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

[Felix Höfling]

Am 10.01.2014, 11:14 Uhr, schrieb Konrad Hinsen
<address@hidden>:

> Felix Höfling writes:

>  > 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?
>
> Sounds good in principle, but again the devil is in the details.
>
> 1) Having both "minimum" and "maximum" is redundant, as the difference
>    must be "edge".
It's not fully redundant as Olaf pointed out, because the difference may
exceed the edge length by a skin width.

> 2) Any such specification should be optional, for trajectories that
>    don't make any promises.
Of course. I think the minimum/maximum fields would best go to the
particles/.../position group, not in the box.

> 3) In simulation of small-molecule liquids, it is common to apply
>    periodic boundary conditions to the centers of mass of the molecules,
>    rather than to individual atoms. The guarantee on the positions thus
>    applies to something else than the stored coordinates.
>
>    It's OK with me to say that no minimum/maximum should be specified
>    in this situation, but I think it's worth saying so explicitly to
>    avoid misunderstandings.
Sounds like a similar situation as with the skin due to lazy updates of
the image vectors. I suggest to skip the minimum/maximum fields in this
case, or to specify a (not necessarily tight) bounding box of actual atom
positions.

I have removed the offset from the box specification and have added a
suggestion for minimum/maximum, which I called bounding_box. (Since a
minimum value would have to be taken by any of the positions, strictly
speaking.)

Felix