[xcrysden] charge density and electrostatic potential

[Ariadna Blanca Romero]

Hi all

I have a problem to understand what a negative isovalue means when I want to 
visualize the charge density and the electrostatic potential. I am using 
crystal06 to get these.

I know that the charge density is a function dependent on three variables, 
namely x,y and z. I can then ask XCrysDen to collect all the points at which the 
density has a single 

specific value, the isovalue, and connect them through a three-dimensional plot. 
I mean  rho(x,y,z)=C, where C is the isovalue.In the isosurface controlling 
window I get a minimum and maximum grid value. Then I chose a isovalue in this 
range, and I use the option Render +/-isovalue. Using this last option I get two 
color surfaces, one in red and other in blue. The xcrysden site 
(http://www.xcrysden.org/doc/isocontrol.html#render+-) gives an example: 


"when displaying the isosurface of a molecular orbital, then it is a good idea 
to display both positive and negative valued isosurface (for example the 
-0.02/0.02 sqrt(BOHR^3/electrons)). By default the positive isosurface is 
rendered in red, while negative in blue."

The problem comes when I wanto to interpret it for electronic density, which is 
given  in electrons/BHOR^3 by crystal06 and this quantity should be POSITIVE. 
First, the isovalue is the square root of the inverse of the electronic density 
(at least by the units it seems), as is shown in the xcrysden site, so what a 
negative isovalue means????? Does it mean less quantity of electrons????.

On the other hand, when instead of surfaces we have planes, we have to specify 
the lowest and the higest render value. This ones are shown in the thermometer 
which has the label DELTA n(r), Does it means a difference between two isovalues 
or a difference between other quantities to get the isovalues???? and again here 
the question returns about negative isovalues, what does a negative isovalue 
means in the thermometer???? 


In the section for property-planes display parameters we have to select a scale 
function (http://www.xcrysden.org/doc/plane1control.html#__toc__5). Here is 
recomended:

"For example for charge density plots the logarithmic scale is usually more 
appropriate as linear, whereas for charge density difference maps the linear 
scale is usually better"


Why for the same property, just to see the difference maps we have to change the 
scale function ??????  Finally, for the electrostatic potential we have the same 
isosurface controlling window. So, I  guess  the  isosurfaces color ( blue and 
red) have the right meaning for positive and negative charges, isn't  it?


Thanks before hand to help me to clarify my doubts.



Regards, Ariadna



      
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://www.democritos.it/pipermail/xcrysden/attachments/20100903/6e8cd64b/attachment.htm