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[h5md-user] Update on H5MD from Stuttgart

From: Pierre de Buyl
Subject: [h5md-user] Update on H5MD from Stuttgart
Date: Wed, 17 Jul 2013 14:28:28 +0200
User-agent: Mutt/1.5.21 (2010-09-15)

Hi all,

Following a discussion we had this morning with Felix, Olaf and Jonas, here's
what's been discussed and what is proposed.

1. Simple

An "id" dataset seemed necessary. It was discussed on the list and met no
opposition at the time. "id" is favoured over "tag" to underline its "unique
identifier" status.

It was suggested to move the notation section to the top of the specification
for clarity.

Within the box description, the nature of the boundaries of the box were still
missing, although discussed on the list. "type" is to be replaced by "geometry"
and "boundary" is to be added, with the value "open" or "periodic" in each

In relation to the addition of "geometry", the presence of "images" is not
needed in a trajectory group to deduce the periodicity of the positions.

I've made the above changes.

2. Less simple

2.1 "/trajectory"

One change seemed necessary in order for the content of "/trajectory" to be
better defined. Indeed, within some simulation schemes the full trajectory of
the system might include different kind of data.

A rename of "/trajectory" to "/particles" would prevent any such confusion.

2.2 time (in)dependent data

A proposal is made to work in the following way: at any place in the file, a
data (such as /trajectory/protein/position) may be either:
- A dataset (with shape [N]). It does not depend on time.
- A H5MD time-dependent conforming group (see current spec).

This being a not so trivial change (at the scale of H5MD), I'll send a separate
email to the list to discuss it. The idea is that this change would apply also
for the box and for "species" and "mass" where special cases are now in place.

It was nice to discuss this with an additional expert on simulation. The "use
case" of visualization, for instance, led to explicit mention of the box
boundaries and some confusing points could be clarified.



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