VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Thu Aug 01 2013 - 05:06:09 CDT

sorry forgot to include the test file:

cat > text.dx <<EOF
object 1 class gridpositions counts 3 3 3
origin 0 0 0
delta 1 0 0
delta 0 1 0
delta 0 0 1
object 2 class gridconnections counts 3 3 3
object 3 class array type double rank 0 items 27 data follows
0 0 0
0 1 0
0 0 0
0 1 0
1 1 1
0 1 0
0 0 0
0 1 0
0 0 0
object "test data" class field
EOF

On Thu, Aug 1, 2013 at 12:05 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
> 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. 

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