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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shan dong
Posts: 31
Joined: Thu Oct 17, 2019 5:26 am

How to plot symmetric exciton wave function

Post by shan dong » Tue Nov 05, 2019 9:10 am

Dear all,
I'm using "ypp -e w" to plot the exciton wavefunction with a finished HSE-BSE result.The hole position has been fixed on Ti atom in unit cell. But the graph of the distribution of the exciton wave function is irregular. The hole position has moved to the vacuum layer .How to plot symmetric exciton wave function? The hole can be placed in the cell after expansion?

ElecTemp= 0.000000 eV # Electronic Temperature
BoseTemp=-1.000000 eV # Bosonic Temperature
excitons # [R] Excitons
wavefunction # [R] Wavefunction
Format= "x" # Output format [(c)ube/(g)nuplot/(x)crysden]
Direction= "123" # [rlu] [1/2/3] for 1d or [12/13/23] for 2d [123] for 3D
FFTGvecs= 42 Ry # [FFT] Plane-waves
States= "1 - 1" # Index of the BS state(s)
Degen_Step= 0.000000 eV # Maximum energy separation of two degenerate states
MinWeight= 0.00100 # Print transitions with weight => MinWeight
% Cells
11 | 11 | 1 | # Number of cell repetitions in each direction (odd or 1)
%
% Hole
4.240000 | 0.870000 | 11.306000 | # [cc] Hole position in unit cell
%

Many thanks~!
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Shan Dong
PhD student
Beijing Institute of Technology,China

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Daniele Varsano
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Re: How to plot symmetric exciton wave function

Post by Daniele Varsano » Tue Nov 05, 2019 2:32 pm

Dear Shan Dong,
The hole position has moved to the vacuum layer
The hole is placed in the closest point indicated in input belonging to the FFT grid. The higher the FFTGvecs the finer is the grid.
You need to place the hole in the unit cell, then it is displaced accordingly in the central cell after the expansion.
In order to have symmetric wavefunctions the hole needs to be placed near a point where the conduction wavefunctions participating to the excitation
have a symmetric profile.
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/

shan dong
Posts: 31
Joined: Thu Oct 17, 2019 5:26 am

Re: How to plot symmetric exciton wave function

Post by shan dong » Wed Nov 06, 2019 1:47 pm

Daniele Varsano wrote:Dear Shan Dong,
The hole position has moved to the vacuum layer
The hole is placed in the closest point indicated in input belonging to the FFT grid. The higher the FFTGvecs the finer is the grid.
You need to place the hole in the unit cell, then it is displaced accordingly in the central cell after the expansion.
In order to have symmetric wavefunctions the hole needs to be placed near a point where the conduction wavefunctions participating to the excitation
have a symmetric profile.
Best,
Daniele
Dear Daniele,
Thanks for your reply. I use qe6.2 and yambo4.4. I have increased the FFTGvecs value to 120Ry. The the distribution of the exciton wave function was changed, but the hole position also moved to the vacuum layer.Could it be that the z-axis of this crystal is not perpendicular to the xy plane. How can I fix the hole position after expansion of the cell?

ElecTemp= 0.000000 eV # Electronic Temperature
BoseTemp=-1.000000 eV # Bosonic Temperature
excitons # [R] Excitons
wavefunction # [R] Wavefunction
Format= "x" # Output format [(c)ube/(g)nuplot/(x)crysden]
Direction= "123" # [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)
Degen_Step= 0.000000 eV # Maximum energy separation of two degenerate states
MinWeight= 0.00100 # Print transitions with weight => MinWeight
% Cells
7 | 7 | 1 | # Number of cell repetitions in each direction (odd or 1)
%
% Hole
2.385000 | 1.68800 | 10.23800 | # [cc] Hole position in unit cell
%
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Shan Dong
PhD student
Beijing Institute of Technology,China

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Daniele Varsano
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Re: How to plot symmetric exciton wave function

