Siesta

WARNING! Removed 20244 elements which connect electrodes across the device region!

Asked by Elder Augusto Viana Mota

Dear SIESTA users,
I has been this trouble when I trying to do transport calculations in TranSIESTA. I got this message in the output file:

"WARNING! Removed 20244 elements which connect electrodes across the device region!

And the results of this way:

"siesta: Final energy (eV):
siesta: Band Struct. = NaN
siesta: Kinetic = NaN
siesta: Hartree = NaN
siesta: Eldau = 0.000000
siesta: Eso = 0.000000
siesta: Ext. field = 0.000000
siesta: Enegf = 0.000000
siesta: Exch.-corr. = NaN
siesta: Ion-electron = NaN
siesta: Ion-ion = 229983.013721
siesta: Ekinion = 0.000000
siesta: Total = NaN
siesta: Fermi = -4.256064

siesta: Stress tensor (static) (eV/Ang**3):
siesta: NaN NaN NaN
siesta: NaN NaN NaN
siesta: NaN NaN NaN

siesta: Constrained stress tensor (static) (eV/Ang**3):
siesta: NaN NaN NaN
siesta: NaN NaN NaN
siesta: NaN NaN NaN

siesta: Cell volume = 29558.281308 Ang**3

siesta: Pressure (static):
siesta: Solid Molecule Units
siesta: NaN NaN Ry/Bohr**3
siesta: NaN NaN eV/Ang**3
siesta: NaN NaN kBar
(Free)E+ p_basis*V_orbitals = NaN
(Free)Eharris+ p_basis*V_orbitals = NaN

siesta: Electric dipole (a.u.) = NaN NaN NaN
siesta: Electric dipole (Debye) = NaN NaN NaN
>> End of run: 22-APR-2020 22:22:59
Job completed"

What is happening? How can I fixed it?

This is my input file:

#########################################
############# By E. A. V. Mota #################
#########################################
mkdir cont

for i in `seq -w 0.00 0.05 0.50`

cp -r cont $i
cd $i
cp ../*.psf .
cp -r ../Lead .

cat > POPGN26_ScatPos.fdf <<EOF

# ---------------------------------------------------------------------------#
# Name and Label #
# ---------------------------------------------------------------------------#

SystemName POPGN26_ScatPos
SystemLabel POPGN26_ScatPos

#--------------------------------------------------#
# k-point sampling #
#--------------------------------------------------#
%block kgrid_Monkhorst_Pack
      1 0 0 0.0
      0 1 0 0.0
      0 0 1 0.0
%endblock kgrid_Monkhorst_Pack

#%block PS.Lmax
# C 2
# H 1
#%endblock

#--------------------------------------------------#
# Basis Set #
#--------------------------------------------------#
PAO.BasisType split
PAO.BasisSize DZP
PAO.SplitNorm 0.15
#PAO.SplitNormH 0.50
PAO.EnergyShift 0.01 Ry

#----------------------------------------------------------------------#
# Exchange-correlation functionals options #
#----------------------------------------------------------------------#
MeshCutoff 300 Ry
#MeshSubDivisions 2
XC.functional GGA
XC.authors PBE

#----------------------------------------------------------------#
# Self-Consistent-Field loop options #
#----------------------------------------------------------------#
MinSCFIterations 0
MaxSCFIterations 500
SCF.Mixer.Method pulay
SCF.Mixer.History 6
SCF.Mixer.Weight 0.02
SCF.DM.Tolerance 0.0001
DM.UseSaveDM .true.
SCF.Mix.First .true.

#------------------------------------------------------------------#
# Calculation of the Electronic Structure #
#------------------------------------------------------------------#
SolutionMethod transiesta
Diag.ParallelOverK F

#--------------------------------------------------------------------------#
# Occupation of electronic states and Fermi level #
#--------------------------------------------------------------------------#
ElectronicTemperature 300 K
OccupationFunction MP

#------------------------------------------------------#
# Structural relaxation #
#------------------------------------------------------#
MD.NumCGSteps 0

#--------------------------------------------------#
# Output options #
#--------------------------------------------------#
WriteMullikenPop 1
WriteForces T
SaveHS T

