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Re: [h5md-user] Variable-size particle groups

From: Pierre de Buyl
Subject: Re: [h5md-user] Variable-size particle groups
Date: Tue, 29 May 2012 20:19:15 +0200
User-agent: Mutt/1.5.21 (2010-09-15)


On Tue, May 29, 2012 at 11:19:44AM +0200, Olaf Lenz wrote:
> Hi!
> This is my first contribution here, therefore let me quickly introduce
> myself: I'm Olaf Lenz, maintainer of the MD package ESPResSo
> (http://espressomd.org), intended for coarse-grained MD simulations. I'm
> working at the Institute for Computational Physics at Stuttgart
> University, Germany. I learned about H5MD from Felix Höfling, with whom
> I am currently giving a course on soft matter research.
> H5MD is compelling to us, as we are working on coarse-grained
> simulations, and compared to atomistic simulations, we need a lot of
> flexibility in a format to store our simulations, as basically
> everything can change throughout a coarse-grained simulation.

Welcome to this list! It's nice for H5MD to have the input from someone who
works on such a package.

> After Peter's mailing, I have had a first thorough look at H5MD. From
> our point of view, Peter describes a very valid point - the number of
> particles in a simulation can vary. This is not only true in the case of
> grand-canonical simulations, but also other state-of-the-art-schemes
> have a varying particle number, e.g. the ADResS-scheme, where the level
> of detail might vary in different regions. As an example, think of a
> protein-water simulation, where the protein and the surrounding nm of
> water is simulated on an atomistic level of detail, while the water
> further away is simulated on a coarse-grained level with less
> interaction sites per water molacule. I believe that this kind of
> schemes will become more important in the future, so allowing to store
> trajectories with varying particle number may become important.
> On 05/29/2012 10:15 AM, Felix Höfling wrote:
> >> H5MD implements an optional dataset “range” inside each
> >> trajectory subgroup, next to the other datasets groups “step” and
> >> “time”.
> Besides making the format more complex, as Felix remarked, I believe
> that forcing Peter's definition upon the format would also have major
> impact upon parallel IO.
> I think a relatively simple solution to avoid making the format more
> complex while still allowing for varying particle number would be to
> specify that if the subgroup "range" exists in a time-dependent dataset,
> the subgroup "value" is to be interpreted in the way Peter described,
> otherwise it uses the simple definition.

For the time being, at least, one could also keep this addition to H5MD on the
specification page but "in discussion" and agree later on it. As the discussion
that follows Peter's message suggests, parallel issues have to be considered
carefully before settling for a solution.


> - -- 
> Dr. rer. nat. Olaf Lenz
> Institut für Computerphysik, Pfaffenwaldring 27, D-70569 Stuttgart
> Phone: +49-711-685-63607
> Version: GnuPG v2.0.18 (GNU/Linux)
> Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/
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