Post by Daniele Varsano » Wed Nov 06, 2019 2:56 pm

Dear Shan Dong,
How can I fix the hole position after the expansion of the cell?
From the picture, it is not very clear what is going wrong. The problem seems a displacement in the z-direction and this should be not changed after expansion as you have just one unit of repetition. The only way I can see to spot the problem, is to plot it just in the unit cell and verify it is in the correct place. Note that the points of the grid are the one reported in the output so you can for instance look at a 2D plot in the xz or yz plane, by plotting in gnuplot format you will have the list of the available grid points (I do not remember if the origin of the grid is shifted to the position of the hole) and see which is the best point where to place the hole.
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/

shan dong
Posts: 31
Joined: Thu Oct 17, 2019 5:26 am

Re: How to plot symmetric exciton wave function

Post by shan dong » Thu Nov 07, 2019 10:19 am

Daniele Varsano wrote:Dear Shan Dong,
How can I fix the hole position after the expansion of the cell?
From the picture, it is not very clear what is going wrong. The problem seems a displacement in the z-direction and this should be not changed after expansion as you have just one unit of repetition. The only way I can see to spot the problem, is to plot it just in the unit cell and verify it is in the correct place. Note that the points of the grid are the one reported in the output so you can for instance look at a 2D plot in the xz or yz plane, by plotting in gnuplot format you will have the list of the available grid points (I do not remember if the origin of the grid is shifted to the position of the hole) and see which is the best point where to place the hole.
Best,
Daniele
Dear Daniele,Thanks for your reply.I have plotted it in the unit cell. It is strange that I fixed the Hole position at (2.5819000 | 1.6463800 | 9.963600 | ),in the output file it appeared in (2.486037 | 1.636834 | 9.985248 | )(it seems right), But in the XSF structure file it went to (1.06318,0.8866172,5.34048).


ElecTemp= 0.000000 eV # Electronic Temperature
BoseTemp=-1.000000 eV # Bosonic Temperature
excitons # [R] Excitons
wavefunction # [R] Wavefunction
Format= "x" # Output format [(c)ube/(g)nuplot/(x)crysden]
Direction= "13" # [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)
Degen_Step= 0.000000 eV # Maximum energy separation of two degenerate states
MinWeight= 0.00100 # Print transitions with weight => MinWeight
% Cells
1 | 1 | 1 | # Number of cell repetitions in each direction (odd or 1)
%
% Hole
2.5819000 | 1.6463800 | 9.963600 | # [cc] Hole position in unit cell
%
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Shan Dong
PhD student
Beijing Institute of Technology,China

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Daniele Varsano
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Re: How to plot symmetric exciton wave function

Post by Daniele Varsano » Thu Nov 07, 2019 10:46 am

Dear Shan,
looking at your files it seems to me that the hole is placed correctly.
In xsf file:
-1 1.31555 0.86617 5.28397
16 1.70998 0.86617 10.38214
......
The atom indicated with -1 is the hole position, which is the same as you indicated after Bohr-> Angstrom conversion.
Is it possible you are assigning the hole value in Angstrom instead of Bohr?

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/

kli103
Posts: 15
Joined: Wed May 20, 2020 7:25 am
Location: University of California, Santa Cruz

Re: How to plot symmetric exciton wave function

Post by kli103 » Wed Sep 02, 2020 7:35 am

Dear Yambo developers,

Is the unit of the isosurface of exciton wavefunction generated by ypp electron/bohr^3?

Best regards,
Kejun
Kejun Li
PhD student,
Department of Physics,
University of California, Santa Cruz
E-mail: kli103@ucsc.edu

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Daniele Varsano
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Re: How to plot symmetric exciton wave function

Post by Daniele Varsano » Wed Sep 02, 2020 8:20 am

Dear Kejun,

please note that the exciton wave function is normalised to its maximum, i.e. its maximum value is set to one.
If you do not want to normalise it, you need to change in the code:
ypp//ypp/modules/YPP_SET_defaults.F

Code: Select all

129  l_sp_wf=.false.
130  l_norm_to_one=.true.
131  output_fname=' '
l_norm_to_one=.false.
and recompile.

In this case the maximum of the WFs will depend on the position of the hole.

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/

kli103
Posts: 15
Joined: Wed May 20, 2020 7:25 am
Location: University of California, Santa Cruz

Re: How to plot symmetric exciton wave function

Post by kli103 » Wed Sep 02, 2020 7:20 pm

Dear Daniele,

Thanks for answering my question.

Best,
Kejun
Kejun Li
PhD student,
Department of Physics,
University of California, Santa Cruz
E-mail: kli103@ucsc.edu

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 » Sat Feb 06, 2021 1:09 pm

Dear Developers,

I'm trying to get exciton wavefunction for MoS2 after finishing the g0w0+BSE calculation. When using the tag "ypp" after editing the input ( attcahed) file with "ypp -e w" command, I'm getting the following error
[06] Excitonic Properties
=========================


[ERROR] STOP signal received while in :[06] Excitonic Properties

[ERROR] ndb.BSS_diago not found
Can someone please help me with this?
Please find the attachment.
Best,
Pushpendra
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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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