Errors about the the integration range and the atom coordinates |
- Date: 2025/04/03 00:03
- Name: Kieran
<masrfa@googlemail.com>
- Dear All,
I am trying to calculate the electric charge conductance for graphene with the NEGF method.The input file was written below.
Input file in the Step 1.
#======================================================================================#
# File Name
System.CurrrentDirectory ./ # default=./
System.Name Lead-Graphene
level.of.stdout 1 # default=1 (1-3)
level.of.fileout 0 # default=1 (0-2)
DATA.PATH /public21/soft/openmx/openmx3.9/DFT_DATA19/
NEGF.output_hks on
NEGF.filename.hks lead-graphene.hks
NEGF.Output.for.TranMain off
NEGF.tran.energydiv 100 # default=200
NEGF.tran.energyrange -10 10 1.0e-3 # default=-10.0 10.0 5.0e-3 (eV)
NEGF.tran.Kgrid 1 1 # default= 1 1
Species.Number 1
# Definition of Atomic Species
<Definition.of.Atomic.Species
C C6.0-s2p2d1 C_PBE19
Definition.of.Atomic.Species>
# Atoms
Atoms.Number 8
Atoms.SpeciesAndCoordinates.Unit Ang # Ang|AU
<Atoms.SpeciesAndCoordinates
1 C 0.000000000 0.000000000 10.000000000000000 2.0 2.0
2 C 2.130390000 1.230000000 10.000000000000000 2.0 2.0
3 C 0.710129999 1.230000000 10.000000000000000 2.0 2.0
4 C 2.840519999 0.000000000 10.000000000000000 2.0 2.0
5 C 4.260780000 0.000000000 10.000000000000000 2.0 2.0
6 C 6.391170000 1.230000000 10.000000000000000 2.0 2.0
7 C 4.970909999 1.230000000 10.000000000000000 2.0 2.0
8 C 7.101299999 0.000000000 10.000000000000000 2.0 2.0
Atoms.SpeciesAndCoordinates>
Atoms.UnitVectors.Unit Ang # Ang|AU
<Atoms.UnitVectors
8.5215600000 0.0000000000 0.0000000000
0.0000000000 2.4600000000 0.0000000000
0.0000000000 0.0000000000 20.000000000
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 350.0 # 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 100 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 0.020 # default=0.40
scf.Mixing.History 20 # default=5
scf.Mixing.StartPulay 7 # 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 100 #
MD.Opt.criterion 1.0e-4 # default=1.0e-4 (a.u.)
# Band dispersion
Band.dispersion off # on|off, default=off
Band.Nkpath 4
<Band.kpath
100 0.5 0.0 0.0 0.5 0.5 0.0 K M
100 0.5 0.5 0.0 0.0 0.5 0.0 M K'
100 0.0 0.5 0.0 0.0 0.0 0.0 K' G
100 0.0 0.0 0.0 0.5 0.0 0.0 G K
Band.kpath>
# DOS and PDOS
Dos.fileout off # on|off, default=off
Dos.Erange -15.0 25.0 # default = -20 20
Dos.Kgrid 600 1 1 # default = Kgrid1 Kgrid2 Kgrid3
DosGauss.fileout off
DosGauss.Num.Mesh 4000
DosGauss.Width 0.01
#======================================================================================#
The Input file in the Step 2.
