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ERROR: PAOs of atoms of L|C|R can overlap only to the next nearest region.
Date: 2023/11/21 14:32
Name: Tom

Dear sir:
  When I use openMX to calculate Transport Properties with NEGF,there is one error interrupts the process.
I would appreciate it if you could help me with this.


The error is as follows:

TRAN_Check_Region()

The length between atomA=17(region C) and atomB=1(region L) is too short for the transport calculation.
distance=11.183786 rcutA=7.000000 rcutB=7.000000

ERROR: PAOs of atoms of L|C|R can overlap only to the next nearest region.


---Below is the input fileF

-------------------Lead-l.dat----------------
#
#      File Name     
#

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

NEGF.output_hks    on             
NEGF.filename.hks  lead-H-l.hks

#
# Definition of Atomic Species
#

Species.Number                    3
<Definition.of.Atomic.Species
Co Co6.0H-s2p2d1 Co_PBE19H
Cr Cr6.0-s2p2d1 Cr_PBE19
Al Al7.0-s2p1d1 Al_PBE19
Definition.of.Atomic.Species>

#
# Atoms
#

Atoms.Number      16
Atoms.SpeciesAndCoordinates.Unit  Ang # Ang|AU
<Atoms.SpeciesAndCoordinates
1  Al      0.000000  0.000000  19.854701 1.5 1.5 0 0 0 0 0 off
2  Al      0.000000  2.821000  16.999797 1.5 1.5 0 0 0 0 0 off
3  Al      2.821000  0.000000  16.999797 1.5 1.5 0 0 0 0 0 off
4  Al      2.821000  2.821000  19.854701 1.5 1.5 0 0 0 0 0 off
5  Cr      2.821000  0.000000  19.854701 8 6 0 0 0 0 0 off
6  Cr      2.821000  2.821000  16.999797 8 6 0 0 0 0 0 off
7  Cr      0.000000  0.000000  16.999797 8 6 0 0 0 0 0 off
8  Cr      0.000000  2.821000  19.854701 8 6 0 0 0 0 0 off
9  Co      1.410500  1.410500  18.427142 10 7 0 0 0 0 0 off
10 Co      1.410500  4.231500  18.427142 10 7 0 0 0 0 0 off
11 Co      1.410500  4.231500  15.572452 10 7 0 0 0 0 0 off
12 Co      1.410500  1.410500  15.572452 10 7 0 0 0 0 0 off
13 Co      4.231500  1.410500  15.572452 10 7 0 0 0 0 0 off
14 Co      4.231500  4.231500  15.572452 10 7 0 0 0 0 0 off
15 Co      4.231500  4.231500  18.427142 10 7 0 0 0 0 0 off
16 Co      4.231500  1.410500  18.427142 10 7 0 0 0 0 0 off
Atoms.SpeciesAndCoordinates>
Atoms.UnitVectors.Unit            Ang # Ang|AU
<Atoms.UnitVectors
  0.000000  0.000000  8.52
  5.709500  0.000000  0.000000
  0.000000  5.709500  0.000000
Atoms.UnitVectors>

#
# SCF or Electronic System
#
scf.XcType GGA-PBE # LDA|LSDA-CA|LSDA-PW|GGA-PBE
scf.SpinPolarization on # On|Off|NC
scf.SpinOrbit.Coupling Off # On|Off, default=off
scf.Constraint.NC.Spin Off
scf.Hubbard.U  off # on|off, default=off
scf.DFTU.Type 1 # 1:Simplified(Dudarev)|2:General, default=1)
scf.Hubbard.Occupation dual # onsite|full|dual, default=dual
scf.ElectronicTemperature 300.0 # default=300 (K)
scf.energycutoff 220.0 # default=150 (Ry)
scf.maxIter 3000 # default=40
scf.EigenvalueSolver band # DC|GDC|Cluster|Band
scf.Kgrid 50 1 1  # means n1 x n2 x n3
scf.Generation.Kpoint regular # regular|MP
scf.Mixing.Type rmm-diisk # Simple|Rmm-Diis|Gr-Pulay|Kerker|Rmm-Diisk
scf.Init.Mixing.Weight 0.05  # default=0.30
scf.Min.Mixing.Weight 0.01  # default=0.001
scf.Max.Mixing.Weight 0.3 # default=0.40
scf.Kerer.factor            10        #default=1.00
scf.Mixing.History          50        # default=5
scf.Mixing.StartPulay      30        # default=6
scf.Mixing.EveryPulay      1          # default=6
scf.criterion 1.0e-6 # default=1.0e-6 (Hartree)
scf.lapack.dste dstevx # dstevx|dstedc|dstegr,default=dstevx
Energy.Decomposiyion      on          #default=off



