Re: [h5md-user] observables: per particle averages or total sums

[Pierre de Buyl]

Hi Felix,

On Mon, Oct 07, 2013 at 11:21:32AM +0200, Felix Höfling wrote:
> Am 04.10.2013, 21:33 Uhr, schrieb Pierre de Buyl
> <address@hidden>:
> 
> >The observables are stated to be "per particle". I'd like to
> >revert that. There
> >are situations where this is just not appropriate.
> >
> >For instance, in MPCD simulations the interaction energy
> >represents energy in
> >the interfacial region for which there is no clear definition of
> >the number of
> >particles.
> >
> Such a constraint on the observables would be a bit too much, indeed. The
> spec was not meant to be restrictive in this direction. The phrase "per
> particle" was merely added as explanation for the standardised
> identifiers, e.g., to say what is meant by "kinetic_energy". Some
> considerations how to make it more flexible and still meaningful:
> 
> The file format should not enforce users to store the average instead of
> the total sum, although I think it is good practice to use the average
> (smaller values with a sensible normalisation and smaller round-off
> errors). In your application, you could store the average along with the
> varying number of particles that contributed to the average.
> 
> The data group has to be verbose about whether the average or the total
> sum is stored, otherwise the information cannot be interpreted properly.
> 
> 1) Very long group names like "kinetic_energy_per_particle" appear weird.
> 
> 2) Making the "particles" attribute/dataset mandatory for averages
> (serving as indicator) is too restrictive as well.
> 
> 3) We could add an attribute "average" which is either "true" or "false",
> or an attribute "type" ...
> 
> I have no definite solution for this yet. Maybe a kind of attribute would
> be the best choice.
> 
> In addition to that, it would be useful to have an optional string
> attribute "description" (for all data groups) which can be as precise as
> the user needs/wants it to be. Such a field, of course, could not be
> parsed automatically (with reasonable effort), but should make things
> clear for a scientifically educated human. It could serve, e.g., as
> display name for H5MD readers, by now a generic reader has to translate
> the group name by replacing "_" by " ".

I thus propose that we even get rid of the suggested names. /observables is
rather free as of now except for those names. Removing them would remove the
need to clarify their definitions :-)

Pierre