From: Axel Kohlmeyer (
Date: Wed Jan 24 2007 - 17:14:53 CST

On Wed, 24 Jan 2007, Robert fiske wrote:

RF> When viewing the spin density of a system (in this case calculation was done
RF> using cpmd) what is the difference between the positive isovalues and the
RF> negative values, is one alpha-beta and the other beta-alpha?

please note, that VMD is (intentionally) mostly ignorant
of all chemistry (which makes it so incredibly flexible,
at the price of that _you_ have to know more about what
you want to do...).

so VMD does not pay any attention to the meaning of what
an iso surface represents.

if you compute a spin density, it _is_ the alpha wavefunction
minus beta (or vice versa depending on the implementation).
according to the definition of what a-b means for a number,
the result is negative, if b > a and positive for a > b.

elementary. :)



p.s.: of course, there is more to the _interpretation_ of
spin polarization (but that is irrelevant of what VMD does).
if you have a system where you 'add' electrons only to the
alpha wavefunction and still find significant areas where
b > a, than this can be an indication of
a) your calculation was wrong,
b) your system has a complicated spin structure (e.g. two
   atoms with local high spin, but in total a low
c) you are doing DFT with self-interaction errors.
d) ... there may be more reasons, but i cannot think of any now.

RF> Thank you for any assistance you can provide
RF> Robert Fiske
RF> Gogonea group
RF> Cleveland State University
RF> _________________________________________________________________
RF> Get Hilary Duff’s homepage with her photos, music, and more.

Axel Kohlmeyer
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
If you make something idiot-proof, the universe creates a better idiot.