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The LEFT lead cannot be superposed on the original cell even after the translation. Check your atomi
Date: 2015/12/08 14:13
Name: Richard Overstreet

I am gettgin the following error with my negf simulation of graphene.

"The LEFT lead cannot be superposed on the original cell even after the translation.
Check your atomic coordinates of the LEFT lead."

I have checked for duplicate or outlying coordinates in the input files but have not found any. I also tried to increase the size of the unit vectors without sucesss.

Here is my lead input file:

#
# File Name
#

System.CurrrentDirectory ./ # default=./
System.Name lead-h20-graphene-o1
level.of.stdout 1 # default=1 (1-3)
level.of.fileout 0 # default=1 (0-2)

NEGF.output_hks on
NEGF.filename.hks lead-h2o-graphene-o1.hks

#
# Definition of Atomic Species
#

Species.Number 3
<Definition.of.Atomic.Species
C C5.0-s2p1 C_CA13
O O7.0-s2p2d1 O_PBE13
H H7.0-s2p1 H_PBE13
Definition.of.Atomic.Species>

#
# Atoms
#

Atoms.Number 43
Atoms.SpeciesAndCoordinates.Unit Ang # Ang|AU
<Atoms.SpeciesAndCoordinates
1 C -1.228 2.127 0.000 2.0 2.0
2 C 0.000 2.836 0.000 2.0 2.0
3 C 1.228 2.127 0.000 2.0 2.0
4 C 2.456 2.836 0.000 2.0 2.0
5 C 3.684 2.127 0.000 2.0 2.0
6 C 4.912 2.836 0.000 2.0 2.0
7 C 6.140 2.127 0.000 2.0 2.0
8 C 7.368 2.836 0.000 2.0 2.0
9 C 8.596 2.127 0.000 2.0 2.0
10 C 9.824 2.836 0.000 2.0 2.0
11 C -1.228 4.963 0.000 2.0 2.0
12 C 0.000 4.254 0.000 2.0 2.0
13 C 1.228 4.963 0.000 2.0 2.0
14 C 2.456 4.254 0.000 2.0 2.0
15 C 3.684 4.963 0.000 2.0 2.0
16 C 4.912 4.254 0.000 2.0 2.0
17 C 6.140 4.963 0.000 2.0 2.0
18 C 7.368 4.254 0.000 2.0 2.0
19 C 8.596 4.963 0.000 2.0 2.0
20 C 9.824 4.254 0.000 2.0 2.0
21 C -1.228 6.381 0.000 2.0 2.0
22 C 0.000 7.090 0.000 2.0 2.0
23 C 1.228 6.381 0.000 2.0 2.0
24 C 2.456 7.090 0.000 2.0 2.0
25 C 3.684 6.381 0.000 2.0 2.0
26 C 4.912 7.090 0.000 2.0 2.0
27 C 6.140 6.381 0.000 2.0 2.0
28 C 7.368 7.090 0.000 2.0 2.0
29 C 8.596 6.381 0.000 2.0 2.0
30 C 9.824 7.090 0.000 2.0 2.0
31 C -1.228 9.217 0.000 2.0 2.0
32 C 0.000 8.508 0.000 2.0 2.0
33 C 1.228 9.217 0.000 2.0 2.0
34 C 2.456 8.508 0.000 2.0 2.0
35 C 3.684 9.217 0.000 2.0 2.0
36 C 4.912 8.508 0.000 2.0 2.0
37 C 6.140 9.217 0.000 2.0 2.0
38 C 7.368 8.508 0.000 2.0 2.0
39 C 8.596 9.217 0.000 2.0 2.0
40 C 9.824 8.508 0.000 2.0 2.0
41 O 4.697 5.314 3.072 3.0 3.0
42 H 5.470 5.400 2.494 0.5 0.5
43 H 3.897 5.585 2.534 0.5 0.5
Atoms.SpeciesAndCoordinates>

Atoms.UnitVectors.Unit Ang # Ang|AU
<Atoms.UnitVectors
14.0000000000000 0.00000000000000 0.00000000000000
0.00000000000000 14.0000000000000 0.00000000000000
0.00000000000000 0.00000000000000 6.00000000000000
Atoms.UnitVectors>

