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ERROR: PAOs of lead atoms can overlap only to the next nearest region.
Date: 2018/07/19 00:47
Name: M.Sh

hello dear openmx users and developers

I have encountered this error while I was calculating BP5* properties. I have calculated band structure etc.for this material. as soon as I put hks input at the top to make it a lead for my negf calculations, I've encountered the following error:


"
The length between atomA=2 and atomB=1 is too short for the transport calculation.
distance=13.575939 rcutA=7.000000 rcutB=7.000000


ERROR: PAOs of lead atoms can overlap only to the next nearest region.

"

I have searched and read about it, but haven't found anything useful. the problem is that the PAO cutoff radius of both P and B are 7. and the distance is 13.57 (as the error says). I don't see how can I overcome this? should I reduce cutoff? is it possible?


*:https://www.nature.com/articles/s41598-017-02011-9

here is the input file & at the end is the full std.out of my run:
ps*: I have put the result of MD of the previous runs..





#
# File Name
#

System.CurrrentDirectory ./ # default=./
System.Name Lead_BP5
level.of.stdout 1 # default=1 (1-3)
level.of.fileout 0 # default=1 (0-2)

NEGF.output_hks on
NEGF.filename.hks Lead-BP5.hks

#
# Definition of Atomic Species
#

Species.Number 2
<Definition.of.Atomic.Species
B B7.0-s2p1 B_PBE13
P P7.0-s2p2 P_PBE13
Definition.of.Atomic.Species>

#
# Atoms
#

Atoms.Number 6
Atoms.SpeciesAndCoordinates.Unit ANG # Ang|AU
<Atoms.SpeciesAndCoordinates # Unit=Ang.
1 B 0.000000000 0.000000000 10.63599990 1.5 1.5
2 P 2.271805000 2.271805000 10.63599970 2.5 2.5
3 P 0.730099300 3.235931100 9.225252000 2.5 2.5
4 P 3.235931100 3.813510700 12.04674770 2.5 2.5
5 P 3.813510700 1.307678900 9.225252000 2.5 2.5
6 P 1.307678900 0.730099300 12.04674770 2.5 2.5
Atoms.SpeciesAndCoordinates>
Atoms.UnitVectors.Unit Ang # Ang|AU
<Atoms.UnitVectors # unit=Ang.
4.54361000000000 0.00000000000000 0.00000000000000
0.00000000000000 4.54361000000000 0.00000000000000
0.00000000000000 0.00000000000000 21.27200000000000
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 # default=300 (K)
scf.energycutoff 200.0 # default=150 (Ry)
scf.maxIter 40 # default=40
scf.EigenvalueSolver band # DC|GDC|Cluster|Band
scf.Kgrid 20 20 5 # means 4x4x4
scf.Mixing.Type rmm-diis # 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 0.040 # default=0.40
scf.Mixing.History 7 # default=5
scf.Mixing.StartPulay 5 # default=6
scf.criterion 1.0e-6 # default=1.0e-6 (Hartree)

#
# MD or Geometry Optimization
#

MD.Type opt # Nomd|Constant_Energy_MD|Opt
MD.maxIter 30 # default=1
MD.TimeStep 1 # default=0.5 (fs)
MD.Opt.criterion 1.0e-5 # default=1.0e-4 (Hartree/bohr)


#
# DOS and PDOS
#

Dos.fileout off # on|off, default=off
Dos.Erange -20.0 20.0 # default = -20 20
Dos.Kgrid 10 10 1 # default = Kgrid1 Kgrid2 Kgrid3


#
# Band dispersion
#

Band.dispersion off # on|off, default=off
Band.Nkpath 3
<Band.kpath
25 0.0 0.0 0.0 0.5 0.0 0.0 G X
25 0.5 0.0 0.0 0.5 0.5 0.0 X M
25 0.5 0.5 0.0 0.0 0.0 0.0 M G
Band.kpath>




stdout:



The number of threads in each node for OpenMP parallelization is 1.


