VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Jun 10 2009 - 09:43:20 CDT

Ondrej

On Wed, Jun 10, 2009 at 02:54:05PM +0200, Ondrej Marsalek wrote:
[...]

Do you have a volumetric trajectory file format of some kind?

> John, am I reading it right that direct support for volumetric data
> animation (and "unloading") is not coming any time soon? If it was
> close, there would be no point in working on my current code.

It won't be in this version of VMD (1.8.7) but it could be added
to the next version if there's enough interest. The major issue up
to this point is a lack of a standard volumetric trajectory file format.
It sounds like Rob has such a file format however, so he may be an ideal
early user of such a feature. What file format are you reading from for
your work?

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

> On Wed, Jun 10, 2009 at 14:24, John Stone<johns_at_ks.uiuc.edu> wrote:
> >
> > Rob,
> >  At present, you can only load a volumetric data object for all
> > timesteps.  For a subsequent version of VMD I may enable loading
> > these for a trajectory, but to make that feasible, several parts
> > of the VMD volume rendering code need to be GPU-accelerated so that
> > animation of such datasets becomes usable.  For now, you
> > could start with a plugin that loads only volumetric maps from the
> > last timestep.  You might also consider talking to Axel and Jan
> > about projecting onto GTOs and providing the QM data to VMD via
> > the QM plugin APIs.  If you could do that, it would use far less memory
> > than storing the volumetric grids for the properties of interest.
> > We expect to add several new QM related representations in the
> > next version that would likely be of interest to you.
> >
> > Cheers,
> >  John Stone
> >  vmd_at_ks.uiuc.edu
> >
> > On Wed, Jun 10, 2009 at 01:11:34AM -0700, Rob wrote:
> >>
> >>
> >> Hi,
> >>
> >> I'm writing a plugin for Abinit.
> >>
> >> I can read sequential structure geometry files, so that I can
> >> see the atoms move during a structure relaxation, for example.
> >>
> >> Each relaxation step also comes with a charge density distribution
> >> as volumetric data; can I read this also as frames/timesteps?
> >>
> >> I'm writing the plugin right now and I see that the "read_next_timestep"
> >> function is repeatedly called until it returns MOLFILE_EOF.
> >> However, the "read_volumetric_data" is called only once during this
> >> procedure.
> >> Hence, I can have a sequence of atom positions as frames, but only
> >> one volumetric data......
> >>
> >> Or am I doing something wrong?
> >>
> >> Thanks,
> >> Rob.
> >>
> >>
> >>
> >
> > --
> > NIH Resource for Macromolecular Modeling and Bioinformatics
> > Beckman Institute for Advanced Science and Technology
> > University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> > Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
> >  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078
> > 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078