#
# SCF or Electronic System
#

scf.XcType LDA # LDA|LSDA-CA|LSDA-PW|GGA-PBE
scf.SpinPolarization off # On|Off|NC
scf.ElectronicTemperature 600.0 # default=300 (K)
scf.energycutoff 200.0 # 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 200 10 1 # 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 40 # default=5
scf.Mixing.StartPulay 7 # default=6
scf.Mixing.EveryPulay 1 # default=6
scf.criterion 1.0e-10 # default=1.0e-6 (Hartree)

#
# 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.)


#
# Band dispersion
#

Band.dispersion off # on|off, default=off
# if <Band.KPath.UnitCell does not exist,
# the reciprical lattice vector is employed.
Band.Nkpath 1
<Band.kpath
20 0.0 0.0 0.0 0.5 0.0 0.0 G X
Band.kpath>


#
# DOS and PDOS
#

Dos.fileout off # on|off, default=off
Dos.Erange -15.0 25.0 # default = -20 20
Dos.Kgrid 300 300 1 # default = Kgrid1 Kgrid2 Kgrid3

DosGauss.fileout off
DosGauss.Num.Mesh 4000
DosGauss.Width 0.01


Here is the NEGF input file:

#
# File Name
#

System.CurrrentDirectory ./ # default=./
System.Name negf-h20-graphene-o1
level.of.stdout 1 # default=1 (1-3)
level.of.fileout 0 # default=1 (0-2)


NEGF.filename.hks.l lead-h2o-graphene-o1.hks
NEGF.filename.hks.r lead-h2o-graphene-o1.hks

NEGF.Num.Poles 100 # defalut=150
NEGF.scf.Kgrid 1 1 # defalut=1 1

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 -15.0 25.0 5.0e-3 #default=-10.0 10.0 5.0e-3 (eV)
NEGF.Dos.energy.div 200 # default=200
NEGF.Dos.Kgrid 600 1 # default=1 1

NEGF.tran.energydiv 100 # default=200
NEGF.tran.energyrange -7.0 7.0 1.0e-3 # default=-10.0 10.0 1.0e-3 (eV)
NEGF.tran.Kgrid 30 1 # default= 1 1


#
# Definition of Atomic Species
#

Species.Number 3
<Definition.of.Atomic.Species
C C5.0-s2p1 C_CA13
O O7.0-s2p2d1 O_PBE13
H H7.0-s2p1 H_PBE13
Definition.of.Atomic.Species>

#
# Atoms
#

Atoms.Number 43
Atoms.SpeciesAndCoordinates.Unit Ang # Ang|AU
<Atoms.SpeciesAndCoordinates
1 C -1.228 2.127 0.000 2.0 2.0
2 C 0.000 2.836 0.000 2.0 2.0
3 C 1.228 2.127 0.000 2.0 2.0
4 C 2.456 2.836 0.000 2.0 2.0
5 C 3.684 2.127 0.000 2.0 2.0
6 C 4.912 2.836 0.000 2.0 2.0
7 C 6.140 2.127 0.000 2.0 2.0
8 C 7.368 2.836 0.000 2.0 2.0
9 C 8.596 2.127 0.000 2.0 2.0
10 C 9.824 2.836 0.000 2.0 2.0
11 C -1.228 4.963 0.000 2.0 2.0
12 C 0.000 4.254 0.000 2.0 2.0
13 C 1.228 4.963 0.000 2.0 2.0
14 C 2.456 4.254 0.000 2.0 2.0
15 C 3.684 4.963 0.000 2.0 2.0
16 C 4.912 4.254 0.000 2.0 2.0
17 C 6.140 4.963 0.000 2.0 2.0
18 C 7.368 4.254 0.000 2.0 2.0
19 C 8.596 4.963 0.000 2.0 2.0
20 C 9.824 4.254 0.000 2.0 2.0
21 C -1.228 6.381 0.000 2.0 2.0
22 C 0.000 7.090 0.000 2.0 2.0
23 C 1.228 6.381 0.000 2.0 2.0
24 C 2.456 7.090 0.000 2.0 2.0
25 C 3.684 6.381 0.000 2.0 2.0
26 C 4.912 7.090 0.000 2.0 2.0
27 C 6.140 6.381 0.000 2.0 2.0
28 C 7.368 7.090 0.000 2.0 2.0
29 C 8.596 6.381 0.000 2.0 2.0
30 C 9.824 7.090 0.000 2.0 2.0
31 C -1.228 9.217 0.000 2.0 2.0
32 C 0.000 8.508 0.000 2.0 2.0
33 C 1.228 9.217 0.000 2.0 2.0
34 C 2.456 8.508 0.000 2.0 2.0
35 C 3.684 9.217 0.000 2.0 2.0
36 C 4.912 8.508 0.000 2.0 2.0
37 C 6.140 9.217 0.000 2.0 2.0
38 C 7.368 8.508 0.000 2.0 2.0
39 C 8.596 9.217 0.000 2.0 2.0
40 C 9.824 8.508 0.000 2.0 2.0
41 O 4.697 5.314 3.072 3.0 3.0
42 H 5.470 5.400 2.494 0.5 0.5
43 H 3.897 5.585 2.534 0.5 0.5
Atoms.SpeciesAndCoordinates>

