problem in Abinit 2 Aymbo conversion

Forum for discussing issues arising with interfacing the Abinit code (KSS) file with Yambo.

Moderator: Conor Hogan

problem in Abinit 2 Aymbo conversion

Postby devsharma » Thu Nov 05, 2009 10:46 am

hi 2 all,
I tried to convert the KSS file into the yambo inputs but got the following error.
<---> [01] A(binit) 2 Y(ambo)
<---> Checking input file ...yvo_o_DS2_KSS
<---> DBs path set to :.
<---> KSS Header...At line 245 of file hdr_io.f90 (unit = 11, file = 'yvo_o_DS2_KSS')
Fortran runtime error: I/O past end of record on unformatted file
[sushil@localhost Abinit]$

i run the command
.../a2y -F yvo_o_DS2_KSS

My input files is listed below

# Data common to the three different datasets

acell 13.451637 13.451637 11.885054
rprim
1.000000 0.000000 0.000000
0.000000 1.000000 0.000000
0.000000 0.000000 1.000000

#Definition of the atom types
# 24 kind of atoms
# ['O', 'V', 'Y']
ntypat 3
znucl 8 23 39
chkprim 0
#Definition of tha atoms
natom 24
typat 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 2 3 3 3 3
xred
0.0 0.4342 0.2008
0.5 0.9342 0.7008
0.5 0.5658 0.7008
0.0 0.0658 0.2008
0.8158 0.75 0.4508
0.6842 0.25 0.9508
0.5 0.4342 0.2992
0.0 0.9342 0.7992
0.0 0.5658 0.7992
0.5 0.0658 0.2992
0.6842 0.75 0.0492
0.8158 0.25 0.5492
0.1842 0.25 0.5492
0.3158 0.75 0.0492
0.3158 0.25 0.9508
0.1842 0.75 0.4508
0.0 0.25 0.375
0.5 0.75 0.875
0.0 0.75 0.625
0.5 0.25 0.125
0.0 0.75 0.125
0.5 0.25 0.625
0.5 0.75 0.375
0.0 0.25 0.875

diemac 12.0 # Although this is not mandatory, it is worth to

# Definition of the plane-wave basis set
ecut 10.0 # Kinetic energy cut-off, in Hartree

# Definition of the SCF procedure
nstep 500 # Maximum number of SCF cycles

# Step 1: determine the ground state
iscf1 3 # Algorithm: Anderson mixing of the potential
nband1 150 # Number of bands
tolwfr1 1.0d-16 # Tolerance on wavefunctions to stop SCF cycles
kptopt1 1 # Automatic generation of k-points
ngkpt1 4 4 4 # Number of grid points for k-point generation
prtden1 1 # Store electronic density in a file

# Step 2: obtain the Kohn-Sham band structure
getden2 1 # Read electronic density from step 1
iscf2 -2 # Non self-consistent calculation
tolwfr2 1.0d-16 # Tolerance on wavefunctions
nband2 150 # Number of bands for the system
nbandkss2 150 # Number of bands to output to the KSS file
kssform2 3 # Format of the KSS file
kptopt2 1 # Automatic generation of k-points
ngkpt2 4 4 4 # Number of grid points for k-point generation
symmorphi2 1 # Disallow non-symmorphic operations (required)
istwfk2 10*1 # Wavefunction storage mode for each k-point


thanks in advance
dev
Dev Sharma,
Junior Research Fellow
Department of Physics & Astrophysics,
University of Delhi,
India
devsharma
 
Posts: 28
Joined: Wed Oct 14, 2009 5:43 pm

Re: problem in Abinit 2 Aymbo conversion

Postby andrea marini » Thu Nov 05, 2009 10:53 am

devsharma wrote:I tried to convert the KSS file into the yambo inputs but got the following error.
<---> [01] A(binit) 2 Y(ambo)
<---> Checking input file ...yvo_o_DS2_KSS
<---> DBs path set to :.
<---> KSS Header...At line 245 of file hdr_io.f90 (unit = 11, file = 'yvo_o_DS2_KSS')
Fortran runtime error: I/O past end of record on unformatted file
[sushil@localhost Abinit]$


What version af abinit are you using ? Not all the most recent version are still implemented in a2y.

Cheers
Andrea MARINI
Istituto di Struttura della Materia, CNR, (Italy)
User avatar
andrea marini
 
Posts: 447
Joined: Mon Mar 16, 2009 4:27 pm

Re: problem in Abinit 2 Aymbo conversion

Postby devsharma » Thu Nov 05, 2009 12:00 pm

hi,
i am using Abinit 5.7.4.
Thanks
Dev Sharma,
Junior Research Fellow
Department of Physics & Astrophysics,
University of Delhi,
India
devsharma
 
Posts: 28
Joined: Wed Oct 14, 2009 5:43 pm

Re: problem in Abinit 2 Aymbo conversion

Postby andrea marini » Thu Nov 05, 2009 12:11 pm

devsharma wrote:hi,
i am using Abinit 5.7.4.
Thanks


I just checked that a2y works with abinit 5.7.3 and 5.8.0. Please post the input, pseudos and output/log of the abinit run. Maybe there is something wrong in the ground-state run.

