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Error in DOS Calculation
Date: 2022/07/12 09:23
Name: Vipin

Dear Users/Developers,

I am trying to calculate MS2-GaS bilayer heterostructure, calculation finished normally. While running ./DosMain ......val .....vec, I am getting error like "WhatSpecies is not found" as follows

$ ./DosMain MS2-GaS.Dos.val MS2-GaS.Dos.vec
<WhatSpecies is not found
$

I am getting same error in some other material also. However, in most cases it generate .Tetrahedron file. But, in few cases it shows the problem as explained above.


Your help would be appreciable.

Regards,
Vipin
メンテ
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Re: Error in DOS Calculation ( No.1 )
Date: 2022/07/26 14:06
Name: T. Ozaki

Hi,

Could you share the input file (for the OpenMX calculation) which caused the problem?

Regards,

TO
メンテ
Re: Error in DOS Calculation ( No.2 )
Date: 2022/07/27 08:40
Name: Vipin Kumar

Dear Professor,

Following is the input file

#
# This was generated by OpenMX Viewer
DATA.PATH /home/msrc/OPEN/openmx3.9/DFT_DATA19
System.CurrrentDirectory ./
System.Name MoS2-GaS-DOSs
level.of.stdout 1
level.of.fileout 1

Species.Number 3
<Definition.of.Atomic.Species
S S7.0-s2p2d1f1 S_PBE19
Ga Ga7.0-s3p2d2 Ga_PBE19
Mo Mo7.0-s3p2d2f1 Mo_PBE19
Definition.of.Atomic.Species>

Atoms.Number 63
Atoms.SpeciesAndCoordinates.Unit FRAC
<Atoms.SpeciesAndCoordinates
1 Mo 0.0950514 0.2139086 0.3959985 7.0 7.0
2 S 0.1990514 0.1099086 0.3520725 3.0 3.0
3 S 0.1990514 0.1099086 0.4399200 3.0 3.0
4 S 0.1092681 0.2423452 0.6427851 3.0 3.0
5 S 0.1092681 0.2423452 0.5132194 3.0 3.0
6 Ga 0.2274881 0.1241252 0.6125209 6.5 6.5
7 Ga 0.2274881 0.1241252 0.5434836 6.5 6.5
8 Mo 0.0950514 0.5472419 0.3959985 7.0 7.0
9 S 0.1990514 0.4432419 0.3520725 3.0 3.0
10 S 0.1990514 0.4432419 0.4399200 3.0 3.0
11 S 0.1092681 0.5756786 0.6427851 3.0 3.0
12 S 0.1092681 0.5756786 0.5132194 3.0 3.0
13 Ga 0.2274881 0.4574586 0.6125209 6.5 6.5
14 Ga 0.2274881 0.4574586 0.5434836 6.5 6.5
15 Mo 0.0950514 0.8805752 0.3959985 7.0 7.0
16 S 0.1990514 0.7765752 0.3520725 3.0 3.0
17 S 0.1990514 0.7765752 0.4399200 3.0 3.0
18 S 0.1092681 0.9090119 0.6427851 3.0 3.0
19 S 0.1092681 0.9090119 0.5132194 3.0 3.0
20 Ga 0.2274881 0.7907919 0.6125209 6.5 6.5
21 Ga 0.2274881 0.7907919 0.5434836 6.5 6.5
22 Mo 0.4283848 0.2139086 0.3959985 7.0 7.0
23 S 0.5323848 0.1099086 0.3520725 3.0 3.0
24 S 0.5323848 0.1099086 0.4399200 3.0 3.0
25 S 0.4426014 0.2423452 0.6427851 3.0 3.0
26 S 0.4426014 0.2423452 0.5132194 3.0 3.0
27 Ga 0.5608214 0.1241252 0.6125209 6.5 6.5
28 Ga 0.5608214 0.1241252 0.5434836 6.5 6.5
29 Mo 0.4283848 0.5472419 0.3959985 7.0 7.0
30 S 0.5323848 0.4432419 0.3520725 3.0 3.0
31 S 0.5323848 0.4432419 0.4399200 3.0 3.0
32 S 0.4426014 0.5756786 0.6427851 3.0 3.0
33 S 0.4426014 0.5756786 0.5132194 3.0 3.0
34 Ga 0.5608214 0.4574586 0.6125209 6.5 6.5
35 Ga 0.5608214 0.4574586 0.5434836 6.5 6.5
36 Mo 0.4283848 0.8805752 0.3959985 7.0 7.0
37 S 0.5323848 0.7765752 0.3520725 3.0 3.0
38 S 0.5323848 0.7765752 0.4399200 3.0 3.0
39 S 0.4426014 0.9090119 0.6427851 3.0 3.0
40 S 0.4426014 0.9090119 0.5132194 3.0 3.0
41 Ga 0.5608214 0.7907919 0.6125209 6.5 6.5
42 Ga 0.5608214 0.7907919 0.5434836 6.5 6.5
43 Mo 0.7617181 0.2139086 0.3959985 7.0 7.0
44 S 0.8657181 0.1099086 0.3520725 3.0 3.0
45 S 0.8657181 0.1099086 0.4399200 3.0 3.0
46 S 0.7759348 0.2423452 0.6427851 3.0 3.0
47 S 0.7759348 0.2423452 0.5132194 3.0 3.0
48 Ga 0.8941548 0.1241252 0.6125209 6.5 6.5
49 Ga 0.8941548 0.1241252 0.5434836 6.5 6.5
50 Mo 0.7617181 0.5472419 0.3959985 7.0 7.0
51 S 0.8657181 0.4432419 0.3520725 3.0 3.0
52 S 0.8657181 0.4432419 0.4399200 3.0 3.0
53 S 0.7759348 0.5756786 0.6427851 3.0 3.0
54 S 0.7759348 0.5756786 0.5132194 3.0 3.0
55 Ga 0.8941548 0.4574586 0.6125209 6.5 6.5
56 Ga 0.8941548 0.4574586 0.5434836 6.5 6.5
57 Mo 0.7617181 0.8805752 0.3959985 7.0 7.0
58 S 0.8657181 0.7765752 0.3520725 3.0 3.0
59 S 0.8657181 0.7765752 0.4399200 3.0 3.0
60 S 0.7759348 0.9090119 0.6427851 3.0 3.0
61 S 0.7759348 0.9090119 0.5132194 3.0 3.0
62 Ga 0.8941548 0.7907919 0.6125209 6.5 6.5
63 Ga 0.8941548 0.7907919 0.5434836 6.5 6.5
Atoms.SpeciesAndCoordinates>