#----------------------------------------------------------------------------------------------------------------------------#
#---------------------------------------------# TranSIESTA options #--------------------------------------------#
 #---------------------------------------------------------------------------------------------------------------------------#
TS.Voltage $i eV
#------------------------------------------------------------#
# This block set all the chemical #
# potentials of the N electrodes #
#------------------------------------------------------------#
%block TS.ChemPots
  Left
  Right
%endblock TS.ChemPots

#--------------------------------------------------------------------------#
# Setting for the chemical potential named "Left" #
#--------------------------------------------------------------------------#
%block TS.ChemPot.Left
  mu V/2
  contour.eq
    begin
      C-Left
      T-Left
    end
%endblock TS.ChemPot.Left

#---------------------------------------------------------------------------#
# Setting for the chemical potential named "Right" #
#---------------------------------------------------------------------------#
%block TS.ChemPot.Right
  mu -V/2
  contour.eq
    begin
      C-Right
      T-Right
    end
%endblock TS.ChemPot.Right

#---------------------------------------------------------------------------------------------------------------------------------------------#
#------------------------------------# Complex contour integration options #-------------------------------------------#
#---------------------------------------------------------------------------------------------------------------------------------------------#

#----------------------------------------------------------------------------------------------------------------------------------#
#----------------------------------# Equilibriun contour optins #---------------------------------------------------#
#----------------------------------------------------------------------------------------------------------------------------------#

TS.Contours.Eq.Pole 2.5 eV

#-----------------------------------------------------------------#
# Block of the integration curve C-Left #
# in block "countourn.eq" #
#-----------------------------------------------------------------#
%block TS.Contour.C-Left
  part circle
   from -40.0 eV + V/2 to -10 kT + V/2
     points 30
      method g-legendre
%endblock TS.Contour.C-Left

#-----------------------------------------------------------------#
# Block of the integration curve T-Left #
# in block "countourn.eq" #
#-----------------------------------------------------------------#
%block TS.Contour.T-Left
  part tail
   from prev to inf
     points 15
      method g-fermi
%endblock TS.Contour.T-Left

#------------------------------------------------------------------#
# Block of the integration curve C-Right #
# in block "countourn.eq" #
#------------------------------------------------------------------#
%block TS.Contour.C-Right
  part circle
   from -40. eV -V/2 to -10 kT -V/2
     points 30
      method g-legendre
%endblock TS.Contour.C-Right

#------------------------------------------------------------------#
# Block of the integration curve T-Right #
# in block "countourn.eq" #
#------------------------------------------------------------------#
%block TS.Contour.T-Right
  part tail
   from prev to inf
     points 15
      method g-fermi
%endblock TS.Contour.T-Right

#-----------------------------------------------------------------------------------------------------------------------------------------------#
#---------------------------------------------# Non-Equilibriun contour optins #---------------------------------------------#
#-----------------------------------------------------------------------------------------------------------------------------------------------#
TS.Contours.nEq.Eta 0.0001 eV

#------------------------------------------------------------------------#
# Block of the non-equilibriun integration curve #
#------------------------------------------------------------------------#
%block TS.Contours.nEq
  neq-1
%endblock TS.Contours.nEq

#-----------------------------------------------------------------#
# Block of the integration curve neq1 #
#-----------------------------------------------------------------#
%block TS.Contour.nEq.neq-1
  part line
   from -|V|/2 - 5 kT to |V|/2 + 5 kT
     delta 0.01 eV
      method mid-rule
%endblock TS.Contour.nEq.neq-1

#---------------------------------------------------------------------------------------------------------------------------------#
#---------------------------------------------# Electrode options #---------------------------------------------------#
#---------------------------------------------------------------------------------------------------------------------------------#
TS.Elecs.Bulk true
TS.Elecs.DM.Update none
TS.Elecs.GF.ReUse true
TS.Elecs.Eta 0.0001000000 eV

#---------------------------------------------------------------------------------------------------#
#------------------------# Two Electrodes configuration #-------------------------#
#---------------------------------------------------------------------------------------------------#
%block TS.Elecs
  Left
  Right
%endblock TS.Elecs

#----------------------------------------------------------#
# Block of the Left electrode #
#-----------------------------------------------------------#
%block TS.Elec.Left
  HS ./Lead/POPGN_P5_Lead22.TSHS
  chem-pot Left
  semi-inf-dir -a3
  elec-pos begin 1
%endblock TS.Elec.Left

