[CP2K-user] [CP2K:12941] Multiple imaginary frequencies in vibrational analysis
Patrick Gono
patri... at gmail.com
Tue Mar 3 12:30:52 UTC 2020
Dear Jacob,
I apologize, I didn't read your original email careful enough -- you are
trying to validate the NEB results and instead of one you observe multiple
negative frequencies.
In this case, try to make sure the calculations are well converged. You may
also try to reduce the finite difference displacement for the vibrational
calculations.
Sorry once again for the misunderstanding.
Yours sincerely,
Patrick Gono
On Tue, 3 Mar 2020 at 13:24, Patrick Gono <patri... at gmail.com> wrote:
> Dear Jacob,
>
> 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).
>
> 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.
>
> 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,
> https://www.cp2k.org/exercises:2015_ethz_mmm:nacl_free_energy.
>
> 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.
>
> Yours sincerely,
> Patrick Gono
>
> On Tue, 3 Mar 2020 at 10:37, Jacob Jensen <neutr... at gmail.com> wrote:
>
>> Dear All,
>>
>> 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?).
>> 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?
>>
>> I have attached my input, (a part of output) and the coordinate file of
>> the TS. Your advice or suggestion would be much appreciated.
>>
>> Kind regards,
>>
>> Jacob
>>
>> VIB| NORMAL MODES - CARTESIAN DISPLACEMENTS
>> VIB|
>> VIB| 1 2 3
>> VIB|Frequency (cm^-1) -627.437013 -370.258287
>> -12.385518
>> VIB|Intensities 0.000000 0.000000
>> 0.000000
>> VIB|Red.Masses (a.u.) 2.780368 1.414776
>> 3.913531
>> VIB|Frc consts (a.u.) -0.001103 -0.000068
>> -0.000000
>> ATOM EL X Y Z X Y Z X Y
>> Z
>> 65 N 0.07 0.13 -0.15 0.14 -0.05 0.07 -0.13
>> 0.37 0.13
>> 66 C -0.03 -0.24 0.22 -0.01 0.07 -0.05 0.01
>> 0.24 -0.02
>> 67 H -0.41 0.72 -0.16 -0.95 0.05 -0.03 -0.17
>> 0.34 -0.06
>> 68 H 0.15 0.17 -0.15 0.14 -0.11 0.09 0.38
>> 0.52 0.28
>> 69 H -0.04 -0.19 -0.17 0.14 -0.05 0.03 -0.22
>> -0.16 -0.25
>>
>>
>> VIB| 4 5 6
>> VIB|Frequency (cm^-1) 94.311628 142.307646
>> 224.156404
>> VIB|Intensities 0.000000 0.000000
>> 0.000000
>> VIB|Red.Masses (a.u.) 4.349457 2.189311
>> 1.433603
>> VIB|Frc consts (a.u.) 0.000001 0.000002
>> 0.000009
>> ATOM EL X Y Z X Y Z X Y
>> Z
>> 65 N 0.14 0.08 -0.38 0.23 0.12 0.14 0.13
>> -0.02 -0.02
>> 66 C 0.02 0.31 -0.08 0.03 -0.06 0.02 0.13
>> 0.02 -0.01
>> 67 H 0.10 0.18 -0.03 0.44 0.06 -0.02 0.37
>> -0.09 0.03
>> 68 H -0.31 -0.15 -0.47 -0.12 0.20 -0.02 0.61
>> -0.02 0.17
>> 69 H 0.22 0.53 -0.10 0.32 0.59 0.45 0.09
>> -0.45 -0.45
>>
>>
>> VIB| 7 8 9
>> VIB|Frequency (cm^-1) 421.227384 449.047513
>> 749.374099
>> VIB|Intensities 0.000000 0.000000
>> 0.000000
>> VIB|Red.Masses (a.u.) 3.868163 5.072223
>> 1.257520
>> VIB|Frc consts (a.u.) 0.000312 0.000528
>> 0.001015
>> ATOM EL X Y Z X Y Z X Y
>> Z
>> 65 N 0.06 -0.05 0.04 -0.02 -0.10 0.08 -0.08
>> -0.09 0.01
>> 66 C -0.45 0.12 0.17 0.24 0.25 0.48 0.07
>> -0.01 0.01
>> 67 H 0.39 -0.02 0.22 -0.02 0.15 0.52 -0.08
>> 0.27 -0.11
>> 68 H 0.41 -0.21 0.24 -0.35 -0.30 0.03 0.37
>> 0.25 0.08
>> 69 H 0.24 0.14 -0.44 -0.08 -0.08 0.34 0.27
>> 0.72 -0.31
>>
>>
>> VIB| 10 11 12
>> VIB|Frequency (cm^-1) 854.933502 940.779054
>> 1487.032716
>> VIB|Intensities 0.000000 0.000000
>> 0.000000
>> VIB|Red.Masses (a.u.) 1.261018 1.071511
>> 1.088996
>> VIB|Frc consts (a.u.) 0.001725 0.002149
>> 0.013633
>> ATOM EL X Y Z X Y Z X Y
>> Z
>> 65 N -0.02 0.11 -0.01 -0.01 -0.01 0.05 0.03
>> -0.02 0.07
>> 66 C 0.04 -0.07 0.03 0.01 0.01 -0.05 0.00
>> 0.00 0.00
>> 67 H -0.18 -0.49 0.23 0.18 0.63 -0.30 -0.01
>> -0.00 -0.00
>> 68 H -0.10 -0.57 0.23 -0.21 -0.61 0.20 -0.55
>> 0.29 -0.36
>> 69 H 0.12 0.31 -0.39 0.01 -0.05 -0.12 0.12
>> -0.11 -0.67
>>
>>
>> VIB| 13 14 15
>> VIB|Frequency (cm^-1) 3078.134845 3178.790354
>> 3420.829077
>> VIB|Intensities 0.000000 0.000000
>> 0.000000
>> VIB|Red.Masses (a.u.) 1.083814 1.061101
>> 1.079557
>> VIB|Frc consts (a.u.) 0.249102 0.277381
>> 0.378480
>> ATOM EL X Y Z X Y Z X Y
>> Z
>> 65 N -0.00 -0.00 -0.00 0.01 -0.02 -0.06 -0.07
>> 0.03 0.00
>> 66 C -0.00 -0.03 -0.08 -0.00 -0.00 0.00 0.00
>> -0.00 0.00
>> 67 H 0.01 0.38 0.92 0.00 -0.00 -0.02 -0.00
>> -0.00 -0.01
>> 68 H -0.00 0.02 0.01 -0.39 0.35 0.82 0.05
>> -0.07 -0.19
>> 69 H 0.02 -0.01 0.00 0.21 -0.09 0.00 0.91
>> -0.30 0.18
>>
>>
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>
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