[xcrysden] charge density and electrostatic potential

[Tone Kokalj]

On Fri, 2010-09-03 at 16:36 +0000, Ariadna Blanca Romero wrote:
> 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.

As for the charge density, the negative value typically appears only for
charge density difference plots, and it indicates charge deficit
regions.

As for the electrostatic potential (elpot), negative values indicate
electron reach regions. Imagine for example a polar molecules, say HF,
then you will have negative region around F and positive around H (i.e.
you can consider this as a representation of dipole pointing from
negative elpot region to positive elpot region).


> 
> "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????.

Don't confuse molecular orbitals and charge density!

Molecular orbitals (say for molecules) can be chosen as being real; not
in general true for crystals. For the latter reason, I believe (not
sure) you can only plot the square moduli of molecular/crystal orbitals
in CRYSTAL06 (i.e. \Phi^2, associated charge density), and in this case
you only plot the "positive" isovalue. However if you would plot the
real molecular orbital than the "+/-" isovalue button is useful.



> 
> 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

No the symbol \Delta is there for convenience only (now I see it causes
confusion): would you plot the charge density difference, then you would
need a \Delta symbol, which cannot be input by keyword!

If you plot a plain charge density, delete the \Delta symbol.

> 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 ?????? 
> 

For difference maps you simply keep the linear scale, however for plain
charge density the logarithmic scale is also very useful (depends on the
purpose). It is obviously up to you which scale to choose.

> 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?

Yes, blue is negative, red is positive.

Regards, Tone

-- 
Anton Kokalj
J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia 
(tel: +386-1-477-3523 // fax:+386-1-477-3822)

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