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Re: [h5md-user] box and observables

From: Konrad Hinsen
Subject: Re: [h5md-user] box and observables
Date: Wed, 25 Sep 2013 11:42:37 +0200

Peter Colberg writes:

 > > Next, the reader: if there is a single box group but differently
 > > sampled positions for different subsystems, reading the box
 > > information is a lot of work and slow.
 > Well, this is the essence of the step/time scheme.
 > I added a section [1] on the use of the step/time datasets, which
 > refers to the binary search, upon which the step/time scheme relies.
 > This is the basic building block for any H5MD program.
 > [1] http://h5md.nongnu.org/implementation.html

So the idea is that we have only a single box information for the
whole trajectory, right? My impression is that Felix still disagrees.

In that case, the following sentence must be removed from the

  A specific requirement for box groups inside particles is that the
  step and time datasets exactly match those of the corresponding
  position groups, which may be accomplished by hard-linking the

If left in, this indirectly implies that all position data must be
sampled on the same time grid.

 > For the case of all data that depends on the box for interpretation,
 > the replicated box groups complicate the matter, while providing no
 > benefit, as a step/time lookup is needed anyway.

I agree that if there is only a single set of box information per
trajectory, then it would be best to have it once in a single place.

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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