VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Sun Dec 04 2011 - 23:27:48 CST

as an example, you may want to check out the two videos featured
on this page. http://sites.google.com/site/akohlmey/software/vrpn-icms
they are available in up to 720p (HD) format and were created with
Tachyon on a cluster using the outlined procedure with ffmpeg
in 1080p with suitably high video data rate (they were postprocessed
by youtube for reduced storage/data rate).

cheers,
     axel.

On Mon, Dec 5, 2011 at 12:19 AM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
> On Sun, Dec 4, 2011 at 10:35 PM, David Cohen-Tanugi <dctanugi_at_mit.edu> wrote:
>> Dear All,
>
> dear david,
>
>> What are the most effective ways of rendering high-quality and long movies
>> from VMD trajectories?
>>
>> I have been using VMD to visualize long (1000+ frames) trajectories of
>> molecular dynamics simulations from LAMMPS, and I haven't yet found an
>> efficient way to render these trajectories into high-quality videos. My
>> Macbook Pro is quick enough for most purposes but at 2-3 minutes per frame
>> in Tachyon Internal with ambient occlusion, it seems much more logical to
>> export the job to a parallel cluster on many nodes.
>
> sure, and it is a fairly straightforward thing to do.
>
>> In that context, what is the most straightforward and efficient way to
>> render and encode a very long, high-quality movie from a VMD session?
>> Strategies that leverage parallelized cluster computing would be greatly
>> appreciated!
>
> the general strategy would be to do visualization, rendering, and
> movie generation as separate steps. for the visualization, you
> can create input files for Tachyon from within VMD through a
> loop construct. those can then be transferred to a cluster (or
> you can use a previously saved state and generate the render
> inputs directly on the cluster) and then rendered into individual
> pictures in batch mode. Tachyon can be compiled for threading
> or MPI parallelization on top of that you can parallelize over the
> individual input scripts (but it is usually more effective to bundle
> multiple inputs into a single submit script). if you are limited by
> disk space, you may want to compile Tachyon with jpeg support
> or convert the default TGA format files into high-quality (85-95)
> jpeg files. the final step would be to convert the individual
> image frames into an mpeg/quicktime/divx/avi/mp4/whatever
> format movie with your favorite tool.
>
> this will require some custom scripting, but a lot of the required
> script code is either straightforward to write from scratch or can
> be adapted from the vmd movie maker plugin.
>
> for the quality setting, you should take into account the image
> and quality loss through the video compression (depending on
> the selected video data rate), which benefits from avoiding hard
> contrasts, "pure" colors (especially red) and smoothing/antialiasing.
>
> HTH,
>    axel.
>
>> Many thanks,
>> David
>>
>> David Cohen-Tanugi | Ph.D. Candidate | Jeffrey C. Grossman Group |
>> Massachusetts Institute of Technology | Department of Materials Science &
>> Engineering | 609-902-6850 | dctanugi_at_mit.edu | www.mit.edu/~dctanugi/
>
>
>
> --
> Dr. Axel Kohlmeyer
> akohlmey_at_gmail.com  http://goo.gl/1wk0
>
> College of Science and Technology
> Temple University, Philadelphia PA, USA. 

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science and Technology
Temple University, Philadelphia PA, USA.