Re: [h5md-user] fix remaining imprecisions - particle position

[Felix Höfling]

Am 09.01.2014, 09:36 Uhr, schrieb Konrad Hinsen
<address@hidden>:

> 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.
>
> So I would like to propose a minor change to your description:
>
>  > The component $d$ of the absolute position of particle $i$ is then
>  > computed as $R_{id} = r_{id}  + L_d a_{id}$, where $\vec r_i$ is
>
> If the simulation permits the definition of an absolute position for
> each particle, the absolute position of particle $i$ is then ...

In some sense, this case is already included in the current version. If
`image` is absent, the `position` data are taken as absolute positions
(which then are all inside the box). However, the file format doesn't say
anything about the existence of a meaningful (continuous) trajectory. Do
you see a need for such information?

>  > Finally, I am still wondering about the meaning of the `offset`
>  > field, given that we give no guarantees on the limits of the
>  > positions. What could anybody do with this value?
>
> I have been wondering about this for a while...

Originally, `offset` together with `edges` was meant to provide the range
of folded particle positions. As of Olaf's pointing at the box skin, this
use has become meaningless. As nobody is using `offset` AFAIK, we may drop
it in favour of `minimum` and `maximum` which provide a guarantee on the
range of particle positions. What do you think?

Felix