WWarning: XX grid is not uniform. Gamma point only
Moderators: Davide Sangalli, andrea.ferretti, myrta gruning, Daniele Varsano
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- Location: Fudan University, Shanghai, China
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WWarning: XX grid is not uniform. Gamma point only
Dear Developers,
I am tryingtrying to use YAMBO to calculate the absorption of two-dimensional Tellurene. We failed at the initialization step with the error message listed below. Could you please tell me how to fix this problem? Thank you!
Best regards,
Hao Zhang
<---> [01] CPU structure, Files & I/O Directories
<---> [02] CORE Variables Setup
<---> [02.01] Unit cells
<---> [02.02] Symmetries
<---> [02.03] RL shells
<---> Shells finder |########################################| [100%] --(E) --(X)
<05s> [02.04] K-grid lattice
<05s> [WARNING]Impossible to define the grid unit vectors
<05s> [WARNING]Trying to expand the k-grid
<05s> Grid dimensions : 1 1 6
<05s> [02.05] Energies [ev] & Occupations
<05s> [03] Transferred momenta grid
<05s> [WARNING][RL indx] 2 equivalent points in the rlu grid found
<05s> [RL indx] X grid is not uniform. Gamma point only.
<05s> [04] Timing Overview
<05s> [05] Game Over & Game summary
I am tryingtrying to use YAMBO to calculate the absorption of two-dimensional Tellurene. We failed at the initialization step with the error message listed below. Could you please tell me how to fix this problem? Thank you!
Best regards,
Hao Zhang
<---> [01] CPU structure, Files & I/O Directories
<---> [02] CORE Variables Setup
<---> [02.01] Unit cells
<---> [02.02] Symmetries
<---> [02.03] RL shells
<---> Shells finder |########################################| [100%] --(E) --(X)
<05s> [02.04] K-grid lattice
<05s> [WARNING]Impossible to define the grid unit vectors
<05s> [WARNING]Trying to expand the k-grid
<05s> Grid dimensions : 1 1 6
<05s> [02.05] Energies [ev] & Occupations
<05s> [03] Transferred momenta grid
<05s> [WARNING][RL indx] 2 equivalent points in the rlu grid found
<05s> [RL indx] X grid is not uniform. Gamma point only.
<05s> [04] Timing Overview
<05s> [05] Game Over & Game summary
You do not have the required permissions to view the files attached to this post.
Dr. Hao Zhang
Department of Optical Science and Engineering, Fudan University,Shanghai 200433, China
http://homepage.fudan.edu.cn/zhanghao/
Department of Optical Science and Engineering, Fudan University,Shanghai 200433, China
http://homepage.fudan.edu.cn/zhanghao/
- Daniele Varsano
- Posts: 3816
- Joined: Tue Mar 17, 2009 2:23 pm
- Contact:
Re: WWarning: XX grid is not uniform. Gamma point only
Dear Hao Zhang,
problems sometimes can arise for non-diagonal cells, you can try to use a different algorithm that usually solves the problem.
This is activated by adding the keyword:
in your setup input file.
Or, if you want by adding verbosity when bulding-up the input file:
and remove the comment to the NoDiagSC variable.
Best,
Daniele
problems sometimes can arise for non-diagonal cells, you can try to use a different algorithm that usually solves the problem.
This is activated by adding the keyword:
Code: Select all
NoDiagSC
Or, if you want by adding verbosity when bulding-up the input file:
Code: Select all
yambo -i -V all
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/
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/
-
- Posts: 39
- Joined: Thu Aug 23, 2018 9:18 am
- Location: Fudan University, Shanghai, China
- Contact:
Re: WWarning: XX grid is not uniform. Gamma point only
Dear Daniele,
Thank you for the reply. The error at the initialization step disappear, but when I generate the in file by using 'yambo -x -g n -p p', the content in the VIM interface is empty.
I have attached the r_setup here. Could you please tell me how to fix it? Thank you!
Hao
Thank you for the reply. The error at the initialization step disappear, but when I generate the in file by using 'yambo -x -g n -p p', the content in the VIM interface is empty.
I have attached the r_setup here. Could you please tell me how to fix it? Thank you!
Hao
Daniele Varsano wrote: ↑Thu May 28, 2020 4:03 pm Dear Hao Zhang,
problems sometimes can arise for non-diagonal cells, you can try to use a different algorithm that usually solves the problem.
This is activated by adding the keyword:in your setup input file.Code: Select all
NoDiagSC
Or, if you want by adding verbosity when bulding-up the input file:and remove the comment to the NoDiagSC variable.Code: Select all
yambo -i -V all
Best,
Daniele
You do not have the required permissions to view the files attached to this post.
