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#195 Periodic repetition of coloured planes

None
closed-fixed
nobody
None
5
2013-03-26
2012-09-06
Daniel Jones
No

If I have a system and I wish to display some function as a colour map projected on a plane, I can do this in Jmol using
$ isosurface plane {x y z}{x1 y1 z1}{x2 y2 z2} map "data.dat"

If the system is made periodic and I want to display a supercell, because it's easier to see the system when you look at more than a single repeat unit, I can reload a supercell in Jmol using e.g.
$ load "<model_file>" { 2 2 2 }

I now want to make a colour map onto a plane of some data
$ isosurface plane {x y z}{x1 y1 z1}{x2 y2 z2} map "data.dat"
This only plots a plane in the original repeat unit.

If I then use
$ isosurface lattice { 2 2 2 }

This makes periodic repeats of the plane (and displays multiple planes)

Is it possible to make periodic representation of the data, and map it to a larger single plane in the visualisation? Perhaps a 2D equivalent command for the
$ isosurface lattice
command.
e.g.
$ isosurface extendPlane { x y }.
Might work.

Discussion

  • Bob Hanson
    Bob Hanson
    2012-09-08

    Daniel, I think I have it. Please try the latest rendition of http://chemapps.stolaf.edu/jmol/Jmol-13.zip

    This version of Jmol includes a new isosurface option. You will use the LATTICE option after the MAP keyword to indicate that the mapped data itself is periodic and that you want to extend the plane over a translational lattice associated with that data set:

    isosurface plane {x y z}{x1 y1 z1}{x2 y2 z2} map LATTICE {2 2 2} "data.dat"

    Let's see if that does the trick.

     
  • Daniel Jones
    Daniel Jones
    2012-09-10

    Hi Bob,

    Sorry for the delay, just got round to trying it, works like a charm!

    Thanks very much,
    Dan

     
  • Bob Hanson
    Bob Hanson
    2012-09-10

    Please be sure to get the latest version of Jmol -- http://chemapps.stolaf.edu/jmol/Jmol-13.zip It was while working on this that I discovered the problem with saving isosurface information in the state.

     
  • Bob Hanson
    Bob Hanson
    2013-03-26

    • status: open --> closed-fixed
    • milestone: -->