#------------------------------------------------------------#
# Block of the Right electrode #
#------------------------------------------------------------#
%block TS.Elec.Right
  TSHS ./Lead/POPGN_P5_Lead22.TSHS
  chem-pot Right
  semi-inf-dir +a3
  elec-pos end -1
%endblock TS.Elec.Right

#-----------------------------------------------------------------------------------------------------------------------------------------#
#--------------------------------------------------------# TBTrans options #---------------------------------------------------#
#-----------------------------------------------------------------------------------------------------------------------------------------#
TBT.Elecs.Eta 0.0001 eV
TBT.T.Eig 3
TBT.DOS.A true

#--------------------------------------------------------------#
# Block to select the device atoms #
# in scattering region #
#--------------------------------------------------------------#
%block TBT.Atoms.Device
atom [ 53 -- 208 ]
%endblock

#------------------------------------------------------------------------#
# Block of the non-equilibriun integration curve #
#------------------------------------------------------------------------#
%block TBT.Contours
  neq
%endblock TBT.Contours

#------------------------------------------------------------------------#
# Block of the integration curve neq #
#------------------------------------------------------------------------#
%block TBT.Contour.neq
  part line
   from -0.25000 eV to 0.25000 eV
    delta 0.001000 eV
     method mid-rule
%endblock TBT.Contour.neq

#------------------------------------------------------------------------------------------------------------------------------------#
#------------------------------------------------# System options #-------------------------------------------------------#
#------------------------------------------------------------------------------------------------------------------------------------#

%block ChemicalSpeciesLabel
  1 1 H
  2 6 C
  3 7 N
%endblock ChemicalSpeciesLabel

NumberOfAtoms 260
NumberOfSpecies 3
LatticeConstant 1.0 Ang
%block LatticeVectors
    20.000000000 0.000000000 0.000000000
     0.000000000 38.964000000 0.000000000
     0.000000000 0.000000000 37.930244980
%endblock LatticeVectors
AtomicCoordinatesFormat Ang
%block AtomicCoordinatesAndAtomicSpecies
    10.000000000 11.920911466 0.508262446 2 # 1
    10.000000000 21.101187750 0.422837617 2 # 2
    10.000000000 17.880052690 0.486982144 2 # 3
    10.000000000 27.035594822 0.340359482 2 # 4
    10.000000000 13.297950386 0.809526663 2 # 5
    10.000000000 22.445562837 0.729533620 2 # 6
    10.000000000 16.511237083 0.800509225 2 # 7
    10.000000000 25.657305742 0.644924671 2 # 8
    10.000000000 11.040704848 1.602241860 2 # 9
    10.000000000 20.176168753 1.516305261 2 # 10
    10.000000000 18.795552159 1.594612283 2 # 11
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    10.000000000 9.940930207 1.601445447 1 # 13
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    10.000000000 13.297771463 2.392362174 2 # 15
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    10.000000000 25.651275323 2.227809855 2 # 18
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    10.000000000 17.880052690 4.280006642 2 # 29
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    10.000000000 21.101187750 34.560058099 2 # 236
    10.000000000 17.880052690 34.624202626 2 # 237
    10.000000000 27.035594822 34.477579964 2 # 238
    10.000000000 13.297950386 34.946747145 2 # 239
    10.000000000 22.445562837 34.866754102 2 # 240
    10.000000000 16.511237083 34.937729707 2 # 241
    10.000000000 25.657305742 34.782145153 2 # 242
    10.000000000 11.040704848 35.739462342 2 # 243
    10.000000000 20.176168753 35.653525743 2 # 244
    10.000000000 18.795552159 35.731832765 2 # 245
    10.000000000 27.910077044 35.569776726 2 # 246
    10.000000000 9.940930207 35.738665929 1 # 247
    10.000000000 29.009948705 35.577302087 1 # 248
    10.000000000 13.297771463 36.529582656 2 # 249
    10.000000000 22.423579387 36.448915144 2 # 250
    10.000000000 16.517291349 36.536133656 2 # 251
    10.000000000 25.651275323 36.365030337 2 # 252
    10.000000000 11.919068313 36.832773768 2 # 253
    10.000000000 21.095676643 36.751171792 3 # 254
    10.000000000 17.889996420 36.849084547 2 # 255
    10.000000000 27.023873476 36.664046884 2 # 256
    10.000000000 14.190377088 37.632675274 2 # 257
    10.000000000 23.344177334 37.530633607 2 # 258
    10.000000000 15.611227636 37.631678293 2 # 259
    10.000000000 24.760250467 37.479445703 2 # 260
%endblock AtomicCoordinatesAndAtomicSpecies
==================================================
==================================================

