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Re: [h5md-user] box and observables
From: |
Konrad Hinsen |
Subject: |
Re: [h5md-user] box and observables |
Date: |
Wed, 25 Sep 2013 11:42:37 +0200 |
Peter Colberg writes:
> > Next, the reader: if there is a single box group but differently
> > sampled positions for different subsystems, reading the box
> > information is a lot of work and slow.
>
> Well, this is the essence of the step/time scheme.
>
> I added a section [1] on the use of the step/time datasets, which
> refers to the binary search, upon which the step/time scheme relies.
> This is the basic building block for any H5MD program.
>
> [1] http://h5md.nongnu.org/implementation.html
So the idea is that we have only a single box information for the
whole trajectory, right? My impression is that Felix still disagrees.
In that case, the following sentence must be removed from the
specification:
A specific requirement for box groups inside particles is that the
step and time datasets exactly match those of the corresponding
position groups, which may be accomplished by hard-linking the
datasets.
If left in, this indirectly implies that all position data must be
sampled on the same time grid.
> For the case of all data that depends on the box for interpretation,
> the replicated box groups complicate the matter, while providing no
> benefit, as a step/time lookup is needed anyway.
I agree that if there is only a single set of box information per
trajectory, then it would be best to have it once in a single place.
Konrad.
--
---------------------------------------------------------------------
Konrad Hinsen
Centre de Biophysique Moléculaire, CNRS Orléans
Synchrotron Soleil - Division Expériences
Saint Aubin - BP 48
91192 Gif sur Yvette Cedex, France
Tel. +33-1 69 35 97 15
E-Mail: research AT khinsen DOT fastmail DOT net
http://dirac.cnrs-orleans.fr/~hinsen/
ORCID: http://orcid.org/0000-0003-0330-9428
Twitter: @khinsen
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- Re: [h5md-user] box and observables, (continued)
- Re: [h5md-user] box and observables, Konrad Hinsen, 2013/09/23
- Re: [h5md-user] box and observables, Felix Höfling, 2013/09/23
- Re: [h5md-user] box and observables, Peter Colberg, 2013/09/23
- Re: [h5md-user] box and observables, Felix Höfling, 2013/09/24
- Re: [h5md-user] box and observables, Peter Colberg, 2013/09/24
- Re: [h5md-user] box and observables, Konrad Hinsen, 2013/09/24
- Re: [h5md-user] box and observables, Peter Colberg, 2013/09/24
- Re: [h5md-user] box and observables, Peter Colberg, 2013/09/24
- Re: [h5md-user] box and observables, Felix Höfling, 2013/09/25
- Re: [h5md-user] box and observables, Felix Höfling, 2013/09/25
- Re: [h5md-user] box and observables,
Konrad Hinsen <=
- Re: [h5md-user] box and observables, Felix Höfling, 2013/09/25
- Re: [h5md-user] box and observables, Konrad Hinsen, 2013/09/25
- Re: [h5md-user] box and observables, Peter Colberg, 2013/09/25
- Re: [h5md-user] box and observables, Felix Höfling, 2013/09/25
- Re: [h5md-user] box and observables, Peter Colberg, 2013/09/25
- Re: [h5md-user] box and observables, Pierre de Buyl, 2013/09/24
- Re: [h5md-user] box and observables, Peter Colberg, 2013/09/23
- Re: [h5md-user] box and observables, Felix Höfling, 2013/09/23
- Re: [h5md-user] box and observables, Peter Colberg, 2013/09/23
- Re: [h5md-user] box and observables, Pierre de Buyl, 2013/09/24