Feature Requests item #3565251, was opened at 2012-09-06 02:30
Message generated for change (Comment added) made by drdanj
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Category: None
Group: None
Status: Open
Priority: 5
Private: No
Submitted By: Daniel Jones (drdanj)
Assigned to: Nobody/Anonymous (nobody)
Summary: Periodic repetition of coloured planes
Initial Comment:
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.
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>Comment By: Daniel Jones (drdanj)
Date: 2012-09-10 08:03
Message:
Hi Bob,
Sorry for the delay, just got round to trying it, works like a charm!
Thanks very much,
Dan
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Comment By: Bob Hanson (hansonr)
Date: 2012-09-08 04:54
Message:
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.
----------------------------------------------------------------------
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