Re: [h5md-user] Make "time" optional?

[Pierre de Buyl]

Hi all!

On Mon, Jul 14, 2014 at 10:01:24AM +0200, Felix Höfling wrote:
> >Am 11.07.2014 16:09 schrieb "Konrad Hinsen"
> ><address@hidden>:
> >
> >>Hi everyone,
> >>
> >>Now that I have started to use H5MD seriously, I also start to notice
> >>problems with it. One of them is the obligatory presence of a "time"
> >>dataset. I want to store a Monte-Carlo trajectory which consists of a
> >>sequence of configurations, but without any associated time values.
> >>If I want to respect the H5MD specification, I have to make up
> >>numbers, which is not a good habit to take.
> >>
> >>Is there any reason why "time" was made obligatory?

Ha! I remember well having wished (not on list, mind you) that time should not
be mandatory. step is so that you have a proper integer-based indexing of
evolution. I am not sure that the discussion took place :-/

> Am 11.07.2014, 17:51 Uhr, schrieb Olaf Lenz <address@hidden>:
> 
> >...and adding to that, can we also make the "step" optional? Weird
> >as this
> >may sound, we would also have to invent step numbers.
> >
> >Olaf
> >
> 
> Dear Konrad and Olaf,
> 
> We have had some discussion on the time dataset in the context of Monte
> Carlo simulations. If I remember well the outcome was that in the case of
> no physical time, time is simply identical (=linked) to step. Our
> intentation was to have no optional parts in the core H5MD element---for
> the sake of making reading simple.
> 
> Whether such a decision was wise or not, I don't know. But it has been
> fixed now for H5MD 1.x. Making step or time optional would break
> compatibility with 1.0 and would make 1.0 basically obsolete. Thus I don't
> think it is a good idea. Nevertheless, I am open to extend the
> interpretation of step/time (but the fields must be present). For example,
> step could also just numerate the snapshots stored, without reference to
> any simulation order.

Actually, allowing time to be missing we could make the reading software default
to use time instead. Would that break anything?

> Note that for a single snapshot only, the data are stored in a simple HDF5
> dataset without step/time.

In a more general idea about step/time, I have an idea since a long time. I
didn't want it for H5MD 1.0 to avoid any confusion. But storing step and time
when step is simply step[i] = STEP_SIZE*i and time[i] = STEP_SIZE*DT*i is a bit
of a waste. We could define a proper setup for regularly sampled data, for which
step[0], STEP_SIZE, time[0] and DT should be given.

P