*******************************************************
*******************************************************
Welcome to OpenMX Ver. 3.8.5
Copyright (C), 2002-2014, T. Ozaki
OpenMX comes with ABSOLUTELY NO WARRANTY.
This is free software, and you are welcome to
redistribute it under the constitution of the GNU-GPL.
*******************************************************
*******************************************************



<Input_std> Your input file was normally read.
<Input_std> The system includes 2 species and 6 atoms.

*******************************************************
PAO and VPS
*******************************************************

<SetPara_DFT> PAOs of species B were normally found.
<SetPara_DFT> PAOs of species P were normally found.
<SetPara_DFT> VPSs of species B were normally found.
B_PBE13.vps is j-dependent.
In case of scf.SpinOrbit.Coupling=off,
j-dependent pseudo potentials are averaged by j-degeneracy,
which corresponds to a scalar relativistic treatment.
<SetPara_DFT> VPSs of species P were normally found.
P_PBE13.vps is j-dependent.
In case of scf.SpinOrbit.Coupling=off,
j-dependent pseudo potentials are averaged by j-degeneracy,
which corresponds to a scalar relativistic treatment.

*******************************************************
Fourier transform of PAO and projectors of VNL
*******************************************************

<FT_PAO> Fourier transform of pseudo atomic orbitals
<FT_NLP> Fourier transform of non-local projectors
<FT_ProExpn_VNA> Fourier transform of VNA separable projectors
<FT_VNA> Fourier transform of VNA potentials
<FT_ProductPAO> Fourier transform of product of PAOs


TRAN_Check_Region_Lead()

The length between atomA=2 and atomB=1 is too short for the transport calculation.
distance=13.575939 rcutA=7.000000 rcutB=7.000000


ERROR: PAOs of lead atoms can overlap only to the next nearest region.

メンテ
Page: [1]

Re: ERROR: PAOs of lead atoms can overlap only to the next nearest region. ( No.1 )
Date: 2018/07/19 15:15
Name: Mitsuaki Kawamura  <mkawamura@issp.u-tokyo.ac.jp>

Dear Dr. M. Sh

Hello,

> ERROR: PAOs of lead atoms can overlap only to the next nearest region.

This message indicates that the PAO of atom-1 and the PAO of atom-2 in the next-next cell overlap, and such a situation is not allowed in the NEGF calculation of OpenMX.
Please see this figure
https://drive.google.com/file/d/1BNEE0NWLnqnouXimU4bRFcnv_sMfbEnv/view?usp=sharing
and the "Rule 2" in the manual
http://www.openmx-square.org/openmx_man3.8/node116.html

You can overcome this issue by using 2×1×1 supercell.
https://drive.google.com/file/d/11LgiRqTkUE3NNYQg9fNVvKTNvEmFdqUX/view?usp=sharing
Atoms.Number 12
Atoms.SpeciesAndCoordinates.Unit Ang
<Atoms.SpeciesAndCoordinates
1 B 0.0000000 0.0000000 10.6359999 1.5 1.5
2 P 2.2718050 2.2718050 10.6359997 2.5 2.5
3 P 0.7300993 3.2359311 9.2252520 2.5 2.5
4 P 3.2359311 3.8135107 12.0467477 2.5 2.5
5 P 3.8135107 1.3076789 9.2252520 2.5 2.5
6 P 1.3076789 0.7300993 12.0467477 2.5 2.5
7 B 4.5436100 0.0000000 10.6359999 1.5 1.5
8 P 6.8154150 2.2718050 10.6359997 2.5 2.5
9 P 5.2737093 3.2359311 9.2252520 2.5 2.5
10 P 7.7795411 3.8135107 12.0467477 2.5 2.5
11 P 8.3571207 1.3076789 9.2252520 2.5 2.5
12 P 5.8512889 0.7300993 12.0467477 2.5 2.5
Atoms.SpeciesAndCoordinates>
In this case, there is no overlapping between PAOs between next-next cells.

Best regards,
Mitsuaki Kawamura
メンテ
Re: ERROR: PAOs of lead atoms can overlap only to the next nearest region. ( No.2 )
Date: 2018/07/20 08:10
Name: M.Sh

Dear Mitsuaki Kawamura

Thank you very much for your clear and complete answer. the pictures were clear and helpful too. it solved my problem.
メンテ

Page: [1]

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