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

[Pierre de Buyl]

Hello,

So, we're back where we were a few weeks ago. My suggestion was to go for
/trajectory/group1/box
instead of
/trajectory/group1/position/box
but with the requirement that position/step and box/step be equal (time also,
indeed).

I am not very enthusiastic about having position and box not respecting
"value,step,time" by the letter...

P

On Mon, Nov 19, 2012 at 08:51:49PM +0100, Felix Höfling wrote:
> Am 19.11.2012, 20:17 Uhr, schrieb Peter Colberg
> <address@hidden>:
> 
> >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).
> >
> 
> This is precisely what my suggestion addresses. Each time series in
> trajectory has its own box data, located in
> 
> /trajectory/group/position/box
> 
> using the identical time grid as the trajectory data. If all groups
> use the same time grid, one may use links and there is no
> redundancy. In the case of arbitrary time grids, there may be some
> redundancy in the stored data, which however consumes almost no
> space.
> 
> Thereby, we don't need sophisticated reverse lookups, interpolation
> between time steps or whatever. The box data are enforced to match
> by index with the trajectory data.
> 
> The box data in observables are completely independent and may
> stored on a totally different time grid. But they may also simply
> share one unique box group by a link.
> 
> >>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 is a misunderstanding, see above.
> 
> Felix
>