VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Fri Nov 22 2019 - 10:29:22 CST

On Fri, Nov 22, 2019 at 10:34 AM Anthony Ruth <Anthony.J.Ruth.12_at_nd.edu>
wrote:

>
> The biggest waste in my current setup is that few atoms move each frame
> but all of the atoms are repeated in the file for every frame. For example,
> the first frame is given by an .xyz file. The next frame has only the
> changes relative to the first frame, e.g. atom1 moved to (5,3,0)
> atom5 moved to (4,4,0). Is there a filetype or a combination of
> filetypes that VMD could interpret this kind of information from and would
> obtain the same set of frames as printing a full structure for each frame?
>

I am not aware of a file format currently that supports this kind of setup
(but I don't know all of them well enough; as you noticed there are just
too many of them), but it should be possible to implement a custom file
type reader, that would be based on an existing file type and then keeps a
copy of the coordinates around and updates them with the delta information
you have. please note, that this file will still expand to having the
coordinates for every atom at every step stored in RAM, as that is a
requirement of how VMD stores information. When writing a custom file
format, you could also make it compress text with gzip, bzip2 or similar
and then decompress on-the-fly when reading those files. that might provide
additional storage savings while maintaining a simple file format
underneath.

The other option I as looking at is a simple binary encoded format. Do you
> have a recommendation on a commonly used binary format?
>

An option to perhaps look into would be the .xtc format, that gromacs
supports. This is a fixed precision (not floating point) binary format,
that can compress data by storing only the delta of the coordinates between
frames. That may help reducing size without writing a "deltaxyz" kind of
custom file reader.

axel.

>
> regards,
> Anthony Ruth
> Condensed Matter Theory
> University of Notre Damee
> 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.