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Re: [h5md-user] [EXTERNAL] Re: H5MD box group

From: Olaf Lenz
Subject: Re: [h5md-user] [EXTERNAL] Re: H5MD box group
Date: Wed, 30 Apr 2014 11:17:32 +0200

Konrad was faster in his reply than I was. I have nothing to add to his explanation.


2014-04-30 8:58 GMT+02:00 Konrad Hinsen <address@hidden>:
Hi David,

 > The main reason I’m interested in an offset element is because of the way LAMMPS does
 > its boundaries. LAMMPS stores its triclinic bounding box as [xlo, xhi], [ylo, yhi],
 > [zlo, zhi], [xy, xz, yz].

Thanks for your explanations. To make sure I interpret them correctly,
here's my summary of the past discussions on this list in the light of
what you describe.

1. The topology of a periodic system is fully described by a set of
   basis vectors. There is no need for any additional information
   for defining the physics of a simulation universe. In particular,
   there is no "box" with any physical properties of relevance, even
   though it can be convenient to think in terms of a "simulation box".

2. Many simulation programs adopt additional conventions for technical
   convenience, such as "all atom coordinates are in [0, X)" or
   "the centers of mass of all molecules are in [-X/2, X/2).

3. Some programs use the additional freedom of having coordinates
   "out of the box" for arranging molecules nicely for visualization.

The idea of storing a "box offset" is usually related to point 2.
However, having the offset in the trajectory is of use only if
the conventions are fully respected, and also written down somewhere.
Since there are too many different conventions, and we didn't want
to decide on a single one, we ended up not having a box offset in
the basic H5MD specification.

My understanding of your proposal is that LAMMPS has its own
convention as well, and that you want to store trajectories that
respect and document this convention. I think this would be best done
in the form of an H5MD module that specifies not only how and where to
store the offset, but also which promises about the coordinates it

BTW, I am really happy about your project, since LAMMPS is a much more
widely used program than any of those that support H5MD today. It's
a big step towards world domination for H5MD ;-)

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

Dr. rer. nat. Olaf Lenz
Institut für Computerphysik, Allmandring 3, D-70569 Stuttgart
Phone: +49-711-685-63607

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