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Ghost states_band structure
Date: 2022/10/15 19:13
Name: Amina   <aminacharef60@gmail.com>

Dear all,
I am trying to study the band structure and DOS of a molecule adsorbed on boron nitride nanotube.
For the Bare BNNT, I got a perfect band structure and DOS.
But when I add the molecule, I got some ghost states in the band structure above and below the fermi level. Meanwhile, there is none ghost states in the DOS.

Can you tell me please where is the problem? I don’t know how to send a photo to explain more ?

Below the input file I used (OpenMx 3.8)
#
# BNNT
#
System.CurrrentDirectory ./ # default=./
System.Name band_BNNT_mol
level.of.stdout 1 # default=1 (1-3)
level.of.fileout 1 # default=1 (0-2)

#
# Definition of Atomic Species
#

Species.Number 5
<Definition.of.Atomic.Species
N N7.0-s2p1 N_PBE13
B B9.0-s2p1 B_PBE13
O O7.0-s2p1 O_PBE13
C C7.0-s2p1 C_PBE13
H H7.0-s2p1 H_PBE13
Definition.of.Atomic.Species>

#
# Atoms
#

Atoms.Number 411
Atoms.SpeciesAndCoordinates.Unit Ang # Ang|AU
<Atoms.SpeciesAndCoordinates
1 N 17.90814809 12.50000624 1.67417008 2.5 2.5
2 B 17.85604309 12.50000654 0.21515648 1.5 1.5
…………………………………………………………………………………………………
..................................................................................................................................
Atoms.SpeciesAndCoordinates>
Atoms.UnitVectors.Unit Ang # Ang|AU
<Atoms.UnitVectors
25.00000000 0.00000000 0.00000000
0.00000000 25.00000000 0.00000000
0.00000000 0.00000000 29.87173000
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 100.0 # default=300 (K)
scf.energycutoff 150.0 # default=150 (Ry)
scf.maxIter 40 # default=40
scf.EigenvalueSolver Band # DC|GDC|Cluster|Band
scf.Kgrid 1 1 1 # means n1 x n2 x n3
scf.Mixing.Type rmm-diis # Simple|Rmm-Diis|Gr-Pulay|Kerker|Rmm-Diisk
scf.Init.Mixing.Weight 0.30 # default=0.30
scf.Min.Mixing.Weight 0.001 # default=0.001
scf.Max.Mixing.Weight 0.400 # default=0.40
scf.Mixing.History 15 # default=5
scf.Mixing.StartPulay 4 # default=6
scf.criterion 1.0e-8 # default=1.0e-6 (Hartree)


scf.dftD on # on|off, default=off
DFTD.Unit Ang # Ang|AU
DFTD.rcut_dftD 100.0 # default=100 (DFTD.Unit)
DFTD.d 20.0 # default=20.0
DFTD.scale6 0.75 # default=0.75
DFTD.IntDirection 1 1 1 # default=1 1 1 (1:on 0:off)

#
# MD or Geometry Optimization
#

MD.Type nomd # Nomd|Opt|NVE|NVT_VS|NVT_NH
MD.maxIter 1 # default=1
MD.TimeStep 1 # default=0.5 (fs)
MD.Opt.criterion 1.0e-5 # default=1.0e-4 (Hartree/bohr)

#
# Band dispersion
#
Band.dispersion on # on|off, default=off

# if <Band.KPath.UnitCell does not exist,
# the reciprical lattice vector is employed.
Band.Nkpath 1
<Band.kpath
11 0.0 0.0 0.0 0.0 0.0 0.5 G Z
Band.kpath>

#
# MO output
#

MO.fileout on # on|off
num.HOMOs 1 # default=1
num.LUMOs 1 # default=1
MO.Nkpoint 1 # default=1
<MO.kpoint
0.0 0.0 0.0
MO.kpoint>

#
# DOS and PDOS
#

Dos.fileout on # on|off, default=off
Dos.Erange -6.0 6.0 # default = -20 20
Dos.Kgrid 1 1 11 # default = Kgrid1 Kgrid2 Kgrid3

Thank you so much.
Best regards.
Amina.
メンテ
Page: [1]

Re: Ghost states_band structure ( No.1 )
Date: 2022/10/18 17:07
Name: Amina  <aminacharef60@gmail.com>

Dear all,

No one encountered this issue before ?

Thank you.

メンテ
Re: Ghost states_band structure ( No.2 )
Date: 2022/10/18 18:05
Name: T. Ozaki

Hi,

Could you share the whole input file?
Without knowing it, it might be difficult to see what's happening in your case.

Regards,

TO
メンテ
Re: Ghost states_band structure ( No.3 )
Date: 2022/10/19 18:49
Name: Amina  <aminacharef60@gmail.com>

Dear Professor,

Thank you for your answer.
But I coudn't send it here. There is an error msg! Is there another way please ?

