[gpaw-users] Plot pseudo charge density

Thu Nov 6 14:34:28 CET 2014

Hi,

alternatively, I like to save the charge density as a cube file and then use VESTA for the isosurfaces.

Best Robert
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From: gpaw-users-request at listserv.fysik.dtu.dk [gpaw-users-request at listserv.fysik.dtu.dk]
Sent: 06 November 2014 13:00
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Subject: gpaw-users Digest, Vol 58, Issue 9

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Today's Topics:

   1. Plot pseudo charge density (Niels Bendtsen Halck)
   2. Re: Plot pseudo charge density (Jens J?rgen Mortensen)
   3. Re: Plot pseudo charge density (Rizwan Ahmed)
   4. Re: Plot pseudo charge density (Niels Bendtsen Halck)

----------------------------------------------------------------------

Message: 1
Date: Wed, 5 Nov 2014 12:00:04 +0000
From: Niels Bendtsen Halck <ntben at fysik.dtu.dk>
To: "gpaw-users at listserv.fysik.dtu.dk"
        <gpaw-users at listserv.fysik.dtu.dk>
Subject: [gpaw-users] Plot pseudo charge density
Message-ID:
        <A585DCD3BFF38E4082C1869A63357377858E2E at ait-pex02mbx04.win.dtu.dk>
Content-Type: text/plain; charset="us-ascii"

Hi

I am interested in plotting some isosurfaces with the pseudo charge density.

However most of the solutions that I have found fails for non cubic cells such as the trick at the summer school:
https://wiki.fysik.dtu.dk/gpaw/exercises/faeq.html#making-x-y-plots

Also I have tried VMD which does not generate very nice isosurfaces for some reason and then J-mol. J-mol seems fine but I am unsure if I can get publishable quality images.

I would really like to use Mayavi for it. Do any of you have a script that can do charge density isosurfaces on non-cubic cells?

Sincerely
Niels Bendtsen Halck
Ph.d.-studerende
FYS-CAMD
DTU Fysik
Bygning 307
2800 Kgs. Lyngby
Direkte telefon 45253177
ntben at fysik.dtu.dk
www.fysik.dtu.dk

------------------------------

Message: 2
Date: Wed, 5 Nov 2014 13:20:31 +0100
From: Jens J?rgen Mortensen <jensj at fysik.dtu.dk>
To: Niels Bendtsen Halck <ntben at fysik.dtu.dk>,
        "gpaw-users at listserv.fysik.dtu.dk" <gpaw-users at listserv.fysik.dtu.dk>
Subject: Re: [gpaw-users] Plot pseudo charge density
Message-ID: <545A160F.6060905 at fysik.dtu.dk>
Content-Type: text/plain; charset="windows-1252"; format=flowed

Den 05-11-2014 kl. 13:00 skrev Niels Bendtsen Halck:
> Hi
>
> I am interested in plotting some isosurfaces with the pseudo charge density.
>
> However most of the solutions that I have found fails for non cubic cells such as the trick at the summer school:
> https://wiki.fysik.dtu.dk/gpaw/exercises/faeq.html#making-x-y-plots

The latest development version of ASE should be able to do that:

     $ python -m ase.visualize.mlab -C gpaw abc.gpw

https://wiki.fysik.dtu.dk/ase/ase/visualize/visualize.html#mayavi

Jens J?rgen

>
> Also I have tried VMD which does not generate very nice isosurfaces for some reason and then J-mol. J-mol seems fine but I am unsure if I can get publishable quality images.
>
> I would really like to use Mayavi for it. Do any of you have a script that can do charge density isosurfaces on non-cubic cells?
>
> Sincerely
> Niels Bendtsen Halck
> Ph.d.-studerende
> FYS-CAMD
> DTU Fysik
> Bygning 307
> 2800 Kgs. Lyngby
> Direkte telefon 45253177
> ntben at fysik.dtu.dk
> www.fysik.dtu.dk
> _______________________________________________
> gpaw-users mailing list
> gpaw-users at listserv.fysik.dtu.dk
> https://listserv.fysik.dtu.dk/mailman/listinfo/gpaw-users

------------------------------

Message: 3
Date: Wed, 5 Nov 2014 12:24:36 +0000
From: Rizwan Ahmed <riah at fysik.dtu.dk>
To: Niels Bendtsen Halck <ntben at fysik.dtu.dk>,
        "gpaw-users at listserv.fysik.dtu.dk" <gpaw-users at listserv.fysik.dtu.dk>
Subject: Re: [gpaw-users] Plot pseudo charge density
Message-ID:
        <56DC058B34F1B3478505BEF2EF08E42E8C858A at ait-pex02mbx04.win.dtu.dk>
Content-Type: text/plain; charset="us-ascii"

Hi Niels,

I remember I used VMD once but it did not generate nice isosurfaces as you mentioned.

