Vibrational Analysis
Ali
RNAlo... at gmail.com
Mon Jun 23 16:55:03 UTC 2008
Hi Flo,
Below is a section of my input file. You are correct in that I am
conducting a vibrational analysis on 4 atoms together. From your email
it seems like you were saying that using Frequency, Range and Involved
atoms are mutually exclusive. I actually tried just doing the involved
atoms and I got an error stating that I needed to have range or
frequency in the input.
I am actually interested in determining a frequency that is associated
with all 4 atoms together which is why I chose 4 of them. I guess its
possible that if I did it seperately on the 4 different atoms that the
mode I get from all 4 together will appear in one of the top 4
seperately.
&VIBRATIONAL_ANALYSIS
FULLY_PERIODIC T
!NPROC_REP 2
&MODE_SELECTIVE
FREQUENCY 500
ATOMS 115 117 120 122
EPS_MAX_VAL 1.0E-07
&END
Ali
On Jun 21, 5:21 am, flo <fsch... at pci.uzh.ch> wrote:
> Hi Ali,
>
> could you post the part of your input file related to the vibrational
> analysis?
> From the output, and what you write, it looks like you used a multiple
> definition of the frequencies you are interested in. Using the mode
> selective method, you have to chose what you are looking for:
> Frequency means you are looking for the (nproc/nrep) frequencies
> closest to the selected one.
> Range converges all the frequencies in the Range.
> Involved_atoms is slightly different: the eigenvectors are projected
> on a unit vector constructed out of your chosen atoms. If you chose
> many atoms, you will most likely end up with a low frequent mode
> (since these are more delocalized, and match the constructed vector
> the best). For to clarify since I expect you used this keyword. Using
> four atoms won't give you the frequencies where one of them is
> involved, it will give you the frequencies where all of them are
> involved the most.
> From these three points you have to choose only one, since each
> specifies a way how to create your residuum vector.
>
> The output:
> Since not only frequencies are present which are converged with
> respect to the EPS valuesyou get a list of all the eigenvalues of the
> approximate Hessian and how far they are converged. Since there are
> two EPS values to specify you egt two values (and the last column
> tells you if they are converged with respect to the EPS).
>
> During iteration cycle you can follow which frequencies are the ones
> used for updating the Davidson algorithm. And in the end which have
> been the last ones chosen by the algorthm.
>
> The output created (the VIBRATIONS.mol file uses molden format. Of
> course one could implement different outputs, but since molden is a
> freely available software I think it's convenient to use this format.
> If you want to use a different Program, you will have to convert it to
> a different format.
>
> Of course, the way you select the modes in CP2K can still be improved,
> but with the present methods you can cover most of the stuff you are
> looking for.
> I would suggest: just take one involved atom and use a multiprocessor
> run (nproc/nrep=4 or more), in this way you will get the four modes in
> which the atom moves most. Afterwards restart the calculation
> (MS_RESTART) with the second,third, fourth atom.
>
> Cheers
> Flo
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