Dr. Hao Zhang
Department of Optical Science and Engineering, Fudan University,Shanghai 200433, China
http://homepage.fudan.edu.cn/zhanghao/
Department of Optical Science and Engineering, Fudan University,Shanghai 200433, China
http://homepage.fudan.edu.cn/zhanghao/
- Daniele Varsano
- Posts: 3816
- Joined: Tue Mar 17, 2009 2:23 pm
- Contact:
Re: WWarning: XX grid is not uniform. Gamma point only
Dear Hao Zhang,
this happens because the problem it is not solved, as you can see in the r_setup:
It seems anyway that the kindex database has not been generated but just read from a previous calculation:
You should try to delete the ndb.kindx , run the setup again using the NoDiagSC option and see if your grid is recognized as uniform.
Best,
Daniele
this happens because the problem it is not solved, as you can see in the r_setup:
Code: Select all
X grid is uniform :no,
Code: Select all
[RD./SAVE//ndb.kindx]
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/
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/
-
- Posts: 39
- Joined: Thu Aug 23, 2018 9:18 am
- Location: Fudan University, Shanghai, China
- Contact:
Re: WWarning: XX grid is not uniform. Gamma point only
Thank you very much! It works!
Daniele Varsano wrote: ↑Fri May 29, 2020 11:55 am Dear Hao Zhang,
this happens because the problem it is not solved, as you can see in the r_setup:It seems anyway that the kindex database has not been generated but just read from a previous calculation:Code: Select all
X grid is uniform :no,
You should try to delete the ndb.kindx , run the setup again using the NoDiagSC option and see if your grid is recognized as uniform.Code: Select all
[RD./SAVE//ndb.kindx]
Best,
Daniele
Dr. Hao Zhang
Department of Optical Science and Engineering, Fudan University,Shanghai 200433, China
http://homepage.fudan.edu.cn/zhanghao/
Department of Optical Science and Engineering, Fudan University,Shanghai 200433, China
http://homepage.fudan.edu.cn/zhanghao/
-
- Posts: 39
- Joined: Thu Aug 23, 2018 9:18 am
- Location: Fudan University, Shanghai, China
- Contact:
Re: WWarning: XX grid is not uniform. Gamma point only
Dear Dianiele,
I have finished the calculations of BSE, but the file for macroscropic polarizability is not produced. Could you please tell me how to fix it? Thank you!
Hao
I have finished the calculations of BSE, but the file for macroscropic polarizability is not produced. Could you please tell me how to fix it? Thank you!
Hao
Daniele Varsano wrote: ↑Fri May 29, 2020 11:55 am Dear Hao Zhang,
this happens because the problem it is not solved, as you can see in the r_setup:It seems anyway that the kindex database has not been generated but just read from a previous calculation:Code: Select all
X grid is uniform :no,
You should try to delete the ndb.kindx , run the setup again using the NoDiagSC option and see if your grid is recognized as uniform.Code: Select all
[RD./SAVE//ndb.kindx]
Best,
Daniele
You do not have the required permissions to view the files attached to this post.
Dr. Hao Zhang
Department of Optical Science and Engineering, Fudan University,Shanghai 200433, China
http://homepage.fudan.edu.cn/zhanghao/
Department of Optical Science and Engineering, Fudan University,Shanghai 200433, China
http://homepage.fudan.edu.cn/zhanghao/
- Daniele Varsano
- Posts: 3816
- Joined: Tue Mar 17, 2009 2:23 pm
- Contact:
Re: WWarning: XX grid is not uniform. Gamma point only
Dear Hao Zhang,
the polarizability is printed when reduced dimension systems are detected.
Unfortunately, your cell setup is not recognized as a 2D system, see the report file:
To make yambo recognize the system as 2D you should rotate your unit cell in such a way to have the third dimension orthogonal to the plane where the system lies e.g.:
Two comments:
1. if you are not interested in intensities the o-2D_G0W0_WR.eps_q1_diago_bse output (containing very small numbers see here the reason why it happens) is proportional to the polarizability.
2. Please note that in your BSE calculations you are not including the GW corrections, in order to do that you need to set
to read the previous calculated GW quasiparticle energies, or model them with a scissor correction:
Best,
Daniele
the polarizability is printed when reduced dimension systems are detected.
Unfortunately, your cell setup is not recognized as a 2D system, see the report file:
Code: Select all
[WARNING] Non-periodic geometry and unit cell are incompatible
Code: Select all
CELL_PARAMETERS
a11 a12 0
a21 a22 0
0. 0. a33
1. if you are not interested in intensities the o-2D_G0W0_WR.eps_q1_diago_bse output (containing very small numbers see here the reason why it happens) is proportional to the polarizability.
2. Please note that in your BSE calculations you are not including the GW corrections, in order to do that you need to set
Code: Select all
KfnQPdb= "E < ./2D_G0W0_WR/ndb.QP"
Code: Select all
% KfnQP_E
scissor_value | 1.000000 | 1.000000 | # [EXTQP BSK BSS] E parameters (c/v) eV|adim|adim
%
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/
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/