VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Fri Aug 21 2015 - 12:05:44 CDT

On Fri, Aug 21, 2015 at 11:05 AM, Ozan Dernek <ozandernek_at_gmail.com> wrote:

> Hello,
>
> I am trying to visualize my Bader charge calculation. I stumbled upon a
> few web sites that say it can be done by creating two isosurfaces, and
> assigning same values with opposite signs to isovalue to them.
>

​what you describe sounds like instructions to visualize *wavefunctions​*
or *orbitals*.

However, I cannot get any visual from the isosurface that i assigned a
> negative isovalue. The reason behind this is when I load the volumetric
> surface, the minimum isovalue is higher than zero. At this point, how can I
> visualize the Bader charge analysis.
>

​i don't understand what you are saying. bader analysis should give you
coordinates of attractors, not a density. a density is the *input* for it.
..and a density is by definition​
​
​ always positive.​ that said, some codes allow to output the individually
partitioned densities (primarily) for debugging purposes. but the main
point of doing a bader analysis is to get the *integral* density for these
partitioned volumes as a charge.

> PS: Dear John Stone helped a lot, but anybody experienced with the problem
> could be more helpful. Also, could you explain (or any source that I can
> learn from) what isovalue represents in this issue.
>

https://en.wikipedia.org/wiki/Isosurface
​
​i think at this point, you should consult with your adviser or tutor and
ask for more detailed explanations. this is really about understanding the
science of what you are doing and not about using VMD correctly.

axel.​

>
> Regards,
> Ozan Dernek
>
> 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.