On Thu, Jan 09, 2014 at 09:36:18AM +0100, Konrad Hinsen wrote:
Olaf Lenz writes:
> In some cases it makes sense to store the particle coordinates in
> absolute coordinates in a periodic system even when they are
> outside the primary box (for example when tracking the MSD of the
> particle). In that case 'image' would not be defined. Also, it
> might make sense to store coordinates outside the primary box even
> when 'image' is used (for example, it is common practice that
> particles can walk out of the box up to skin/2 before the image is
> updated for performance reasons.
There is one more case I have encountered in practice: all positions
are folded into the box and nothing whatsoever is stored to permit the
reconstruction of absolute coordinates. This is appropriate e.g. for
many
Monte-Carlo algorithms where the notion of a trajectory in time doesn't
exist, or doesn't matter for analysis.
I have the impression that with a minor update one can use the following
reasoning(assuming cuboid geometry):
read position
if coordinate i is of type 'periodic' and 'image' is present
then
compute position_i += image_i*edges_i
else
position is fine the way it is
end if
The modification would be to remove "Otherwise, the data indicate
absolute
positions in space." Then, the following cases are ok:
- periodic position, with no 'image', such as the Monte Carlo mentioned
above.
- periodic positions, with 'image'
- absolute position: as long as there is no 'image' element, you can
store
absolute positions even if the boundary is periodic.
Olaf, does that reply to your query about the MSD?
Pierre