I was interested in plotting planner xy-average potential along z. So, I generated cube files and wrote a script to do planner xy-avg along z and then plot. if you interested in it, I can send it to you,

BR,

Rizwan
________________________________________
From: gpaw-users-bounces at listserv.fysik.dtu.dk [gpaw-users-bounces at listserv.fysik.dtu.dk] on behalf of Niels Bendtsen Halck [ntben at fysik.dtu.dk]
Sent: Wednesday, November 05, 2014 1:00 PM
To: gpaw-users at listserv.fysik.dtu.dk
Subject: [gpaw-users] Plot pseudo charge density

Hi

I am interested in plotting some isosurfaces with the pseudo charge density.

However most of the solutions that I have found fails for non cubic cells such as the trick at the summer school:
https://wiki.fysik.dtu.dk/gpaw/exercises/faeq.html#making-x-y-plots

Also I have tried VMD which does not generate very nice isosurfaces for some reason and then J-mol. J-mol seems fine but I am unsure if I can get publishable quality images.

I would really like to use Mayavi for it. Do any of you have a script that can do charge density isosurfaces on non-cubic cells?

Sincerely
Niels Bendtsen Halck
Ph.d.-studerende
FYS-CAMD
DTU Fysik
Bygning 307
2800 Kgs. Lyngby
Direkte telefon 45253177
ntben at fysik.dtu.dk
www.fysik.dtu.dk
_______________________________________________
gpaw-users mailing list
gpaw-users at listserv.fysik.dtu.dk
https://listserv.fysik.dtu.dk/mailman/listinfo/gpaw-users

------------------------------

Message: 4
Date: Wed, 5 Nov 2014 12:38:54 +0000
From: Niels Bendtsen Halck <ntben at fysik.dtu.dk>
To: Jens J?rgen Mortensen <jensj at fysik.dtu.dk>,
        "gpaw-users at listserv.fysik.dtu.dk" <gpaw-users at listserv.fysik.dtu.dk>
Subject: Re: [gpaw-users] Plot pseudo charge density
Message-ID:
        <A585DCD3BFF38E4082C1869A6335737785AE5D at ait-pex02mbx04.win.dtu.dk>
Content-Type: text/plain; charset="iso-8859-1"

Is the latest development version more recent than the used at the Summer School?

Because this is just what I did and it failed stating something like

Generic Warning: In /builddir/build/BUILD/VTK/Graphics/vtkGridSynchronizedTemplates3D.cxx, line 280
Cannot compute gradient of grid

Sincerely
Niels Bendtsen Halck
Ph.d.-studerende
FYS-CAMD
DTU Fysik
Bygning 307
2800 Kgs. Lyngby
Direkte telefon 45253177
ntben at fysik.dtu.dk
www.fysik.dtu.dk
________________________________________
Fra: Jens J?rgen Mortensen
Sendt: 5. november 2014 13:20
Til: Niels Bendtsen Halck; gpaw-users at listserv.fysik.dtu.dk
Emne: Re: [gpaw-users] Plot pseudo charge density

Den 05-11-2014 kl. 13:00 skrev Niels Bendtsen Halck:
> Hi
>
> I am interested in plotting some isosurfaces with the pseudo charge density.
>
> However most of the solutions that I have found fails for non cubic cells such as the trick at the summer school:
> https://wiki.fysik.dtu.dk/gpaw/exercises/faeq.html#making-x-y-plots

The latest development version of ASE should be able to do that:

     $ python -m ase.visualize.mlab -C gpaw abc.gpw

https://wiki.fysik.dtu.dk/ase/ase/visualize/visualize.html#mayavi

Jens J?rgen

>
> Also I have tried VMD which does not generate very nice isosurfaces for some reason and then J-mol. J-mol seems fine but I am unsure if I can get publishable quality images.
>
> I would really like to use Mayavi for it. Do any of you have a script that can do charge density isosurfaces on non-cubic cells?
>
> Sincerely
> Niels Bendtsen Halck
> Ph.d.-studerende
> FYS-CAMD
> DTU Fysik
> Bygning 307
> 2800 Kgs. Lyngby
> Direkte telefon 45253177
> ntben at fysik.dtu.dk
> www.fysik.dtu.dk
> _______________________________________________
> gpaw-users mailing list
> gpaw-users at listserv.fysik.dtu.dk
> https://listserv.fysik.dtu.dk/mailman/listinfo/gpaw-users

------------------------------

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