EOF

mpirun -np 8 siesta41b4 < POPGN26_ScatPos.fdf | tee POPGN26_BiasPos.out

cd ..
rm -rf cont
mkdir cont

cp ./$i/POPGN26_ScatPos.TSDE ./$i/POPGN26_ScatPos.TSHS ./$i/POPGN26_ScatPos.DM cont # copy these files for continuation of the next bias step.

done

I really appreciate if someone could helpe me!
Besta regards!

Msc. Elder A. V. Mota

Question information

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Elder Augusto Viana Mota
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Revision history for this message
Nick Papior (nickpapior) said : 		#1

Always check the SCF convergence, it seems to me you just think it will always converge? It won't.
Perhaps this is related to too high mixing weights, etc.

Also, this warning:
"WARNING! Removed 20244 elements which connect electrodes across the device region!

This will always be shown for gamma-only calculations since it tries to guess the "incorrect" PBC in the semi-infinite direction.

Revision history for this message
Elder Augusto Viana Mota (eavmota) said : 		#2

Dear Nick,
Thank you for answering my question. I have some doubts about the answer::

1. I used the value of 0.02 for mixing, and I believe that value is already low. Is there a minimum acceptable value for good accuracy? For example: "Decrease the value until 0.0001"?

This is the SCF part of the output file is that:

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

outcell: Unit cell vectors (Ang):
       20.000000 0.000000 0.000000
        0.000000 38.964000 0.000000
        0.000000 0.000000 37.930245

outcell: Cell vector modules (Ang) : 20.000000 38.964000 37.930245
outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000
outcell: Cell volume (Ang**3) : 29558.2813
<dSpData1D:S at geom step 0
  <sparsity:sparsity for geom step 0
    nrows_g=3220 nrows=408 sparsity=.0225 nnzs=233666, refcount: 7>
  <dData1D:(new from dSpData1D) n=233666, refcount: 1>
refcount: 1>
new_DM -- step: 1
Initializing Density Matrix...

Attempting to read DM, EDM from TSDE file... Failed...
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=3220 nrows=408 sparsity=.0225 nnzs=233666, refcount: 8>
  <dData2D:DM n=233666 m=1, refcount: 1>
refcount: 1>

transiesta: Initialization run using siesta

No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 259 208
New grid distribution: 1
           1 1: 108 1: 108 1: 50
           2 1: 108 1: 108 51: 100
           3 1: 108 1: 108 101: 150
           4 1: 108 1: 108 151: 200
           5 1: 108 109: 216 1: 50
           6 1: 108 109: 216 51: 100
           7 1: 108 109: 216 101: 150
           8 1: 108 109: 216 151: 200

InitMesh: MESH = 216 x 432 x 400 = 37324800
InitMesh: (bp) = 108 x 216 x 200 = 4665600
InitMesh: Mesh cutoff (required, used) = 300.000 307.362 Ry
ExtMesh (bp) on 0 = 172 x 176 x 114 = 3451008
New grid distribution: 2
           1 1: 108 1: 83 1: 100
           2 1: 108 84: 108 1: 100
           3 1: 108 1: 83 101: 200
           4 1: 108 84: 108 101: 200
           5 1: 108 134: 216 1: 100
           6 1: 108 109: 133 1: 100
           7 1: 108 134: 216 101: 200
           8 1: 108 109: 133 101: 200
New grid distribution: 3
           1 1: 108 1: 76 1: 100
           2 1: 108 77: 108 1: 100
           3 1: 108 1: 76 101: 200
           4 1: 108 77: 108 101: 200
           5 1: 108 141: 216 1: 100
           6 1: 108 109: 140 1: 100
           7 1: 108 141: 216 101: 200
           8 1: 108 109: 140 101: 200
Setting up quadratic distribution...
ExtMesh (bp) on 0 = 172 x 151 x 164 = 4259408
PhiOnMesh: Number of (b)points on node 0 = 896400
PhiOnMesh: nlist on node 0 = 5483100