---------------------------Lead-r.dat----------------------------------------------
#
#      File Name     
#

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

NEGF.output_hks    on             
NEGF.filename.hks  lead-H-r.hks


#
# Definition of Atomic Species
#

Species.Number                    3
<Definition.of.Atomic.Species
Co Co6.0H-s2p2d1 Co_PBE19H
Cr Cr6.0-s2p2d1 Cr_PBE19
Al Al7.0-s2p1d1 Al_PBE19
Definition.of.Atomic.Species>

#
# Atoms
#

Atoms.Number      16
Atoms.SpeciesAndCoordinates.Unit  Ang # Ang|AU
<Atoms.SpeciesAndCoordinates
1  Al      0.000000  0.000000  1.800212 1.5 1.5 180 0 0 0 0 off
2  Al      0.000000  2.821000  4.654942 1.5 1.5 180 0 0 0 0 off
3  Al      2.821000  0.000000  4.654942 1.5 1.5 180 0 0 0 0 off
4  Al      2.821000  2.821000  1.800212 1.5 1.5 180 0 0 0 0 off
5  Cr      2.821000  0.000000  1.800212 8 6 180 0 0 0 0 off
6  Cr      2.821000  2.821000  4.654942 8 6 180 0 0 0 0 off
7  Cr      0.000000  0.000000  4.654942 8 6 180 0 0 0 0 off
8  Cr      0.000000  2.821000  1.800212 8 6 180 0 0 0 0 off
9  Co      1.410500  1.410500  3.227557 10 7 180 0 0 0 0 off
10 Co      1.410500  4.231500  3.227557 10 7 180 0 0 0 0 off
11 Co      1.410500  4.231500  6.082287 10 7 180 0 0 0 0 off
12 Co      1.410500  1.410500  6.082287 10 7 180 0 0 0 0 off
13 Co      4.231500  1.410500  6.082287 10 7 180 0 0 0 0 off
14 Co      4.231500  4.231500  6.082287 10 7 180 0 0 0 0 off
15 Co      4.231500  4.231500  3.227557 10 7 180 0 0 0 0 off
16 Co      4.231500  1.410500  3.227557 10 7 180 0 0 0 0 off
Atoms.SpeciesAndCoordinates>
Atoms.UnitVectors.Unit            Ang # Ang|AU
<Atoms.UnitVectors
  0.000000  0.000000  8.52
  5.709500  0.000000  0.000000
  0.000000  5.709500  0.000000     
Atoms.UnitVectors>


#
# SCF or Electronic System
#

scf.XcType GGA-PBE # LDA|LSDA-CA|LSDA-PW|GGA-PBE
scf.SpinPolarization on # On|Off|NC
scf.SpinOrbit.Coupling Off # On|Off, default=off
scf.Constraint.NC.Spin Off
scf.Hubbard.U off # on|off, default=off
scf.DFTU.Type 1 # 1:Simplified(Dudarev)|2:General, default=1)
scf.Hubbard.Occupation dual # onsite|full|dual, default=dual
scf.ElectronicTemperature 300.0 # default=300 (K)
scf.energycutoff 220.0 # default=150 (Ry)
scf.maxIter 3000 # default=40
scf.EigenvalueSolver band # DC|GDC|Cluster|Band
scf.Kgrid 50 1 1 # means n1 x n2 x n3
scf.Generation.Kpoint regular # regular|MP
scf.Mixing.Type rmm-diisk # Simple|Rmm-Diis|Gr-Pulay|Kerker|Rmm-Diisk
scf.Init.Mixing.Weight 0.05  # default=0.30
scf.Min.Mixing.Weight 0.01  # default=0.001
scf.Max.Mixing.Weight 0.45 # default=0.40
scf.Kerer.factor            10        #default=1.00
scf.Mixing.History          50        # default=5
scf.Mixing.StartPulay      30        # default=6
scf.Mixing.EveryPulay      1          # default=6
scf.criterion 1.0e-6 # default=1.0e-6 (Hartree)
scf.lapack.dste dstevx # dstevx|dstedc|dstegr,default=dstevx
Energy.Decomposiyion      on          #default=off



