3
$\begingroup$

I am using SIESTA 4.1.5 version, I have done electrode Calculation using K-grid values 3X3X100 for both the electrodes, and currently i am doing transmission calculation, I tried different K-grid values like 3 × 3 × 100, 3 × 3 × 1,3 × 3 × 3,3 × 3 × 300, etc. in transmission calculation but I am getting Error like this:

Electrode: Left is a Gamma-only calculation, this is not feasible.
Erroneous electrode setup, check out-put

How can I fix this problem?


Thanks for this reply Sir, I searched in the output file of electrode calculation, i was not unable find but it is written in output file of electrode calculation that the K-points displacement in the 3 input could be 0.0 0.5 other than this, I didn't found anything different.

code for electrode and scattering region calculation input and output electrode input:

SystemName  leftAu
SystemLabel leftAu

# Atomic coordinates
NumberOfAtoms 36
AtomicCoordinatesFormat Ang
%block AtomicCoordinatesAndAtomicSpecies
   1.705900000000      4.978000000000     -2.885900000000 1
   3.266300000000      5.634400000000     -0.551300000000 1
   3.440400000000      7.281600000000     -2.912000000000 1
   4.568100000000      4.627500000000     -2.919400000000 1
   5.000900000000      7.938100000000     -0.577400000000 1
   5.175000000000      9.585300000000     -2.938000000000 1
   6.128600000000      5.283900000000     -0.584800000000 1
   6.302600000000      6.931200000000     -2.945500000000 1
   7.430300000000      4.277000000000     -2.952900000000 1
   6.735400000000     10.241800000000     -0.603400000000 1
   6.909500000000     11.889000000000     -2.964100000000 1
   7.863100000000      7.587600000000     -0.610900000000 1
   8.037200000000      9.234800000000     -2.971500000000 1
   8.990800000000      4.933400000000     -0.618300000000 1
   9.164900000000      6.580700000000     -2.979000000000 1
  10.292500000000      3.926500000000     -2.986400000000 1
   8.470000000000     12.545400000000     -0.629500000000 1
   8.644100000000     14.192700000000     -2.990100000000 1
   9.597700000000      9.891300000000     -0.636900000000 1
   9.771700000000     11.538500000000     -2.997600000000 1
  10.725300000000      7.237100000000     -0.644400000000 1
  10.899400000000      8.884300000000     -3.005000000000 1
  11.853000000000      4.582900000000     -0.651800000000 1
  12.027100000000      6.230200000000     -3.012500000000 1
  13.154700000000      3.576000000000     -3.019900000000 1
  10.204600000000     14.849100000000     -0.655500000000 1
  10.378600000000     16.496300000000     -3.016200000000 1
  11.332200000000     12.194900000000     -0.663000000000 1
  11.506300000000     13.842200000000     -3.023600000000 1
  12.459900000000      9.540800000000     -0.670400000000 1
  12.634000000000     11.188000000000     -3.031100000000 1
  13.587500000000      6.886600000000     -0.677900000000 1
  13.761600000000      8.533800000000     -3.038500000000 1
  14.715200000000      4.232400000000     -0.685300000000 1
  14.889300000000      5.879700000000     -3.046000000000 1
  16.017000000000      3.225500000000     -3.053400000000 1         
%endblock AtomicCoordinatesAndAtomicSpecies

# UNIT CELL

%block LatticeVectors
    18.00000    18.00000    18.00000
    18.00000    18.00000    18.00000
    18.00000    18.00000    18.00000
%endblock LatticeVectors


# K-points

%block kgrid_Monkhorst_Pack
3    0   0    0.0
0    3   0    0.0
0    0   100  0.0
%endblock kgrid_Monkhorst_Pack


# Chemical species

NumberOfSpecies 1
%block ChemicalSpeciesLabel
  1  79 Au 
%endblock ChemicalSpeciesLabel

# Basis set variables
PAO.BasisType split
PAO.SplitTailNorm true
PAO.SplitNorm 0.15
PAO.BasisSize SZP

# General variables

#NeglNonOverlapInt   True
ElectronicTemperature  300 K
SolutionMethod    diagon 
MeshCutoff           150. Ry
xc.functional         GGA           # Exchange-correlation functional
xc.authors            PBE 
SpinPolarized false 
PAO.EnergyShift    0.01 eV
          # Exchange-correlation version

