<div dir="ltr"><div>Dear Jacob,</div><div><br></div><div>Imaginary frequencies are a consequence of your geometry not being an energy minimum. By construction, you are trying to study saddle points, which are not energy minima, and hence negative eigenvalues of the dynamical matrix are to be expected. In general, negative frequencies indicate the studied structure is not stable at finite temperature (which is evidently true for saddle points / transition states).<br></div><div><br></div><div>In the case you are evaluating minimum energy geometries (such as the initial and final configuration in your simulations), the existence of negative frequencies points to an insufficient geometry optimization. You may try to reduce EPS_SCF even further to achieve better wave function optimization, and at the same time reduce the geometry optimization convergence parameters. If you use the BFGS algorithm, reduce TRUST_RADIUS to make the convergence more stable. If your configuration really corresponds to an energy minimum, then no negative frequencies should be present in the spectrum at all.</div><div><br></div><div>If you need to assess the energy profile of some reaction at finite temperatures, you may want to resort to the so-called Blue Moon sampling technique, which is an analog to NEB but uses ab-initio molecular dynamics at finite temperature instead of static 0K calculations. See, for instance, <a href="https://www.cp2k.org/exercises:2015_ethz_mmm:nacl_free_energy">https://www.cp2k.org/exercises:2015_ethz_mmm:nacl_free_energy</a>.</div><div><br></div><div>To answer your question about the validity of "freezing" the substrate -- this is conventionally done and generally accepted to be okay, especially if you only care about the differences between e.g. zero point energies or vibrational entropies of different adsorbed configurations.</div><div><br></div><div>Yours sincerely,</div><div>Patrick Gono<br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Tue, 3 Mar 2020 at 10:37, Jacob Jensen <<a href="mailto:neutr...@gmail.com">neutr...@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr">Dear All,<div><br></div><div><div>I'm doing vibrational analysis in order to validate some of the saddle points achieved from the NEB calculations. I have a system consist of impinging molecules on the metal surface, so for doing vib. analysis, I have fixed all the metal slab's atoms and only tried to do the calculation for the molecules adsorbed on the surface (I don't know how valid this is! Any thoughts?).</div><div>The problem is, even though the keyword FULLY_PERIODIC is set to False by default for removing the rotational frequencies, I still get three imaginary frequencies which I have no clue where they are coming from. Do you have any idea about the source of these "extra" imaginary frequencies? Or in another words, what is your best suggested strategy to get a single imaginary frequency for the validation of the results coming from NEB calculations?</div><div><br></div><div>I have attached my input, (a part of output) and the coordinate file of the TS. Your advice or suggestion would be much appreciated.