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

From: Felix Höfling
Subject: Re: [h5md-user] tentative of synthesis: parameters, box size, particle number
Date: Fri, 07 Oct 2011 15:38:01 +0200
User-agent: Opera Mail/11.51 (Linux)

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>:
Hi everyone,

There has been a lot of traffic on the list and I couldn't keep up. I'll try to make a synthesis of my suggestions, remarks and questions.

Please, if possible, keep the discussion in this single thread so as to remain focused on these items.

1. parameters "subgroups"
- I think it is a good idea to devise a few (let us keep it to a minimum) shared parameters and to put program parameters in "/parameters/program_name". - In my opinion, time-dependent information should not be in "parameters" but in "observables".

The idea behind moving 'particle_number' and 'box' to /parameters was that they should become mandatory for a H5MD file, while the /observables group is optional. I have encountered several situations where both information is essential for the further interpretion of the data, independent of where the data come from (trajectory or observables). Of course, they could be time-dependent datasets (as we have in both trajectory and observables so far).

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
- The offset should be given, each in their "H5MD containter" with step and time. - How different is what we do with respect to, for instance, PDB or gromacs ? see the manual of gromacs, chapter 3, §3.1 and §3.2 at http://www.gromacs.org/ second news item or direct link ftp://ftp.gromacs.org/pub/manual/manual-4.5.4.pdf
      pdb http://www.wwpdb.org/documentation/format33/sect8.html
Good question, we should look that up.

- If we put all of that in "observables" (not parameters), then a H5MD file with only the trajectory group will be useless. Do we agree on that ?
I agree, that's why I would like to move it to the parameters group.

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'?

Best regards,

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