#======================================================================================#
# File Name
System.CurrrentDirectory ./ # default=./
System.Name negf-graphene
level.of.stdout 1 # default=1 (1-3)
level.of.fileout 0 # default=1 (0-2)
DATA.PATH /public21/soft/openmx/openmx3.9/DFT_DATA19/
NEGF.filename.hks.l lead-graphene.hks
NEGF.filename.hks.r lead-graphene.hks
NEGF.Num.Poles 100 # default=150
NEGF.scf.Kgrid 1 1 # default=1 1
NEGF.SCF.Iter.Band 50
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 100 # default=200
NEGF.Dos.Kgrid 1 1 # default=1 1
# Transmission & Eigen Channel
NEGF.tran.Analysis on # default on
NEGF.tran.energydiv 100 # default=200
NEGF.tran.energyrange -15 5.1 5.0e-3 # default=-10.0 10.0 1.0e-3 (eV)
NEGF.tran.Kgrid 1 1 # default= 1 1
NEGF.tran.Channel on # default on
NEGF.Channel.Nkpoint 1 # default=1
<NEGF.Channel.kpoint
0.0 0.0
NEGF.Channel.kpoint> # default 0.0 0.0
NEGF.Channel.Nenergy 3 # default=1
<NEGF.Channel.energy
-3.849658618020418
-4.349658618020418
-4.549658618020418
NEGF.Channel.energy> # default 0.0
NEGF.Channel.Num 3 # defualt=5(for collinear), 10(for Non-collinear)
# Definition of Atomic Species
Species.Number 1
<Definition.of.Atomic.Species
C C6.0-s2p2d1 C_PBE19
Definition.of.Atomic.Species>
# Atoms
Atoms.SpeciesAndCoordinates.Unit Ang # Ang|AU
Atoms.Number 64
<Atoms.SpeciesAndCoordinates
1 C 8.521560000 0.000000000 10.000000000000000 2.0 2.0
2 C 10.65195000 1.230000000 10.000000000000000 2.0 2.0
3 C 9.231689999 1.230000000 10.000000000000000 2.0 2.0
4 C 11.36207999 0.000000000 10.000000000000000 2.0 2.0
5 C 12.78234000 0.000000000 10.000000000000000 2.0 2.0
6 C 14.91273000 1.230000000 10.000000000000000 2.0 2.0
7 C 13.49246999 1.230000000 10.000000000000000 2.0 2.0
8 C 15.62285999 0.000000000 10.000000000000000 2.0 2.0
9 C 17.04312000 0.000000000 10.000000000000000 2.0 2.0
10 C 19.17351000 1.230000000 10.000000000000000 2.0 2.0
11 C 17.75324999 1.230000000 10.000000000000000 2.0 2.0
12 C 19.88363999 0.000000000 10.000000000000000 2.0 2.0
13 C 21.30390000 0.000000000 10.000000000000000 2.0 2.0
14 C 23.43429000 1.230000000 10.000000000000000 2.0 2.0
15 C 22.01402999 1.230000000 10.000000000000000 2.0 2.0
16 C 24.14441999 0.000000000 10.000000000000000 2.0 2.0
17 C 25.56468000 0.000000000 10.000000000000000 2.0 2.0
18 C 27.69507000 1.230000000 10.000000000000000 2.0 2.0
19 C 26.27480999 1.230000000 10.000000000000000 2.0 2.0
20 C 28.40519999 0.000000000 10.000000000000000 2.0 2.0
21 C 29.82546000 0.000000000 10.000000000000000 2.0 2.0
22 C 31.95585000 1.230000000 10.000000000000000 2.0 2.0
23 C 30.53558999 1.230000000 10.000000000000000 2.0 2.0
24 C 32.66597999 0.000000000 10.000000000000000 2.0 2.0
25 C 34.08624000 0.000000000 10.000000000000000 2.0 2.0
26 C 36.21663000 1.230000000 10.000000000000000 2.0 2.0
27 C 34.79636999 1.230000000 10.000000000000000 2.0 2.0
28 C 36.92675999 0.000000000 10.000000000000000 2.0 2.0
29 C 38.34702000 0.000000000 10.000000000000000 2.0 2.0
30 C 40.47741000 1.230000000 10.000000000000000 2.0 2.0
31 C 39.05714999 1.230000000 10.000000000000000 2.0 2.0
32 C 41.18753999 0.000000000 10.000000000000000 2.0 2.0
33 C 42.60780000 0.000000000 10.000000000000000 2.0 2.0
34 C 44.73819000 1.230000000 10.000000000000000 2.0 2.0
35 C 43.31792999 1.230000000 10.000000000000000 2.0 2.0
36 C 45.44831999 0.000000000 10.000000000000000 2.0 2.0
37 C 46.86858000 0.000000000 10.000000000000000 2.0 2.0
38 C 48.99897000 1.230000000 10.000000000000000 2.0 2.0
39 C 47.57870999 1.230000000 10.000000000000000 2.0 2.0
40 C 49.70909999 0.000000000 10.000000000000000 2.0 2.0
41 C 51.12936000 0.000000000 10.000000000000000 2.0 2.0
42 C 53.25975000 1.230000000 10.000000000000000 2.0 2.0
43 C 51.83948999 1.230000000 10.000000000000000 2.0 2.0
44 C 53.96987999 0.000000000 10.000000000000000 2.0 2.0
45 C 55.39014000 0.000000000 10.000000000000000 2.0 2.0
46 C 57.52053000 1.230000000 10.000000000000000 2.0 2.0
47 C 56.10026999 1.230000000 10.000000000000000 2.0 2.0
48 C 58.23065999 0.000000000 10.000000000000000 2.0 2.0
49 C 59.65092000 0.000000000 10.000000000000000 2.0 2.0
50 C 61.78131000 1.230000000 10.000000000000000 2.0 2.0
51 C 60.36104999 1.230000000 10.000000000000000 2.0 2.0
52 C 62.49143999 0.000000000 10.000000000000000 2.0 2.0
53 C 63.91170000 0.000000000 10.000000000000000 2.0 2.0
54 C 66.04209000 1.230000000 10.000000000000000 2.0 2.0
55 C 64.62182999 1.230000000 10.000000000000000 2.0 2.0
56 C 66.75221999 0.000000000 10.000000000000000 2.0 2.0
57 C 68.17248000 0.000000000 10.000000000000000 2.0 2.0
58 C 70.30287000 1.230000000 10.000000000000000 2.0 2.0
59 C 68.88260999 1.230000000 10.000000000000000 2.0 2.0
60 C 71.01299999 0.000000000 10.000000000000000 2.0 2.0
61 C 72.43326000 0.000000000 10.000000000000000 2.0 2.0
62 C 74.56365000 1.230000000 10.000000000000000 2.0 2.0
63 C 73.14338999 1.230000000 10.000000000000000 2.0 2.0
64 C 75.27377999 0.000000000 10.000000000000000 2.0 2.0
Atoms.SpeciesAndCoordinates>
# Lead-Left
LeftLeadAtoms.Number 8
<LeftLeadAtoms.SpeciesAndCoordinates # Unit=Ang.
