transiesta <scat.fdf>scat.out coor: Wrong number of atoms found in AtomicCoordinatesAndAtomicSpecies block ERROR STOP from Node: 0

Asked by Mandar Jatkar on 2019-06-11

While running this code i am getting following error.
coor: Atomic-coordinates input format = Cartesian coordinates
coor: (in Angstroms)
coor: Wrong number of atoms found in AtomicCoordinatesAndAtomicSpecies block
ERROR STOP from Node: 0
coor: Wrong number of atoms found in AtomicCoordinatesAndAtomicSpecies block
ERROR STOP from Node: 0

SystemName scat
SystemLabel scat

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# SPECIES AND BASIS

# Number of species
NumberOfSpecies 2
%block ChemicalSpeciesLabel
 1 42 Mo
 2 16 S
%endblock ChemicalSpeciesLabel
PAO.BasisSize SZP
PAO.EnergyShift 0.005 Ry
XC.functional LDA
XC.authors CA

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# K-points

%block kgrid_Monkhorst_Pack
 2 0 0 0.0
 0 2 0 0.0
 0 0 2 0.0
%endblock kgrid_Monkhorst_Pack

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# Structure
NumberOfAtoms 75
LatticeConstant 1.0 Ang

%block LatticeVectors
20.00000000 0.00000000000 0.0000000000
0.00000000 28.0646883677 0.0000000000
0.000000000 0.00000000000 4.26258
%endblock LatticeVectors

AtomicCoordinatesFormat Ang
%block AtomicCoordinatesAndAtomicSpecies
9.946816 11.60039385 2.81228216 1
9.946816 12.79040909 3.55614061 1
9.946816 11.59980471 1.45007376 1
9.946816 14.03329915 2.83951307 1
9.946816 15.27643513 3.55592641 1
9.946816 12.78972579 0.70643938 1
9.946816 14.03304096 1.42323176 1
9.946816 16.46541174 2.81211064 1
9.053184 17.37870274 3.05152764 2
9.946816 15.2764249 0.70665452 1
9.946816 16.46532993 1.45002433 1
9.946816 17.72657708 1.02390291 2
9.946816 10.3398653 3.23897475 2
9.946816 10.33811128 1.02547066 2
10.946816 17.00680874 3.30316864 2

%endblock AtomicCoordinatesAndAtomicSpecies

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# SCF variables

DM.MixSCF1 T
MaxSCFIterations 300 # Maximum number of SCF iter
DM.MixingWeight 0.05 # 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
TS.MixH yes

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# MD variables

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

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# Output variables

WriteMullikenPop 1
WriteBands .true.
SaveRho .true.
SaveDeltaRho .false.
SaveHS .false.
SaveElectrostaticPotential True
SaveTotalPotential no
WriteCoorXmol .true.
WriteMDXmol .true.
WriteMDhistory .false.
WriteEigenvalues yes

BandLinesScale ReciprocalLatticeVectors
%block BandLines
1 0 0 0
50 0 0 0.5
%endblock Bandlines

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# Transmission
TS.TBT.NPoints 101
TS.TBT.Emin -0.5 eV
TS.TBT.Emax 0.5 eV

TS.TBT.NEigen 9

# Bias voltage
TS.Voltage $i eV
TS.biasContour.NumPoints 20

# Transiesta: electrode definition:
# LEFT ELECTRODE
TS.HSFileLeft ./elec.TSHS
TS.ReplicateA1Left 1
TS.ReplicateA2Left 1
TS.NumUsedAtomsLeft 20
TS.BufferAtomsLeft 0
# RIGHT ELECTRODE
TS.HSFileRight ./elec.TSHS
TS.ReplicateA1Right 1
TS.ReplicateA2Right 1
TS.NumUsedAtomsRight 20
TS.BufferAtomsRight 0

# SPECIES AND ATOMS
# DYNAMICS
TS.UseBulkInElectrodes T
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Question information

Language:
English Edit question
Status:
Answered
For:
Siesta Edit question
Assignee:
No assignee Edit question
Last query:
2019-06-12
Last reply:
2019-06-12
Nick Papior (nickpapior) said : #1

I think the error message is pretty clear.

You specify that there are 75 atoms in your atoms-block, but there isn't!

Mandar Jatkar (jatkarmandar) said : #2

I specified to 16 , Still I am facing same error

Nick Papior (nickpapior) said : #3

Please try and count the number of atoms in your block. :)

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