[Pw_forum] Some questions about vibrational modes

Torstein Fjermestad torstein.fjermestad at kjemi.uio.no
Fri Oct 12 09:50:26 CEST 2012

 Dear all,

 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?

 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?

 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?

 Thank you in advance for your help.

 Yours sincerely,

 Torstein Fjermestad
 University of Oslo,

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