1 C 0.000000000 0.000000000 10.000000000000000 2.0 2.0
2 C 2.130390000 1.230000000 10.000000000000000 2.0 2.0
3 C 0.710129999 1.230000000 10.000000000000000 2.0 2.0
4 C 2.840519999 0.000000000 10.000000000000000 2.0 2.0
5 C 4.260780000 0.000000000 10.000000000000000 2.0 2.0
6 C 6.391170000 1.230000000 10.000000000000000 2.0 2.0
7 C 4.970909999 1.230000000 10.000000000000000 2.0 2.0
8 C 7.101299999 0.000000000 10.000000000000000 2.0 2.0
LeftLeadAtoms.SpeciesAndCoordinates>
# Lead-Right
RightLeadAtoms.Number 8
<RightLeadAtoms.SpeciesAndCoordinates # Unit=Ang.
1 C 76.69404000 0.000000000 10.000000000000000 2.0 2.0
2 C 78.82443000 1.230000000 10.000000000000000 2.0 2.0
3 C 77.40416999 1.230000000 10.000000000000000 2.0 2.0
4 C 79.53455999 0.000000000 10.000000000000000 2.0 2.0
5 C 80.95482000 0.000000000 10.000000000000000 2.0 2.0
6 C 83.08521000 1.230000000 10.000000000000000 2.0 2.0
7 C 81.66494999 1.230000000 10.000000000000000 2.0 2.0
8 C 83.79533999 0.000000000 10.000000000000000 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 350.0 # default=150 (Ry)
scf.maxIter 100 # default=40
scf.EigenvalueSolver NEGF # DC|GDC|Cluster|Band
#scf.lapack.dste dstevx # dstegr|dstedc|dstevx, default=dstegr
scf.Kgrid 100 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 0.020 # default=0.30
scf.Min.Mixing.Weight 0.020 # default=0.001
scf.Max.Mixing.Weight 0.050 # default=0.40
scf.Mixing.History 100 # default=5
scf.Mixing.StartPulay 20 # default=6
scf.criterion 1.0e-7 # default=1.0e-6 (Hartree)
scf.Kerker.factor 30.0 # default=1
NEGF.Poisson.Solver FFT
#======================================================================================#
The calculation in the step 1 was done normally; while the calculation in the step 2 was aborted abnormally. Here are the error message.
#======================================================================================#
Intrinsic chemical potential (eV) of the leads
Left lead: -4.349658702530
Right lead: -4.349658702530
add voltage = 0.0000 (eV) to the left lead: new ChemP (eV): -4.3497
add voltage = 0.0000 (eV) to the right lead: new ChemP (eV): -4.3497
Parameters for the integration of the non-equilibrium part
lower bound: -4.349658702530 (eV)
upper bound: -4.349658702530 (eV)
energy step: 0.020000000000 (eV)
number of steps: 0
Warning: the energy step you specified is larger than the integration range.
The RIGHT lead cannot be superposed on the original cell even after the translation.
Check your atomic coordinates of the RIGHT lead.
#======================================================================================#
I have already set NEGF.tran.energyrange -15 5.1 5.0e-3. The upper and lower bounds are different. Would anyone please tell me why the upper and lower bound are same (-4.349658702530 (eV)) in the output file and the 'energy step you specified is larger than the integration range'?
Another enquiry is that why 'The RIGHT lead cannot be superposed on the original cell even after the translation'?
Thank you in advance.
Kieran
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