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Re: [h5md-user] tentative of synthesis: parameters, box size, particle n

From: Pierre de Buyl
Subject: Re: [h5md-user] tentative of synthesis: parameters, box size, particle number
Date: Mon, 10 Oct 2011 12:04:29 +0200

Le 7 oct. 2011 à 15:38, Felix Höfling a écrit :

Am 07.10.2011, 08:46 Uhr, schrieb Pierre de Buyl

Le 15 sept. 2011 à 18:09, Felix Höfling a écrit :
Am 14.09.2011, 09:39 Uhr, schrieb Pierre de Buyl <address@hidden>:
Please, if possible, keep the discussion in this single thread so as to remain focused on these items.
1. parameters "subgroups"
Well, "observables" is, in my view, all that changes during the simulation, which is the case of the box size. The box volume, for instance, is a proper physical observable.

Sure (although a fixed box size would be a bit boring).

2. box size
A file should always, in my opinion, contain the observables group.
I go on after point 3.

This is to be discussed. I prefer a separate paramters group which is
mandatory, the trajectory or observables group may be present or not,
independently of each other. A H5MD file may also used as input of a
simulation, then the trajectory group makes perfectly sense while
'observables' should contain the outcome of the simulation. And there are
other parameters like space dimension that would not fit well into the
observables group.
Konrad and Peter, what do you think?

3. particle numbers
- I prefer the option where the data is in a single dataset [:][N_species].
   - It should be in "observables".
- It should not be mandatory, as some simulation/experiments may work with no "particle number" or with a fixed particle number, in this situtation having a time-dependent dataset is overkill.
An MD simulation without particles appears weird to me ... What do you mean with that? The time-dependent dataset could contain a single entry only, of course, which would be valid for all later times (until the next 'update' if it exists).
Well, I hope H5MD will be able, at some point, to store
   - MD simulations. reasonable expectation :-)
- Experimentally relevant structures (crystallography data, for instance) so that one can put it into a simulation program. - "Only" the observables: Sometimes, I don't need the full trajectory. So I want to copy the H5MD file without the trajectory group. I still keep, thanks to the observables group, info on energy conservation, center of mass motion for selected colloidal compounds, chemical kinetics, box size, ... - Other kind of simulations, for instance lattice or kinetic simulations. In the former, trajectory (or a newly-named group) would contain the state of the lattice sites while in the latter, you may store only distributions (space dependent, position dependent or dependent on both).

I'm not sure whether H5MD shall cover all types of simulations. I prefer
to stick to particle-based methods.
I've had already some need to store concentration fields or density
distributions. Shall we agree on a common format here as well, or would
this be too early? While time-dependent fields (a field depends on
position in addition) fit well into a subgroup /observables/fields
(including some information on the position grid), distributions are not
time-dependent. Does that justify a root group 'distributions'?

These are only plans for use of H5MD, not especially something that would
be part of the specification. But the storage, for instance, of the
time-dependent observables in the H5MD manner makes it worthwhile to
consider other uses.

But none of this is meant for immediate inclusion (even, for no inclusion
at all) in H5MD. This was just to support the discussion on the
organization of the file.

I think that we should agree on a simple criterion for "observabes", for
     - any time-dependent data should go in observables.
     - all data needed to start the simulation (number of dimensions, ...)
should go in parameters.


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