Re: [h5md-user] box data as part of trajectory/position

[Peter Colberg]

On Mon, Nov 19, 2012 at 07:44:42PM +0100, Felix Höfling wrote:
> The main motivation is the issue with potentially different sampling
> intervals of different particle groups, which remains unresolved if
> only a single box group is stored. In my proposal, the box
> information relevant for each snapshot of a particle group is
> stored, ensuring data consistency and simplifying the access of
> particle coordinates. Further, it avoids dependencies across
> different root groups.

That is a different issue.

If variable box information needs to be available for different sets
of times T_A and T_B (e.g., with regard to trajectory or observable
datasets), then the box/time dataset is the superset of T_A and T_B.

But this remark shows that we need to clarify lookup by time/step.
Only if two H5MD data groups have identical time/step datasets, one
may assume that two data elements with the same index refer to the
same time/step. Otherwise, one must lookup the element index using
the time/step dataset (e.g., using bisection).

> BTW, if your old files shall be read by a future H5MD reader that
> expects the box information in trajectory, you may simply add a link
> from trajectory to observables.

Current H5MD files have a data group /observables/box.
A reader complying with your proposal expects /trajectory/box.

This was my last comment on the issue, regardless of outcome ;-).

Regards,
Peter