Atoms.UnitVectors.Unit Ang
<Atoms.UnitVectors
10.2264000 0.0000000 0.0000000
-5.1132000 8.8563222 0.0000000
0.0000000 0.0000000 35.8138000
Atoms.UnitVectors>

scf.XcType GGA-PBE
scf.SpinPolarization off
scf.ElectronicTemperature 300.0
scf.energycutoff 220.0
scf.maxIter 100
scf.EigenvalueSolver band
scf.Kgrid 2 2 1
scf.Mixing.Type rmm-diisk
scf.Init.Mixing.Weight 0.05
scf.Min.Mixing.Weight 0.01
scf.Max.Mixing.Weight 0.30
scf.Mixing.History 25
scf.Mixing.StartPulay 15
scf.criterion 1.0e-7

MD.Type nomd
MD.maxIter 1
MD.TimeStep 1.0
MD.Opt.criterion 0.0003



Band.dispersion off
Band.Nkpath 3
<Band.kpath
30 0.000000 0.000000 0.000000 0.500000 0.000000 0.000000 G M
17 0.500000 0.000000 0.000000 0.333333 0.333333 0.000000 M K
34 0.333333 0.333333 0.000000 0.000000 0.000000 0.000000 K G
Band.kpath>

Dos.fileout on
Dos.Erange -10.0 10.0
Dos.Kgrid 45 45 1



#
# partial charge calculation
#

partial.charge off #on|off, default=off
partial.charge.energy.window 2.0 # in eV


メンテ
Re: Error in DOS Calculation ( No.3 )
Date: 2022/07/28 02:23
Name: Yung-Ting Lee

Following the input file, I obtain DOS by DosMain with "mos2-GaS-DOSs.Dos.val" and "mos2-GaS-DOSs.Dos.vec" successfully. There is no problem in my Linux computer.

DOS figure : https://ppt.cc/f7B16x .

