Re: [h5md-user] Update on H5MD from Stuttgart

[Peter Colberg]

On Wed, Jul 17, 2013 at 09:25:45PM +0200, Pierre de Buyl wrote:
> On Wed, Jul 17, 2013 at 11:30:54AM -0400, Peter Colberg wrote:
> > On Wed, Jul 17, 2013 at 02:28:28PM +0200, Pierre de Buyl wrote:
> > > 2.1 "/trajectory"
> > > 
> > > One change seemed necessary in order for the content of "/trajectory" to 
> > > be
> > > better defined. Indeed, within some simulation schemes the full 
> > > trajectory of
> > > the system might include different kind of data.
> > > 
> > > A rename of "/trajectory" to "/particles" would prevent any such 
> > > confusion.
> > 
> > This needs a detailed explanation.
> > 
> > What kind of simulation schemes and data were you discussing?
> > In which cases is /trajectory not appropriate?
> > 
> > What about simulations without particles, e.g., Lattice-Boltzmann?
> 
> This is precisely one of the simulation types that motivated the change. For
> now, "/trajectory" holds particle data only. The idea is that if someone doing
> Lattice Boltzmann wants to store that it would go in "/fields", "/fluid",
> "/lattice_boltzmann", "/whatever". That is not part of the H5MD specification,
> it could come later.

Since this is the only remaining change towards the H5MD v1.0 release:

I agree with renaming "/trajectory" to "/particles".

With regard to Lattice-Boltzmann, I suggest to include in the
Discussion section a proposal to use "/fields/<subgroup>/density"
and "/fields/<subgroup>/velocity" for Lattice-Boltzmann density
and velocity fields.

@Olaf: Since I use multi-particle collision dynamics instead of
Lattice-Boltzmann, it would be great if you and your team could
provide feedback on the needed data elements.

Regards,
Peter