ts: Using electrode: Left for Hartree correction
ts: Grid fraction plane 0.00056
ts: Grid point plane (Ang): 0.00000 0.00000 0.02139
ts-Vha: -0.17117E-09 eV

stepf: Methfessel-Paxton step function
       Using Hermite-Gauss polynomials of order 1
ts-Vha: -0.15160E-01 eV

siesta: Program's energy decomposition (eV):
siesta: Ebs = -12674.674177
siesta: Eions = 63325.725641
siesta: Ena = 13460.355987
siesta: Ekin = 27538.004843
siesta: Enl = -3068.700052
siesta: Eso = 0.000000
siesta: Eldau = 0.000000
siesta: DEna = -1151.754003
siesta: DUscf = 164.247937
siesta: DUext = 0.000000
siesta: Enegf = 0.000000
siesta: Exc = -13898.325714
siesta: eta*DQ = 0.000000
siesta: Emadel = 0.000000
siesta: Emeta = 0.000000
siesta: Emolmec = 0.000000
siesta: Ekinion = 0.000000
siesta: Eharris = -39921.233838
siesta: Etot = -40281.896641
siesta: FreeEng = -40281.910794

        iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV)
   scf: 1 -39921.233838 -40281.896641 -40281.910794 1.927809 -6.135367 9.366906
timer: Routine,Calls,Time,% = IterSCF 1 147.366 11.68
ts-Vha: -0.14823E-01 eV
   scf: 2 -40307.095148 -40295.084006 -40295.104259 0.009573 -6.108813 7.916860
ts-Vha: -0.14267E-01 eV
   scf: 3 -40316.124492 -40321.764548 -40321.766730 0.054527 -5.989550 5.908457
ts-Vha: -0.14387E-01 eV
   scf: 4 -40321.866173 -40321.922877 -40321.923202 0.004884 -5.979746 5.588569
ts-Vha: -0.12301E-01 eV
   scf: 5 -40238.308580 -40290.088410 -40290.092091 0.037273 -6.018436 10.632877
ts-Vha: -0.71123E-02 eV
   scf: 6 -39353.237720 -40062.301905 -40062.316421 0.193461 -4.954515 27.377983
ts-Vha: -0.73924E-02 eV
   scf: 7 -40230.754227 -40152.352854 -40152.363587 0.041983 -4.685029 22.921523
ts-Vha: -0.70898E-02 eV
   scf: 8 -40145.108107 -40150.493731 -40150.508692 0.024483 -4.790258 23.091490
ts-Vha: -0.13929E-01 eV
   scf: 9 -40179.717768 -40314.212793 -40314.227391 0.129288 -4.309705 7.107832
ts-Vha: -0.15047E-01 eV
   scf: 10 -40265.522568 -40319.973402 -40319.961602 0.069793 -4.485708 7.624188
ts-Vha: -0.15169E-01 eV
   scf: 11 -40339.192634 -40331.312235 -40331.308517 0.040625 -4.901976 5.548671
ts-Vha: -0.17266E-01 eV
   scf: 12 -40227.824167 -40291.454880 -40291.443962 0.056484 -4.508113 10.843701
ts-Vha: -0.20007E-01 eV
   scf: 13 -40213.975359 -40316.907824 -40316.923079 0.105074 -4.710737 7.151132
ts-Vha: -0.19130E-01 eV
   scf: 14 -40291.263269 -40327.617274 -40327.610492 0.079372 -4.358538 5.809127
ts-Vha: -0.16037E-01 eV
   scf: 15 -40341.199201 -40339.266573 -40339.281897 0.028907 -4.251503 2.497209
ts-Vha: -0.14975E-01 eV
   scf: 16 -40313.685737 -40331.024329 -40331.040211 0.035604 -4.248891 4.639559
ts-Vha: -0.14179E-01 eV
   scf: 17 -40282.082155 -40310.194111 -40310.191094 0.024976 -4.341602 8.780581
ts-Vha: -0.12268E-01 eV
   scf: 18 -40280.961275 -40296.259607 -40296.251802 0.017714 -4.534274 10.891458
ts-Vha: -0.15939E-01 eV
