Error in NEGF |
- Date: 2016/07/22 17:34
- Name: Keshav Raheja
- I am trying to run NEGF for Black Phosphorus based device. PFA my input file and lead files. I run the lead file first and it exits normally. After that I try the input file, it shows the following error:
"The LEFT lead cannot be superposed on the original cell even after the translation.
Check your atomic coordinates of the LEFT lead."
The files are as follows:
## lead file
System.CurrrentDirectory ./ # default=./
System.Name Lead-BP_Keshav
#DATA.PATH ../../DFT_DATA13
level.of.stdout 1 # default=1 (1-3)
level.of.fileout 1 # default=1 (0-2)
NEGF.output_hks on
NEGF.filename.hks lead-chain_BP.hks
NEGF.Output.for.TranMain off
NEGF.tran.energydiv 200 # default=200
NEGF.tran.energyrange -3 2 1.0e-1 # default=-10.0 10.0 5.0e-3 (eV)
NEGF.tran.Kgrid 3 3 # default= 1 1
# Definition of Atomic Species
#
Species.Number 1
<Definition.of.Atomic.Species
P P7.0-s1p1 P_PBE13
Definition.of.Atomic.Species>
#
# Atoms
#
Atoms.Number 8
Atoms.SpeciesAndCoordinates.Unit Ang # Ang|AU
<Atoms.SpeciesAndCoordinates
1 P 0.0 0.0 0.0 2.0 3.0
2 P 1.417 0.0 1.635 2.0 3.0
3 P 2.215 2.144 1.635 2.0 3.0
4 P 3.632 2.144 0.0 2.0 3.0
5 P 0.0 0.0 3.27 2.0 3.0
6 P 3.632 2.144 3.27 2.0 3.0
7 P 4.43 0.0 3.27 2.0 3.0
8 P 4.43 0.0 0.0 2.0 3.0
Atoms.SpeciesAndCoordinates>
Atoms.UnitVectors.Unit Ang # Ang|AU
<Atoms.UnitVectors
0.000000 0.000000 12.842313918
5.50696373 0.000000 0.00000
0.000000 3.179447 0.00000
Atoms.UnitVectors>
#
# SCF or Electronic System
#
scf.XcType GGA-PBE # LDA|LSDA-CA|LSDA-PW|GGA-PBE
scf.SpinPolarization off # On|Off|NC
scf.ElectronicTemperature 300.0 # default=300 (K)
scf.energycutoff 150.0 # default=150 (Ry)
scf.maxIter 100 # default=40
scf.EigenvalueSolver Band # DC|GDC|Cluster|Band
scf.lapack.dste dstevx # dstegr|dstedc|dstevx, default=dstegr
scf.Kgrid 4 12 12 # means n1 x n2 x n3
scf.Mixing.Type rmm-diisk # Simple|Rmm-Diis|Gr-Pulay|Kerker|Rmm-Diisk
scf.Init.Mixing.Weight 0.010 # default=0.30
scf.Min.Mixing.Weight 0.001 # default=0.001
scf.Max.Mixing.Weight 0.020 # default=0.40
scf.Mixing.History 20 # default=5
scf.Mixing.StartPulay 7 # default=6
scf.criterion 1.0e-8 # default=1.0e-6 (Hartree)
Band.dispersion on # on|off, default=off
Band.Nkpath 1
<Band.kpath
15 0.0 0.0 0.0 0.5 0.0 0.0 g X
Band.kpath>
#
# MD or Geometry Optimization
#
MD.Type Nomd # Opt|EF|BFGS|RF|DIIS
MD.Opt.DIIS.History 6 # default=3
MD.Opt.StartDIIS 7 # default=5
MD.Opt.EveryDIIS 6 # default=10
MD.maxIter 200 #
MD.Opt.criterion 1.0e-4 # default=1.0e-4 (a.u.)
