How to plot symmetric exciton wave function

Anything regarding the post-processing utility (e.g. excitonic wavefunction analysis) is dealt with in this forum.

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Daniele Varsano
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Re: How to plot symmetric exciton wave function

Post by Daniele Varsano » Sun Feb 07, 2021 10:05 am

Dear Pushpendra,
in order to plot excitonic wave function yambo need to read the eigenvector of the BSE.
It seems that the database containing them (ndb.BSS_diago) is not found neither in the SAVE directory nor in the 2D_WR_WC directory. Check if it exists.
If it is not there, possible reasons are:
1) It is contained in a different directory (you used a different directory as -J in the BSE calculation)
2) Check that BSE run finished correctly
3) You did not diagonalise the BSE, but you solved it in an iterative way (haydock), in order to plot the exc-wf you need a direct diagonalization:

Code: Select all

BSSmod= "d"
and add the

Code: Select all

WRbsWF
keyword in your input in order write eigenvectors.

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/

pyadav
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Re: How to plot symmetric exciton wave function

Post by pyadav » Sun Feb 07, 2021 1:04 pm

Dear Daniele,

Thank you for the reply. I'll follow the pointed suggestions.

wishes,
Pushpendra
Pushpendra Yadav
Ph.D. Research Scholar
Quantum Transport and Theory Group
Department of Physics
Indian Instittute of Technology Kanpur, India.

https://sites.google.com/site/amitkag1/

pyadav
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Re: How to plot symmetric exciton wave function

Post by pyadav » Thu Feb 11, 2021 9:33 am

Dear Developers,

I'm trying to get exciton wavefunction in real space and I'm using the input attached. I'm getting one hole position that seems to be going out of the given supercell. My aim to get the excitonic plot like the one attached for MoS2 that is done using Yambo code itself. Can someone please help me with how to get that?

Reference doi - 10.1103/PhysRevB.88.045412
Attachment link - https://www.dropbox.com/s/6qpdbfafxoeitg9/file.rar?dl=0

Thanks and regards,
Pushpendra
Pushpendra Yadav
Ph.D. Research Scholar
Quantum Transport and Theory Group
Department of Physics
Indian Instittute of Technology Kanpur, India.

https://sites.google.com/site/amitkag1/

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Daniele Varsano
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Re: How to plot symmetric exciton wave function

Post by Daniele Varsano » Thu Feb 11, 2021 9:53 am

Dear Pushendra,
the hole is in the closest point of the grid you indicated in the input file considering the unit cell repetitions in x and y direction.
From the xsf file:

Code: Select all

 3.37173   6.20501   0.40000
Looking at coordinate of your system (in xsf file) it seems to me your structure is centred in the middle of the cell in the x direction, while you are
putting the hole near the origin. What you need to do is placing the z coordinate of the hole also in the middle of the cell.

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/

pyadav
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Joined: Thu Nov 26, 2020 2:56 pm
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Re: How to plot symmetric exciton wave function

Post by pyadav » Fri Feb 19, 2021 5:56 pm

Dear Daniel,

I got the exciton wavefunction data and now able to fix the hole position at the desired place. Now I have an issue that the color plot surface (plotted in xcrysden) is not exactly in the atomic plane [Mo plane (x-y)] where my hole is placed. The images with the xsf data are attached. It would be very helpful for me if you could have a look and help me out with this.
Attachment link - https://www.dropbox.com/s/57jx30m3101b6j0/file.rar?dl=0

Thanks.
Pushpendra
Pushpendra Yadav
Ph.D. Research Scholar
Quantum Transport and Theory Group
Department of Physics
Indian Instittute of Technology Kanpur, India.

https://sites.google.com/site/amitkag1/

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Daniele Varsano
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Re: How to plot symmetric exciton wave function

