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Re: [h5md-user] fields of observable group

From: Felix Höfling
Subject: Re: [h5md-user] fields of observable group
Date: Fri, 09 Sep 2011 15:25:56 +0200
User-agent: Opera Mail/11.51 (Linux)

On Wed, 07 Sep 2011 11:03:19 +0200, Konrad Hinsen <address@hidden> wrote:

On 6 Sep, 2011, at 11:00 , Felix Höfling wrote:

If we restrict to isometric transformations, the matrix shall be
orthogonal. This appears to be pretty general already, see

Indeed. I don't see any point in going beyond isometric transformations for atomic systems.

Good. Is the qualification "for atomic systems" necessary? What about, e.g., complex-shaped colloids (ellipsoids, tetraeders, ...), but there isometric transformations should do the job as well, right?

It think about two optional attributes "transformation" and "shift"
attached to the "box" group. They hold datasets of ranks 3 and 2,
respectively: a square matrix and a vector for each copy of the stored
particle coordinates.

For the applications I can think off, it would be excessive to store transformations for each configuration (i.e. each time step). The situation of variable box size and shape can be solved by storing the transformations in fractional coordinates, as it is the habit in crystallography. A truncated octahedral, for example, would have a symmetry transformation saying "translate by 1/2 of each lattice vector".

Fractional coordinates is an excellent solution. Then, the symmetry transformations shall be stored as (static) attributes to the box group.


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