# SCF variables

DM.MixSCF1   T
MaxSCFIterations      1000           # Maximum number of SCF iter
DM.MixH               T    
DM.MixingWeight       0.01          # New DM amount for next SCF cycle
DM.Tolerance          1.d-5         # Tolerance in maximum difference
DM.UseSaveDM          .true.          # to use continuation files
DM.NumberPulay         5

# MD variables

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

# Output variables

WriteMullikenPop                1
WriteBands                      .true.
SaveRho                         .true.
SaveDeltaRho                    .true.
SaveHS                          .true.
SaveElectrostaticPotential      yes
SaveTotalPotential              yes
WriteCoorXmol                   .true.
WriteMDXmol                     .true.
WriteMDhistory                  .true.
WriteEigenvalues                yes
SaveTotalPotential              .true.

electrode output file:

siesta: WARNING: XV file not found

siesta: Atomic coordinates (Bohr) and species
siesta:      3.22369   9.40706  -5.45356  1        1
siesta:      6.17241  10.64748  -1.04181  1        2
siesta:      6.50142  13.76024  -5.50288  1        3
      ...........

siesta: Automatic unit cell vectors (Ang):
siesta:   26.046637    0.000000    0.000000
siesta:    0.000000   24.902307    0.000000
siesta:    0.000000    0.000000   13.056737

siesta: System type = molecule  

initatomlists: Number of atoms, orbitals, and projectors:     36   324   684

coxmol: Writing XMOL coordinates into file leftAu.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                    =        1
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                                 =   150.0000 Ry
redata: Net charge of the system                    =     0.0000 |e|
redata: Min. number of SCF Iter                     =        0
redata: Max. number of SCF Iter                     =     1000
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 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                        =     0.000010
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                       = Diagonalization
redata: Electronic Temperature                      =   299.9978 K
redata: Fix the spin of the system                  =   F
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                 =     0.010000
mix.SCF:    Mixing weight                        =     0.010000
mix.SCF:    SVD condition                        = 0.1000E-07
redata: Save all siesta data in one NC              =   F
redata: ***********************************************************************

%block SCF.Mixers
  Pulay
%endblock SCF.Mixers

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

  # Mixing options
  weight 0.0100
  weight.linear 0.0100
  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:   396.000000
Total ionic charge:   396.000000

* ProcessorY, Blocksize:    6   6


* Orbital distribution balance (max,min):    12     6

k-point displ. along   3 input, could be:     0.00    0.50
 Kpoints in:          459 . Kpoints trimmed:          455

siesta: k-grid: Number of k-points =   455
siesta: k-grid: Cutoff (effective) =    37.353 Ang
siesta: k-grid: Supercell and displacements
siesta: k-grid:    3   0   0      0.000
siesta: k-grid:    0   3   0      0.000
siesta: k-grid:    0   0 100      0.000

diag: Algorithm                                     = D&C
diag: Parallel over k                               =   F
diag: Use parallel 2D distribution                  =   T
diag: Parallel block-size                           = 6
diag: Parallel distribution                         =     6 x     8
diag: Used triangular part                          = Lower
diag: Absolute tolerance                            =  0.100E-15
diag: Orthogonalization factor                      =  0.100E-05
diag: Memory factor                                 =  1.0000


ts: **************************************************************
ts: Save H and S matrices                           =    T
ts: Save DM and EDM matrices                        =    T
ts: Only save the overlap matrix S                  =    F
ts: **************************************************************

************************ Begin: TS CHECKS AND WARNINGS ************************
************************ End: TS CHECKS AND WARNINGS **************************


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

outcell: Unit cell vectors (Ang):
       26.046637    0.000000    0.000000
        0.000000   24.902307    0.000000
        0.000000    0.000000   13.056737

outcell: Cell vector modules (Ang)   :   26.046637   24.902307   13.056737
outcell: Cell angles (23,13,12) (deg):     90.0000     90.0000     90.0000
outcell: Cell volume (Ang**3)        :   8468.8790
<dSpData1D:S at geom step 0
  <sparsity:sparsity for geom step 0
    nrows_g=324 nrows=12 sparsity=.0285 nnzs=2990, refcount: 7>
  <dData1D:(new from dSpData1D) n=2990, refcount: 1>
refcount: 1>
new_DM -- step:     1
Initializing Density Matrix...