Post by Daniele Varsano » Fri Feb 19, 2021 6:38 pm

Dear Pushpendra,
please first
by default the plane is set at the half of the cell, and the Mo atom plane is not exactly centred.
Anyway, what matters is the position of the hole and not where the plotted plane is shown, so you can do is just shift the plotted plane where you desire by editing the xsf file:

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 BEGIN_BLOCK_DATAGRID_2D
   Generated with YPP  4   4   0
   BEGIN_DATAGRID_2D
    109  109
     0.00000   0.00000  12.50
    28.44900   0.00000   0.00000
   -14.22450  24.63755   0.00000
and change the z coordinate of the origin from (0.00000 0.00000 12.50) to (0.00000 0.00000 12.11).

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/

pyadav
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Re: How to plot symmetric exciton wave function

Post by pyadav » Fri Feb 19, 2021 7:24 pm

Dear Daniele,

Thank you so much for the very quick reply and for clarifying the doubts.

Best wishes,
Pushpendra
Pushpendra Yadav
Ph.D. Research Scholar
Quantum Transport and Theory Group
Department of Physics
Indian Instittute of Technology Kanpur, India.

https://sites.google.com/site/amitkag1/

pyadav
Posts: 42
Joined: Thu Nov 26, 2020 2:56 pm
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Re: How to plot symmetric exciton wave function

Post by pyadav » Wed Aug 04, 2021 1:45 pm

Dear team yambo,

What does it mean by the line -

Code: Select all

 [WARNING] 3 excitonic states added to the USER selection to preserve degeneracy
?

My input for the exciton WF for the 1st exciton peak calculation is the following-

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excitons                         # [R] Excitonic properties
wavefunction                     # [R] Wavefunction
Format= "x"                      # Output format [(c)ube/(g)nuplot/(x)crysden]
Direction= "12"                   # [rlu] [1/2/3] for 1d or [12/13/23] for 2d [123] for 3D
FFTGvecs= 120            Ry    # [FFT] Plane-waves
States= "1 - 1"                  # Index of the BS state(s)
BSQindex= 1                      # Q-Index of the BS state(s)
Degen_Step= 0.010000       eV    # Maximum energy separation of two degenerate states
% Cells
 14 | 14 | 1 |                             # Number of cell repetitions in each direction (odd or 1)
%
% Hole
 -0.000002787 | 3.175575905 | 24.590300392 |        # [cc] Hole position in unit cell (positive)
%
Also if for the 1st exciton peak, my above input is correct, then how do I plot the second exciton peak separately? And how do I calculate exciton radius from this?

Thanks,
Pushpendra
Pushpendra Yadav
Ph.D. Research Scholar
Quantum Transport and Theory Group
Department of Physics
Indian Instittute of Technology Kanpur, India.

https://sites.google.com/site/amitkag1/

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Daniele Varsano
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Re: How to plot symmetric exciton wave function

Post by Daniele Varsano » Thu Aug 05, 2021 9:37 am

Dear Pushendra,

yambo consider a linear combination of exciton wave functions when it founds degenerate excitons.
Excitons are considered degenerate if their energy difference is lower than a threshold.
The threshold can be set by input with the variable:

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Degen_Step= 0.010000       eV 
If you set it to zero you will treat each exciton as non-degenerate and you can analyse them separately.

About exciton radius, once you have the plot you can try to fit with a suitable model e.g. hydrogen like wfs along a direction.
To do that you need to perform some post-processing by yourself, for instance you can have the output in cube format from yambo and then slice the data
in one direction and finally fit them.

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/

pyadav
Posts: 42
Joined: Thu Nov 26, 2020 2:56 pm
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Re: How to plot symmetric exciton wave function

Post by pyadav » Thu Aug 05, 2021 11:47 am

Thank you so much, Daniele!
Pushpendra Yadav
Ph.D. Research Scholar
Quantum Transport and Theory Group
Department of Physics
Indian Instittute of Technology Kanpur, India.

https://sites.google.com/site/amitkag1/

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