Error in generating r_setup file

Concerns any physical issues arising during the setup step (-i option). This includes problems with symmetries, k/q-point sets, and so on. For technical problems (running in parallel, etc), refer to the Technical forum.

Moderators: Davide Sangalli, andrea.ferretti, myrta gruning, Daniele Varsano

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Daniele Varsano
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Re: Error in generating r_setup file

Post by Daniele Varsano » Tue Oct 01, 2019 10:19 am

Dear Yang,
I have tried to lower the kinetic energy cut-off in scf calculation. But the total G vector number doesn't vary with the kinetic energy cut-off.
This is a bit strange, it should change by definition. The number of G-vectors is determined by the ecutrho input variable. If you do not have defined, it is set to 4 times the cutoff for the wavenfution (ecutwfc), assuming you are using norm-conserving pseudopotential. In case you are using ultrasoft pseudos, this is an experimental feature in Yambo and it is strongly discouraged.

If you want you can post your nscf input file of QE and we will have look. Actually, I do not know where the problem in reading the ns.db1 database comes from, maybe someone more expert than me in netcdf library can help you on this issue. In any case a calculation with 20M G-vector I would say that it is unfeasable.
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/

andrea.ferretti
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Re: Error in generating r_setup file

Post by andrea.ferretti » Tue Oct 01, 2019 10:44 am

Dear Yang,

the ratio of charge density and wfc plane waves (defined by ecutrho and ecutwfc, respectively) is far from ~8, which should be
the expected value when ecutrho=4*ecutwfc (as is mathematically defined for norm-conserving pseudopot).
The numbers you obtain are quite suspicious.
Are you setting ecutrho independently ?
Can you post your scf/nscf input ? (without this I think we won't be able to help much further).

take care
Andrea
Andrea Ferretti, PhD
CNR-NANO-S3 and MaX Centre
via Campi 213/A, 41125, Modena, Italy
Tel: +39 059 2055322; Skype: andrea_ferretti
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Davide Sangalli
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Re: Error in generating r_setup file

Post by Davide Sangalli » Tue Oct 01, 2019 5:17 pm

Can you post the output of

Code: Select all

ncdump -v DIMENSIONS SAVE/ns.db1
Best,
D.
Davide Sangalli, PhD
CNR-ISM, Division of Ultrafast Processes in Materials (FLASHit) and MaX Centre
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el16yz
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Re: Error in generating r_setup file

Post by el16yz » Wed Oct 02, 2019 1:04 pm

Dear Andrea and Daniele,

Yes, you are right. I set ecutrho independently and didn't reset it when I changed kinetic energy cut-off before. That is why the G-vector keep unchanging. The problem is solved now. The number of G vector decreases to 4885279 after I change ecutrho. And Yambo can work now. Thank you very much. It is really helpful.

Best,
Yang
Yang Zhou
PhD student
University of Leeds
United Kingdom

pyadav
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Re: Error in generating r_setup file

Post by pyadav » Thu Jul 29, 2021 8:35 am

Dear Team Yambo,

I'm facing the following issue when I'm trying to generate the SAVE file using p2y command.
The error comes out as

Code: Select all

[ERROR] Writing File ./SAVE//ns.db1; Variable  NOT DEFINED; Permission denied
.

Help needed.

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: Error in generating r_setup file

Post by Daniele Varsano » Thu Jul 29, 2021 8:48 am

Dear Pushpendra,

do you have the right permission to write files in the directory you are running?
If you can write files, then please provide more details (yambo release / log file before the error etc / any other info can help to post the problem).

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: Error in generating r_setup file

Post by pyadav » Thu Jul 29, 2021 11:52 am

Dear Daniele,

Yes, I have permission to write files in the same directory ( for example the quantum espresso calculation is running smoothly in the same directory).
I'm using the Yambo 5.0.0 (yambo master).

Also, when I'm running yambo with the already created 'SAVE' database it is showing the following error-

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Reading File ./SAVE//ns.db1; Variable  NOT DEFINED; NetCDF: HDF error
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: Error in generating r_setup file

Post by Daniele Varsano » Thu Jul 29, 2021 12:42 pm

Dear Pushendra,
it seems there are some problems with compilation/lining of the netcdf libraries.
Can you post your config.log 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/

pyadav
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Re: Error in generating r_setup file

Post by pyadav » Thu Aug 05, 2021 11:55 am

Dear Daniele,

Sorry for the late reply.
We have checked that there are no permission problems in the concerned folder.
Apparently, it is encountering some "undefined variable" during the p2y writing phase.

I'm attaching here the config.log file of the installation.
config.log

Thank you,
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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