Re: [h5md-user] H5MD discussions

[Peter Colberg]

On Fri, Jun 17, 2011 at 06:04:14PM +0200, Felix Höfling wrote:
> Hi Pierre,
> 
> Am 17.06.2011, 17:39 Uhr, schrieb Pierre de Buyl <address@hidden>:
> 
> >>3) Specification of a box with non-orthogonal edges requires
> >>more than giving just two corners, it also requires some
> >>information about the angles. To me, it appears more direct if
> >>the edge vectors of the box would be stored for this general
> >>case. This would imply two datasets: "offset" and "edges", where
> >>the latter is a d×d matrix with the edge vectors as rows. For a
> >>cuboid box of lengths L_x, L_y, L_z centered around the origin,
> >>one would have:
> >>
> >>offset (-L_x/2, -L_y/2, -L_z/2)
> >>edges ((L_x, 0, 0), (0, L_y, 0), (0, 0, L_z))
> >>time (0)
> >>step (0)
> >>
> >>This suggestion contains some redundancy (e.g., the zeros), but
> >>appears the most general and manageable to me.
> >This is nice.
> >How is it redundant ?
> I thought one could save some numbers by specifying relative angles
> between the edges. But this is cumbersome, and maybe it requires the
> same amount of data.

The description of box via "edges" seems a good idea to me. For a
periodic box, the edges alone already provide a full description,
and the offset may be discarded by a reader if wished.

This is for example the case with VMD, which is only interested in the
unit cell edge lengths and angles, not its absolute offset. Therefore
the description with edge vectors seems more suitable than absolute
lower left / upper right corner coordinates.

http://www.ks.uiuc.edu/Research/vmd/plugins/doxygen/structmolfile__timestep__t.html

Peter

-- 
Peter Colberg
Chemical Physics Theory Group
Department of Chemistry
University of Toronto
Toronto, Ontario M5S 3H6
Canada
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Website: http://www.chem.utoronto.ca/~pcolberg/