</div><div><br></div><div>Kind regards,</div><div><br></div><div>Jacob</div><div><br></div><div><div> VIB| NORMAL MODES - CARTESIAN DISPLACEMENTS</div><div> VIB|</div><div> VIB| 1 2 3</div><div> VIB|Frequency (cm^-1) <span style="background-color:rgb(255,255,0)">-627.437013</span> <span style="background-color:rgb(255,255,0)"> -370.258287 </span> <span style="background-color:rgb(255,255,0)">-12.385518</span></div><div> VIB|Intensities 0.000000 0.000000 0.000000</div><div> VIB|Red.Masses (a.u.) 2.780368 1.414776 3.913531</div><div> VIB|Frc consts (a.u.) -0.001103 -0.000068 -0.000000</div><div> ATOM EL X Y Z X Y Z X Y Z</div><div> 65 N 0.07 0.13 -0.15 0.14 -0.05 0.07 -0.13 0.37 0.13</div><div> 66 C -0.03 -0.24 0.22 -0.01 0.07 -0.05 0.01 0.24 -0.02</div><div> 67 H -0.41 0.72 -0.16 -0.95 0.05 -0.03 -0.17 0.34 -0.06</div><div> 68 H 0.15 0.17 -0.15 0.14 -0.11 0.09 0.38 0.52 0.28</div><div> 69 H -0.04 -0.19 -0.17 0.14 -0.05 0.03 -0.22 -0.16 -0.25</div><div><br></div><div><br></div><div> VIB| 4 5 6</div><div> VIB|Frequency (cm^-1) 94.311628 142.307646 224.156404</div><div> VIB|Intensities 0.000000 0.000000 0.000000</div><div> VIB|Red.Masses (a.u.) 4.349457 2.189311 1.433603</div><div> VIB|Frc consts (a.u.) 0.000001 0.000002 0.000009</div><div> ATOM EL X Y Z X Y Z X Y Z</div><div> 65 N 0.14 0.08 -0.38 0.23 0.12 0.14 0.13 -0.02 -0.02</div><div> 66 C 0.02 0.31 -0.08 0.03 -0.06 0.02 0.13 0.02 -0.01</div><div> 67 H 0.10 0.18 -0.03 0.44 0.06 -0.02 0.37 -0.09 0.03</div><div> 68 H -0.31 -0.15 -0.47 -0.12 0.20 -0.02 0.61 -0.02 0.17</div><div> 69 H 0.22 0.53 -0.10 0.32 0.59 0.45 0.09 -0.45 -0.45</div><div><br></div><div><br></div><div> VIB| 7 8 9</div><div> VIB|Frequency (cm^-1) 421.227384 449.047513 749.374099</div><div> VIB|Intensities 0.000000 0.000000 0.000000</div><div> VIB|Red.Masses (a.u.) 3.868163 5.072223 1.257520</div><div> VIB|Frc consts (a.u.) 0.000312 0.000528 0.001015</div><div> ATOM EL X Y Z X Y Z X Y Z</div><div> 65 N 0.06 -0.05 0.04 -0.02 -0.10 0.08 -0.08 -0.09 0.01</div><div> 66 C -0.45 0.12 0.17 0.24 0.25 0.48 0.07 -0.01 0.01</div><div> 67 H 0.39 -0.02 0.22 -0.02 0.15 0.52 -0.08 0.27 -0.11</div><div> 68 H 0.41 -0.21 0.24 -0.35 -0.30 0.03 0.37 0.25 0.08</div><div> 69 H 0.24 0.14 -0.44 -0.08 -0.08 0.34 0.27 0.72 -0.31</div><div><br></div><div><br></div><div> VIB| 10 11 12</div><div> VIB|Frequency (cm^-1) 854.933502 940.779054 1487.032716</div><div> VIB|Intensities 0.000000 0.000000 0.000000</div><div> VIB|Red.Masses (a.u.) 1.261018 1.071511 1.088996</div><div> VIB|Frc consts (a.u.) 0.001725 0.002149 0.013633</div><div> ATOM EL X Y Z X Y Z X Y Z</div><div> 65 N -0.02 0.11 -0.01 -0.01 -0.01 0.05 0.03 -0.02 0.07</div><div> 66 C 0.04 -0.07 0.03 0.01 0.01 -0.05 0.00 0.00 0.00</div><div> 67 H -0.18 -0.49 0.23 0.18 0.63 -0.30 -0.01 -0.00 -0.00</div><div> 68 H -0.10 -0.57 0.23 -0.21 -0.61 0.20 -0.55 0.29 -0.36</div><div> 69 H 0.12 0.31 -0.39 0.01 -0.05 -0.12 0.12 -0.11 -0.67</div><div><br></div><div><br></div><div> VIB| 13 14 15</div><div> VIB|Frequency (cm^-1) 3078.134845 3178.790354 3420.829077</div><div> VIB|Intensities 0.000000 0.000000 0.000000</div><div> VIB|Red.Masses (a.u.) 1.083814 1.061101 1.079557</div><div> VIB|Frc consts (a.u.) 0.249102 0.277381 0.378480</div><div> ATOM EL X Y Z X Y Z X Y Z</div><div> 65 N -0.00 -0.00 -0.00 0.01 -0.02 -0.06 -0.07 0.03 0.00</div><div> 66 C -0.00 -0.03 -0.08 -0.00 -0.00 0.00 0.00 -0.00 0.00</div><div> 67 H 0.01 0.38 0.92 0.00 -0.00 -0.02 -0.00 -0.00 -0.01</div><div> 68 H -0.00 0.02 0.01 -0.39 0.35 0.82 0.05 -0.07 -0.19</div><div> 69 H 0.02 -0.01 0.00 0.21 -0.09 0.00 0.91 -0.30 0.18</div><div><br></div><div><br></div></div><div></div></div></div>
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