[CP2K-user] [CP2K:12627] VIBRATIONAL_ANALYSIS of a single adsorbed molecule on a surface: What is the best computational procedure?

[Stefano Ferrero]

Dear Patrick,

Thank you very much for your help
Kind regards

Stefano Ferrero

Il Gio 12 Dic 2019, 08:15 Patrick Gono <patri... at gmail.com> ha scritto:

> 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:
> https://pubs.acs.org/doi/10.1021/acscatal.8b01120
>
> 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
>>
>>
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