[Paraview] Gaussian cube files

[Roberto Di Remigio]

The package is DIRAC and is dedicated to relativistic calculations. For our
purposes we produce cube files, that is we simply calculate the properties
to be visualized on a grid of points and then print to file. As I said,
this is ok if you want to plot one thing at a time but for more elaborate
things it's too cumbersome (in my opinion).
For example, Molekel can't do that. Molden can in principle, but I didn't
manage to do it. So I thought about ParaView.
Since we are free to choose whatever format for the visualization output, I
was really interested in this vtkMolecule facility. If we could provide to
ParaView some kind of "native" format things would be much easier. In my
case, I would like to visualize:
1. atoms and bonds;
2. isodensity surfaces;
3. isodensity surfaces color mapped with the electrostatic potential;
4. isosurfaces for the electrostatic potential.

However, in general, we would be interested in plotting molecular orbitals,
magnetic current densities and so on.

Il giorno 16 marzo 2012 01:40, Marcus D. Hanwell <marcus.hanwell at kitware.com
> ha scritto:

> This work was only recently merged into VTK, and is not exposed in
> ParaView at all right now. We are working on additional chemical
> structure visualization and analysis in dedicated applications, and
> adding features to VTK where appropriate. Right now there is not much
> more than a small set of chemistry classes.
>
> What package are you using? I am interested in the type of work you
> are doing, and how you are currently using ParaView.
>
> Marcus
>
> On Thu, Mar 15, 2012 at 5:14 PM, Roberto Di Remigio
> <roberto.diremigio at gmail.com> wrote:
> > Is there some sort of guide about this part of the VTK code? I mean, I am
> > working with an electronic structure package and it would be great if
> there
> > was a way to "interface" it with ParaView.
> >
> > Il giorno 15 marzo 2012 16:48, Marcus D. Hanwell
> > <marcus.hanwell at kitware.com> ha scritto:
> >
> >> On Thu, Mar 15, 2012 at 11:29 AM, Roberto Di Remigio
> >> <roberto.diremigio at gmail.com> wrote:
> >> > Sorry for taking the discussion out of the mailing list! I hadn't
> >> > noticed.
> >> > I tried with the Resample filter and it worked.
> >> > For future use, I summarize what I did:
> >> > 1. open first cube file (containing the density);
> >> > 2. plot the isodensity surface;
> >> > 3. open second cube file (containing the electrostatic potential);
> >> > 4. use Resample With Dataset filter. Select Gridded Data of the second
> >> > cube
> >> > file as Input and Contour of the first cube file as Source.
> >> > This should do it.
> >> > Thank you again for your answers
> >> >
> >> Just to add that we have added more chemistry to VTK, in the form of
> >> Blue Obelisk Data Repository for atom colors, radii, symbols, names,
> >> etc along with things like a vtkMolecule data structure and a simple
> >> bond perceiver. This should hopefully gain some exposure in future
> >> ParaView releases so that it is easier to view molecular structure and
> >> related data.
> >>
> >> Marcus
> >
> >
> >
> >
> > --
> > Roberto Di Remigio
> >
>



-- 
Roberto Di Remigio
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://www.paraview.org/pipermail/paraview/attachments/20120316/8d6e7bc3/attachment.htm>