[CP2K-user] [CP2K:16241] Re: Using TAMkin with CP2K - how is CP2K diagonalizing the Hessian matrix?

[Eugene]

This is defenetly late responce but in order to keep information there is a 
reason for responce. I don't know units in CP2K output, but CP2K save 
Hessian in unformatted bynary file, which can be easily read and then 
diagonalized. The sqrt of eigenvalues is freqeuncy of vibrational modes 
wich can be converted to cm-1 by factor multiplying, where the factor is:
sqrt(Hartree/AMU/Bohr2Angstrom)*1/2/pi/Angstrom/c*sqrt(massunit/Bohr2Angstrom)/1)10**5
Hartree=4.359748536313086e-18
AMU=1.6605402e-27
Bohr2Angstrom=0.529177207423948
massunit=a_mass/e_mass
a_mass=1.660538782e-27
e_mass=9.10938215e-31
I've wrote convertor from cp2k hessian file format to FORCE_CONSTANTS file 
format (see attachment). Using PHONOPY one can write dynamical matrix, plot 
eigenvectors and lot of other things. 

Best wishes,
Eugene
среда, 10 июня 2020 г. в 16:56:53 UTC+3, tfjer... at gmail.com: 

> Dear all, 
>
> I would like to use TAMkin (http://molmod.github.io/tamkin/) to compute 
> thermodynamic properties from the vibrational frequencies computed with 
> CP2K.
> As I have understood it, the way TAMkin works is to read and diagonalize 
> the Hessian matrix printed in the CP2K output.
> When I compare the frequencies obtained with TAMkin with those obtained 
> with cp2k, the values are not the same (Compare column 2 and 3 in the table 
> below). 
>
> The first task is then to understand how CP2K computes the frequencies. To 
> investigate this, I copied the Hessian matrix from the CP2K output (printed 
> below the string "Hessian in cartesian coordinates") and pasted it into 
> Excel and saved it as a csv file. This file I read into python and 
> diagonalized the Hessian with numpy. The frequencies I get are different 
> from those printed in the cp2k output file (compare column 3 and 4 in the  
> table below). 
> I have assumed that the units of the Hessian matrix in the cp2k output 
> file are Ry*bohr-2*kamu-1 (kamu = 1000*amu). This assumption is based on 
> trial and error; it was what got me closest to the cp2k frequencies. 
>
>
> Table 1: The eight lowest frequencies. There are 48 in total.
>
> frequencies
>
> TAMkin / 
> cm-1
>
> cp2k / 
> cm-1
>
> Diag., cp2k Hessian / 
> cm-1
>
> 1
>
> 31.1
>
> 27.3
>
> 32.6
>
> 2
>
> 38.3
>
> 40.8
>
> 40.1
>
> 3
>
> 47.7
>
> 51.0
>
> 50.2
>
> 4
>
> 74.7
>
> 74.0
>
> 78.2
>
> 5
>
> 82.0
>
> 80.0
>
> 85.8
>
> 6
>
> 111.0
>
> 109.9
>
> 116.3
>
> 7
>
> 223.7
>
> 224.1
>
> 234.3
>
> 8
>
> 245.6
>
> 246.3
>
> 257.3
>
> What is wrong with my calculation?
> What steps should be done to go from the Hessian to the frequencies?
>
> The Hessian in csv format, the python script and the cp2k output file are 
> attached. 
>
> Thanks a lot for your help.
>
> Regards,
> Torstein Fjermestad
>  
>
>
>

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