   scf: 19 -40332.272401 -40316.097384 -40316.092154 0.031893 -4.179586 7.312923
ts-Vha: -0.93873E-02 eV
   scf: 20 -40055.170790 -40206.635131 -40206.645924 0.057949 -4.227163 18.159665
ts-Vha: -0.17025E-01 eV
   scf: 21 -39599.794913 -40183.732764 -40183.727326 0.207531 -4.353811 19.181048
ts-Vha: -0.13883E-01 eV
   scf: 22 -40141.247357 -40315.083883 -40315.080779 0.156168 -4.299259 8.025257
ts-Vha: -0.14749E-01 eV
   scf: 23 -40345.382617 -40339.941840 -40339.948669 0.048964 -4.241049 2.864728
ts-Vha: -0.15940E-01 eV
   scf: 24 -40334.399755 -40340.042792 -40340.037924 0.025699 -4.320215 2.700916
ts-Vha: -0.15530E-01 eV
   scf: 25 -40341.602429 -40341.031744 -40341.023824 0.005820 -4.297774 2.321201
ts-Vha: -0.16147E-01 eV
   scf: 26 -40340.214410 -40340.669098 -40340.665753 0.003353 -4.283292 2.500561
ts-Vha: -0.16376E-01 eV
   scf: 27 -40339.710695 -40340.225505 -40340.219634 0.003239 -4.318142 2.656668
ts-Vha: -0.15488E-01 eV
   scf: 28 -40339.810926 -40340.038373 -40340.034420 0.003449 -4.295808 2.745360
ts-Vha: -0.15145E-01 eV
   scf: 29 -40341.281417 -40340.700680 -40340.697103 0.002980 -4.295695 2.488388
ts-Vha: -0.17141E-01 eV
   scf: 30 -40270.234306 -40322.127772 -40322.114551 0.062540 -4.279954 6.922126
ts-Vha: -0.16710E-01 eV
   scf: 31 -40323.678273 -40340.325636 -40340.323151 0.063588 -4.238023 2.289219
ts-Vha: -0.16677E-01 eV
   scf: 32 -40341.982482 -40341.220612 -40341.214325 0.003168 -4.255020 1.726721
ts-Vha: -0.17138E-01 eV
   scf: 33 -40338.247746 -40339.864475 -40339.860267 0.004864 -4.241038 2.469742
ts-Vha: -0.16527E-01 eV
   scf: 34 -40321.737002 -40332.132611 -40332.125804 0.011899 -4.315138 4.781137
ts-Vha: -0.15451E-01 eV
   scf: 35 -40345.078654 -40341.692107 -40341.687025 0.022143 -4.253242 1.502969
ts-Vha: -0.17461E-01 eV
   scf: 36 -40337.497789 -40340.122756 -40340.120449 0.013272 -4.274280 2.219966
ts-Vha: -0.15167E-01 eV
   scf: 37 -40288.903387 -40328.339449 -40328.343118 0.061063 -4.218780 5.689313
ts-Vha: -0.16478E-01 eV
   scf: 38 -40316.467738 -40338.774651 -40338.772803 0.065039 -4.284622 2.958757
ts-Vha: -0.15560E-01 eV
   scf: 39 -40341.828044 -40340.398506 -40340.392951 0.003935 -4.291928 2.316894
ts-Vha: -0.14995E-01 eV
   scf: 40 -40339.613930 -40340.029812 -40340.021928 0.002214 -4.294179 2.523432
ts-Vha: -0.13773E-01 eV
   scf: 41 -40343.145859 -40341.806427 -40341.816011 0.010689 -4.292269 1.714737
ts-Vha: -0.13827E-01 eV
   scf: 42 -40340.316103 -40341.210341 -40341.203788 0.008846 -4.276603 2.021523
ts-Vha: -0.12839E-01 eV
   scf: 43 -40343.462899 -40342.525148 -40342.532351 0.008253 -4.271945 1.252690
ts-Vha: -0.10848E-01 eV
   scf: 44 -40308.516958 -40333.237923 -40333.256796 0.040812 -4.246503 4.488955
ts-Vha: -0.12706E-01 eV
   scf: 45 -40337.865686 -40342.732749 -40342.740508 0.039526 -4.262371 1.047581
ts-Vha: -0.12979E-01 eV
   scf: 46 -40341.958518 -40342.373490 -40342.376912 0.002703 -4.272834 1.353804
