[Pw_forum] Some questions about vibrational modes

Stefano Baroni baroni at sissa.it
Sun Oct 14 19:27:15 CEST 2012

On Oct 12, 2012, at 9:50 AM, Torstein Fjermestad wrote:

> With the purpose of obtaining the Gibbs free energy, I am computing the 
> vibrational modes of a system. The system is a microporous zeotype 
> material with an extra-framework species (Si(OH)4) located in the pore. 
> The vibrational modes were obtained by first optimizing the structure 
> with increased accuracy ( forc_conv_thr=1.0d-5, etot_conv_thr=1.0d-6). 
> Thereafter I did a phonon calculation with the tr2_ph option set to 
> 1.0e-14. I had expected three of the vibrational modes to correspond to 
> a translation of all atoms in the unit cell in one direction. This 
> happens indeed for the lowest mode (mode 1, frequency = 3 cm-1) which 
> corresponds to a translation in the z direction. Modes 3 (frequency = 29 
> cm-1)  and 4 (frequency = 30 cm-1) show a translation of the framework 
> atoms in the y and x direction respectively, but the Si(OH)4 species is 
> not translating with the framework atoms. Is such a behavior expected?

NO. This however may happen if your system has other "quasi-soft" mode that are almost degenerate with acoustic modes. I know very little of your system but I can imagine that the "extra-framework" species is associated with "rattle" modes that, if the cage is larger than the species itself may become soft. I do not know if the difference in the behaviors along the z axis and in the xy plane may be due to the anisotropy of the cage, or if by accident (i.e. numerics) the modes rattle mode along z is more tightly coupled with the cage motion than the xy modes are ... Please let us know more.

> When calculating the vibrational contribution to the Gibbs free energy, 
> one should not include modes corresponding to a translation of the whole 
> unit cell, but what about cases such as mode 3 and 4 where the Si(OH)4 
> species is not translating with the rest of the atoms? How are such 
> cases treated correctly?

I think they should be treated as low-frequency modes, as they probably are. (not sure about the numbering, though: one of them is probably a mized rattle-translation mode)

> Another issue concerns the extra-framework species Si(OH)4. In mode 2 
> (frequency = 23 cm-1) and 5 (frequency = 51 cm-1) this is being 
> translated while the rest of the atoms are relatively static. Wouldn't 
> it be better to treat these modes as translations instead of vibrations? 
> In that case, how is this done correctly?

ah! ah! you said it! mode 2 is a rattle mode, and so is mode 5! I am curious about the rattle mode in the z direction. Has it a larger frequency? Can you make a sense of it?
> Thank you in advance for your help.

Hope you had some ...

Cheers - SB

Stefano Baroni -  http://stefano.baroni.me, stefanobaroni (skype)
on leave of absence from SISSA, Trieste, presently at the Department of Materials, EPF Lausanne (untill March 2013)

La morale est une logique de l'action comme la logique est une morale de la pensée - Jean Piaget

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