 70 0.011168 -0.142770 3.086536
siesta: 71 0.011883 -0.142710 3.086800
siesta: 72 0.012845 -0.142159 3.086516
siesta: 73 -0.036945 0.049650 2.169009
siesta: 74 -0.037334 0.050823 2.169126
siesta: 75 -0.036546 0.050330 2.168246
siesta: 76 0.004067 -0.200134 -0.243011
siesta: 77 0.003974 -0.199828 -0.242815
siesta: 78 0.004242 -0.199672 -0.242898
siesta: 79 0.024043 0.243046 -2.121901
siesta: 80 0.023991 0.242963 -2.121747
siesta: 81 0.023609 0.243033 -2.121749
siesta: 82 0.000005 3.342693 -5.372543
siesta: 83 0.000614 3.342409 -5.371498
siesta: 84 0.001607 3.341476 -5.372916
siesta: 85 0.004716 6.840294 5.715495
siesta: 86 0.003909 6.840307 5.715840
siesta: 87 0.005149 6.840136 5.715373
siesta: 88 -0.017880 0.837101 1.910175
siesta: 89 -0.019096 0.837272 1.910539
siesta: 90 -0.018538 0.837076 1.909767
siesta: 91 -0.027910 -4.798043 -1.793049
siesta: 92 -0.028048 -4.797316 -1.793023
siesta: 93 -0.027247 -4.796972 -1.792749
siesta: 94 -0.010233 -1.658044 0.216631
siesta: 95 -0.010239 -1.657955 0.216633
siesta: 96 -0.010283 -1.657992 0.216637
siesta: 97 0.022157 -2.744367 -1.592177
siesta: 98 0.022477 -2.744720 -1.591969
siesta: 99 0.022832 -2.744923 -1.592475
siesta: 100 -0.002308 -2.636955 1.163764
siesta: 101 -0.002284 -2.636897 1.163533
siesta: 102 -0.002521 -2.637239 1.163600
siesta: 103 0.004695 0.071583 1.128731
siesta: 104 0.004916 0.071599 1.128492
siesta: 105 0.005092 0.071267 1.128130
siesta: 106 -0.003743 -0.011398 -0.055815
siesta: 107 -0.003720 -0.011533 -0.055869
siesta: 108 -0.003610 -0.011485 -0.055903
siesta: 109 -0.000071 -0.109754 -1.096918
siesta: 110 0.000007 -0.109875 -1.096903
siesta: 111 0.000036 -0.109931 -1.096796
siesta: 112 0.002824 0.235810 -1.465606
siesta: 113 0.002989 0.235957 -1.465774
siesta: 114 0.002770 0.235826 -1.465477
siesta: 115 -0.012201 0.364180 1.555697
siesta: 116 -0.012189 0.364323 1.555725
siesta: 117 -0.012363 0.363860 1.555828
siesta: 118 0.007944 -0.023616 1.155247
siesta: 119 0.007949 -0.023475 1.154967
siesta: 120 0.008229 -0.023668 1.154907
siesta: 121 -0.004095 -0.082250 -0.021539
siesta: 122 -0.004233 -0.082312 -0.021575
siesta: 123 -0.004118 -0.082306 -0.021525
siesta: 124 -0.000150 -0.042225 -1.173539
siesta: 125 -0.000185 -0.042204 -1.173486
siesta: 126 -0.000303 -0.042201 -1.173472
siesta: 127 0.002770 0.075095 -1.574046
siesta: 128 0.003014 0.074500 -1.573881
siesta: 129 0.003121 0.074455 -1.573866
siesta: 130 -0.011962 0.077498 1.611354
siesta: 131 -0.012328 0.077165 1.611150
siesta: 132 -0.012013 0.077060 1.611285
siesta: 133 0.008323 -0.043007 1.200447
siesta: 134 0.008121 -0.043008 1.200525
siesta: 135 0.008605 -0.043135 1.200076
siesta: ----------------------------------------
siesta: Tot -0.060129 0.119866 -0.092391

siesta: Stress tensor (static) (eV/Ang**3):
siesta: 0.004719 0.000166 0.000174
siesta: 0.000088 0.018702 -0.003823
siesta: 0.000157 -0.004978 -0.008835

siesta: Cell volume = 5150.872104 Ang**3

siesta: Pressure (static):
siesta: Solid Molecule Units
siesta: -0.00005295 -0.00001547 Ry/Bohr**3
siesta: -0.00486191 -0.00141998 eV/Ang**3
siesta: -7.78972919 -2.27508946 kBar
(Free)E+ p_basis*V_orbitals = -89132.423162
(Free)Eharris+ p_basis*V_orbitals = -89132.424324

siesta: Electric dipole (a.u.) = 0.000000 0.000000 -0.127518
siesta: Electric dipole (Debye) = 0.000000 0.000000 -0.324118
ts-Vha: 0.55022E+00 eV

dhscf: Vacuum level (max, mean) = -0.098671 -0.283228 eV

>> End of run: 30-MAR-2021 11:04:18
Job completed

Revision history for this message
Nick Papior (nickpapior) said : 		#6

You have missed that in one case the dQ is on the order of 350 electrons. Thus your device is only occupied with 0.3 electrons. So that run is faulty and cannot be trusted in any way.

Please ALWAYS carefully examine the output and ensure that charges make sense and are not off by a lot.
We have put in place some tolerance in a later version that should catch this.

For now, you should restart that calculation (from scratch).

Revision history for this message
xiaoboy (xiaoboy) said : 		#7

Thanks for your comments.
Could you please talk about the detail reasons for this problem.
Thanks.

Revision history for this message
Best Nick Papior (nickpapior) said : 		#8

Restarting from TSDE files can sometimes cause this. And too high mixing weights as well.

Revision history for this message
xiaoboy (xiaoboy) said : 		#9

Thanks Nick Papior, that solved my question.