VMD-L Mailing List

From: Axel Kohlmeyer (axel.kohlmeyer_at_theochem.ruhr-uni-bochum.de)
Date: Tue Aug 24 2004 - 09:56:02 CDT

On Tue, 24 Aug 2004, Keith Refson wrote:

KF> Dear VMD developers,

hello keith,

KF>
KF> I am seeing a problem displaying periodic images of the
KF> attached PDB file. The spatial relationship between the
KF> periodic images is clearly not correct for repeats in the
KF> Y and Z directions, but appears OK only for X. This is most
KF> clearly seen by choosing a "dynamicbonds" representation for
KF> "name Mg00 O00" and CPK for "all". The MgO layer should
KF> be an infinite periodic solid.
KF>
KF> I guess that the periodic image generation is not able to
KF> cope with the non-orthogonal axes of the cell.

exactly. IIRC, this has been discussed on VMD-L and
i occasionally get (painfully) reminded myself.

KF>
KF> A couple of supplementary questions:
KF>
KF> 1) Is there any way of adding bonds between periodic images
KF> - for a layer structure this would be the correct display mode.

not directly. the best suggestion so far, was to write a small
program that adds copies (of parts) of the unit cell to the
file and then have the periodic images overlap.

KF> 2) Is there any way of actually drawing the unit cell box?

if you create a faked gaussian cube file, you can use the
isosurface representation.

alternatively, you can draw directly with vmd graphics commands,
see, e.g.
http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/cpmd-vmd/part2.html#chap4_sect6

for an example (using a cubic cell). this can probably be easily
adapted to your needs.

hope that helps,
        axel.

KF> Thanks
KF>
KF> Keith Refson
KF> 

-- 
=======================================================================
Dr. Axel Kohlmeyer                        e-mail: axel.kohlmeyer_at_rub.de
Lehrstuhl fuer Theoretische Chemie          Phone: ++49 (0)234/32-26673
Ruhr-Universitaet Bochum - NC 03/53         Fax:   ++49 (0)234/32-14045
D-44780 Bochum  http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/
=======================================================================