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Re: [h5md-user] New commits, "id" and rc

From: Felix Höfling
Subject: Re: [h5md-user] New commits, "id" and rc
Date: Tue, 31 Jul 2012 17:45:23 +0200
User-agent: Opera Mail/12.00 (Linux)

Hi Pierre,

I apologise for having been silent over such a long time. I've been pretty busy with another project and have done neither much programming nor simulations lately, although I did some data analysis of H5MD files. I think the proposed H5MD format is in a good shape for a first release and has seen some testing in a few applications so far.

Regarding additional datasets in trajectory like "id": we may suggest a commonly used name, but not enforce that such datasets are present. This would be in line with "species" or "force" and the "observables" group.

I have some minor suggestions for "observables", see the attached commit. Mainly, I think we should make it possible to have subgroups for storing partial pressures or partial energy contributions. Global quantities shall be stored at the top level still. If you agree I will upload the commit.

@Peter: If I remember correctly, in HALMD/master the box group is currently created in the trajectory group, which makes the iteration over particle groups a bit cumbersome. So I was glad to see that it is not so in the H5MD proposal (I already wanted to suggest moving it somewhere else.)

Some more comments:

– We shall agree on either British or American orthography (organization vs. standardised).

– The group "profiling" may be dropped and be considered as program-specific (it is not forbidden by the format to store such groups at the root level).

– For the future, I would find the following root groups useful, bearing in mind that the format must not be overspecified:

"dynamics" for storing time correlation functions like the mean-square displacement, such data can not be interpreted as a time series and the datasets will thus have a very different structure

"structure" for storing static correlation functions like the static structure factor or the pair distribution function. These data, however, may be interpreted as a time series (including averages over finite pieces of the simulation run) and we have to discuss about a sensible structure and place for such data. In contrast to simple observables, they carry additional parameters like a wavenumber grid and do not necessarily belong to a single simulation step.

"fields" for storing binned quantities like a one-dimensional density profile or a three-dimensional velocity field. Such data sets describe the transition from particle-based MD to continuous (albeit discretised) fields. From a technical point of view, they have similar requirements like the static structure factor.

Best wishes,

Am 28.07.2012, 22:32 Uhr, schrieb Pierre de Buyl <address@hidden>:

Hi all,

I'd like to know wether there are remarks on my recents commits.

H5MD has stabilized since some time and is in a very usable state. I've cleaned
a bit the draft.

I'd like to release a "0.1" version of H5MD. As a first step, I'd like to tag
the current (modulo "id", see below) version as 0.1-rc1.

Before that, I think that the "id" information should be included. Defining it already seems a way to future proof a building block that matters in the case of
spatial sorting of particles, including parallel coding.

"id" would be included in a similar way to "position": in the "trajectory" group, and of shape [var,N] where var is the time stepping and N the number of

Comments and input welcome :-)



PS: despite the low activity on the list, I believe that at least Felix, Peter and me are still using the file format for our software, which gives sense to
agree on a release.

Dr Felix Höfling
Max Planck Institute for Intelligent Systems
(formerly Max Planck Institute for Metals Research)
Heisenbergstr. 3
70569 Stuttgart

Phone:  +49 711 689 1938
Fax:    +49 711 689 1922

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