Cheers
Andrea MARINI
Istituto di Struttura della Materia, CNR, (Italy)
User avatar
andrea marini
 
Posts: 447
Joined: Mon Mar 16, 2009 4:27 pm

Re: problem in Abinit 2 Aymbo conversion

Postby devsharma » Thu Nov 05, 2009 3:14 pm

hi sir,
I tried to attach the files , using upload attachment --> browse(setting the path)--> add the files
but on the top a mssg is coming in red colour.
The extension is not allowed even i am not giving any extension.
Please tell me . how to attach the files on the forum.And sir, log files is 12.1 MB. Is it possible to attach such a large file on forum ???
Thanks,
Well, till the time being, I am sending you the inputs/outputs files on ur email id ,
Please have a look .
Thanks
With regards
DEV
Dev Sharma,
Junior Research Fellow
Department of Physics & Astrophysics,
University of Delhi,
India
devsharma
 
Posts: 28
Joined: Wed Oct 14, 2009 5:43 pm

Re: problem in Abinit 2 Aymbo conversion

Postby andrea marini » Thu Nov 05, 2009 3:18 pm

devsharma wrote:I tried to attach the files , using upload attachment --> browse(setting the path)--> add the files
but on the top a mssg is coming in red colour.
The extension is not allowed even i am not giving any extension.
Please tell me . how to attach the files on the forum.And sir, log files is 12.1 MB. Is it possible to attach such a large file on forum ???


Try creating a tar.gz file. It is an accepted format and the size is strongly reduced.

devsharma wrote:Thanks,
Well, till the time being, I am sending you the inputs/outputs files on ur email id ,


Please use the forum as all of us can try to help you.

Cheers
Andrea MARINI
Istituto di Struttura della Materia, CNR, (Italy)
User avatar
andrea marini
 
Posts: 447
Joined: Mon Mar 16, 2009 4:27 pm

Re: problem in Abinit 2 Aymbo conversion

Postby Conor Hogan » Thu Nov 05, 2009 3:26 pm

Dev,
The Abinit output log file can be huge. You can probably also cut out the thousands of lines of GS convergence info as well...but make sure to post everything regarding the KSS file.
Conor
Dr. Conor Hogan
CNR-ISM, via Fosso del Cavaliere, 00133 Roma, Italy;
Department of Physics and European Theoretical Spectroscopy Facility (ETSF),
University of Rome "Tor Vergata".
User avatar
Conor Hogan
 
Posts: 143
Joined: Tue Mar 17, 2009 12:17 pm

Re: problem in Abinit 2 Aymbo conversion

Postby devsharma » Fri Nov 06, 2009 9:23 am

hi sir,
i have attached the Input file, Pseudo potentials, Output files and log file.
Please have a look and help.
Thanks a lot
take care
You do not have the required permissions to view the files attached to this post.
Dev Sharma,
Junior Research Fellow
Department of Physics & Astrophysics,
University of Delhi,
India
devsharma
 
Posts: 28
Joined: Wed Oct 14, 2009 5:43 pm

Re: problem in Abinit 2 Aymbo conversion

Postby myrta gruning » Sat Nov 07, 2009 2:43 pm

Dear Dev,

The input, output and log you sent seems OK. I generated the KSS file from your input and converted with a2y without any problem. I tested with 5.6.4 and 5.8.3 (I do not have the specific version you are using). I reduced some of the parameters (see below) to make the test quicker, but since the failure you met is in the header, it should not have any influence. Furthermore I have converted very large KSS files without such problem.

I have some comments/suggestions regarding your abinit input.
1. You are using GGAs. Note that Yambo support only LDA , so if you want to be consistent, you should use LDA for the pseudo and the DFT calculation. This has not influence on the conversion of the KSS, since yambo will give a warning and switch to LDA, anyway. Only this inconsistency may introduce an error in your calculations.
2. In the self consistent calculations (first dataset) you are asking for 150 bands (nband1) with a very strict criterion on the convergence of the wavefunctions (tolwfr1) . This is making your calculation lengthier and heavier than needed. In the self consistent abinit run the main quantity is the ground state electron density obtained by minimizing the total energy. So in the scf run I would suggest not to specify the number of bands (nband1) (abinit will choose the bands that are needed for this run, that are usually OK for systems with a finite gap) and to change the criteria for convergence to toldfe1 (<=1.d-8 is usually fine). Read the abinit documentation for more details.

Coming back to your problem I would suggest
1. to check if the KSS was not fully written for some reason. From your log it should be about 58 Mb, check this is the case.
2. since the run does not take very long try again to generate the KSS file. Run abinit again and see if you met the same problem with the new KSS file (just for a test you can reduce some parameters). If possible double-check with another abinit version.
I don't know if others may have more suggestions. Well if this fails, we should look at more "exotic" things...

Regards,

Myrta
Dr Myrta Grüning
Atomistic Simulation Centre
Queen's University Belfast - Northern Ireland

http://www.researcherid.com/rid/B-1515-2009
User avatar
myrta gruning
 
Posts: 303
Joined: Tue Mar 17, 2009 11:38 am

Re: problem in Abinit 2 Aymbo conversion

Postby devsharma » Sat Nov 07, 2009 5:18 pm

Dear myrta gruning,
Thanks a lot for your suggestions. I will follow your instructions, and if some problem occur, will be back to all of you.
:D
thanks
take care
dev
Dev Sharma,
Junior Research Fellow
Department of Physics & Astrophysics,
University of Delhi,
India
devsharma
 
Posts: 28
Joined: Wed Oct 14, 2009 5:43 pm

Next

Return to Abinit

Who is online

Users browsing this forum: No registered users and 1 guest