-------------------------NEGF-0.0.dat----------------------------------------------------
#
# File Name
#

System.CurrrentDirectory        ./    # default=./
System.Name                    negf-H-0.0
level.of.stdout                  1    # default=1 (1-3)
level.of.fileout                  1    # default=1 (0-2)

#
# NEGF
#

NEGF.filename.hks.l    lead-H-l.hks
NEGF.filename.hks.r    lead-H-r.hks

NEGF.SCF.Iter.Band        100      # default=6
NEGF.Num.Poles            200      # defalut=150
NEGF.scf.Kgrid            3 3    # defalut=1 1,k point

NEGF.bias.voltage          0.0      # default=0.0 (eV),source drain voltage
NEGF.bias.neq.im.energy    0.01      # default=0.01 (eV)
NEGF.bias.neq.energy.step  0.02      # default=0.02 (eV)
NEGF.Poisson.Solver        FD      # FD/FFT,default=FD
#NEGF.gate.voltage          0.1      # default=0.0ev,gate voltage

#
# NEGF DOS
#

Dos.fileout                off      # on|off, default=off
NEGF.Dos.energyrange      -20.0 20.0 1.0e-4  #default=-10.0 10.0 5.0e-3 (eV)
NEGF.Dos.energy.div        4000      # default=200
NEGF.Dos.Kgrid            100 100      # default=1 1

#
# Transmission & Eigen Channel Analysis
#

NEGF.tran.Analysis          on      # default on,transmission,total current,conductance
NEGF.tran.CurrentDensity    on      # default on,Real-space charge/spin current density
NEGF.tran.energyrange  -5 5 0.005  # default=-10.0 10.0 5.0e-3 (eV)
NEGF.tran.energydiv        200      # default=200
NEGF.tran.Kgrid          4 4      # default= 1 1,larger than that by NEGF.scf.Kgrid



NEGF.tran.Channel          on      # default on,Eigenchannel analysis
NEGF.Channel.Nkpoint        1      # default 1
<NEGF.Channel.kpoint
0.0  0.0
NEGF.Channel.kpoint>                # default 0.0  0.0
NEGF.Channel.Nenergy        1      # default 1
<NEGF.Channel.energy
0.0
NEGF.Channel.energy>                # default 0.0
NEGF.Channel.Num            5        # defualt=5(for collinear), 10(for Non-collinear)




#
# Definition of Atomic Species
#

Species.Number                    4
<Definition.of.Atomic.Species
P      P7.0-s2p2d1      P_PBE19
Al    Al7.0-s2p1d1      Al_PBE19
Co    Co6.0H-s2p2d1 Co_PBE19H
Cr    Cr6.0-s2p2d1 Cr_PBE19
Definition.of.Atomic.Species>


#
# Atoms
#

Atoms.SpeciesAndCoordinates.Unit  Ang # Ang|AU


Atoms.Number        8
<Atoms.SpeciesAndCoordinates
1  Al      0.000000  0.000000  12.892508 1.5 1.5
2  Al      0.000000  2.821000  10.138919 1.5 1.5
3  Al      2.821000  0.000000  10.138919 1.5 1.5
4  Al      2.821000  2.821000  12.892508 1.5 1.5
5  P      1.410500  1.410500  11.515607 2.5 2.5
6  P      1.410500  4.231500  8.762231 2.5 2.5
7  P      4.231500  1.410500  8.762231 2.5 2.5
8  P      4.231500  4.231500  11.515607 2.5 2.5
Atoms.SpeciesAndCoordinates>

Atoms.UnitVectors.Unit            Ang # Ang|AU

#<Atoms.UnitVectors
# 0.000 0.000  4.88
# 10.000 0.000 0.000
# 0.000 24.000 0.000
#Atoms.UnitVectors>


