VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Thu Aug 01 2013 - 05:05:03 CDT

On Thu, Aug 1, 2013 at 10:43 AM, Norman Geist
<norman.geist_at_uni-greifswald.de> wrote:
> Hi experts,
>
>
>
> while I’m in the NAMD mailing list since years, now I needed to join here
> too, to find some help regarding the following problem.
>
>
>
> Unfortunately I’m sure having found a BUG in the DX file format reader in
> VMD. As it seems and as I understood the corresponding code, the dx reader
> computes the box size (needed to map the scalar data back to angstom) from
> gridsize and gridspacing like: (pseudo code)
>
>
>
> Box[X|Y|Z] = gridsize[X|Y|Z] * ((gridspacing[X|Y|Z]-1) > 0 ?
> (gridspacing[X|Y|Z]-1) : 1)
>
>
>
> But this doesn’t make sense. The delta values for each axis already tells
> the spacing between the grids. Multiplied with the number of grids per axis
> is already supposed to result in the correct box dimensions. But the current
> implementation always misses one times the gridspacing, so why -1??

to turn a "general grid" into a "periodic grid".

http://www.xcrysden.org/doc/XSF.html#__toc__12

consider this simple example, which results in a proper cube.

axel.

> As I’m currently writing a TCL script, that computes the “per particle”
> temperature and puts them together in a configurable grid, which I wanted to
> visualize via the volume slice representation, this behavior is unusable for
> me. As I sometimes have quite large gridspacings here, for example to show
> the temperature distribution in one axis only. Like a box having {140 40 40}
> and I use spacing {10 40 40} would result in a X-distribution only. But also
> when using 1A spacing, the volume slice will be 1 times spacing too small in
> all upper box boundaries what makes it impossible to assign the data to the
> right atoms visually. To show that this is not a problem of my dx files, let
> me say that also the VMDs PME Electrostatics dx files show the same
> behavior, although both files are correct due the opendx standard.
>
>
>
> Some more examples:
>
>
>
> Gridsize Spacing expected_Box resulting_Box
>
> 1x 1 x 1 30x30x30 30x30x30 30x30x30
>
> 3 x 3 x 3 10x10x10 30x30x30 20x20x20
>
> 6 x 6 x 6 5 x 5 x 5 30x30x30 25x25x25
>
> 10x10x10 3 x 3 x 3 30x30x30 27x27x27
>
>
>
> For now I can cheat by saving my dx files with wrong delta values, so the
> resulting box size fits, but what about other dx files, also from PME?
>
>
>
> Please find some time to fix this.
>
>
>
> Thank you very much
>
>
>
> Norman Geist 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
International Centre for Theoretical Physics, Trieste. Italy.