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Re: [h5md-user] Update on H5MD from Stuttgart
From: |
Pierre de Buyl |
Subject: |
Re: [h5md-user] Update on H5MD from Stuttgart |
Date: |
Sun, 21 Jul 2013 22:43:03 +0200 |
User-agent: |
Mutt/1.5.21 (2010-09-15) |
Hi all,
A quick update on time-(in)dependent data.
On Wed, Jul 17, 2013 at 09:25:45PM +0200, Pierre de Buyl wrote:
> On Wed, Jul 17, 2013 at 11:30:54AM -0400, Peter Colberg wrote:
> > On Wed, Jul 17, 2013 at 02:28:28PM +0200, Pierre de Buyl wrote:
> > > 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.
>
> Glad to hear that. I am quite prudent about that but it would simplify the
> specification.
I pushed modifications and found a surprise issue.
In the box specification, one stores edges and offset as attributes for time
independent boxes. This goes against the new idea that any data is a dataset or
a H5MD group. Still, datasets make sense in "/trajectory" (for species or
masses, say) but attributes are more appropriate for a box edges and offset.
I also updated https://github.com/pdebuyl/pyh5md (on branch time_data_optional)
and the code is (in my opinion) simpler than previously.
Still, almost all that was discussed is going well :-)
Pierre