[CP2K-user] [CP2K:12626] VIBRATIONAL_ANALYSIS of a single adsorbed molecule on a surface: What is the best computational procedure?

Patrick Gono patri... at gmail.com
Thu Dec 12 07:15:24 UTC 2019

Dear Stefano,

The general assumption here is that the vibrational spectrum of the slab is
not in any way perturbed by the adsorbed molecule. Hence, you can run a
VIBRATIONAL_ANALYSIS calculation with all atoms fixed, with the exception
of the adsorbed molecule. That way, you will only have to calculate a very
small subset of all vibrational modes and greatly speed up the process.

The thermodynamic corrections (zero point energy, vibrational entropy,
possibly internal energy) can then be extracted from the computed
frequencies. However, the description of the THERMOCHEMISTRY keyword
mentions gas-phase molecules only. In any case, you might still want to
verify you are getting the correct corrections yourself, manually.

Have a look at:
Cramer, C. J. Essentials of Computational Chemistry: Theories and Models,
2nd ed.; Wiley, Chichester, 2004; pp 355–366

or the supporting information of:

Yours sincerely,
Patrick Gono

On Wed, Dec 11, 2019 at 3:24 PM Stefano Ferrero <
stefano.... at edu.unito.it> wrote:

> Dear CP2K experts,
> I have just started using CP2K and I would be really thankful if anybody
> can help me.
> My question is on calculating frequencies of a molecule (as CO) adsorbed
> on a surface (an ice surface in my case).
> I will work with energy differences so, there is no need of a vibrational
> analysis of the entire system but just of a fragment of it.
> I have to zoom in on the frequencies of the adsorbed molecule and the most
> interacting water which will be the most perturbed modes with respect to
> gas phase frequecies
> Looking at other threads,I found that CP2K has the keyword MODE_SELECTIVE
> with which I can zoom in to specific vibrational modes.
> 1) How does it do that? Is it displacing and calculating forces just for
> the atom on which I ask to zoom in on?
>     Can I use the keyword THERMOCHEMISTRY with the MODE_SELECTIVE one in
> order to obtain the ZPE and thermal correction for just the modes I zoomed
> in on?
> 2) Would it be better to fix (with CONSTRAINT + FIXED_ATOMS) all atoms for
> which I do not want calculate the normal modes, in order to speed up the
> calculation?
>     Are there any problems with this "partial Hessian approach"?
>     Would it be possible to use the THERMOCHEMISTRY keyword in this case?
> 3) Which one will be the best way to calculate the frequencies of just the
> adsorbate plus the most interacting water molecules from the surface,
> keeping in mind that I have to make the thermochemical analysis on that
> little
>    fragment of the entire system?
> Thank you for your help!
> Stefano Ferrero
> ------------------------
> Indirizzo istituzionale di posta elettronica degli studenti e dei laureati
> dell'Università degli Studi di Torino
> Official University of Turin email address for students and graduates
> --
> You received this message because you are subscribed to the Google Groups
> "cp2k" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to cp... at googlegroups.com.
> To view this discussion on the web visit
> https://groups.google.com/d/msgid/cp2k/f2a83185-793e-4ba2-a33f-ed9c6521474d%40googlegroups.com
> <https://groups.google.com/d/msgid/cp2k/f2a83185-793e-4ba2-a33f-ed9c6521474d%40googlegroups.com?utm_medium=email&utm_source=footer>
> .
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://lists.cp2k.org/archives/cp2k-user/attachments/20191212/0021d3a5/attachment.htm>

More information about the CP2K-user mailing list