Re: Visualization for Dummies

• To: mathgroup at smc.vnet.net
• Subject: [mg113456] Re: Visualization for Dummies
• From: Daniel Huber <dh at metrohm.com>
• Date: Fri, 29 Oct 2010 06:29:22 -0400 (EDT)
• References: <iabc7s\$5l6\$1@smc.vnet.net>

Hi Hauke,
in vibrational analysis the displacements of atoms are given as vectors
(e.g. of the maximal or relative amplitudes), either in absolute or
internal coordinates. For a graphics you need them in absolute coordinates.
To get a nice movie, you need to multiply these displacement vectors by
a time dependend factor, e.g. Sin[w t] where t is the time and w the
frequeny (needed if you have more than one normal mode simultaniously).
The atom position at time t would then be:
equilibrium position+ Sin[w t] displacement vector.
With this you can now create a bunch of graphics for different times.
cheers, Daniel

On 28.10.2010 10:28, Hauke Reddmann wrote:
> And dummy still I am, so I pester you, even if
> the problem is probably trivial :-)
>
> I have a list1 {{atom-id 1, x1,y1,z1},{atom-id 2, ...
> and several lists2 {{atom-id 1, dx1,dy1,dz1},{atom-id 2, ...
> The first list holds the coordinates of the atoms,
> and the seconds the displacements due to vibrations.
>
> E.g.
>
> o===c===o  c={{C,0,0,0},{O,-4,0,0},{O,4,0,0}}
>   oc======o l1={{C,2,0,0},{O,-1,0,0},{O,-1,0,0}}
>   o==c==o l2={{C,0,0,0},{O,-1,0,0},{O,1,0,0}}
>
> In this example I obviously don't need Mathematica
> to recognize l1 as asymmetric and l2 as symmetric
> stretch of the CO2 molecule. But mine is a tad
> larger. :-)
> So do you have a standard proggie p(c,l1,l2) who
> outputs a nice "movie" of the vibration? Note that
> I'm still on v5.2 (if it works, don't change it :-)
> but can upgrade to v7 if I have no choice.

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