#
# Lead-Left
#

LeftLeadAtoms.Number 10
<LeftLeadAtoms.SpeciesAndCoordinates # Unit=Ang.
1 C -1.228 0.709 0.000 2.0 2.0
2 C 0.000 0.000 0.000 2.0 2.0
3 C 1.228 0.709 0.000 2.0 2.0
4 C 2.456 0.000 0.000 2.0 2.0
5 C 3.684 0.709 0.000 2.0 2.0
6 C 4.912 0.000 0.000 2.0 2.0
7 C 6.140 0.709 0.000 2.0 2.0
8 C 7.368 0.000 0.000 2.0 2.0
9 C 8.596 0.709 0.000 2.0 2.0
10 C 9.824 0.000 0.000 2.0 2.0
LeftLeadAtoms.SpeciesAndCoordinates>


#
# Lead-Right
#

RightLeadAtoms.Number 10
<RightLeadAtoms.SpeciesAndCoordinates # Unit=Ang.
1 C -1.228 10.635 0.000 2.0 2.0
2 C 0.000 11.344 0.000 2.0 2.0
3 C 1.228 10.635 0.000 2.0 2.0
4 C 2.456 11.344 0.000 2.0 2.0
5 C 3.684 10.635 0.000 2.0 2.0
6 C 4.912 11.344 0.000 2.0 2.0
7 C 6.140 10.635 0.000 2.0 2.0
8 C 7.368 11.344 0.000 2.0 2.0
9 C 8.596 10.635 0.000 2.0 2.0
10 C 9.824 11.344 0.000 2.0 2.0
RightLeadAtoms.SpeciesAndCoordinates>

#
# SCF or Electronic System
#

scf.XcType LDA # LDA|LSDA-CA|LSDA-PW|GGA-PBE
scf.SpinPolarization off # On|Off|NC
scf.ElectronicTemperature 600.0 # default=300 (K)
scf.energycutoff 200.0 # 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 1 1 1 # 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 0.100 # default=0.40
scf.Mixing.History 40 # default=5
scf.Mixing.StartPulay 10 # default=6
scf.Kerker.factor 1.0 # default=1.0
scf.criterion 1.0e-7 # default=1.0e-6 (Hartree)
メンテ
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Re: The LEFT lead cannot be superposed on the original cell even after the translation. Check your atomi ( No.1 )
Date: 2015/12/08 21:05
Name: Artem Pulkin

So how much atoms do you have in the lead: 10 or 43?
メンテ
Re: The LEFT lead cannot be superposed on the original cell even after the translation. Check your atomi ( No.2 )
Date: 2015/12/09 05:31
Name: Richard Overstreet

10 In the graphene negf example the device region is put in the lead input file.
メンテ
Re: The LEFT lead cannot be superposed on the original cell even after the translation. Check your atomi ( No.3 )
Date: 2015/12/09 21:03
Name: Artem Pulkin

I have no idea about graphene example but if you have 10 atoms in the lead you should have 10 atoms in your lead file (the one with "NEGF.output_hks on"). Instead, you have 43 atoms there. That's the problem.
メンテ

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