<div dir="ltr">Dear all, <div><br></div><div>I would like to use TAMkin (<a href="http://molmod.github.io/tamkin/">http://molmod.github.io/tamkin/</a>) to compute thermodynamic properties from the vibrational frequencies computed with CP2K.</div><div>As I have understood it, the way TAMkin works is to read and diagonalize the Hessian matrix printed in the CP2K output.</div><div>When I compare the frequencies obtained with TAMkin with those obtained with cp2k, the values are not the same (Compare column 2 and 3 in the table below). </div><div><br></div><div>The first task is then to understand how CP2K computes the frequencies. To investigate this, I copied the Hessian matrix from the CP2K output (printed below the string "Hessian in cartesian coordinates") and pasted it into Excel and saved it as a csv file. This file I read into python and diagonalized the Hessian with numpy. The frequencies I get are different from those printed in the cp2k output file (compare column 3 and 4 in the table below). </div><div>I have assumed that the units of the Hessian matrix in the cp2k output file are Ry*bohr-2*kamu-1 (kamu = 1000*amu). This assumption is based on trial and error; it was what got me closest to the cp2k frequencies. </div><div><br></div><div><br></div><div>Table 1: The eight lowest frequencies. There are 48 in total.</div><div><table class="MsoTableGrid" border="1" cellspacing="0" cellpadding="0" style="border-collapse: collapse; border-width: initial; border-style: none;">
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<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:
normal"><span lang="IT">frequencies</span><o:p></o:p></p>
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<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:
normal"><span lang="IT">TAMkin / <br>
cm-1<o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:
normal"><span lang="IT">cp2k / <br>
cm-1<o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:
normal"><span lang="IT">Diag., cp2k Hessian / <br>
cm-1<o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:
normal"><span lang="IT">1<o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:
normal"><span lang="IT">31.1<o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:
normal"><span lang="IT">27.3<o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:
normal"><span lang="IT">32.6<o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:
normal"><span lang="IT">2<o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:
normal"><span lang="IT">38.3<o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:
normal"><span lang="IT">40.8<o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:
normal"><span lang="IT">40.1<o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:
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<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:
normal"><span lang="IT">47.7<o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:
normal"><span lang="IT">51.0<o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:
normal"><span lang="IT">50.2<o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:
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<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:
normal"><span lang="IT">74.7<o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:
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<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:
normal"><span lang="IT">78.2<o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:
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<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:
normal"><span lang="IT">82.0<o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:
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<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:
normal"><span lang="IT">85.8<o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:
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<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:
normal"><span lang="IT">111.0<o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:
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<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:
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<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:
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<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:
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<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:
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<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:
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<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:
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<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:
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<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:
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<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:
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</tbody></table></div><div><br></div><div>What is wrong with my calculation?</div><div>What steps should be done to go from the Hessian to the frequencies?</div><div><br></div><div>The Hessian in csv format, the python script and the cp2k output file are attached. </div><div><br></div><div>Thanks a lot for your help.</div><div><br></div><div>Regards,</div><div>Torstein Fjermestad</div><div> </div><div><br></div><div><br></div></div>