<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><br><div><div>On Aug 26, 2009, at 10:47 PM, Denny Jackson wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">Hello,<br></blockquote><div><br></div>Hi Denny:</div><div><br><blockquote type="cite"><br>I am having trouble understanding the output from ph.x in the matdyn file. I am looking at Barium Titanate in the cubic phase, but with broken symmetry and then relaxed. <br>I'm trying to compare the linear response frequencies from ph.x to frozen phonon frequencies. From what I understand, the diagonalized dynamical matrix should give displacements of each atom. So in the output:<br> <br>omega( 4) = 3.763989 [THz] = 125.553988 [cm-1]<br> ( 0.097362 0.000000 -0.116603 0.000000 -0.288197 0.000000 ) <br> ( -0.066349 0.000000 0.077204 0.000000 0.200853 0.000000 ) <br> ( -0.169282 0.000000 0.204883 0.000000 0.421687 0.000000 ) <br> ( -0.159112 0.000000 0.218980 0.000000 0.474827 0.000000 ) <br> ( -0.184271 0.000000 0.191581 0.000000 0.474679 0.000000 ) <br><br>each column gives the real and imaginary components of the displacements in cartesian coordinates. I could not find what units these values have, first of all. I assume they are unitless and are a fraction of the lattice parameter. <br></blockquote><div><br></div>the answer is, "does not matter". vibrational mode are identified by the direction and the relative magnitude of each atom's displacement. the absolute magnitude is a matter of convention. hope it is clear why it has to be so. if not, please revert to us and I'll try to explain.</div><div><br><blockquote type="cite"> Also, each column should add up to zero to preserve symmetry, should it not? For higher frequencies in this calculation the columns do indeed add up to zero, but for lower frequencies (and negative frequencies) this is not the case. Does this indicate a problem with my pw calculation or something else? <br></blockquote><div><br></div>not sure what you mean by "preserve the symmetry". what is sure is that zone-center acoustic modes correspond to a rigid translation of the whole crystal. for these modes, the atomic displacements certainly do not sum to zero. the other modes have to be orthogonal to acoustic ones, and that's why their displacements sum to zero. beware, though, that orthogonality holds with respect to the "vibrational metric" which is proportional to a diagonal matrix with the atomic masses on the diagonal ...</div><div><br><blockquote type="cite">Is there a resource for good documentation on the matdyn file I have overlooked? <br></blockquote><div><br></div>not that I know, but a good textbook on lattice dynamics (such as Born and Huang or Botteger) and/or molecular vibrations may help clarify some of the general concepts you need to master to understand what ph.x does ...</div><div><br></div><div>Stefano B</div><div><br></div><br><br><div apple-content-edited="true"> <span class="Apple-style-span" style="border-collapse: separate; 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"><div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 12px; ">---</span></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 12px; ">Stefano Baroni - SISSA</span></font><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 12px; "> </span></font><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 12px; ">&</span></font><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 12px; "> </span></font><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 12px; ">DEMOCRITOS National Simulation Center - Trieste</span></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 12px; "><a href="http://stefano.baroni.me">http://stefano.baroni.me</a> [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype)</span></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 12px/normal Helvetica; min-height: 14px; font-size: 12px; "><br style="font-size: 12px; "></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 12px/normal Helvetica; min-height: 14px; font-size: 12px; "><span class="Apple-style-span" style="font-size: 14px; "><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 12px; ">La morale est une logique de l'action comme la logique est une morale de la pensée - Jean Piaget</span></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 12px; "><br></span></font></div></span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 12px; ">Please, if possible, don't</span></font><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 12px; "> </span></font><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 12px; ">send me MS Word or PowerPoint attachments</span></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 12px; ">Why? See:</span></font><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 12px; "> </span></font><font class="Apple-style-span" color="#0023E9" size="3"><span class="Apple-style-span" style="font-size: 12px; "><a href="http://www.gnu.org/philosophy/no-word-attachments.html">http://www.gnu.org/philosophy/no-word-attachments.html</a></span></font></div><div><font class="Apple-style-span" color="#0023E9" size="3"><span class="Apple-style-span" style="font-size: 12px; "><br class="webkit-block-placeholder"></span></font></div></div></div></span><br class="Apple-interchange-newline"></div></span><br class="Apple-interchange-newline"></div></span><br class="Apple-interchange-newline"></div></span><br class="Apple-interchange-newline"></div></span><br class="Apple-interchange-newline"> </div><br></body></html>