Dear all,
how I can see the crystal structure of input data and know that xangst coordinate chooses give the geometry considered.
ie, is there a softwear to visualize ABINIT input and output file.
best regards
visualization input and output files
Moderators: MMNSchmitt, gonze
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spamrefuse
- Posts: 35
- Joined: Wed Jan 20, 2010 3:08 am
Re: visualization input and output files
Hi Ham,
I believe there's not much vizualization software that can import Abinit in/output files directly.
My choice for vizualization is VMD (http://www.ks.uiuc.edu/Research/vmd/) which can handle
easily 'home-made' plugins to convert alien formats into its own.
I have written a plugin to read Abinit output files (GEO, DEN) into VMD.
(It can't handle the Abinit input file, because its syntax is far too flexible).
I'm about to share my Abinit plugin with the VMD developers; if you're interested in an
early version, I can share that with you.
Cheers!
I believe there's not much vizualization software that can import Abinit in/output files directly.
My choice for vizualization is VMD (http://www.ks.uiuc.edu/Research/vmd/) which can handle
easily 'home-made' plugins to convert alien formats into its own.
I have written a plugin to read Abinit output files (GEO, DEN) into VMD.
(It can't handle the Abinit input file, because its syntax is far too flexible).
I'm about to share my Abinit plugin with the VMD developers; if you're interested in an
early version, I can share that with you.
Cheers!
Re: visualization input and output files
Dear spamrefuse
Just to clarify my situation, my subject is graphene crystal, and I want to draw
the geometry and have the coordinates for the return xangst parameter in the input file of ABINIT.
Does VDM can do this job and for the output file is that it allows to trace the DOS and
band structure of this material !!
Best regards
Just to clarify my situation, my subject is graphene crystal, and I want to draw
the geometry and have the coordinates for the return xangst parameter in the input file of ABINIT.
Does VDM can do this job and for the output file is that it allows to trace the DOS and
band structure of this material !!
Best regards
-
Alain_Jacques
- Posts: 279
- Joined: Sat Aug 15, 2009 9:34 pm
- Location: Université catholique de Louvain - Belgium
Re: visualization input and output files
Hello Ham,
The most "integrated" visualization software working with Abinit is probably V_Sim - http://inac.cea.fr/sp2m/L_Sim/V_Sim/index.en.html
It is running on *nix and Windows. The most obvious way to try it is to install the distribution package under Ubuntu - it's on the repositories.
Kind regards,
Alain
The most "integrated" visualization software working with Abinit is probably V_Sim - http://inac.cea.fr/sp2m/L_Sim/V_Sim/index.en.html
It is running on *nix and Windows. The most obvious way to try it is to install the distribution package under Ubuntu - it's on the repositories.
Kind regards,
Alain
Re: visualization input and output files
try the ab2xsf script attached, and read it with XCrysDen (remove the .in I had to add to get the forum to upload the script file).
matthieu
matthieu
- Attachments
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ab2xsf.in- (6.72 KiB) Downloaded 1372 times
Matthieu Verstraete
University of Liege, Belgium
University of Liege, Belgium
Re: visualization input and output files
Thank you very much for your reply Mr matthieu
I would like to get your Email adresse for contacting you
best regards.
I would like to get your Email adresse for contacting you
best regards.
Re: visualization input and output files
Dear all:
I used ab2xsf to read abinit input file in the following format:
ab2xsf < file.in > trialabinittoXCrys.xsf;
where file.in is abinit input file.
But trialabinittoXCrys.xsf is empty. Any suggestions? Thank you for your input.
I used ab2xsf to read abinit input file in the following format:
ab2xsf < file.in > trialabinittoXCrys.xsf;
where file.in is abinit input file.
But trialabinittoXCrys.xsf is empty. Any suggestions? Thank you for your input.
Re: visualization input and output files
ab2xsf is a script, and does not read from stdin
ab2xsf filename.out > stuff.xsf
it will not read the input file, only the out or log file from an abinit run.
NB: you can also try a script included in the abinit package in ./scripts/deprecated/abi2xsf
Matthieu
ab2xsf filename.out > stuff.xsf
it will not read the input file, only the out or log file from an abinit run.
NB: you can also try a script included in the abinit package in ./scripts/deprecated/abi2xsf
Matthieu
Matthieu Verstraete
University of Liege, Belgium
University of Liege, Belgium
Re: visualization input and output files
Dear Matthieu:
Thank you very much. I figured out that even "cut3d" can create the .xsf output from DEN file. I also tested the ab2xsf the way you suggested. Structure visualization works either way.
Thank you very much. I figured out that even "cut3d" can create the .xsf output from DEN file. I also tested the ab2xsf the way you suggested. Structure visualization works either way.