merged database not read by yambo
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- Posts: 13
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merged database not read by yambo
Dear developers,
I am trying to calculate the BSE spectra reading the GW corrections from a merged database with Yambo 5.0.
First I calculate the GW corrections for multiple couples of bands and then I merged the database with ypp.
After that I use bse.in reading from the merged database.
However, Yambo is not able to read the database where the corrections are stored. I reproduced the error in hBN and I attach here the input/report/log files.
Thank you for your help and your time.
Best regards.
Riccardo Reho
Utrecht University, Netherlands
I am trying to calculate the BSE spectra reading the GW corrections from a merged database with Yambo 5.0.
First I calculate the GW corrections for multiple couples of bands and then I merged the database with ypp.
After that I use bse.in reading from the merged database.
However, Yambo is not able to read the database where the corrections are stored. I reproduced the error in hBN and I attach here the input/report/log files.
Thank you for your help and your time.
Best regards.
Riccardo Reho
Utrecht University, Netherlands
You do not have the required permissions to view the files attached to this post.
- Daniele Varsano
- Posts: 3838
- Joined: Tue Mar 17, 2009 2:23 pm
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Re: merged database not read by yambo
Dear Riccardo,
the correct syntax to read the database in the use input file is:
there is a missing "<" in your input.
Best,
Daniele
the correct syntax to read the database in the use input file is:
Code: Select all
KfnQPdb= "E < ../gw_merged/gw_merged_morebands/ndb.QP" # [EXTQP BSK BSS] Database action
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/
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- Posts: 13
- Joined: Mon Apr 26, 2021 3:39 pm
Re: merged database not read by yambo
Dear Daniele,
Thank you for your reply. I am sorry but in order to give you a general input file I deleted that character.
This is the original input file that I used for the calculation with the real path. As you can see I used the '<'.
Looking forward to your reply.
Best,
Riccardo
Thank you for your reply. I am sorry but in order to give you a general input file I deleted that character.
This is the original input file that I used for the calculation with the real path. As you can see I used the '<'.
Looking forward to your reply.
Best,
Riccardo
You do not have the required permissions to view the files attached to this post.
- Daniele Varsano
- Posts: 3838
- Joined: Tue Mar 17, 2009 2:23 pm
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Re: merged database not read by yambo
Dear Riccardo,
many thanks for reporting?
indeed there is an I/O problem in reading the database. We need to inspect to understand what went wrong.
1) Please verify that the needed file exists in the indicated directory:
/gpfs/scratch/pr1eme00/pr1eme09/hBN/new/gw_merged/gw_merged_morebands/ndb.QP
2) If so, as I believe, can you post the ndb.QP file?
3) If we cannot spot any particular problem we need to reproduce you error.
Best,
Daniele
many thanks for reporting?
indeed there is an I/O problem in reading the database. We need to inspect to understand what went wrong.
1) Please verify that the needed file exists in the indicated directory:
/gpfs/scratch/pr1eme00/pr1eme09/hBN/new/gw_merged/gw_merged_morebands/ndb.QP
2) If so, as I believe, can you post the ndb.QP file?
3) If we cannot spot any particular problem we need to reproduce you error.
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/
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- Posts: 13
- Joined: Mon Apr 26, 2021 3:39 pm
Re: merged database not read by yambo
Dear Daniele,
This is the ndb.QP database obtained after I merged with ypp. As you can see it is named by default as 'ndb.QP_merged_1_gw_ppa'. I already tried to call it from the bse part both with his original name and after renaming it with ndb.QP. I thought it could have been some small mistake like that.
Thanks
Riccardo
This is the ndb.QP database obtained after I merged with ypp. As you can see it is named by default as 'ndb.QP_merged_1_gw_ppa'. I already tried to call it from the bse part both with his original name and after renaming it with ndb.QP. I thought it could have been some small mistake like that.
Thanks
Riccardo
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- Daniele Varsano
- Posts: 3838
- Joined: Tue Mar 17, 2009 2:23 pm
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Re: merged database not read by yambo
Dear Riccardo,
many thanks, we will inspect it and probably we will need to reproduce the problem.
