<div dir="ltr">Hi<div><br></div><div>In case the method suggested by Matt doesn't work or for whatever reason you don't want to touch the source code, you may also consider to perform the vibrational analysis (with frozen atoms) using the CP2K/ASE interface, see e.g.:</div><div><br></div><div><a href="https://wiki.fysik.dtu.dk/ase/ase/vibrations/vibrations.html">https://wiki.fysik.dtu.dk/ase/ase/vibrations/vibrations.html</a></div><div><br></div><div>You can write a file of the vibrational modes and visualise it using Jmol, see <a href="https://wiki.fysik.dtu.dk/ase/ase/vibrations/vibrations.html#ase.vibrations.Vibrations.write_jmol">https://wiki.fysik.dtu.dk/ase/ase/vibrations/vibrations.html#ase.vibrations.Vibrations.write_jmol</a></div><div><br></div><div>A very short introduction of the CP2K/ASE interface is included in the end of this presentation: </div><div><br></div><div><a href="https://www.cp2k.org/_media/events:2016_summer_school:cp2k-uk-summer-school-sanliang-ling.pdf">https://www.cp2k.org/_media/events:2016_summer_school:cp2k-uk-summer-school-sanliang-ling.pdf</a></div><div><br></div><div>SL<br></div><div><br></div></div><div class="gmail_extra"><br><div class="gmail_quote">On 26 September 2016 at 16:51, Tobias Kraemer <span dir="ltr"><<a href="mailto:161brun...@gmail.com" target="_blank">161brun...@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div style="color:rgb(0,0,0);font-family:Calibri,Arial,Helvetica,sans-serif;font-size:16px">Hi Matt,</div><div style="color:rgb(0,0,0);font-family:Calibri,Arial,Helvetica,sans-serif;font-size:16px"><br></div><div style="color:rgb(0,0,0);font-family:Calibri,Arial,Helvetica,sans-serif;font-size:16px"><br></div><div style="color:rgb(0,0,0);font-family:Calibri,Arial,Helvetica,sans-serif;font-size:16px">thanks for your suggestion. I will pass this on to the people at our supercomputer, I wouldn't want to mess around with the code. But they can certainly provide assistance. I'll see if this works, but at least it is clear now where the problem lies.</div><div style="color:rgb(0,0,0);font-family:Calibri,Arial,Helvetica,sans-serif;font-size:16px"><br></div><div style="color:rgb(0,0,0);font-family:Calibri,Arial,Helvetica,sans-serif;font-size:16px">Tobi</div><div><div class="h5"><br>On Monday, September 26, 2016 at 3:51:28 PM UTC+2, Tobias Kraemer wrote:<blockquote class="gmail_quote" style="margin:0;margin-left:0.8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Dear all,<div><br></div><div><br></div><div>I have run a vibrational analysis on an optimised structure, thereby keeping a number of atoms fixed through setting spatial constraints. This is essentially the idea of the Partial Hessian Vibrational Analysis (PHVA) approach. Now, I have realised that although the normal modes are printed in the output file, there is no molden-compatible file </div><div>for visualisation of the modes (in particular important for verifying transition states). I have defined this in the input (also attached as file), and for a full vibrational analysis (i.e. no constraints) this works without problems. I always obtain this file. For various reasons, it would be very useful to output this file in any case. Could this be looked into by someone. </div><div><br></div><div>Thanks for your comments</div><div><br></div><div><br></div><div>Tobias</div><div><br><div><br></div><div><p style="font-size:11px;line-height:normal;font-family:Menlo;background-color:rgb(255,246,220)"><span>&MOLDEN_VIB</span></p>
<p style="font-size:11px;line-height:normal;font-family:Menlo;background-color:rgb(255,246,220)"><span> FILENAME=frequencies.mol</span></p>
<p style="font-size:11px;line-height:normal;font-family:Menlo;background-color:rgb(255,246,220)"><span> &END</span></p></div></div></div></blockquote></div></div></div><div class="HOEnZb"><div class="h5">
<p></p>
-- <br>
You received this message because you are subscribed to the Google Groups "cp2k" group.<br>
To unsubscribe from this group and stop receiving emails from it, send an email to <a href="mailto:cp2k+uns...@googlegroups.com" target="_blank">cp2k+unsubscribe@googlegroups.<wbr>com</a>.<br>
To post to this group, send email to <a href="mailto:cp...@googlegroups.com" target="_blank">cp...@googlegroups.com</a>.<br>
Visit this group at <a href="https://groups.google.com/group/cp2k" target="_blank">https://groups.google.com/<wbr>group/cp2k</a>.<br>
For more options, visit <a href="https://groups.google.com/d/optout" target="_blank">https://groups.google.com/d/<wbr>optout</a>.<br>
</div></div></blockquote></div><br></div>