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Re: [h5md-user] Particle tracking


From: Olaf Lenz
Subject: Re: [h5md-user] Particle tracking
Date: Tue, 03 Sep 2013 17:40:49 +0200
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Hi!

It looks to me as though reading the positions from an h5md-file is
becoming pretty difficult meanwhile.
I would suggest to implement a h5md library in C that provides functions
to read the particle trajectory (and possibly other structures later
on). Such a library can serve both as a reference implementation as well
as a library that can be interfaced from various languages.

The basic idea would be that the library initially allows to loop over
all timesteps and provides functions to initialize the loop, go to the
next timestep, and get the positions in the current timestep. The
positions will be ordered; this means that e.g. the id will have to be
handled, etc.

Of course, such a library will not be able to handle all possible cases
efficiently, but it can show how to handle them at all.

I even know who is going to implement it: my student helpers that are
working on the VMD plugin. They have to write C-functions to read the
positions anyway, so we just have to factor out these functions into the
library.

Olaf


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