<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><div>On Oct 12, 2012, at 9:50 AM, Torstein Fjermestad wrote:</div><div><br></div><blockquote type="cite"><div>With the purpose of obtaining the Gibbs free energy, I am computing the <br> vibrational modes of a system. The system is a microporous zeotype <br> material with an extra-framework species (Si(OH)4) located in the pore. <br> The vibrational modes were obtained by first optimizing the structure <br> with increased accuracy ( forc_conv_thr=1.0d-5, etot_conv_thr=1.0d-6). <br> Thereafter I did a phonon calculation with the tr2_ph option set to <br> 1.0e-14. I had expected three of the vibrational modes to correspond to <br> a translation of all atoms in the unit cell in one direction. This <br> happens indeed for the lowest mode (mode 1, frequency = 3 cm-1) which <br> corresponds to a translation in the z direction. Modes 3 (frequency = 29 <br> cm-1) and 4 (frequency = 30 cm-1) show a translation of the framework <br> atoms in the y and x direction respectively, but the Si(OH)4 species is <br> not translating with the framework atoms. Is such a behavior expected?<br></div></blockquote><div><br></div>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.</div><div><br></div><div>WHAT ABOUT MODE #2?</div><div> <br><blockquote type="cite"><div>When calculating the vibrational contribution to the Gibbs free energy, <br> one should not include modes corresponding to a translation of the whole <br> unit cell, but what about cases such as mode 3 and 4 where the Si(OH)4 <br> species is not translating with the rest of the atoms? How are such <br> cases treated correctly?<br></div></blockquote><div><br></div>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)</div><div><br><blockquote type="cite"><div>Another issue concerns the extra-framework species Si(OH)4. In mode 2 <br> (frequency = 23 cm-1) and 5 (frequency = 51 cm-1) this is being <br> translated while the rest of the atoms are relatively static. Wouldn't <br> it be better to treat these modes as translations instead of vibrations? <br> In that case, how is this done correctly?<br></div></blockquote><div><br></div>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?</div><div> <br><blockquote type="cite"><div>Thank you in advance for your help.<br></div></blockquote><div><br></div>Hope you had some ...</div><div><br></div><div>Cheers - SB</div><div><br></div><div>
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