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

[Pierre de Buyl]

Hi Felix,

On Mon, Sep 17, 2012 at 04:26:45PM +0200, Felix Höfling wrote:
> Hi Pierre,
> 
> Am 17.09.2012, 15:18 Uhr, schrieb Pierre de Buyl
> <address@hidden>:
> 
> >A conclusion would be that "box" is mandatory within a trajectory
> >group with
> >identical "step" and "time" datasets (that may or not be linked,
> >this is an
> >implementation detail). Then, as you write, wether or not it is
> >also found in
> >"observables" depends on the simulation.
> >
> 
> Mostly yes. I just thought that datasets position/box/{time,step} are not
> needed as they coincide with position/time and position/step by
> definition. The reader would refer to the latter (and ignore box/time if
> present). Thereby consistency
> would be automatically ensured without demanding that position/box/time ≡
> position/time. But I have no strong preference here, my main point was to
> provide the box information along with the position data in trajectory.
> 
> So you may link the current box group from observables, but the reader is
> adviced to access the time and step information from the datasets in
> position rather than box.
> 
> In my diagram above I noted a slight mistake. It meant it to look like
> this, box is at the same level as value:
> 
> trajectory
>      \-- group1
>      |  \-- position
>      |    \-- value
>      |    \-- step
>      |    \-- time
>      |    \-- box
>      |         +-- type
>      |         \-- edges [D][D]
>      |         \-- offset [D]
> 

Ok, this is quite different. I see a small problem with that: "box" does not
appear with a normal H5MD group structure. Also, one may one to also use the box
information (that give the box volume) along with the velocity and species data.
This is not very natural with this organization. I propose to make "box" at the
same level as "position", "velocity" and "species" but make it mandatory to have
equal time and step than "position".

Thoughts on that?

Pierre