Re: [h5md-user] [h5md-commit] [SCM] UNNAMED PROJECT branch, master, updated. c234149781bfa9f5dc81aa139038e7dc6689b64d

[Felix Höfling]

Am 31.05.2013, 13:01 Uhr, schrieb Pierre de Buyl  
<address@hidden>:

> Hi,
>
> On Wed, May 29, 2013 at 03:01:57PM +0200, Felix Höfling wrote:
> > Am 29.05.2013, 13:48 Uhr, schrieb Pierre de Buyl
> > <address@hidden>:
> >
> > >I would like to make the "particles" attribute optional. It is
> > >useless in many
> > >cases.
> >
> > We should try to minimise the number of optional items and thus the
> > variants a data group can have. Otherwise evaluating the file
> > becomes really difficult since one has to check every time whether a
> > certain piece of information is present or not. The decision whether
> > a certain piece of data is present or not should happen at the level
> > of the data groups.
>
> HDF5 is quite powerful with respect to this kind of check. We should not  
> make
> optional something that has to be present anytime, but we should not  
> refrain
> from making optional data optional.
>
> > Concerning the "particles" attribute: it does not hurt to store the
> > information (just a few bytes), but one is in real trouble if one
> > needs it and it is missing. And I think it is good practice to store
> > some statistical information along with averaged data.
>
> My concern is that this attribute is not always needed and may even be
> misleading. Whether in experiments or simulations, not every observable  
> is
> associated to a number of particles. A few examples:
>   - A quantity associated with a thermostat, such as a program for the
>     temperature.
>   - State of a PRNG. This is in my opinion a very valid usecase. If a  
> code uses
>     H5MD, it should be able to store a maximum amount of data in the  
> H5MD file.
>     As the state of a PRNG depends of the time and can be used for
>     checkpointing, it is very well suited for the observables group.
>   - Data about simulated or measured actuators or probes.
>
> Sticking a mandatory "particles" attribute makes no sense for those  
> usecases. As
> the need for it is frequent I still think that it should be a reserved  
> and
> optional attribute name.
>
> Pierre

Hi Pierre,

Thanks for providing these examples. The /observables group is intended  
for physical observables that are averages over a (sub)set of particles.  
And the primary target of H5MD are molecular simulations. Let me respond  
to your examples:

Thermostat variables should be stored inside /trajectory since the time  
evolution of each degree of freedom is resolved. Things like the  
thermostat energy, however, deserve a place in /observables. Here, the  
number of degrees of freedom may replace the particle number.

Experimental data of a different kind (e.g., the time series read from a  
voltmetre indicating a cantilever position) may go to a different root  
group. Alternatively, the user is free to set the "particle" number (or  
number of d.o.f.) to 1.

For the state of a PRNG, I would prefer to store it inside /parameters as  
it heavily depends on the simulation program.

Does this answer your objections?

Felix