The command lines are printed as below for your reference.
------------------------------------------------------------------------------------------
$ /home/***/openmx/openmx3.9/source/DosMain mos2-GaS-DOSs.Dos.val mos2-GaS-DOSs.Dos.vec
Max of Spe_Total_CNO = 26
1 1 101 102 103 101 102 103 201 202 203 204 205 301 302 303 304 305 306 307
1 1 1 101 102 103 101 102 103 201 202 203 204 205 201 202 203 204 205
1 1 1 101 102 103 101 102 103 201 202 203 204 205 201 202 203 204 205 301 302 303 304 305 306 307
<mos2-GaS-DOSs.Dos.val>
<mos2-GaS-DOSs>
Which method do you use?, Tetrahedron(1), Gaussian Broadening(2)
1
Do you want Dos(1) or PDos(2)?
1
<Dos_Tetrahedron> start
<Dos_Tetrahedron> make mos2-GaS-DOSs.DOS.Tetrahedron
$ ls
mos2-GaS-DOSs.bulk.xyz MoS2-GaS-DOSs.dat# mos2-GaS-DOSs.Dos.val mos2-GaS-DOSs.FermiSurf0.bxsf mos2-GaS-DOSs.md2 mos2-GaS-DOSs.tden.cube mos2-GaS-DOSs.xyz
mos2-GaS-DOSs.cif mos2-GaS-DOSs.dden.cube mos2-GaS-DOSs.Dos.vec MoS2-GaS-DOSs.log mos2-GaS-DOSs.out mos2-GaS-DOSs.v0.cube
MoS2-GaS-DOSs.dat mos2-GaS-DOSs.DOS.Tetrahedron mos2-GaS-DOSs.ene mos2-GaS-DOSs.md mos2-GaS-DOSs_rst mos2-GaS-DOSs.vhart.cube
------------------------------------------------------------------------------------------

Best regards,
Yung-Ting Lee
メンテ
Re: Error in DOS Calculation ( No.4 )
Date: 2022/07/28 10:42
Name: T. Ozaki

Hi,

Did you move the .Dos.val and .Dos.vec files from the machine you performed with OpenMX to another machine you performed with DosMain?
I wonder that such a treatment may cause the trouble you encountered.

Regards,

TO
メンテ
Re: Error in DOS Calculation ( No.5 )
Date: 2022/07/29 08:52
Name: Vipin

Dear Prof. Ozaki,

>>> Did you move the .Dos.val and .Dos.vec files from the machine you performed with OpenMX to another machine you performed with DosMain?

No Prof.

Instead, I copy and pasted from other folder to the current working folder in the same machine. Also, I did not copy and pasted from "WORK" directory to the current working folder.

I hope this could not create problem. As I did same thing for other works and going smooth. It is creating this problem in some cases.

I am in trouble now. Any help will be appreciated.

Regards,
Vipin
メンテ
Re: Error in DOS Calculation ( No.6 )
Date: 2022/07/29 17:12
Name: Naoya Yamaguchi

Dear Vipin,

Can you show output for the following command?

$ head -n 22 MS2-GaS.Dos.val

The above command should be executed at a directory including `MS2-GaS.Dos.val`.

Regards,
Naoya Yamaguchi
メンテ
Re: Error in DOS Calculation ( No.7 )
Date: 2022/07/29 13:11
Name: T. Ozaki

Hi,

The .Dos.val and .Dos.vec files that I obtained using your input have the following size:

$ ls -l MoS2-GaS-DOSs.Dos.v*
-rw-rw-r-- 1 ozaki ozaki 8018664 Jul 29 10:43 MoS2-GaS-DOSs.Dos.val
-rw-rw-r-- 1 ozaki ozaki 4313979000 Jul 29 10:43 MoS2-GaS-DOSs.Dos.vec

I wonder that your MoS2-GaS-DOSs.Dos.val might be broken or imcomplete.

Adding an compiler option "-Dxt3" to CC in the makefile for the compilation may solve the problem.

Regards,

TO
メンテ
Re: Error in DOS Calculation ( No.8 )
Date: 2022/07/30 09:03
Name: Vipin

Dear Yamaguchi,

Following is the output of the command you asked. However, it gives nothing.

$ head -n 22 MoS2-GaS.Dos.val
$

Regards,
Vipin
メンテ
Re: Error in DOS Calculation ( No.9 )
Date: 2022/07/30 09:07
Name: Vipin

Dear Prof. Ozaki,

The .Dos.val and .Dos.vec files I obtained have the following size:

$ ls -l MoS2-GaS-DOSs.Dos.v*
-rw-rw-r-- 1 msrc msrc 0 Jul 20 17:10 MoS2-GaS-DOSs.Dos.val
-rw-rw-r-- 1 msrc msrc 0 Jul 20 17:10 MoS2-GaS-DOSs.Dos.vec
$


Could you please guide me how to solve this problem then?

Regards,
Vipin
メンテ
Re: Error in DOS Calculation ( No.10 )
Date: 2022/07/30 10:19
Name: T. Ozaki

Hi,

Your files are empty.
The size of files I got is large (~4GB) due to the setting:

Dos.Kgrid 45 45 1

Could you try a set of small numbers of kgrids, and see what happens as you gradually increase these numbers?
I guess that the problem must come from your disk system, and at a certain point, the disk system cannot handle such large files.

Please also note that there is another way to calculate DOS for such a case with a large number of k-points.
http://www.openmx-square.org/openmx_man3.9/node71.html

Regards,

TO
メンテ

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