[gpaw-users] Plot pseudo charge density

Filip Anselm Rasmussen fras at fysik.dtu.dk
Thu Nov 6 14:39:19 CET 2014 

I was coincidentally having the same problem with MayaVi and found a 
solution for plotting isosurfaces of non-orthorgonal cells. It is now 
implemented in the plot() function in the ase.visualize.mlab module.
If you find any errors with it please report back - I have only 
performed one test.

- Filip


On 2014-11-06 14:34, Robert Warmbier wrote:
> Hi,
>
> alternatively, I like to save the charge density as a cube file and then use VESTA for the isosurfaces.
>
> Best Robert
> ________________________________________
> From: gpaw-users-request at listserv.fysik.dtu.dk [gpaw-users-request at listserv.fysik.dtu.dk]
> Sent: 06 November 2014 13:00
> To: gpaw-users at listserv.fysik.dtu.dk
> 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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