VMD-L Mailing List

From: Edward Lyman (edward.lyman_at_gmail.com)
Date: Mon Mar 11 2013 - 20:23:55 CDT

and...I figured it out. put the z loop on the outside.

On Mon, Mar 11, 2013 at 5:41 PM, Edward Lyman <edward.lyman_at_gmail.com>wrote:

> Hi all,
>
> I am trying to figure out how the values are listed in the dx file written
> by vmd. Below I copy a reply from Axel from a couple years back to a
> similar Q. My question regards the ordering of the values... does
>
> *ordered z fast, y medium, and x slow
>
> *mean that as I roll through the values in the dx file, I read first a
> row along z, then move one grid point along y and read another row of z,
> and repeat until I have read a slice in the first yz plane? Then, move one
> grid point in x and read another plane of yz values?
>
> In other words, if I wanted to read the data into a 3 dim array indexed by
> x, y, and z, what should the order of my loops be?
>
> Best,
> Ed
>
>
> *> here is the blurb from the dx file reader in VMD that may be helpful: *
> *> *
> *> /* DX potential maps *
> *> Â * *
> *> Â * Format of the file is: *
> *> Â * # Comments *
> *> Â * . *
> *> Â * . *
> *> Â * . *
> *> Â * object 1 class gridpositions counts xn yn zn *
> *> Â * origin xorg yorg zorg *
> *> Â * delta xdel 0 0 *
> *> Â * delta 0 ydel 0 *
> *> Â * delta 0 0 zdel *
> *> Â * object 2 class gridconnections counts xn yn zn *
> *> Â * object 3 class array type double rank 0 items { xn*yn*zn }
> [binary] *
> *> data follows *
> *> Â * f1 f2 f3 *
> *> Â * f4 f5 f6 f7 f8 f9 *
> *> Â * . *
> *> Â * . *
> *> Â * . *
> *> Â * object "Dataset name" class field *
> *> *
> *> Â * Where xn, yn, and zn are the number of data points along each
> axis; *
> *> Â * xorg, yorg, and zorg is the origin of the grid, assumed to be in
> angstroms; *
> *> Â * xdel, ydel, and zdel are the scaling factors to convert grid units
> to *
> *> Â * angstroms. *
> *> Â * *
> *> Â * Grid data follows, with a single or multiple values per line
> (maximum *
> *> Â * allowed linelength is hardcoded into the plugin with ~2000 chars),
> *
> *> Â * ordered z fast, y medium, and x slow. *
> *> Â * *
> *> Â */ *
>