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Re: [h5md-user] box and observables

From: Konrad Hinsen
Subject: Re: [h5md-user] box and observables
Date: Fri, 20 Sep 2013 13:01:14 +0200

Peter Colberg writes:

 > Great! If it's rather small, please feel free to send the compressed
 > output of "h5dump -A" and the Mosaic file. I am sure some of the
 > subscribers would be interested to see a typical example of which
 > data elements are needed for a protein simulation.

Here it comes. There is no separate Mosaic file, all the Mosaic data
is in the group "mosaic" which sits at the root level right next
to "h5md" and the other groups.

If you want to get an idea about what is stored inside the Mosaic group,
it's probably better to look at an XML file with a Mosaic definition
for a protein:


The XML and HDF5 representations of Mosaic are exactly interconvertible,
but optimized for different types of use.

 > Do you already have suggestions for a H5MD protein module?

I could write down a complete specification by now, but I prefer to
have tested all aspects of the specification in real life before doing
so. Which is what I am currently working on. The missing pieces
are (1) periodic boundary conditions (needs extensions to pyh5md) and
(2) subgroups defined by Mosaic "selections" (needs to be implemented
in my trajectory writer and in the viewer).

 > So it is not a mistake; but I would agree it seems inconsistent that
 > box is stored for each subsystem in "particles", and only stored once
 > in "observables".

My understanding is that the "box" information in each subgroup under
"particles" can be different. Otherwise, why have it in each subgroup?
But if it can be different, then which one should be linked to

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
ORCID: http://orcid.org/0000-0003-0330-9428
Twitter: @khinsen

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