ERROR!
Too many characters.
Please write within 10000 double-byte characters

Thank you.
Best regards.
Amina.
メンテ
Re: Ghost states_band structure ( No.4 )
Date: 2022/10/20 14:50
Name: T. Ozaki

Hi

>But when I add the molecule, I got some ghost states in the band structure above and below the fermi level.

Could you show us the band dispersion?
How did you conclude that the states can be attributed to ghost states?

Regards,

TO
メンテ
Re: Ghost states_band structure ( No.5 )
Date: 2022/10/23 04:54
Name: Amina  <aminacharef60@gmail.com>

Dear professor,

There is the band structure and DOS of BNNT (13.0) after adsorption....> https://ibb.co/x5yh4zn

If you provide me with an address email, I will send you the whole input file, because I couldn't put here all the atoms coordinates.

Thank you so much for your help.
Best regards.
Amina.

メンテ
Re: Ghost states_band structure ( No.6 )
Date: 2022/10/28 03:48
Name: Amina  <aminacharef60@gmail.com>

There is the new link to the band structure and DOS of BNNT (13.0) after adsorption....> https://ibb.co/80XNRn4

Thank you.
メンテ
Re: Ghost states_band structure ( No.7 )
Date: 2022/10/28 09:29
Name: T. Ozaki

Hi,

Please let us know which band can be regarded as the ghost states.

Regards,

TO
メンテ
Re: Ghost states_band structure ( No.8 )
Date: 2022/10/31 16:44
Name: Amina  <aminacharef60@gmail.com>

Dear professor,

I specified in red color the ghost states .....> https://ibb.co/56D5M6D
Could you tell me please the reason I obtained those ghost states after adsorption? Is it related to the software OpenMX? Or something else?

Thank you.
Best regards.
Amina.
メンテ
Re: Ghost states_band structure ( No.9 )
Date: 2022/11/01 23:51
Name: T. Ozaki  <t-ozaki@issp.u-tokyo.ac.jp>

Hi,

Is there a possibility that the 'ghost' states can be attributed to the localized state of molecule?
Could you try the Gaussian broadening method for the calculation of DOS, and zoom in the energy region?
I wonder that the DOS near the Fermi level may have a small weight and be invisible in the current scale.
If you do not mind, could you send me your input file to the e-mail in the thread.

Regards,

TO
メンテ
Re: Ghost states_band structure ( No.10 )
Date: 2022/11/07 16:34
Name: T. Ozaki

Hi,

With the input file you sent me by email, I noticed that the SCF does not converge.
So, I changed a couple of parameters as

scf.Mixing.Type rmm-diisk
scf.Init.Mixing.Weight 0.010
scf.Min.Mixing.Weight 0.001
scf.Max.Mixing.Weight 0.200
scf.Mixing.History 15
scf.Mixing.StartPulay 10

and got the SCF convergence with v3.9.
Please take a look at the DOS and band: https://www.openmx-square.org/forum/img/band.pdf

The states around the Fermi level should be attributed to those of the molecule.

Regards,

TO

メンテ
Re: Ghost states_band structure ( No.11 )
Date: 2022/11/09 19:03
Name: Amina

Dear professor,

Thank you so much for your reply.

Could you tell me please how did you notice that the SCF didn’t converge?
Did you choose a very small width for the Gaussian broadening method?

Thank you.
Best regards.
メンテ
Re: Ghost states_band structure ( No.12 )
Date: 2022/11/11 11:14
Name: T. Ozaki

Hi,

>Could you tell me please how did you notice that the SCF didn’t converge?

As explained in the manual: https://www.openmx-square.org/openmx_man3.9/node16.html
one can confirm the SCF convergence in the out file as

***********************************************************
***********************************************************
SCF history at MD= 1
***********************************************************
***********************************************************

SCF= 1 NormRD= 1.000000000000 Uele= -3.523169099731
SCF= 2 NormRD= 0.181517404404 Uele= -3.686855123738
SCF= 3 NormRD= 0.449067381009 Uele= -4.193062144919
SCF= 4 NormRD= 0.541215648203 Uele= -4.381387140154
SCF= 5 NormRD= 0.509921689399 Uele= -4.352426233337
SCF= 6 NormRD= 0.004026023243 Uele= -3.886371199720
SCF= 7 NormRD= 0.000838640096 Uele= -3.889312346884
SCF= 8 NormRD= 0.000420666755 Uele= -3.889396659132
SCF= 9 NormRD= 0.000241013350 Uele= -3.889362708861
SCF= 10 NormRD= 0.000573725679 Uele= -3.889427222948
SCF= 11 NormRD= 0.000000150516 Uele= -3.889316043314
SCF= 12 NormRD= 0.000000001917 Uele= -3.889316014533
SCF= 13 NormRD= 0.000000000005 Uele= -3.889316014156
SCF= 14 NormRD= 0.000000000001 Uele= -3.889316014146



>Did you choose a very small width for the Gaussian broadening method?

I used 0.02 eV for that.


Regards,

TO
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