Re: [h5md-user] fields of observable group

[Felix Höfling]

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
> > http://en.wikipedia.org/wiki/Euclidean_group.
>
> 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.

Felix