Yambo Community Forum

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

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

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

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:

Code: Select all

NoDiagSC

in your setup input file.

Or, if you want by adding verbosity when bulding-up the input file:

Code: Select all

yambo -i -V all

and remove the comment to the NoDiagSC variable.

Best,
Daniele

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

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:

Code: Select all

 X grid is uniform     :no, 

It seems anyway that the kindex database has not been generated but just read from a previous calculation:

Code: Select all

[RD./SAVE//ndb.kindx]

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

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

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:

Code: Select all

 X grid is uniform     :no, 

It seems anyway that the kindex database has not been generated but just read from a previous calculation:

Code: Select all

[RD./SAVE//ndb.kindx]

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

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