inizialization and databases

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.

Moderator: Daniele Varsano

inizialization and databases

Postby samazadi » Thu May 12, 2011 4:06 pm

Dear Developers

I try to use 'yambo -g n' command to create yambo.in file for GW calculations, but some problem happens, because
the yambo.in file is:

# __ __ ________ ___ __ __ _______ ______
# /_/\/_/\ /_______/\ /__//_//_/\ /_______/\ /_____/\
# \ \ \ \ \\::: _ \ \\::\| \| \ \\::: _ \ \\:::_ \ \
# \:\_\ \ \\::(_) \ \\:. \ \\::(_) \/_\:\ \ \ \
# \::::_\/ \:: __ \ \\:.\-/\ \ \\:: _ \ \\:\ \ \ \
# \::\ \ \:.\ \ \ \\. \ \ \ \\::(_) \ \\:\_\ \ \
# \__\/ \__\/\__\/ \__\/ \__\/ \_______\/ \_____\/
#
# GPL Version 3.2.3 Revision 676
# http://www.yambo-code.org
#
setup # [R INI] Initialization


and nothing more !!
would you help me to overcome this problem ?
Thanks in advance.

Cheers
Sam
********************************************
Sam Azadi
Institute of Physical Chemistry and
Center for Computational Sciences
Johannes Gutenberg University Mainz
Staudinger Weg 9
D-55128 Mainz
Germany
azadi@uni-mainz.de
+49/(0)6131/39-26844
*******************************************
Sam Azadi
Institute of Physical Chemistry and
Center for Computational Sciences
Johannes Gutenberg University Mainz
Staudinger Weg 9
D-55128 Mainz
Germany
azadi@uni-mainz.de
+49/(0)6131/39-26844
samazadi
 
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Location: Mainz, Germany

Re: Linking problem

Postby Daniele Varsano » Thu May 12, 2011 5:22 pm

Dear Sam,

did you run the setup first?
Please check if you have the setup databases (db.gopes, db.kinx, etc) in the SAVE directory.
Next if you want to perform a GW calculation, you need also to calculate the screened potential,
so build the input as
yambo -p p -g n
for instance, in the case you want to use the plasmon-pole approximation.


Cheers,

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/
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Re: Linking problem

Postby samazadi » Fri May 20, 2011 1:37 pm

Dear Daniele

p2y generates SAVE directory, *.db1 and *.wf but in the setup run (yambo without any input) I get this error:

yambo: cannot access CORE database (SAVE/*db1 and/or SAVE/*wf)

could you help me to solve this problem ?
I attached config.log file.

Bests
Sam
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*******************************************
Sam Azadi
Institute of Physical Chemistry and
Center for Computational Sciences
Johannes Gutenberg University Mainz
Staudinger Weg 9
D-55128 Mainz
Germany
azadi@uni-mainz.de
+49/(0)6131/39-26844
samazadi
 
Posts: 21
Joined: Fri Apr 15, 2011 11:24 am
Location: Mainz, Germany

Re: Linking problem

Postby Daniele Varsano » Fri May 20, 2011 3:08 pm

Dear Sam,
have you checked in the forum if you can find the answer to your problem?
For instance, please have a look to this posts.

Cheers,

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/
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Re: inizialization and databases

Postby samazadi » Fri May 20, 2011 8:00 pm

Dear Daniele

I have "/usr/local/lib/libnetcdf.a" and "/usr/local/include/netcdf.h"
but when I do:

./configure --with-iotk="/home/sam/espresso-4.2.1/iotk" --with-p2y=4.0 --with-netcdf-lib="/usr/local/lib/" --with-netcdf-include="/usr/local/include/"

yambo doesn't link to them:

checking for NetCDF in /usr/local/lib/... no
# [ ] NETCDF/Large Files

also I found this error in config.log file:
**************************
use netcdf
1
Fatal Error: Can't open module file 'netcdf.mod' for reading at (1): No such file or directory
configure:13006: $? = 1
configure: failed program was:
| program main
| use netcdf
| end
configure:12999: mpif90 -c -M/usr/local/include/ -O3 -mtune=native conftest.f90 >&5
Warning: Using -M <directory> is deprecated, use -J instead
conftest.f90:2.10:
*******************************
Thanks for your help.

Ciao,
Sam
*******************************************
Sam Azadi
Institute of Physical Chemistry and
Center for Computational Sciences
Johannes Gutenberg University Mainz
Staudinger Weg 9
D-55128 Mainz
Germany
azadi@uni-mainz.de
+49/(0)6131/39-26844
samazadi
 
Posts: 21
Joined: Fri Apr 15, 2011 11:24 am
Location: Mainz, Germany

Re: inizialization and databases

Postby claudio » Mon May 23, 2011 4:43 pm

Dear Sam

please try the new version of Yambo, version 3.2.4:

http://www.yambo-code.org/download.php

we improved the configuration script to link the netcdf.

let us know
Claudio
Claudio Attaccalite
Institut Neel, CNRS/UJF ABINEEL group
25 rue des Martyrs BP 166, Bâtiment D
38042 Grenoble cedex 9 France
web site: http://www.attaccalite.com
Freely download scientific books from: http://www.freescience.info
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Re: inizialization and databases

Postby samazadi » Tue May 24, 2011 10:56 am

Dear Claudio

I tried the new version, but still there is same problem.
I attached config.log file.
Thanks for your help.

Ciao
Sam
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*******************************************
Sam Azadi
Institute of Physical Chemistry and
Center for Computational Sciences
Johannes Gutenberg University Mainz
Staudinger Weg 9
D-55128 Mainz
Germany
azadi@uni-mainz.de
+49/(0)6131/39-26844
samazadi
 
Posts: 21
Joined: Fri Apr 15, 2011 11:24 am
Location: Mainz, Germany

Re: inizialization and databases

Postby claudio » Tue May 24, 2011 11:17 am

Dear Sam

the problem is that you do not have the file "netcdf.mod" that is the one requires by Yambo

if you have ubuntu just install libnetcdf-dev

otherwise download netcdf and compiler with fortran support

cla
Claudio Attaccalite
Institut Neel, CNRS/UJF ABINEEL group
25 rue des Martyrs BP 166, Bâtiment D
38042 Grenoble cedex 9 France
web site: http://www.attaccalite.com
Freely download scientific books from: http://www.freescience.info
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Re: inizialization and databases

Postby samazadi » Tue May 24, 2011 3:30 pm

Dear Claudio

I installed libnetcdf-dev, there is no more problem in configure
but there is an error in making (more precisely at Linking yambo ).
I attached error. I really appreciate your help.

Ciao
Sam
*******************************************
Sam Azadi
Institute of Physical Chemistry and
Center for Computational Sciences
Johannes Gutenberg University Mainz
Staudinger Weg 9
D-55128 Mainz
Germany
azadi@uni-mainz.de
+49/(0)6131/39-26844
samazadi
 
Posts: 21
Joined: Fri Apr 15, 2011 11:24 am
Location: Mainz, Germany

Re: inizialization and databases

Postby samazadi » Tue May 24, 2011 3:32 pm

error file of previous email.
Sam
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*******************************************
Sam Azadi
Institute of Physical Chemistry and
Center for Computational Sciences
Johannes Gutenberg University Mainz
Staudinger Weg 9
D-55128 Mainz
Germany
azadi@uni-mainz.de
+49/(0)6131/39-26844
samazadi
 
Posts: 21
Joined: Fri Apr 15, 2011 11:24 am
Location: Mainz, Germany

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