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Noisy output for sden.cube file
Date: 2020/03/01 01:54
Name: Maedeh   <rasekh.maede@gmail.com>

Dear OpenMX developers,
Hi,

For some structures, I see that the "sden.cube" output file of OpenMX is not a clear picture (I use VESTA visualization). It looks like all the colors are scattered all over the cell and it is a noisy picture. I wish I could upload a picture here to show what I mean.
I always ignore it because I don't need that but I would like to know the reason.
have you ever faced this problem?

Best regards,
Maedeh
メンテ
Page: [1]

Re: Noisy output for sden.cube file ( No.1 )
Date: 2020/03/01 08:05
Name: T. Ozaki

Hi,

The data in the cube files are output in 4 decimal digits.
I wonder that this may cause such a noisy visualization in some situations.
Please give us a minimum input file, which produces such a cube file,
so that we can figure out the cause.

Regards,

TO
メンテ
Re: Noisy output for sden.cube file ( No.2 )
Date: 2020/03/01 16:27
Name: Maedeh  <rasekh.maede@gmail.com>

Dear professor Ozaki,

This is one of them:



Species.Number 2
<Definition.of.Atomic.Species
H H6.0-s2p1 H_PBE13
C C6.0-s2p2d1 C_PBE13
Definition.of.Atomic.Species>

Atoms.Number 20
Atoms.SpeciesAndCoordinates.Unit FRAC
<Atoms.SpeciesAndCoordinates
1 C 0.2128830 0.6666670 0.5000000 2.0 2.0
2 C 0.2949170 0.8333330 0.5000000 2.0 2.0
3 C 0.2128830 0.3333330 0.5000000 2.0 2.0
4 C 0.3769500 0.6666670 0.5000000 2.0 2.0
5 C 0.4589830 0.8333330 0.5000000 2.0 2.0
6 C 0.2949170 0.1666670 0.5000000 2.0 2.0
7 C 0.3769500 0.3333330 0.5000000 2.0 2.0
8 C 0.5410170 0.6666670 0.5000000 2.0 2.0
9 C 0.6230500 0.8333330 0.5000000 2.0 2.0
10 C 0.4589830 0.1666670 0.5000000 2.0 2.0
11 C 0.5410170 0.3333330 0.5000000 2.0 2.0
12 C 0.7050830 0.6666670 0.5000000 2.0 2.0
13 C 0.7871170 0.8333330 0.5000000 2.0 2.0
14 C 0.6230500 0.1666670 0.5000000 2.0 2.0
15 C 0.7050830 0.3333330 0.5000000 2.0 2.0
16 C 0.7871170 0.1666670 0.5000000 2.0 2.0
17 H 0.1499520 0.7945230 0.5000000 0.5 0.5
18 H 0.1499520 0.2054770 0.5000000 0.5 0.5
19 H 0.8500480 0.7054770 0.5000000 0.5 0.5
20 H 0.8500480 0.2945230 0.5000000 0.5 0.5
Atoms.SpeciesAndCoordinates>

Atoms.UnitVectors.Unit Ang
<Atoms.UnitVectors
15.0000000 0.0000000 0.0000000
0.0000000 4.2625800 0.0000000
0.0000000 0.0000000 15.0000000
Atoms.UnitVectors>


#
# SCF or Electronic System
#

scf.XcType GGA-PBE # LDA|LSDA-CA|LSDA-PW
scf.SpinPolarization on # On|Off|NC
scf.ElectronicTemperature 300.0 # default=300 (K)
scf.energycutoff 300 # default=150 (Ry)
scf.maxIter 100 # default=40
scf.EigenvalueSolver band # Recursion|Cluster|Band
scf.Kgrid 1 27 1 # means 4x4x4
scf.Mixing.Type rmm-diisk # Simple|Rmm-Diis|Gr-Pulay
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 20 # default=5
scf.Mixing.StartPulay 10 # default=6
scf.Mixing.EveryPulay 1 # default=5
scf.criterion 1.0e-6 # default=1.0e-6 (Hartree)



Best regards,
Maedeh
メンテ
Re: Noisy output for sden.cube file ( No.3 )
Date: 2020/03/01 16:43
Name: Maedeh  <rasekh.maede@gmail.com>

you can click on this link to see the output image:

https://pasteboard.co/IX2PfTF.jpg

メンテ
Re: Noisy output for sden.cube file ( No.4 )
Date: 2020/03/02 17:50
Name: T. Ozaki

Hi,

I have tested your input file, and found the reason
why we have such a noisy picture.

The system is found to be non-magnetic, and the spin density at each point
is around 10^{-16} or less. So, the values are beyond significant digits
of double precision. So, the output data in the sden.cube file do not have
enough accuray, resulting in such a noisy picture.

And to discuss such a small difference may be physically and numerically meaningless.

Regards,

TO
メンテ
Re: Noisy output for sden.cube file ( No.5 )
Date: 2020/03/04 17:02
Name: Maedeh  <rasekh.maede@gmail.com>

Dear professor Ozaki,

Thanks,
but this doesn't happen for all non-magnetic systems. and I think I have seen this problem also in some magnetic systems.
anyway, I will keep this in my mind and if I have more examples, I will post here.

Best regards,
Maedeh
メンテ

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