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

[Olaf Lenz]

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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.

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.

Olaf

- -- 
Dr. rer. nat. Olaf Lenz
Institut für Computerphysik, Pfaffenwaldring 27, D-70569 Stuttgart
Phone: +49-711-685-63607
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