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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 09:47:54 +0200

Peter Colberg writes:

 > On Fri, Sep 20, 2013 at 01:01:14PM +0200, Konrad Hinsen wrote:
 > > My understanding is that the "box" information in each subgroup under
 > > "particles" can be different. Otherwise, why have it in each subgroup?
 > > But if it can be different, then which one should be linked to
 > > "observables"?
 > That would be a new interpretation.
 > H5MD started with a single box group, located at /particles/box.

OK, so the idea is that there is a single dataset or time series with
box information for the whole trajectory. I didn't see this clearly
stated anywhere.

 > Then it was noted that the special box group is misplaced in
 > /particles, next to the subsystem groups.

The main inconvenience is that it prevents any subsystem from being
called "box". That's not much of restriction semantically, but it
requires all software to treat "box" differently from any other group

 > So box was moved and replicated to the subsystem groups. Then the
 > discussion about the observables group came up, and it was
 > replicated to observables…

At least it would have been consistent to move it to the subsystem
groups there as well.

 > Why don't we just move the box to the H5MD root?

Fine with me. If it's meant to be the one and only box information for
the trajectory, it might as well be at the root level.

A single box group for the whole file raises some practical issues,
however. Suppose I have two subsystems (in my typical case "protein"
and "solvent") sampled at different time steps: the protein very
frequently, the solvent much less so. I thought that each subsystem
could have its own box data with the same sampling, which makes
reading both together quite straightforward.

With a single box group, finding the right box step to go with a
specific subsystem position step can be very expensive, since H5MD
makes no guarantees about matching information in different subgroups.
It is reasonable to assume that data with the same step number goes
together, of course, but that step number can be in very different
positions in the data array. H5MD doesn't even guarantee that step
numbers are monotonically increasing, so finding the box step for a
given position step could at worst require reading the complete box
time series.

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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