[Pw_forum] frequency of NO molecule

Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu
Thu Sep 7 16:01:52 CEST 2006

> >  nat_todo=2, <== Here we specify number of atoms to be displaced.
> >  /
> >  0.0 0.0 0.0
> >  31 32 <== Here we specify atom index in our supercell.
> >
> > That's it. Later I found that INPUT_PH has a mention regarding this.
> in this way you just calculate and diagonalize the 6 x 6 submatrix of the
> dynamical matrix.
> In principle it should be possible to reconstruct an approximate dynamical
> matrix from the above calculation and the dynamical matrix of the surface
> without NO. I don't know how useful this would be, though.

how about including several atoms in the neighborhood of the adsorbed
molecule? this is how it works in CPMD: you pick an atoms (or pick a
reference coordinate) and set a radius and then do the vibrational analysis
for those atoms and keep the rest fixed. this way you include at least the
contributions from the near neighbors, have the rest as 'static background',
and still save a lot of (cpu) time.


> > I wish that this procedure could be explained very clearly in the manual
> > in coming version.
> it is not clearly explained right now because it is a seldom-used feature
> (and one that should be carefully used). If you have any specific suggestions
> to improve the manual, feel free to suggest them

> Paolo
> --
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Axel Kohlmeyer   akohlmey at cmm.chem.upenn.edu   http://www.cmm.upenn.edu
  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.

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