Attempting to read DM from file... Failed...
DM filled with atomic data:
<dSpData2D:DM initialized from atoms
  <sparsity:sparsity for geom step 0
    nrows_g=324 nrows=12 sparsity=.0285 nnzs=2990, refcount: 8>
  <dData2D:DM n=2990 m=1, refcount: 1>
refcount: 1>
No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps:      30     230
New grid distribution:   1
           1       1:   96    1:   16    1:    7
           2       1:   96    1:   16    8:   14
           3       1:   96    1:   16   15:   20
          .......

InitMesh: MESH =   192 x   192 x   100 =     3686400
InitMesh: (bp) =    96 x    96 x    50 =      460800
InitMesh: Mesh cutoff (required, used) =   150.000   150.176 Ry
ExtMesh (bp) on 0 =   168 x    92 x    79 =     1221024
New grid distribution:   2
           1      44:   96    1:   22    1:   34
           2      36:   43    1:   22    1:   40
           3      42:   96   23:   31   46:   50
           4      21:   35    1:   24   41:   45
           5       1:   20    1:   24    1:   40
          ....
Setting up quadratic distribution...
ExtMesh (bp) on 0 =   125 x    98 x   106 =     1298500
PhiOnMesh: Number of (b)points on node 0 =                39644
PhiOnMesh: nlist on node 0 =               232730

stepf: Fermi-Dirac step function

siesta: Program's energy decomposition (eV):
siesta: Ebs     =     -4008.186821
siesta: Eions   =     31343.136906
siesta: Ena     =       127.262206
siesta: Ekin    =     20794.072458
siesta: Enl     =    -15707.362626
siesta: Eso     =         0.000000
siesta: Edftu   =         0.000000
siesta: DEna    =        -4.980730
siesta: DUscf   =        13.886775
siesta: DUext   =         0.000000
siesta: Exc     =     -7721.736615
siesta: eta*DQ  =         0.000000
siesta: Emadel  =         0.000000
siesta: Emeta   =         0.000000
siesta: Emolmec =         0.000000
siesta: Ekinion =         0.000000
siesta: Eharris =    -33806.017259
siesta: Etot    =    -33841.995438
siesta: FreeEng =    -33842.068095

        iscf     Eharris(eV)        E_KS(eV)     FreeEng(eV)     dDmax    Ef(eV) dHmax(eV)
   scf:    1   -33806.017259   -33841.995438   -33842.068095  0.383586 -4.299979  6.458168
timer: Routine,Calls,Time,% = IterSCF        1    1229.819  99.92
   scf:    2   -33843.275716   -33842.647545   -33842.720352  0.009007 -4.323171  5.968842
   scf:    3   -33846.714056   -33846.257633   -33846.334987  0.103917 -4.600736  1.648266 ....................

SCF Convergence by DM+H criterion
max |DM_out - DM_in|         :     0.0000017710
max |H_out - H_in|      (eV) :     0.0007986776
SCF cycle converged after 36 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:      30     230

siesta: E_KS(eV) =           -33847.9636

siesta: E_KS - E_eggbox =    -33847.9636

siesta: Atomic forces (eV/Ang):
----------------------------------------
   Tot    0.003138   -0.002314   -0.000862
----------------------------------------
   Max    1.995833
   Res    0.779961    sqrt( Sum f_i^2 / 3N )
----------------------------------------
   Max    1.995833    constrained

I have not included some part of electrode output...

scattering region input:

SystemName  CpolyPTN2
SystemLabel CpolyPTN2

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

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

%block PAO.BasisSizes
C  DZP
H  DZP
S  DZP
Au SZP
%endblock PAO.BasisSizes

PAO.EnergyShift  0.01 eV

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

%block kgrid_Monkhorst_Pack
3   0   0      0.0
0   3   0      0.0
0   0   100    0.0
%endblock kgrid_Monkhorst_Pack

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

# UNIT CELL

%block LatticeVectors
18.00000    00.00000    0.000000
00.00000    18.00000    0.000000
00.00000    00.00000    42.00000
%endblock LatticeVectors

