Re: [h5md-user] particle number

[Felix Höfling]

Hi Pierre,

Am 25.01.2013, 20:19 Uhr, schrieb Pierre de Buyl  
<address@hidden>:

> Hi Felix,
>
> Thanks for relaunching the discussion :-)
>
> On Fri, Jan 25, 2013 at 04:10:49PM +0100, Felix Höfling wrote:
> > 1) The space dimension shall be stored in /parameters+dimension (as
> > integer attribute).
> >
> > In principle, it can be deduced from the size of the box offset, but
> > this appears pretty cumbersome. Apart from handiness, the box may be
> > found either in observables or in trajectory, requiring a
> > distinction of cases—just to obtain the space dimension.
>
> This seems reasonable enough :-)

I've included the space dimension in the draft. Since I can't push to  
git://git.savannah.nongnu.org/h5md.git (why?) I have attached the patch.

> > 2) If data are present only in /observables, the number of particles
> > can not be inferred. My suggestion is to supplement each observable
> > group with an attribute indicating the number of particles that lead
> > to this specific average. (So far, all macroscopic observables
> > result from an average over particles.) Thereby, also partial
> > observables of particle subgroups are handled correctly. The
> > attribute may be attached either to the top groups ('all', 'A', and
> > so on), or to individual data groups like 'total_energy'.
>
> I have mixed feelings about this one. For the moment (this does not mean  
> that
> this should be the final solution, btw) I run multispecies simulations.  
> The
> number of particles is in /observables/solvent_N and is a [:,N_species]  
> dataset.
> In all generality, the number of particles depends on time and on the  
> species.
> The variety of situations makes me think that this should not go into  
> the first
> published version (FPV).
>
> > I believe that both attributes are of sufficient generality to
> > deserve a place in H5MD, and I will add them if there are no urgent
> > objections.
> >
> > BTW, what is missing as well is an (optional) error field (=standard
> > deviation) for the observables. What do you think?
>
> Is this critical for the FPV?

I see that we're running in a similar trouble as with the  
static/fluctuating box size. Nevertheless, I think storing the particle  
number of averaged quantities is an essential feature, two examples:

Example 1: given two subset of particles, the total potential energy per  
particle can not be computed from the subgroups unless the particle number  
is known.

Example 2: computing simple response coefficients like the specific heat  
from energy fluctuations requires the particle number.

The crucial point is to add the possibility to convert a per particle  
quantity in a total quantity. If the particle group contains a mixture (as  
in your case, and also in some of my simulations), the _total_ number of  
particles is stored. (Information about the fluctutating composition of  
the mixture may go in a seperate observable.)

My suggestion is to store the particle number either in an attribute  
attached to the observable if it is fixed in time or in a dataset next to  
value/time/step if it fluctuating. The naming may be "number",  
"particle_number", or simply "count".

What do you think?

Best regards,

Felix

PS: Your replies to the mailing list are often only CC to the list, is  
this by intention? Opera's mail client doesn't recognise such mails as  
belonging to the discussion in the list.

0001-Add-attribute-dimension-to-parameters-group.patch
Description: Text Data