In the meanwhile, as it seems the calculations are not heavy I suggest you to repeat a calculation including all the QP correction in a single run so that you can avoid to merge databases.
Best,
Daniele
many thanks, we will inspect it and probably we will need to reproduce the problem.
In the meanwhile, as it seems the calculations are not heavy I suggest you to repeat a calculation including all the QP correction in a single run so that you can avoid to merge databases.
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/
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- Posts: 13
- Joined: Mon Apr 26, 2021 3:39 pm
Re: merged database not read by yambo
Dear Daniele,
Thank you for your help. This was a test system. The actual system is a supercell of 42 atoms with a 9x9x1 k-mesh and spin-orbit.
I wanted to report here in the Forum the test system that we used in the school to help with finding the error.
Best,
Riccardo
Thank you for your help. This was a test system. The actual system is a supercell of 42 atoms with a 9x9x1 k-mesh and spin-orbit.
I wanted to report here in the Forum the test system that we used in the school to help with finding the error.
Best,
Riccardo
- Daniele Varsano
- Posts: 3838
- Joined: Tue Mar 17, 2009 2:23 pm
- Contact:
Re: merged database not read by yambo
Dear Riccardo,
ok i see. We will try to reproduce the error and fix it.
Daniele
ok i see. We will try to reproduce the error and fix it.
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/
- Daniele Varsano
- Posts: 3838
- Joined: Tue Mar 17, 2009 2:23 pm
- Contact:
Re: merged database not read by yambo
Dear Riccardo,
unfortunately I was not able to reproduce your error and the database is read correctly, next the code stop as in your input file there an inconsistency between BSENGBlk (4Ha) and NGsBlkXs (4Ry). Anyway the merged database is read correctly, also when using the same database you post.
I used the last GPL release.
Note that the same problem you are experiencing i.e.:
I have also found when I misspelled the name of the file, so the file was not found.
So what I can suggest you is:
* Update to the newest release ( Version 5.0.3)
* be sure your are addressing the correct file, to be 100% sure you can set in the SAVE directory and setting KfnQPdb= "E < ./SAVE/ndb.QP_merged_1_gw_ppa" or in the same directory you are running omitting the SAVE. In any case the name of the file is not an issue.
Best,
Daniele
unfortunately I was not able to reproduce your error and the database is read correctly, next the code stop as in your input file there an inconsistency between BSENGBlk (4Ha) and NGsBlkXs (4Ry). Anyway the merged database is read correctly, also when using the same database you post.
I used the last GPL release.
Note that the same problem you are experiencing i.e.:
Code: Select all
[WARNING]I/O problems in reading QP database
So what I can suggest you is:
* Update to the newest release ( Version 5.0.3)
* be sure your are addressing the correct file, to be 100% sure you can set in the SAVE directory and setting KfnQPdb= "E < ./SAVE/ndb.QP_merged_1_gw_ppa" or in the same directory you are running omitting the SAVE. In any case the name of the file is not an issue.
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/
- Daniele Varsano
- Posts: 3838
- Joined: Tue Mar 17, 2009 2:23 pm
- Contact:
Re: merged database not read by yambo
Dear Riccardo,
it is possible that the length of the string is causing problems:
/gpfs/scratch/pr1eme00/pr1eme09/hBN/new/gw_merged/gw_merged_morebands/ndb.QP
you should try to provide a relative path instead of the absolute path e.g. if you are running in the directory,
/gpfs/scratch/pr1eme00/pr1eme09/hBN/new/
you can assign:
./gw_merged/gw_merged_morebands/ndb.QP
Best,
Daniele
it is possible that the length of the string is causing problems:
/gpfs/scratch/pr1eme00/pr1eme09/hBN/new/gw_merged/gw_merged_morebands/ndb.QP
you should try to provide a relative path instead of the absolute path e.g. if you are running in the directory,
/gpfs/scratch/pr1eme00/pr1eme09/hBN/new/
you can assign:
./gw_merged/gw_merged_morebands/ndb.QP
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/