# Atomic coordinates
NumberOfAtoms 168
AtomicCoordinatesFormat Ang
%block AtomicCoordinatesAndAtomicSpecies
    1.705900000000      4.978000000000     -2.885900000000 4
    3.266300000000      5.634400000000     -0.551300000000 4
    3.440400000000      7.281600000000     -2.912000000000 4
    4.568100000000      4.627500000000     -2.919400000000 4
    5.000900000000      7.938100000000     -0.577400000000 4
    5.175000000000      9.585300000000     -2.938000000000 4
    6.128600000000      5.283900000000     -0.584800000000 4
    6.302600000000      6.931200000000     -2.945500000000 4
    7.430300000000      4.277000000000     -2.952900000000 4
    6.735400000000     10.241800000000     -0.603400000000 4
    6.909500000000     11.889000000000     -2.964100000000 4
    7.863100000000      7.587600000000     -0.610900000000 4
    8.037200000000      9.234800000000     -2.971500000000 4
    8.990800000000      4.933400000000     -0.618300000000 4
    9.164900000000      6.580700000000     -2.979000000000 4
   10.292500000000      3.926500000000     -2.986400000000 4
    8.470000000000     12.545400000000     -0.629500000000 4
    8.644100000000     14.192700000000     -2.990100000000 4
    9.597700000000      9.891300000000     -0.636900000000 4
    9.771700000000     11.538500000000     -2.997600000000 4
   10.725300000000      7.237100000000     -0.644400000000 4
   10.899400000000      8.884300000000     -3.005000000000 4
   11.853000000000      4.582900000000     -0.651800000000 4
   12.027100000000      6.230200000000     -3.012500000000 4
   13.154700000000      3.576000000000     -3.019900000000 4
   10.204600000000     14.849100000000     -0.655500000000 4
   10.378600000000     16.496300000000     -3.016200000000 4
   11.332200000000     12.194900000000     -0.663000000000 4
   11.506300000000     13.842200000000     -3.023600000000 4
   12.459900000000      9.540800000000     -0.670400000000 4
   12.634000000000     11.188000000000     -3.031100000000 4
   13.587500000000      6.886600000000     -0.677900000000 4
   13.761600000000      8.533800000000     -3.038500000000 4
   14.715200000000      4.232400000000     -0.685300000000 4
   14.889300000000      5.879700000000     -3.046000000000 4
   16.017000000000      3.225500000000     -3.053400000000 4
    4.826800000000      6.290800000000      1.783300000000 4
    6.387300000000      6.947300000000      4.117800000000 4
    6.561400000000      8.594500000000      1.757200000000 4
    7.947800000000      7.603700000000      6.452400000000 4
    8.121800000000      9.251000000000      4.091800000000 4
    7.689000000000      5.940400000000      1.749700000000 4
    9.249500000000      6.596800000000      4.084300000000 4
    8.295900000000     10.898200000000      1.731100000000 4
    9.682300000000      9.907400000000      6.426400000000 4
    9.856400000000     11.554600000000      4.065700000000 4
    9.423600000000      8.244000000000      1.723700000000 4
    9.508200000000      8.260200000000      8.787000000000 4
   10.810000000000      7.253200000000      6.418900000000 4
   10.984100000000      8.900500000000      4.058300000000 4
   10.551300000000      5.589900000000      1.716200000000 4
   12.111700000000      6.246300000000      4.050800000000 4
   10.030500000000     13.201900000000      1.705100000000 4
   11.158100000000     10.547700000000      1.697600000000 4
   12.285800000000      7.893500000000      1.690200000000 4
   13.413500000000      5.239400000000      1.682700000000 4
   ...... some coordintaes are removed because of limit in characters
%endblock AtomicCoordinatesAndAtomicSpecies  
==================================================
==================================================
# General variables

PAO.SplitTailNorm  .true.
PAO.SplitNorm   0.15
ElectronicTemperature  300 K 
MeshCutoff           150. Ry
xc.functional         GGA           # Exchange-correlation functional
xc.authors            PBE
SpinPolarized .false.
SolutionMethod transiesta

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

DM.MixSCF1   T
MaxSCFIterations      1000          
SCF.MixAfterConvergence  .false.
NeglNonOverlapInt     .true.       
DM.MixingWeight       0.01          
DM.Tolerance          1.d-5        
DM.UseSaveDM         .true.          
DM.Require.Energy.Convergence  .true.
DM.NumberPulay         5
Diag.DivideAndConquer  no
Diag.ParallelOverK     .true.
UseSaveData         .true.
LongOutput          .true.

