[Smeagol-discuss] Problem: Leads decimation
Barraza-lopez, Salvador
sbl3 at mail.gatech.edu
Wed Feb 25 15:06:47 GMT 2009
Your extended molecule has to accommodate your leads. In other words, your extended molecule should include at least 2*10 atoms.
-Salvador.
----- Original Message -----
From: "asa aravindh" <mails2asa at gmail.com>
To: smeagol-discuss at lists.tchpc.tcd.ie
Sent: Wednesday, February 25, 2009 1:40:11 AM GMT -05:00 US/Canada Eastern
Subject: Re: [Smeagol-discuss] Problem: Leads decimation
Dear all...
I have already posted a question regarding the leads decimation error.
Could somebody please point out out of what reason , such an error is coming. I have been trying with simple systems to figure out the error.. Even when I use the bccFe(001) as both leads and EM part error persists.
Am I making some error in the geomtery of the leads and scattering part??
I am pasting here my inputs for the bcc Fe (001) .. Could anybody help me please..
---------------------------------------------------------------------------------------------------------------------------------------
Leads
---------------------------------------------------------------------------------------------------------------------------------------
SystemName Fe TRANS
SystemLabel Fe.chain.pol
NumberOfAtoms 10
NumberOfSpecies 1
WriteCoorStep
WriteMullikenPop 1
PAO.EnergyShift 0.01 Ry
%block Chemical_Species_Label
1 26 Fe
%endblock Chemical_Species_Label
LatticeConstant 1.00 Ang
%block LatticeVectors
28.66 0.000 0.000 1
0.000 28.66 0.000 1
0.000 0.000 5.732 1
%endblock LatticeVectors
AtomicCoordinatesFormat Ang
%block AtomicCoordinatesAndAtomicSpecies
0.000 0.000 0.000 1 Fe 1
2.866 0.000 0.000 1 Fe 2
0.000 2.866 0.000 1 Fe 3
2.866 2.866 0.000 1 Fe 4
1.433 1.433 1.433 1 Fe 5
0.000 0.000 2.866 1 Fe 6
2.866 0.000 2.866 1 Fe 7
0.000 2.866 2.866 1 Fe 8
2.866 2.866 2.866 1 Fe 9
1.433 1.433 4.299 1 Fe 10
%endblock AtomicCoordinatesAndAtomicSpecies
%block kgrid_Monkhorst_Pack
1 0 0 0.0
0 1 0 0.0
0 0 100 0.0
%endblock kgrid_Monkhorst_Pack
MD.TypeOfRun cg # Type of dynamics:
MD.NumCGsteps 0 # Number of CG steps for
# coordinate optimization
MD.MaxCGDispl 0.1 Ang # Maximum atomic displacement
# in one CG step (Bohr)
MD.MaxForceTol 0.04 eV/Ang # Tolerance in the maximum
# atomic force (Ry/Bohr)
BandLinesScale ReciprocalLatticeVectors
xc.functional GGA # 'LDA', 'GGA'
xc.authors PBE #'CA'='PZ', 'PW92', 'PBE'SpinPolarized T # 'T', 'F'
MeshCutoff 200. Ry # Equivalent plane wave cutoff for the grid
MaxSCFIterations 10
NeglNonOverlapInt T # 'F'=do not neglect
SolutionMethod diagon
ElectronicTemperature 300 K # Default value
SaveElectrostaticPotential T
BulkTransport T
BulkLeads LR
----------------------------------------------------------------------------------------------------------------------------------------
Scattering part
----------------------------------------------------------------------------------------------------------------------------------------
SystemName fe-scatter TRANS # Descriptive name of the system
SystemLabel fe-scatter.chain # Short name for naming files
NumberOfAtoms 15 # Number of atoms
NumberOfSpecies 1 # Number of species
PAO.EnergyShift 0.01 Ry
#PAO.BasisType split # Type of basis ('nones', 'nonodes', 'split')
#PAO.SplitNorm 0.15 # Amount of norm carried by the second zeta
#%block ChemicalSpeciesLabel
# 1 79 Au
#%endblock ChemicalSpeciesLabel
#%block Chemical_Species_Label
# 1 26 Fe
#%endblock Chemical_Species_Label
#LatticeConstant 1.00 Ang
%block Chemical_Species_Label
1 26 Fe
%endblock Chemical_Species_Label
LatticeConstant 1.00 Ang
%block LatticeVectors
28.66 0.000 0.000 1
0.000 28.66 0.000 1
0.000 0.000 8.595 1
%endblock LatticeVectors
AtomicCoordinatesFormat Ang
%block AtomicCoordinatesAndAtomicSpecies
0.000 0.000 0.000 1 Fe 1
2.866 0.000 0.000 1 Fe 2
0.000 2.866 0.000 1 Fe 3
2.866 2.866 0.000 1 Fe 4
1.433 1.433 1.433 1 Fe 5
0.000 0.000 2.866 1 Fe 6
2.866 0.000 2.866 1 Fe 7
0.000 2.866 2.866 1 Fe 8
2.866 2.866 2.866 1 Fe 9
1.433 1.433 4.299 1 Fe 10
0.000 0.000 5.732 1 Fe 11
2.866 0.000 5.732 1 Fe 12
0.000 2.866 5.732 1 Fe 13
2.866 2.866 5.732 1 Fe 14
1.433 1.433 7.165 1 Fe 15
%endblock AtomicCoordinatesAndAtomicSpecies
#kgrid_cutoff 0. Ang
%block kgrid_Monkhorst_Pack
1 0 0 0.0
0 1 0 0.0
0 0 1 0.0
%endblock kgrid_Monkhorst_Pack
xc.functional GGA # 'LDA', 'GGA'
xc.authors PBE #'CA'='PZ', 'PW92', 'PBE'SpinPolarized T # 'T', 'F'
FixSpin F
TotalSpin 0.0
NonCollinearSpin F # 'T', 'F'
MeshCutoff 200. Ry # Equivalent plane wave cutoff for the grid
MaxSCFIterations 100
DM.MixingWeight 0.2
DM.NumberPulay 3 # Pulay convergency accelerator
DM.MixSCF1 F
DM.PulayOnFile F # Store in memory ('F') or in files ('T')
DM.Tolerance 5.0E-5
NeglNonOverlapInt T # 'F'=do not neglect
SolutionMethod diagon
ElectronicTemperature 300 K # Default value
DM.UseSaveDM T
DM.MixSCF1 F
WriteCoorXmol T
SaveElectrostaticPotential T
SaveHS F # Save the Hamiltonian and Overlap matrices
SaveRho T # Save the valence pseudocharge density
SaveDeltaRho F
WriteDenchar F # Write Denchar output
WriteDMT T
WriteEigenvalues F
WriteMullikenPop 1
EMTransport T
NEnergReal 1000
NEnergImCircle 200
NEnergImLine 50
NPoles 20
VInitial 0.d0 eV
VFinal 0.01 eV
NIVPoints 1
Delta 1.d-5
EnergLowestBound -1.4d0 Ry
NSlices 1
TrCoefficients T
AtomLeftVCte 2
AtomRightVCte 7
NTransmPoints 800
InitTransmRange 1.0d0 Ry
FinalTransmRange 1.8d0 Ry
PeriodicTransp T
InitTransport F
HartreeLeadsBottom -0.705 eV
HartreeLeadsLeft 0.000 Ang
HartreeLeadsRight 22.400 Ang
%block SaveBiasSteps
0 1
%endblock SaveBiasSteps
#Blocksize 2
---------------------------------------------------------------------------------------------
Thanks and regards,
Asa
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