ts-Vha: -0.12792E-01 eV
   scf: 47 -40342.974807 -40342.703166 -40342.712893 0.003283 -4.270677 1.087630
ts-Vha: -0.12426E-01 eV
   scf: 48 -40343.030438 -40342.881287 -40342.893158 0.002120 -4.266773 0.894976
ts-Vha: -0.12690E-01 eV
   scf: 49 -40342.628636 -40342.763199 -40342.773118 0.001774 -4.267584 1.027635
ts-Vha: -0.12626E-01 eV
   scf: 50 -40342.806128 -40342.784864 -40342.794742 0.000329 -4.268453 1.000534
ts-Vha: -0.11989E-01 eV
   scf: 51 -40337.463915 -40341.734929 -40341.767108 0.020781 -4.242584 1.726560
ts-Vha: -0.12738E-01 eV
   scf: 52 -40339.989016 -40342.655558 -40342.664193 0.021247 -4.272498 1.130323
ts-Vha: -0.12595E-01 eV
   scf: 53 -40342.886198 -40342.776314 -40342.786554 0.001588 -4.271122 1.003695
ts-Vha: -0.12529E-01 eV
   scf: 54 -40343.209982 -40343.018635 -40343.026533 0.002713 -4.256868 0.646926
ts-Vha: -0.12440E-01 eV
   scf: 55 -40343.234596 -40343.174954 -40343.189249 0.004065 -4.254523 0.159051
ts-Vha: -0.12384E-01 eV
   scf: 56 -40343.176293 -40343.182876 -40343.199736 0.001447 -4.254013 0.054247
ts-Vha: -0.12443E-01 eV
   scf: 57 -40343.138716 -40343.171173 -40343.185030 0.001796 -4.255195 0.195996
ts-Vha: -0.12384E-01 eV
   scf: 58 -40343.051607 -40343.153996 -40343.173612 0.003951 -4.254069 0.258681
ts-Vha: -0.12486E-01 eV
   scf: 59 -40343.089002 -40343.168168 -40343.181718 0.003972 -4.254811 0.218395
ts-Vha: -0.12448E-01 eV
   scf: 60 -40343.185809 -40343.185117 -40343.201326 0.001679 -4.254341 0.020238
ts-Vha: -0.12406E-01 eV
   scf: 61 -40343.149042 -40343.173241 -40343.191677 0.001463 -4.254109 0.152966
ts-Vha: -0.12429E-01 eV
   scf: 62 -40343.188737 -40343.184588 -40343.201379 0.001091 -4.254471 0.021862
ts-Vha: -0.12431E-01 eV
   scf: 63 -40343.184851 -40343.185153 -40343.201356 0.000377 -4.254784 0.025239
ts-Vha: -0.12413E-01 eV
   scf: 64 -40343.185129 -40343.185183 -40343.201579 0.000114 -4.255143 0.011723
ts-Vha: -0.12399E-01 eV
   scf: 65 -40343.183983 -40343.184743 -40343.201500 0.000237 -4.255327 0.017734
ts-Vha: -0.12399E-01 eV
   scf: 66 -40343.185291 -40343.185058 -40343.201632 0.000117 -4.255446 0.004006
ts-Vha: -0.12395E-01 eV
   scf: 67 -40343.185095 -40343.185077 -40343.201638 0.000028 -4.255583 0.003278
ts-Vha: -0.12394E-01 eV
   scf: 68 -40343.185206 -40343.185147 -40343.201645 0.000044 -4.255724 0.003030
ts-Vha: -0.12394E-01 eV
   scf: 69 -40343.185101 -40343.185125 -40343.201652 0.000050 -4.255855 0.001322
ts-Vha: -0.12397E-01 eV
   scf: 70 -40343.185128 -40343.185126 -40343.201654 0.000026 -4.255918 0.001217
ts-Vha: -0.12400E-01 eV
   scf: 71 -40343.185135 -40343.185131 -40343.201655 0.000006 -4.255918 0.001217
ts-Vha: -0.12401E-01 eV
   scf: 72 -40343.185133 -40343.185132 -40343.201655 0.000006 -4.255937 0.001199
ts-Vha: -0.12399E-01 eV
   scf: 73 -40343.185134 -40343.185133 -40343.201656 0.000039 -4.256114 0.000639

