Re: [Jmol-users] Visualising isodensity surfaces in crystals using Jmol

[Robert H. <ha...@st...>]

Hi, Dan,

Yes, the CASTEP reader is very good, and what you probably want to do is
first load the model as a CASTEP file, then add the surface. The advantage
then is that you get the full symmetry and unit cell of the model along
with the surface, and then you can do some thing simple such as

isosurface rho 0.08 "Si2.cube"
isosurface lattice {2 2 1}

this gives you  the periodicity that you are looking for.

We are working  very closely with CASTEP developers, so there is a lot
there you can do. Have you seen J-ICE? (Google that.)

Bob Hanson

On Mon, Sep 3, 2012 at 1:15 PM, Daniel Jones <
dan...@ma...> wrote:

>  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
>
>
>
>
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-- 
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Chemistry Department
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr


If nature does not answer first what we want,
it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900