AW: vmd-l: Occupancy maps

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Mon Aug 12 2013 - 00:14:36 CDT

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
the file. The delta scaling factors usually just give the spacing between
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
be able to translate the grid points to cartesian coordinates again, to
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
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).
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
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
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 info like origin etc
>
> [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

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