####
## Input file
System.CurrrentDirectory ./ # default=./
System.Name NEGF-BP_Keshav
#DATA.PATH ../../DFT_DATA13
level.of.stdout 1 # default=1 (1-3)
level.of.fileout 1 # default=1 (0-2)
NEGF.filename.hks.l lead-chain_BP.hks
NEGF.filename.hks.r lead-chain_BP.hks
NEGF.Num.Poles 150 # default=150
NEGF.scf.Kgrid 12 12 # default=1 1
NEGF.SCF.Iter.Band 10
NEGF.bias.voltage 0.0 # default=0.0 (eV)
NEGF.bias.neq.im.energy 0.01 # default=0.01 (eV)
NEGF.bias.neq.energy.step 0.02 # default=0.02 (eV)
Dos.fileout off # on|off, default=off
NEGF.Dos.energyrange -3.0 2.0 5.0e-1 #default=-10.0 10.0 5.0e-3 (eV)
NEGF.Dos.energy.div 200 # default=200
NEGF.Dos.Kgrid 3 3 # default=1 1
NEGF.tran.energydiv 3000 # default=200
NEGF.tran.energyrange -3 2 0.0001 # default=-10.0 10.0 1.0e-3 (eV)
NEGF.tran.Kgrid 3 3 # default= 1 1
#
# Definition of Atomic Species
#
Species.Number 1
<Definition.of.Atomic.Species
P P7.0-s1p1 P_PBE13
Definition.of.Atomic.Species>
#
# Atoms
#
Atoms.SpeciesAndCoordinates.Unit Ang # Ang|AU
Atoms.Number 8
<Atoms.SpeciesAndCoordinates
1 P 0.0 0.0 0.0 2.0 3.0
2 P 1.417 0.0 1.635 2.0 3.0
3 P 2.215 2.144 1.635 2.0 3.0
4 P 3.632 2.144 0.0 2.0 3.0
5 P 0.0 0.0 3.27 2.0 3.0
6 P 3.632 2.144 3.27 2.0 3.0
7 P 4.43 0.0 3.27 2.0 3.0
8 P 4.43 0.0 0.0 2.0 3.0
Atoms.SpeciesAndCoordinates>
#
# Lead-Left
#
LeftLeadAtoms.Number 8
<LeftLeadAtoms.SpeciesAndCoordinates # Unit=Ang.
1 P 0.0 0.0 -5.0 2.0 3.0
2 P 1.417 0.0 -3.365 2.0 3.0
3 P 2.215 2.144 -3.635 2.0 3.0
4 P 3.632 2.144 -5.0 2.0 3.0
5 P 0.0 0.0 -1.73 2.0 3.0
6 P 3.632 2.144 -1.73 2.0 3.0
7 P 4.43 0.0 -1.73 2.0 3.0
8 P 4.43 0.0 -5.0 2.0 3.0
LeftLeadAtoms.SpeciesAndCoordinates>
#
# Lead-Right
#
RightLeadAtoms.Number 8
<RightLeadAtoms.SpeciesAndCoordinates # Unit=Ang.
1 P 0.0 0.0 5.0 2.0 3.0
2 P 1.417 0.0 6.635 2.0 3.0
3 P 2.215 2.144 6.635 2.0 3.0
4 P 3.632 2.144 5.0 2.0 3.0
5 P 0.0 0.0 8.27 2.0 3.0
6 P 3.632 2.144 8.27 2.0 3.0
7 P 4.43 0.0 8.27 2.0 3.0
8 P 4.43 0.0 5.0 2.0 3.0
RightLeadAtoms.SpeciesAndCoordinates>
#
# SCF or Electronic System
#
scf.XcType GGA-PBE # LDA|LSDA-CA|LSDA-PW|GGA-PBE
scf.SpinPolarization off # On|Off|NC
scf.ElectronicTemperature 300.0 # default=300 (K)
scf.energycutoff 150.0 # default=150 (Ry)
scf.maxIter 200 # default=40
scf.EigenvalueSolver NEGF # DC|GDC|Cluster|Band
scf.lapack.dste dstevx # dstegr|dstedc|dstevx, default=dstegr
scf.Kgrid 4 12 12 # means n1 x n2 x n3
scf.Mixing.Type rmm-diisk # Simple|Rmm-Diis|Gr-Pulay|Kerker|Rmm-Diisk
scf.Init.Mixing.Weight 0.020 # default=0.30
scf.Min.Mixing.Weight 0.020 # default=0.001
scf.Max.Mixing.Weight 0.100 # default=0.40
scf.Mixing.History 40 # default=5
scf.Mixing.StartPulay 20 # default=6
#scf.Kerker.factor 1.0 # default=1.0
scf.criterion 1.0e-5 # default=1.0e-6 (Hartree)
####
Kindly help me out.
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Re: Error in NEGF