The calculated wavefunction didn't show in xsf file

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The calculated wavefunction didn't show in xsf file

Postby Tianshu » Mon May 14, 2018 3:03 pm

Dear developers,

I want to plot wavefunctions for each level in excitonic spectrum based my completed GW+BSE results. I follow the steps on http://www.yambo-code.org/wiki/index.php?title=How_to_analyse_excitons. However, when I run command "ypp -F ypp_wf.in -e w" to get xsf file, but the xsf file only show some atomic structure. The input file used for this step is as following:
Code: Select all
excitons
wavefunction
Direction =       '13'
BoseTemp = -1.000000e+00 eV
ElecTemp = 0.000000e+00 eV
Format =        'x'
% Cells
 11 | 1 | 11 |
%
States =    '1 - 1'
Degen_Step = 0.010000 eV
FFTGvecs = 10 Ry
% Hole
 0.0 | 24.45 | 0.0 |
%
MinWeight = 0.010000

So is this problem related to the chosen hole position or other cause? Waiting for your response. Thank you for your help and patience.

Best regards,
Tianshu Li
Jilin University, China
Tianshu
 
Posts: 27
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Re: The calculated wavefunction didn't show in xsf file

Postby Daniele Varsano » Mon May 14, 2018 3:12 pm

Dear Tianshu,
from the input file, I cannot see anything wrong.
Can you please post your r_setup file and the standard output you have when you type
>ypp -F ypp_wf.in


Best,
Daniele
Dr. Daniele Varsano
S3-CNR Institute of Nanoscience and MaX Center, Italy
MaX - Materials design at the Exascale
http://www.nano.cnr.it
http://www.max-centre.eu/
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Re: The calculated wavefunction didn't show in xsf file

Postby Tianshu » Tue May 15, 2018 2:10 am

Dear Daniele,

Thank you for your response. I attached the r_setup and o-bse_y.exc_2d_1.xsf file from command 'ypp -F ypp_wf.in'. Also I add the output file named 'o-bse_y.exc_E_sorted' and 'o-bse_y.exc_I_sorted', which I got from 'ypp -F ypp.in -e s'. I'm not sure is this helpful. Thank you for your help and patience.

Best regards,
Tianshu
Jilin University, China
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College of Materials Science and Engineering,
Jilin University, China
Institute http://dmse.jlu.edu.cn/?mod=info&act=view&id=502
Tianshu
 
Posts: 27
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Re: The calculated wavefunction didn't show in xsf file

Postby Daniele Varsano » Tue May 15, 2018 12:21 pm

Dear Tianshu Li,
please sign your post with your affiliation. You can do once for all by filling the signature in your profile.
Now, it seems to me that your xsf file is correct, as you can see after the atomic system specification, starts the volumetric data of your
wave function:
line 534
Code: Select all
BEGIN_BLOCK_DATAGRID_2D
   Generated with YPP  4   1   3
   BEGIN_DATAGRID_2D

I do not know what software you are using to visualize it, it looks that VESTA has a bug has it is not able to process data having the origin in the y direction and data on xz plane.
Just, as a proof, by switching lines 538-540 as:
Code: Select all
  36.35554   0.00000   0.00000
  0.00000  11.13345   0.00000
 0.00000   0.00000  49.59734

you can see your wfs, but of course, displayed on a bad scale and on a different plane.
Maybe the problem can be overcome by setting correctly the boundary in VESTA, but I'm not an expert and I cannot help on that.

XCRYSDEN should read correctly your file. Now I do not have xcrysden installed on my machine so I cannot verify that directly with your file.
In alternative you can plot 3D isosurface, probably it should work also with VESTA.

Best,
Daniele
Dr. Daniele Varsano
S3-CNR Institute of Nanoscience and MaX Center, Italy
MaX - Materials design at the Exascale
http://www.nano.cnr.it
http://www.max-centre.eu/
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Re: The calculated wavefunction didn't show in xsf file

Postby Tianshu » Wed May 16, 2018 3:21 am

Dear Daniele,

Thank you. I will try it again. Btw, I have two questions. When I got the file named 'o-bse_y.exc_E_sorted', there are a lot of index number corresponding different energy levels. But when I plot the excitonic spectrum, only some of energy levels are shown up. Are the shown levels corresponding to bright states?

On the other hand, I found the first level didn't locate at the first peak position sometimes, just like the figure I attached. I'm not sure is this correct. Waiting for your response. Thank you for your help and patience.

Best regards,
Tianshu
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College of Materials Science and Engineering,
Jilin University, China
Institute http://dmse.jlu.edu.cn/?mod=info&act=view&id=502
Tianshu
 
Posts: 27
Joined: Wed Sep 20, 2017 8:36 am

Re: The calculated wavefunction didn't show in xsf file

Postby Daniele Varsano » Wed May 16, 2018 6:59 am

Dear Thiansu,

In the *exc_E_sorted output file you have excitation energies, their strength and an index corresponding to that excitation as indicated in the header:

Code: Select all
#  E [ev]     Strength   Index


When you plot them of course zero or very low strength will not appear in the plot.

The excitation energies are the pole of the response function so they should match the peak positions, are you sure you are looking at the correct file?
Please check, otherwise post your outputs (*sorted, *eps) and the report file.
Best,
Daniele
Dr. Daniele Varsano
S3-CNR Institute of Nanoscience and MaX Center, Italy
MaX - Materials design at the Exascale
http://www.nano.cnr.it
http://www.max-centre.eu/
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Posts: 2027
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