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Re: [h5md-user] Update on H5MD from Stuttgart

From: Peter Colberg
Subject: Re: [h5md-user] Update on H5MD from Stuttgart
Date: Wed, 17 Jul 2013 11:30:54 -0400
User-agent: Mutt/1.5.21 (2010-09-15)

On Wed, Jul 17, 2013 at 02:28:28PM +0200, Pierre de Buyl wrote:
> Following a discussion we had this morning with Felix, Olaf and Jonas, here's
> what's been discussed and what is proposed.

Pierre, thanks for the heads-up on the meeting!

> 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.

The type of a particle id is not mentioned in the text.

I suppose the particle id is of integer type?

> 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
> dimension.

What is the value of “boundary” in the presence of walls?

Note the definition of a closed system in thermodynamics: The system
is closed with regard to flow of mass, but open with regard to flow
of work and heat. Maybe it should be made explicit that “closed” and
“open” only refers to the flow of mass through the boundaries.

> 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.

This needs a detailed explanation.

What kind of simulation schemes and data were you discussing?
In which cases is /trajectory not appropriate?

What about simulations without particles, e.g., Lattice-Boltzmann?

> 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).

That is a good idea.


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