**From:** Axel Kohlmeyer (*akohlmey_at_gmail.com*)

**Date:** Mon Aug 12 2013 - 01:14:52 CDT

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On Mon, Aug 12, 2013 at 7:14 AM, Norman Geist

<norman.geist_at_uni-greifswald.de> wrote:

*> Hi Andrei,
*

*>
*

*> I'm was working with dx files just a week ago and so already know your
*

*> questions. I was writing a script creating own dx files to visualize the
*

*> temperature distribution through the simulation cell. You can just stay with
*

*> the header like it is. Just put in your own origin(simply the minmax lower
*

*> bounds) and delta values, aswell as a title for the data at the bottom of
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*> the file. The delta scaling factors usually just give the spacing between
*

the dx format as VMD reads it is described here:

http://www.ks.uiuc.edu/Research/vmd/plugins/molfile/dxplugin.html

*> the grid points. As dx is a scalar format, you do not need to save the
*

*> coordinates for each point in this way and so save a lot of disk space. To
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*> be able to translate the grid points to cartesian coordinates again, to
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*> visualize it, you need the scaling factors, which will also point to the
*

*> right box size if multiplied by gridsize. The delta values are computed for
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*> each dimension from boxsize/gridsize. But, for some reason I didn't
*

*> understand so far, VMD will compute the box size from delta*(gridsize-1).
*

i already explained that VMD expects a "general" and not a "periodic"

grid, i.e. the file is providing data for all corners of the described

voxels. that means for a single voxel, you need 8 (= 2x2x2) points,

for 8 (2x2x2) voxels correspondingly 27 (=3x3x3) grid points. for a

periodic data set, the values at the extremes are identical, for a

non-periodic data set, they are not.

is this so difficult to understand? where is the problem?

axel.

*> Therefore if you create own dx file and want the "volslice" to correctly fit
*

*> with the box bounds and the atoms, compute the delta from
*

*> boxsize/(gridsize-1) aswell.
*

*>
*

*> Im not sure if you understood the data block correctly.
*

*>
*

*>> 0 0 0 -> x0 y0 z0
*

*>> 0 0 0 -> x0 y0 z1
*

*>
*

*> I guess you meant:
*

*>
*

*>> 0 -> x0 y0 z0
*

*>> 0 -> x0 y0 z1
*

*>
*

*> Or:
*

*>
*

*>> 0 0 -> (x0 y0 z0) (x0 y0 z1)
*

*>
*

*> The data values will just follow each other. Every number represents one
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*> gridpoint, there are no coordinates. I guess the maximum number of points
*

*> per line was hardcoded in VMD to five. One value per line would also be
*

*> possible and valid.The Z rows, as you pointed out raises 1st, then Y. This
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*> means for a 2x2x2 grid, the data section would look like:
*

*>
*

*> 1.2 3.2 5.09 7.32 9.52 -> (x0 y0 z0) (x0 y0 z1) (x0 y1 z0) (x0 y1
*

*> z1) (x1 y0 z0)
*

*> 4.8 7.2 8.4 -> (x1 y0 z1) (x1 y1 z0) (x1 y1 z1)
*

*>
*

*> Good luck
*

*>
*

*> Norman Geist.
*

*>
*

*>> -----Ursprüngliche Nachricht-----
*

*>> Von: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] Im
*

*>> Auftrag von Andrei Tudor
*

*>> Gesendet: Freitag, 9. August 2013 18:27
*

*>> An: vmd-l_at_ks.uiuc.edu
*

*>> Betreff: vmd-l: Occupancy maps
*

*>>
*

*>> Hello,
*

*>>
*

*>> I am trying to understand the dx files that are made by volmap. This is
*

*>> what I understand until now:
*

*>>
*

*>> [header]
*

*>> header info like origin etc
*

*>> [/header]
*

*>>
*

*>> [data]
*

*>> 0 0 0 -> x0 y0 z0
*

*>> 0 0 0 -> x0 y0 z1
*

*>> 0 0 0 -> x0 y0 z2
*

*>> 0.001294 0 0 -> x0 y0 z3
*

*>>
*

*>> (...)
*

*>>
*

*>> 0 0 0 -> x0 y1 z0
*

*>> 0 0 0 -> x0 y1 z1
*

*>>
*

*>> (...)
*

*>>
*

*>> [/data]
*

*>>
*

*>> So each row of data represents a point on the grid and they are
*

*>> described as I have shown here.
*

*>> This is how I understood that dx works.
*

*>> What I didn't understand is what is represented in each point as 0 0 0.
*

*>> For example, on the row (0.001294 0 0) what does 0.001294 represent?
*

*>>
*

*>> Thank you,
*

*>> Andrei
*

*>
*

*>
*

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

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