Re: [Towhee-users] New to Towhee, want Water in CNT

[Marcus M. <mar...@us...>]

On Thu, Mar 26, 2009 at 3:18 AM, Prashant <pr...@pi...> wrote:

> I am just learning Towhee and want to put molecules/atoms in carbon
> nanotubes by Configurational-Bias Monte Carlo.  I am trying to learn the
> commands accepted in the towhee_input script.  Basically, the
> 'Walt2001_Nanotube' example is perfect except for I only want the water to
> be inside the carbon nanotube, not outside.  What do you suggest I do?
>
> Is it possible to artificially weight all positions outside the CNT to
> suffer a high potential energy penalty?  While that seems like a somewhat
> inelegant solution, I'd rather simply restrict the box to inside the carbon
> nanotube, but I do not know how to make a box that isn't orthorhombic.

Currently, the only way to exclude atoms from a particular region
would be to use a field to apply a high energy penalty as you
described.

While Towhee does allow the box to be non-orthorhombic, it is limited
to unit cells that are a subset of triclinic.  You can fake a
hexogonal lattice by adding an additional unit cell and making it
orthorhombic again.  Still, that is probably not going to help in your
case as there are likely to be some gaps between the nanotubes.

Marcus

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Marcus G. Martin
Director, Useful Bias Incorporated
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