Hi,

Here are three different views of the triazene (N3H3) molecule.

Top left: electron density
Top right: electrostatic potential
Bottom left: Laplacian of the electron density

All the three "clouds" are rendered from .df3 files generated with the help 
of quantum calculation software (gaussian98, if you care). I have been 
playing with isosurfaces as well, but it's not easy to get the scale from 
the .df3 files (all values are between 0 and 1) and there are some issues 
with the onion-like layers in the Laplacian.

-- 
light_source{9+9*x,1}camera{orthographic look_at(1-y)/4angle 30location
9/4-z*4}light_source{-9*z,1}union{box{.9-z.1+x clipped_by{plane{2+y-4*x
0}}}box{z-y-.1.1+z}box{-.1.1+x}box{.1z-.1}pigment{rgb<.8.2,1>}}//Jellby

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Attachments:
Download 'triazene.jpg' (28 KB)

Preview of image 'triazene.jpg'

Very interesting, good work!!!

Regards,
Oleguer


news:417bf122@news.povray.org...
> Hi,
>
> Here are three different views of the triazene (N3H3) molecule.
>
> Top left: electron density
> Top right: electrostatic potential
> Bottom left: Laplacian of the electron density
>
> All the three "clouds" are rendered from .df3 files generated with the
help
> of quantum calculation software (gaussian98, if you care). I have been
> playing with isosurfaces as well, but it's not easy to get the scale from
> the .df3 files (all values are between 0 and 1) and there are some issues
> with the onion-like layers in the Laplacian.
>
> -- 
> light_source{9+9*x,1}camera{orthographic look_at(1-y)/4angle 30location
> 9/4-z*4}light_source{-9*z,1}union{box{.9-z.1+x clipped_by{plane{2+y-4*x
> 0}}}box{z-y-.1.1+z}box{-.1.1+x}box{.1z-.1}pigment{rgb<.8.2,1>}}//Jellby
>

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"Jellby" <jel### [at] M-yahoocom> wrote in message
news:417bf122@news.povray.org...
> Hi,
>
> Here are three different views of the triazene (N3H3) molecule.
>
> Top left: electron density
> Top right: electrostatic potential
> Bottom left: Laplacian of the electron density
>
> All the three "clouds" are rendered from .df3 files generated with the
help
> of quantum calculation software (gaussian98, if you care). I have been

[snip]

Are you using the linux version of gaussian98?
http://www.gausian.com is not responding.

http://www.compuchem.com/gaussian.htm
is about gaussian 03 W for windows, but the download link is
void of any further mention of the software

Any clues on where/how to obtain some version of gaussian?

And,
is it stratightforward to produce the .df3?

tia,
Pan

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Among other things, pan saw fit to write:

> Are you using the linux version of gaussian98?
> http://www.gausian.com is not responding.
> 
> http://www.compuchem.com/gaussian.htm
> is about gaussian 03 W for windows, but the download link is
> void of any further mention of the software
> 
> Any clues on where/how to obtain some version of gaussian?

Yes, we have the linux/unix version of gaussian98 in my department. I can't 
tell you exactly the address you should write to, but gaussian.com was 
working yesterday, so I guess it's a temporary a temporary problem. Anyway, 
gaussian is not free, you may want to try other programs as GAMESS (I'm not 
sure whether it can output electron density data, but it's very likely)

> And,
> is it stratightforward to produce the .df3?

It's easier than it could seem. It's easy to get the density (or potential, 
or laplacian...) in a grid, then all you need is convert the ascii, 
floating-point values to the correct .df3 format.

-- 
light_source{9+9*x,1}camera{orthographic look_at(1-y)/4angle 30location
9/4-z*4}light_source{-9*z,1}union{box{.9-z.1+x clipped_by{plane{2+y-4*x
0}}}box{z-y-.1.1+z}box{-.1.1+x}box{.1z-.1}pigment{rgb<.8.2,1>}}//Jellby

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Hi Jellby,

just a question. What do You think, is it somehow possible to create a 3
dimesional electron density map from a single crystal x-ray measurement,
using povray for the visualisation. Or would it be somehow possible to
calculate a 3df file from a hkl file using fourier synthesis. It's possible
to calculate 2 dimensional electron maps from the data during the structure
refinement. But a 3 dimensional one ???
Nice work by the way.

Shu.

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Jellby wrote:
> Hi,
> 
> Here are three different views of the triazene (N3H3) molecule.
> 
> Top left: electron density
> Top right: electrostatic potential
> Bottom left: Laplacian of the electron density
> 
> All the three "clouds" are rendered from .df3 files generated with the help 
> of quantum calculation software (gaussian98, if you care). I have been 
> playing with isosurfaces as well, but it's not easy to get the scale from 
> the .df3 files (all values are between 0 and 1) and there are some issues 
> with the onion-like layers in the Laplacian.
> 
> 
> 
> ------------------------------------------------------------------------
> 

Very nice. Are you familiar with the Orbitron? 
http://www.shef.ac.uk/chemistry/orbitron/

-- 
Maurice

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Among other things, Shurakai wrote:

> just a question. What do You think, is it somehow possible to create a 3
> dimesional electron density map from a single crystal x-ray measurement,
> using povray for the visualisation. Or would it be somehow possible to
> calculate a 3df file from a hkl file using fourier synthesis. It's
> possible to calculate 2 dimensional electron maps from the data during the
> structure refinement. But a 3 dimensional one ???

No idea, sorry. I have never worked with x-ray experiments, but I guess it 
should theoretically be possible to get the 3D density. If you can obtain 
the density values in a 2D grid, maybe you can combine several planes to 
get a 3D grid...

The images I've shown are from theoretical calculations, and the software 
already outputs a 3D-grid of density data, all that's needed is a format 
conversion.

-- 
light_source{9+9*x,1}camera{orthographic look_at(1-y)/4angle 30location
9/4-z*4}light_source{-9*z,1}union{box{.9-z.1+x clipped_by{plane{2+y-4*x
0}}}box{z-y-.1.1+z}box{-.1.1+x}box{.1z-.1}pigment{rgb<.8.2,1>}}//Jellby

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Among other things, Maurice saw fit to write:

> Very nice. Are you familiar with the Orbitron?
> http://www.shef.ac.uk/chemistry/orbitron/

Yes, I've visited it several times, it's very nice. Note, however, that the 
information displayed there and in my images is different.

-- 
light_source{9+9*x,1}camera{orthographic look_at(1-y)/4angle 30location
9/4-z*4}light_source{-9*z,1}union{box{.9-z.1+x clipped_by{plane{2+y-4*x
0}}}box{z-y-.1.1+z}box{-.1.1+x}box{.1z-.1}pigment{rgb<.8.2,1>}}//Jellby

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Jellby wrote:
> Among other things, Maurice saw fit to write:
> 
> 
>>Very nice. Are you familiar with the Orbitron?
>>http://www.shef.ac.uk/chemistry/orbitron/
> 
> 
> Yes, I've visited it several times, it's very nice. Note, however, that the 
> information displayed there and in my images is different.
> 
Yes, I know.

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