# Lead-Left
#

LeftLeadAtoms.Number        16
<LeftLeadAtoms.SpeciesAndCoordinates          # Unit=Ang.
1  Al      0.000000  0.000000  19.854701 1.5 1.5 0 0 0 0 0 off
2  Al      0.000000  2.821000  16.999797 1.5 1.5 0 0 0 0 0 off
3  Al      2.821000  0.000000  16.999797 1.5 1.5 0 0 0 0 0 off
4  Al      2.821000  2.821000  19.854701 1.5 1.5 0 0 0 0 0 off
5  Cr      2.821000  0.000000  19.854701 8 6 0 0 0 0 0 off
6  Cr      2.821000  2.821000  16.999797 8 6 0 0 0 0 0 off
7  Cr      0.000000  0.000000  16.999797 8 6 0 0 0 0 0 off
8  Cr      0.000000  2.821000  19.854701 8 6 0 0 0 0 0 off
9  Co      1.410500  1.410500  18.427142 10 7 0 0 0 0 0 off
10 Co      1.410500  4.231500  18.427142 10 7 0 0 0 0 0 off
11 Co      1.410500  4.231500  15.572452 10 7 0 0 0 0 0 off
12 Co      1.410500  1.410500  15.572452 10 7 0 0 0 0 0 off
13 Co      4.231500  1.410500  15.572452 10 7 0 0 0 0 0 off
14 Co      4.231500  4.231500  15.572452 10 7 0 0 0 0 0 off
15 Co      4.231500  4.231500  18.427142 10 7 0 0 0 0 0 off
16 Co      4.231500  1.410500  18.427142 10 7 0 0 0 0 0 off
LeftLeadAtoms.SpeciesAndCoordinates>


#
# Lead-Right
#


RightLeadAtoms.Number        16
<RightLeadAtoms.SpeciesAndCoordinates          # Unit=Ang.
1  Al      0.000000  0.000000  1.800212 1.5 1.5 180 0 0 0 0 off
2  Al      0.000000  2.821000  4.654942 1.5 1.5 180 0 0 0 0 off
3  Al      2.821000  0.000000  4.654942 1.5 1.5 180 0 0 0 0 off
4  Al      2.821000  2.821000  1.800212 1.5 1.5 180 0 0 0 0 off
5  Cr      2.821000  0.000000  1.800212 8 6 180 0 0 0 0 off
6  Cr      2.821000  2.821000  4.654942 8 6 180 0 0 0 0 off
7  Cr      0.000000  0.000000  4.654942 8 6 180 0 0 0 0 off
8  Cr      0.000000  2.821000  1.800212 8 6 180 0 0 0 0 off
9  Co      1.410500  1.410500  3.227557 10 7 180 0 0 0 0 off
10 Co      1.410500  4.231500  3.227557 10 7 180 0 0 0 0 off
11 Co      1.410500  4.231500  6.082287 10 7 180 0 0 0 0 off
12 Co      1.410500  1.410500  6.082287 10 7 180 0 0 0 0 off
13 Co      4.231500  1.410500  6.082287 10 7 180 0 0 0 0 off
14 Co      4.231500  4.231500  6.082287 10 7 180 0 0 0 0 off
15 Co      4.231500  4.231500  3.227557 10 7 180 0 0 0 0 off
16 Co      4.231500  1.410500  3.227557 10 7 180 0 0 0 0 off
RightLeadAtoms.SpeciesAndCoordinates>

#
# SCF or Electronic System
#

scf.XcType GGA-PBE # LDA|LSDA-CA|LSDA-PW|GGA-PBE
scf.SpinPolarization on # On|Off|NC
scf.SpinOrbit.Coupling off # On|Off, default=off
scf.Constraint.NC.Spin Off
scf.Hubbard.U off # on|off, default=off
scf.DFTU.Type 1 # 1:Simplified(Dudarev)|2:General, default=1)
scf.Hubbard.Occupation dual # onsite|full|dual, default=dual
scf.ElectronicTemperature  300.0      # default=300 (K)
scf.energycutoff          220.0        # default=150 (Ry)
scf.maxIter                1000        # default=40
scf.Constraint.NC.Spin      off        # On|Off
scf.Constraint.NC.Spin.v    0          # default=0.0 (eV)
scf.EigenvalueSolver      NEGF        # Recursion|Cluster|Band
scf.Kgrid                  5 5 5      # means 4x4x4
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      0.250      # default=0.40
scf.Mixing.History          100        # default=5
scf.Mixing.StartPulay      20        # default=6
scf.Kerker.factor          30.0        # default=1
scf.criterion            3.50e-7      # default=1.0e-6 (Hartree) 10e-9ev
Energy.Decomposiyion      on          #default=off
e
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