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Re: [h5md-user] Subgroups

From: Konrad Hinsen
Subject: Re: [h5md-user] Subgroups
Date: Mon, 23 Sep 2013 15:53:40 +0200

Felix Höfling writes:

 > I'm not sure whether overlapping subgroups are also useful for the data in  
 > "particles". (Maybe one example for a spatial selection: a user wants to  
 > analyse the interfacial region between two liquids, so only a shallow slab  
 > along the interface is stored instead of all particles.) Do you see a  
 > problem here w.r.t. your applications?

Overlapping subgroups are quite relevant for me, in particular the
special case of one subgroup being a subset of another.

In protein simulations, the total system is often decomposed as a tree

                  /      \
                 /        \
            solvent      protein
                        /       \
                       /         \
                   chain A     chain B
              active site  

Observables may be provided at any level. Particle positions are often
stored more frequently at the lower levels than at the upper levels.

It is quite common not to store anything at all for the complete
system, so reconstruction is not my goal either. However, I would like
to be able to say which of the atoms in "chain A" are the ones that
are also in "active site".

I have solved this problem for my own applications in the
"H5MD-Mosaic" module that I am working on, which is why I didn't
insist on this question any longer. Mosaic has an "atom selection"
data item which handles the job quite nicely. I simply require that
for every subgroup in "particles", there is an entry with the same
name in the "mosaic" group at the root level, which is either a Mosaic
universe (i.e. the whole system) or a Mosaic atom selection.

 > Automatic reconstruction of a complete simulation from a H5MD file would  
 > be nice, but there is much more to it than just particle coordinates.  
 > Then, one would have to enter into specifying particle interactions in a  
 > generic way which appears impossible to me.

Well, I am working on that, so I hope you are wrong ;-)

It's clearly a non-trivial problem and I don't expect to finish this
any time soon. Since interactions are arbitrary mathematical
functions, it comes down to defining a domain-specific language for
interactions. The real difficulty is to design such a language in a
way that is both sufficiently flexible to handle all cases and
sufficiently simple to implement for the common cases to make the
approach efficient.

Konrad Hinsen
Centre de Biophysique Moléculaire, CNRS Orléans
Synchrotron Soleil - Division Expériences
Saint Aubin - BP 48
91192 Gif sur Yvette Cedex, France
Tel. +33-1 69 35 97 15
E-Mail: research AT khinsen DOT fastmail DOT net
ORCID: http://orcid.org/0000-0003-0330-9428
Twitter: @khinsen

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