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Re: [h5md-user] box and observables

From: Konrad Hinsen
Subject: Re: [h5md-user] box and observables
Date: Mon, 23 Sep 2013 11:48:27 +0200

Felix Höfling writes:

 > The reason that there are several box groups is primarily that different  
 > subgroups have different sampling intervals. For trajectory subgroups, the  

That was my understanding as well (there is even a sentence saying
so), but apparently Peter disagrees.

 > For this reason (and since the /particle root group may be absent),
 > the box is also stored in /observables where it is considered a
 > physical observable (NPT simulations), not just an appendage to
 > some real data.

Having the box as an observable is indeed quite reasonable.

 > Assuming that there is only one simulation box, the
 > box is not stored inside each particle subgroup but at the main
 > level. Actually, this latter point deviates from the structure in
 > /particles and may be debated.

Now that I understand the reasoning behind the current layout, I'd say
the fundamental problem is elsewhere: it's that the "observables" group
can contain two very distinct kinds of subgroups: those that define
systems-wide observables, and those that group together observables for
different subsystems.

There is no such distinction in the "particles" group, where all data
is stored by subsystem, implying that the whole system is just a special
case of a subsystem.

Why not take the same point of view for "observables"? We'd then have
only subsystem-naming groups at the top level, and all observables, 
including "box", inside them.

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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