[Pw_forum] Some questions about vibrational modes

Torstein Fjermestad torstein.fjermestad at kjemi.uio.no
Fri Oct 19 21:48:45 CEST 2012

 Dear Prof. Baroni,

 First of all, thanks for your help. It is not easy to give an accurate 
 description of a structure and its vibrational modes in an e-mail. I 
 think therefore it would be better to attach a .axsf file so that it 
 would be possible to visualize the modes in xcrysden. Unfortunately, the 
 e-mail with the file attached was rejected because of a too large size 
 (560 kB). However, if you (or anyone else) are interested in having a 
 look at the vibrational modes, I could send the .axsf file directly to 

 Concerning your questions / comments on the translational modes of the 
 Si(OH)4 species.
 I have not been able to identify a rattle mode in the z direction, and 
 I suspect that your
 suggestion that this mode might be tightly coupled to the cage motion 
 is correct. This mode should, by the way, be precisely mode 1, were the 
 whole unit cell is translating in the z direction.
 The difference of the Si(OH)4 translation in the xy plane and the z 
 direction could indeed be due to anisotropy. The Si(OH)4 species is 
 located closer to one of the walls (presumably by non-bonding dispersion 
 interactions) and it might be that the translation in z direction is 
 hindered somehow.

 My problem concerns the computation of Gibbs free energy. However, I do 
 not know whether it is correct to
 exclude modes 3 and 4 from the computation as these modes also involve 
 motions of the Si(OH)4 species in addition to the unit cell translation. 
 I would appreciate very much if someone could help me with this problem.

 Thanks in advance.

 Yours sincerely,

 Torstein Fjermestad
 University of Oslo,


 On Sun, 14 Oct 2012 19:27:15 +0200, Stefano Baroni <baroni at sissa.it> 
> 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 [1], 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
> Links:
> ------
> [1] http://stefano.baroni.me/

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