VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Wed Jun 10 2009 - 08:16:58 CDT

On Wed, 2009-06-10 at 01:11 -0700, Rob wrote:
>
> Hi,
>
> I'm writing a plugin for Abinit.

rob,

> 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?

no. volumetric data sets are currently global data and not
tied to a specific frame number. you can emulate the behavior
you want by using a trace on vmd_frame in the way outlined here:

http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/cpmd-vmd/part5.html#chap7_sect6

a future option, and i may have mentioned it before, would be to
project the whole data set on slater functions and use the new
QM plugin API. however, this would require some coordination,
since we are still ironing out some details and it may need some
more changes to be suitable for more widespread usage. the problem
here is, that you can only work out the details while doing it,
as it is much more complex than passing coordinates to VMD.

> 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......

you can hand over multiple data sets during the read_volumetric_data
step. check out the cube plugin. it supports multi-orbital cubes,
which are effectively interleaved multiple volumetric data sets.

> Or am I doing something wrong?

nope. not really. for the new API you can look at the sources
of gamessplugin, gaussianplugin, or cpmdlogplugin, in order of
completeness (cpmdlogplugin is currently not working due to
pending adjustments to the latest API changes).

cheers,
   axel.

> Thanks,
> Rob.
>
>
> 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.