From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Tue Aug 13 2013 - 03:28:25 CDT
Sounds correct, but 2nd point is at -54.5 -36.5 -57.5
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: Montag, 12. August 2013 17:40
> An: Norman Geist; 'Axel Kohlmeyer'
> Cc: Namd Mailing List; vmd-l_at_ks.uiuc.edu
> Betreff: RE : namd-l: AW: vmd-l: Occupancy maps
>
> 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.
>
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