a2y conversion

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

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a2y conversion

Postby zchen » Thu Oct 06, 2011 7:13 pm

Hi all:
I have problem to use a2y to read the KSS file created by abinit-5.8.4. I have problem to do conversion for abinit-6.0.4 so I think abinit may change the format . This time I used abinit-5.8.4. I used a2y in yambo-3.2.4-r.855.
The error message is:

a2y -F ../tgwo_DS2_KSS

__ __ ______ ____ _____
/\ \ /\ \\ _ \ /"\_/`\/\ _`\ /\ __`\
\ `\`\\/"/ \ \L\ \/\ \ \ \L\ \ \ \/\ \
`\ `\ /" \ \ __ \ \ \__\ \ \ _ <" \ \ \ \
`\ \ \ \ \ \/\ \ \ \_/\ \ \ \L\ \ \ \_\ \
\ \_\ \ \_\ \_\ \_\\ \_\ \____/\ \_____\
\/_/ \/_/\/_/\/_/ \/_/\/___/ \/_____/

<---> [01] A(binit) 2 Y(ambo)
<---> Checking input file ...../tgwo_DS2_KSS
<---> DBs path set to :.
<---> KSS Header...PGFIO/stdio: Invalid argument
PGFIO-F-/BACKSPACE/unit=11/error code returned by host stdio - 22.
File name = ../tgwo_DS2_KSS unformatted, sequential access record = 1
In source file hdr_io.f90, at line number 143

I really do not understand what is wrong.

Thanks

Zhifan Chen
Clark Atlanta University
USA
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Re: a2y conversion

Postby andrea marini » Thu Oct 06, 2011 8:13 pm

It sounds strange. Can you attach a tar file with ALL the files needed to run abinit and reproduce the error ? If you could include in the archive the output/log files of your run it would be useful.

Andrea
Andrea MARINI
Istituto di Struttura della Materia, CNR, (Italy)
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Re: a2y conversion

Postby zchen » Fri Oct 07, 2011 2:04 pm

Andrea:
Thank you very much. I will send you an e-mail attached with a tar file which icludes tgw.in (input file), tgw.files, tgw.out (output), log, 06-C-GGA.fhi (pseudopotential). You can directly run on abinit-5.8.4. In this reply I only include the input file. Cell is a trilevel graphene.

iprcel 45
ndtset 2

# acell below in bohr from outmol
acell
4.67404859755914 4.67404859755914 28.79923717228981

rprim 1.0 0.0 0.0
-0.5 0.8660254037844 0.0
0.0 0. 1.

ntypat 1 # There are 1 types of atom
znucl 6 # The keyword refers to the atomic number
natom 6
typat 6*1

## xangst in unit A from car file
xangst
0.000000000 0.000000000 7.353404149
0.000000000 0.000000000 4.126355324
0.000000000 1.428018156 7.350203770
0.000000000 1.428018156 10.626782270
1.236700000 0.714009078 10.624801083
1.236700000 0.714009078 4.128488910
ecut 26.0 # kinetic energy cut-off, in Hartree, should use 12 , PRB paper
enunit 1
# define k points
kptopt 1
ngkpt 6 6 1
nsym 0
symmorphi 0 # 0 not symmetry not allowed, 1 allowed
nsppol 2
# SCF procedure
prtden1 1
nstep1 150
toldfe1 1.0d-6 # Will stop when, twice in a row, the difference
# between two consecutive evaluations of total energy
# differ by less than toldfe (in Hartree)
diemac 5.0 # Although this is not mandatory, it is worth to
# precondition the SCF cycle. The model dielectric
# function used as the standard preconditioner
# is described in the "dielng" input variable section.
# Here, we follow the prescription for bulk diamond.
diemix 0.5
mkmem 0
mffmem 0
prtvol 2
# DATA set 2. for KSS
iscf2 -2 # non self-consistency, read previous density file
nband2 25
getden2 -1
tolwfr2 1.0d-7 # it is not important as later there is a diago
nstep2 100
npwkss2 0 # planewave of kohn-sham state to build Hamiltonian
nbandkss2 25
kssform2 3
istwfk2 *1


Zhifan Chen
Clark Atlanta University
USA
zchen
 
Posts: 41
Joined: Thu Apr 01, 2010 2:23 pm

Re: a2y conversion

Postby andrea marini » Fri Oct 07, 2011 2:09 pm

zchen wrote:I will send you an e-mail attached with a tar file which icludes tgw.in (input file), tgw.files, tgw.out (output), log, 06-C-GGA.fhi (pseudopotential).
Zhifan Chen
Clark Atlanta University
USA


No e-mail, please. Upload the tar file on the board. Thanks

Andrea
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Re: a2y conversion

Postby zchen » Fri Oct 07, 2011 2:50 pm

Andrea:
I cannot find the way to attach my tar file.


Zhifan Chen
Clark Atlanta University
USA
zchen
 
Posts: 41
Joined: Thu Apr 01, 2010 2:23 pm

Re: a2y conversion

Postby andrea marini » Fri Oct 07, 2011 3:08 pm

zchen wrote:Andrea:
I cannot find the way to attach my tar file.


In the screen where you compose your message there is (below the text window) an "upload attachment" button. Press it and upload the file. If the tar format is not correcly recognized change the extension in .txt.

Hope it help

Andrea
Andrea MARINI
Istituto di Struttura della Materia, CNR, (Italy)
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Re: a2y conversion

Postby zchen » Fri Oct 07, 2011 4:22 pm

Hi all:
Attached is the tar file which include a input file, files file, out put file and the ppseudopotential file. These files allow you to run on abinit. However, after running abinit I cannot do the conversion to yambo using a2y.



Zhifan Chen
Clark Atlanta University
USA
chen3.tar
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Re: a2y conversion

Postby myrta gruning » Mon Oct 10, 2011 9:32 pm

Hallo Zhifan Chen

I think that the problem is that your calculation is spin polarized that is currantly not supported by Yambo.

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

http://www.researcherid.com/rid/B-1515-2009
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Re: a2y conversion

Postby zchen » Tue Oct 11, 2011 6:16 pm

Dr. Gruning:
Thanks. However, after removing the spin the results are the same. May be ABINIT changed output format starting some version. But I do not know


Zhifan chen
Clark Atlanta University
USA
zchen
 
Posts: 41
Joined: Thu Apr 01, 2010 2:23 pm

Re: a2y conversion

Postby myrta gruning » Wed Oct 12, 2011 12:20 pm

Hallo Zhifan Chen

For my production runs I am using the 6.4.2 version and I did not meet any problem with conversion.

However with that version I could not run your input getting problem with not symmetric grid.

I was able to run it with abinit 5.3.4 but only I deleted istwfk2 *1 or changed it to istwfk2 12*1
then I have no problem with conversion with a2y.

So please check your abinit input.

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

http://www.researcherid.com/rid/B-1515-2009
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