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


From: Olaf Lenz
Subject: Re: [h5md-user] fix remaining imprecisions - particle position
Date: Wed, 8 Jan 2014 15:58:35 +0100

Hi all!

Happy New Year!

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. 

To make that clear, I propose to change the last paragraph (starting with "For instance...") with the following paragraph:

    If the component $d$ of `box/boundary` is set to "none" (see below) and `image` is set, the value of the corresponding component $d$ of `image` has to be silently ignored. If the component $d$ of `box/boundary` is set to "periodic", this does neither mean that the element `image` has to exist nor that the position has to be within the primary box. 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 taken from `position`, $\vec a_i$ is taken from `image`, and $\vec L$ from `box/edges`.

Furthermore, I would propose to extend the paragraph "Simulation box" -> "boundary" as follows:

  For those components where `boundary` is set to "none", any value of `edges` or `offset` must be silently ignored.

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?

Olaf


2014/1/7 Felix Höfling <address@hidden>
Am 10.12.2013, 11:54 Uhr, schrieb Felix Höfling <address@hidden>:


* For "position", I can't recall the criterion whether the data are interpreted as "wrapped" or "unwrapped". This should be stated clearly. (BTW, would "folded coordinates" be better instead of "wrapped coordinates"?)


Happy New Year to everybody following the list!

The interpretation of the position data needs clarification still. I have made a suggestion in commit 0989a65, which reads now:

`position`
:   An element that describes the particle positions as coordinate vectors of
    `Float` or `Integer` type. If the element `image` is present as well, the
    data are interpreted as periodically reduced coordinates along the periodic
    directions of the simulation box. Otherwise, the data indicate the absolute
    position in space.

`image`
:   An element that represents the periodic image of the box in which each
    particle is actually located and allows one to unfold periodically reduced
    positions. For the case of time-dependent data, the `image/value` dataset
    is of the same shape as `position/value` and is either of `Float` or
    `Integer` type.

    For instance, given a cuboid box with periodic boundaries, let $\vec r_i$
    be the reduced position of particle $i$ taken from `position`, $\vec a_i$
    its image vector from `image`, and $\vec L$ the space diagonal of the box,
    then component $j$ of the absolute position $\vec R_i$ is given by
    $R_{ij} = r_{ij} + L_j a_{ij}$.

Feedback is most welcome!

Best regards,

Felix




--
Dr. rer. nat. Olaf Lenz
Institut für Computerphysik, Allmandring 3, D-70569 Stuttgart
Phone: +49-711-685-63607

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