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

MD.TypeOfRun       CG
MD.NumCGsteps      00
MD.MaxCGDispl    0.2 Ang
MD.UseSaveCG      .true.                 
MD.MaxForceTol   0.02 eV/Ang
MD.MaxStressTol  0.01 eV/Ang**3
MD.Targetpressure  0 GPa
WriteMDHistory   .true.
WriteMDXMol      .true.

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

WriteMullikenPop                1
WriteBands                      .true.
SaveRho                         .true.
SaveDeltaRho                    .true.
SaveHS                          .true.
SaveElectrostaticPotential      .true. 
SaveTotalPotential              .true.
WriteCoorXmol                   .true.
WriteMDXmol                     .true.
WriteMDhistory                  .true.
WriteEigenvalues                .true.

==================================================
==================================================
# Transiesta

# Bias voltage
TS.Voltage 0.0 eV
%block TS.ChemPots
  Left
  Right
%endblock TS.ChemPots

%block TS.ChemPot.Left
  mu V/2
  contour.eq
    begin
      c-Left
      t-Left
    end
%endblock TS.ChemPot.Left
%block TS.ChemPot.Right
  mu -V/2
  contour.eq
    begin
      c-Right
      t-Right
    end
%endblock TS.ChemPot.Right

TS.Elecs.Bulk true
TS.Elecs.DM.Update none
TS.Elecs.GF.ReUse false
%block TS.Elecs
  Left
  Right
%endblock TS.Elecs

%block TS.Elec.Left
  TSHS ./leftAu.TSHS
  chem-pot Left
  semi-inf-dir -a3
  elec-pos begin 1
  used-atoms 36
%endblock TS.Elec.Left

%block TS.Elec.Right
  TSHS ./rightAu.TSHS
  chem-pot Right
  semi-inf-dir  +a3
  elec-pos end -1
  used-atoms 36
%endblock TS.Elec.Right

TS.Contours.Eq.Pole 2.5 eV
%block TS.Contour.c-Left
  part circle
   from   -40.00000 eV + V/2 to -10. kT + V/2
    points 30
     method g-legendre
%endblock TS.Contour.c-Left
%block TS.Contour.t-Left
  part tail
   from prev to inf
    points 10
     method g-fermi
%endblock TS.Contour.t-Left
%block TS.Contour.c-Right
  part circle
   from   -40.00000 eV - V/2 to -10. kT - V/2
    points 30
     method g-legendre
%endblock TS.Contour.c-Right
%block TS.Contour.t-Right
  part tail
   from prev to inf
    points 10
     method g-fermi
%endblock TS.Contour.t-Right

TS.Contours.nEq.Eta 0.0001 eV
%block TS.Contours.nEq
  neq
%endblock TS.Contours.nEq
%block TS.Contour.nEq.neq
  part line
   from -|V|/2 - 5 kT to |V|/2 + 5 kT
    delta 0.01 eV
     method mid-rule
%endblock TS.Contour.nEq.neq

TBT.DOS.A.All T
TS.SolutionMethod btd
==================================================
==================================================

scattering region output:
siesta: Automatic unit cell vectors (Ang):
siesta:   26.101199    0.000000    0.000000
siesta:    0.000000   25.083477    0.000000
siesta:    0.000000    0.000000   52.409897

siesta: System type = molecule  

initatomlists: Number of atoms, orbitals, and projectors:    168  1608  2912

coxmol: Writing XMOL coordinates into file CpolyPTN2.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                                 =   T
redata: Number of Atomic Species                    =        4
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                                 =   150.0000 Ry
redata: Net charge of the system                    =     0.0000 |e|
redata: Min. number of SCF Iter                     =        0
redata: Max. number of SCF Iter                     =     1000
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 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                        =     0.000010
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   =   T
redata: (free) Energy tolerance for SCF             =     0.000100 eV
redata: Using Saved Data (generic)                  =   T
redata: Use continuation files for DM               =   T
redata: Neglect nonoverlap interactions             =   T
redata: Method of Calculation                       = Transiesta
redata: Fix the spin of the system                  =   F
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                 =     0.010000
mix.SCF:    Mixing weight                        =     0.010000
mix.SCF:    SVD condition                        = 0.1000E-07
redata: Save all siesta data in one NC              =   F


siesta: k-grid: Number of k-points =   455
siesta: k-grid: Cutoff (effective) =    37.625 Ang
siesta: k-grid: Supercell and displacements
siesta: k-grid:    3   0   0      0.000
siesta: k-grid:    0   3   0      0.000
siesta: k-grid:    0   0 100      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

