VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Dec 17 2009 - 13:38:12 CST

Rob,
  At present, the molfile API doesn't provide a means to load
time-varying volumetric data, but this is something on my long-term
TODO list. I plan to add this after we make some significant revisions
to the way volumetric data is stored and managed within VMD.
You might talk to Axel Kohlmeyer about whether you could do
an on the fly projection of the data in your abinit files into
a basis set that VMD understands and then you could use the
QM visualization functionality we've been adding into VMD for
your purposes, and the memory consumption would be a tiny fraction
of what it would be for loading a large number of explicit grids.

When I get a chance, I will look at your code closely
and send you some small corrections to a few places I saw that
needed fixing. Thanks for sharing your code.

Cheers,
  John

On Tue, Dec 15, 2009 at 07:47:08PM -0800, Rob wrote:
>
> Hello,
>
> I'm working on a VMD plugin for the abinit software (www.abinit.org).
>
> A preliminary version is here:
> http://skku.homeip.net/lahaye/vmd/abinitplugin.c
>
> It can read geometry (*_GEO) and charge density (*_DEN) files,
> although the latter has not bee tested for spin polarized data.
>
> It CANNOT read the general input (*.in) and output (*.out) files,
> because the abinit syntax is far to flexible to be able to read all
> different ways of inputting variables.
>
> It automatically reads the subsequent timesteps if the
> geometric input file contains a number (i.e. it increments the
> number in the filename and opens that one next, until it gets
> a non-existing filename).
>
> Some stuff is not implemented yet and certainly there are
> unexpected bugs.....
> So it's not ready yet for official release, but I welcome
> "preview testing".
>
> ---------------------------
>
> Few comments:
> 1. Concerning volumetric data:
> Is it still not possible to read volumetric data as timesteps?
>
> 2. The plugin.filename_extension automagically puts a dot
> inbetween the star and the list given here.
> This is very inconvenient when one wants to get a list of
> files which do not have dots in it (like abinit!).
> This should really be changed to become more general!
>
>
> Regards,
> 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