From: Andrei Tudor (andrei.tudor.1_at_ulaval.ca)
Date: Mon Aug 12 2013 - 10:40:27 CDT
Hello,
Thank you for your answers I think I understood the dx format. Just to make sure I got it, In the next header where delta is 1 for x y and z. This means that the distance between each point is 1 angstrom. So the first point (x0 y0 z0) is at origin and the second (x0 y0 z1) is at 1 angstrom from the origin along the z axis, at -54.5 -36.5 -58.7.
# Data calculated by the VMD volmap function
object 1 class gridpositions counts 113 111 110
origin -54.5 -36.5 -58.5
delta 1 0 0
delta 0 1 0
delta 0 0 1
object 2 class gridconnections counts 113 111 110
object 3 class array type double rank 0 items 1379730 data follows
0 0 0
I hope that this is right.
Andrei
________________________________________
De : owner-namd-l_at_ks.uiuc.edu [owner-namd-l_at_ks.uiuc.edu] de la part de Norman Geist [norman.geist_at_uni-greifswald.de]
Date d'envoi : 12 août 2013 02:47
À : 'Axel Kohlmeyer'
Cc : Namd Mailing List
Objet : AW: namd-l: AW: vmd-l: Occupancy maps
Hi Axel.
Ok, now I got it. Your formerly post just contained the link to the
description of a periodic grid, therefore I thought VMD expects such a one.
Now I see it's vice versa.
Thank you.
Norman Geist.
> -----Ursprüngliche Nachricht-----
> Von: Axel Kohlmeyer [mailto:akohlmey_at_gmail.com]
> Gesendet: Montag, 12. August 2013 08:15
> An: Norman Geist
> Cc: Andrei Tudor; Namd Mailing List
> Betreff: Re: namd-l: AW: vmd-l: Occupancy maps
>
> 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
> > 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
> > 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).
>
> 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
> > 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]
> >> 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.
This archive was generated by hypermail 2.1.6 : Tue Dec 31 2013 - 23:23:33 CST