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Re: [h5md-user] Offset

From: Konrad Hinsen
Subject: Re: [h5md-user] Offset
Date: Wed, 11 Sep 2013 13:13:14 +0200

Pierre de Buyl writes:

 > Some people work with [-L/2:L/2], others with [0:L].
 > offset is there so that users may dump their position data without
 > operation between memory and file, whatever box convention they use.

Do I conclude then that "offset" is supposed to be -L/2 in the first
case, and 0 in the second?

Olaf Lenz writes:

 > I was always wondering about the offset, but I didn't want to start that
 > discussion. Thanks, Konrad. :-/
 > The offset is mathematically irrelevant.

I agree.

 > I also do not see what the offset is needed for in the file.

I'd look at this from a different point of view: if it's there, what
information does it convey? What conclusion can a trajectory reader
draw from it?

 > The only case that I can think of where the offset might be useful is,
 > when it is somehow guaranteed that the positions are all within the
 > primary image that is defined by the offset and the edges.


 > Therefore, from my point of view, the offset is useless and can be
 > removed from the specs.

Or add a guarantee about the positions being in the primary image to
the specs. From my experience, that can be useful information to have.

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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