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Re: [h5md-user] box and observables

From: Felix Höfling
Subject: Re: [h5md-user] box and observables
Date: Wed, 25 Sep 2013 09:52:57 +0200
User-agent: Opera Mail/12.15 (Linux)

Am 25.09.2013, 09:20 Uhr, schrieb Felix Höfling <address@hidden>:

Am 24.09.2013, 18:57 Uhr, schrieb Peter Colberg <address@hidden>:

On Tue, Sep 24, 2013 at 12:51:15PM -0400, Peter Colberg wrote:
> So looking at this purely from the point of view of writing and
> reading positions, a box group per subsystem is highly desirable.

For that specific case, yes, that would be desirable.

A different aspect to consider:

Suppose I wish to display the combined particle positions of two or
more subsystems in a visualization program. If each subsystem has its
own box copy, which box group does the reader read, and which box
groups are discarded? Does the reader need to verify that the box
information of all groups coincides?

As long as we can agree on a single physical box per H5MD root,
agreeing on a single box group to represent this data also avoids
this ambiguity.


If different subsystems are combined, the box information within the respective subgroup is used to unfold the particle positions. That is: all (relevant) box groups are read. The reader does not need to bother whether the box datasets differ or not. I think this is very natural and simple, but I might overlook something.

This is also a situation where the box offset comes into play: the two subgroups could in principle use very different boxes, and the offset allows the reconstruction of the particle positions in a global coordinate frame.

Olaf, what is your experience with such a situation? How would the VMD plugin handle it?


To avoid confusion, let me add that the current draft has only a single box in the observables group. My proposed change was to simply move global observables (including the box) to a subgroup "global" such that there are only subgroups at the "observables" level.

Replicating the box in the various observables subgroups would be a different issue (which appears to be discussed partly in this thread).


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