Hi all,
I'm relatively new to using Jmol, and wondered if you could help me with a
problem.
I would like to visualise the electron isodensity surface in a crystal, and
then repeat the density through repeat units of the unit cell.
I have a .cube file, from which I can plot the density using the command:
$ load "Si2.cube"
$ isosurface rho 0.08 "Si2.cube"
Si2.cube is generated from a CASTEP run, and the castep2cube tool, it is of the
primitive (2 atom) unit cell.
If I use this file for both the geometry and the isodensity surface, I cannot
appear to draw repeat units of the atoms, eg with:
$ load "" { 2 2 2 }
The same 2 atom unit cell is drawn.
One alternative I tried was to use the .cell CASTEP file for the geometry and
then superimpose the surface.
$ load "Si2.cell" { 2 2 2 }
$ isosurface rho 0.08 "Si2.cube"
This plots the required supercell of the Si2. But the isosurface is only
displayed in the volume of the original unit cell. It is difficult to visualise
the electron density in the crystal from looking at the isosurface in a single
repeat unit.
Is there a way to duplicate the isodensity surface throughout the repeated unit
cell?
Finally, is there a way from transforming from the primitive to the
conventional (cubic) unit cell representation in Jmol? If only the primitive
cell is used, the displayed geometry is long and thin, and not ideal to see the
diamond structure of silicon.
Thanks in advance for your help.
Kind regards,
Dan Jones
------------------------------------------------------------------------------
Live Security Virtual Conference
Exclusive live event will cover all the ways today's security and
threat landscape has changed and how IT managers can respond. Discussions
will include endpoint security, mobile security and the latest in malware
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
_______________________________________________
Jmol-users mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/jmol-users