 Kpoints in:            6 . Kpoints trimmed:            5

transiesta: ts_k-point coordinates (Bohr**-1) and weights:
transiesta:    1   -0.042462    0.000000    0.000000       0.222222
transiesta:    2    0.000000    0.000000    0.000000       0.111111
transiesta:    3   -0.042462    0.044185    0.000000       0.222222
transiesta:    4    0.000000    0.044185    0.000000       0.222222
transiesta:    5    0.042462    0.044185    0.000000       0.222222

transiesta: k-grid: Number of Green function k-points =     5
transiesta: k-grid: Supercell and displacements
transiesta: k-grid:    3   0   0      0.000
transiesta: k-grid:    0   3   0      0.000
transiesta: k-grid:    0   0   1      0.000
Electrode: Left is a Gamma-only calculation, this is not feasible.
Erroneous electrode setup, check out-put
Stopping Program from Node:   19
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2
  • $\begingroup$ Your electrode setup is incorrect, please correct lattice vectors, and also, move the atomic coordinates into the unit-cell. There is no need to have them offset $\endgroup$
    – nickpapior
    Jan 20, 2023 at 10:24
  • $\begingroup$ Sir, i have taken the electrode lattice vectors from older (4.0.2) version of same electrodes where it worked properly and substituted in new (4.1.5) electrode.fdf, and also unconstrained atomic coordinates as wells as lattice, but stiil i am getting the same error as gamma only calculation, but the same thing is working in older siesta version. I updated the input and output file in code format. $\endgroup$ Jan 26, 2023 at 5:14

1 Answer 1

4
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This error occurs if the electrode calculation was done only at the Gamma-point.

So I suspect that the flags you say you have put in the electrode calculation has not been accepted, the easiest way to check is to read the output of the electrode calculation. It should clearly specify the k-grid specification.

The problem is that there is no lattice constant definitions, and so the lattice-vectors turn to 0. When the lattice vectors are 0, Siesta will automatically calculate the smallest unit-cell that ensures no supercell couplings, effectively doing a molecule calculation.

This can be seen from your output:

siesta: Automatic unit cell vectors (Ang):
siesta:   26.101199    0.000000    0.000000
siesta:    0.000000   25.083477    0.000000
siesta:    0.000000    0.000000   52.409897

This is clearly not what you put in the file.

The reason for 4.0 to work is that it does not check for supercell connections, it only checks that the k-grid used is not the Gamma point. So any calculations with 4.0 and older would result in an electrode self-energy that is the molecule self-energy, not a semi-infinite electrode! Thus any calculation with 4.0 and this electrode would be wrong!

Please always check your output file to assert that the options you specify are correctly understood.

Secondly, your input lattice vectors like this:

%block LatticeVectors
    18.00000    18.00000    18.00000
    18.00000    18.00000    18.00000
    18.00000    18.00000    18.00000
%endblock LatticeVectors

are not viable lattice vectors. Please adjust them appropriately!

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7
  • $\begingroup$ Sir, I have defined lattice vectors during electrode and scattering calculation carefully but still i am getting Error like Electrode: Left is a Gamma-only calculation, this is not feasible. Erroneous electrode setup, check out-put previously i have used siest v4.0.2 never faced such problem but in 4.1.5 i am gettiing this kind of error $\endgroup$ Jan 22, 2023 at 18:09
  • $\begingroup$ Could you please show the input lattice-vectors (from the fdf file) and what Siesta understands as your lattice-vectors (from the output), put that in your question and lets take it from there. $\endgroup$
    – nickpapior
    Jan 24, 2023 at 7:05
  • $\begingroup$ Input lattice vectors 18.00000 00.00000 00.00000 00.00000 18.00000 00.00000 00.00000 00.00000 10.00000 $\endgroup$ Jan 25, 2023 at 5:34
  • $\begingroup$ Please update your initial question with the input AND output so it is clear from the question. $\endgroup$
    – nickpapior
    Jan 25, 2023 at 7:33
  • $\begingroup$ @ShanmukaRao see the updated response $\endgroup$
    – nickpapior
    Jan 26, 2023 at 8:38

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