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Re: [h5md-user] Particle tracking

From: Pierre de Buyl
Subject: Re: [h5md-user] Particle tracking
Date: Wed, 4 Sep 2013 10:48:54 +0200
User-agent: Mutt/1.5.21 (2010-09-15)

On Tue, Sep 03, 2013 at 12:14:49PM -0400, Pierre de Buyl wrote:
> I just uploaded to the branch test_open at https://github.com/pdebuyl/pyh5md
> in which there is an example of an open system.
> The simulation is a random walk in which the particles disappear when exiting
> the simulation box (similar to Mathieu's problem) and new particles appear
> randomly (i.e. at random times) at the center of the box. Each new particles
> carries a yet unused id. It is thus different than particles moving around
> nodes in a parallel simulations.
> The script show_walk_2d.py displays the trajectory for each id found in the
> system. It is very (very) inefficient but works.

I update the module to allow for fillvalue when creating the data and mask when
writing the data.

The example now only writes data that is not empty. Most of the logic remains in
the "main program", but a large part of it is to resize the "live" data arrays
and not so much HDF5 fiddling.


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