SCF Convergence by DM+H criterion
max |DM_out - DM_in| : 0.0000385620
max |H_out - H_in| (eV) : 0.0006385464
SCF cycle converged after 73 iterations

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

ts-Vha: -0.12399E-01 eV

*** WARNING! Removed 20244 elements which connect electrodes across the device region!

transiesta: We cannot assure cross-boundary connections in Gamma calculations.
transiesta: Ensure that the electrode says: Principal cell is perfect

transiesta: created H and S sparsity pattern:
  <sparsity:(M of: G ((UC of: T T T sparsity for geom step 0)))
    nrows_g=3220 nrows=3220 sparsity=.1150 nnzs=1192236, refcount: 1>

transiesta: created update sparsity pattern:
  <sparsity:G ((UC of: (M of: T T T sparsity for geom step 0)))
    nrows_g=3220 nrows=3220 sparsity=.0880 nnzs=912276, refcount: 1>

*** WARNING! Removed 20244 elements which connect electrodes across the device region!

transiesta: Determining an optimal tri-matrix using: atom+Left
transiesta: Established a near-optimal partition for the tri-diagonal matrix.
BTD partitions (6):
  [ 639, 638, [643] * 2, 644, 13 ]
transiesta: Matrix elements in % of full matrix: 51.74208 %

transiesta: mem of electrodes (static): 12.66MB
transiesta: mem of global update arrays (static): 32.11MB
transiesta: mem of tri-diagonal matrices: 163.72MB
transiesta: Total memory usage: 208.49MB

transiesta: Charge distribution, target = 990.00000
Total charge [Q] : 990.00000
Device [D] : 586.61067
Left [E1] : 190.61067
Left / device [C1] : 7.38933
Right [E2] : 190.61067
Right / device [C2] : 7.38933
Other [O] : 7.38933

ts-q: D E1 C1 E2 C2 dQ
ts-q: NaN 190.611 7.389 190.611 7.389 NaN
ts-Vha: NaN eV

siesta: Program's energy decomposition (eV):
siesta: Ebs = NaN
siesta: Eions = 63325.725641
siesta: Ena = 13460.355987
siesta: Ekin = NaN
siesta: Enl = NaN
siesta: Eso = 0.000000
siesta: Eldau = 0.000000
siesta: DEna = NaN
siesta: DUscf = NaN
siesta: DUext = 0.000000
siesta: Enegf = 0.000000
siesta: Exc = NaN
siesta: eta*DQ = 0.000000
siesta: Emadel = 0.000000
siesta: Emeta = 0.000000
siesta: Emolmec = 0.000000
siesta: Ekinion = 0.000000
siesta: Eharris = NaN
siesta: Etot = NaN
siesta: FreeEng = NaN

        iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV)
ts-scf: 1 NaN NaN NaN 0.000000 -4.256114 0.000000

SCF Convergence by DM+H criterion
max |DM_out - DM_in| : 0.0000000000
max |H_out - H_in| (eV) : 0.0000000000
SCF cycle converged after 1 iterations
timer: Routine,Calls,Time,% = TS 1 790.607 7.05

2. The SFC part of single point calculation converged well, but the TranSIESTA part was weird. I do not know what happened. Could you give me any suggestions on how to resolve this?

3. What is a gamma-only calculation? I researched in the manual, but I did not find anything about it.

Thanks!!!
Msc. Elder A. V. Mota

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

1. You have to try.

2. Could you try and add this to the fdf file: "ForceAuxCell true"

3. Gamma-point? You know the Gamma-point in regards of k-point sampling? If not please ask at your PI.

Revision history for this message
Elder Augusto Viana Mota (eavmota) said : 		#5

I forgot to finished the situation. Sorry!!!
The problem was in the SIESTA compilation. I recompiled in a different way and it's work!
Thanks Nick for your help!

Revision history for this message
hananab (hananab) said : 		#6

Hello,
Thank you for posting this qst, i got the same error in Transiesta Calculation at 0 bias, the calculation converge, but tbt no, and it give the same warning error, i try to run with ForceAuxCell true,
But did you use another solution to solve it ?

Thank you