[CP2K-user] [CP2K:12941] Multiple imaginary frequencies in vibrational analysis
Jacob Jensen
neutr... at gmail.com
Tue Mar 3 13:18:01 UTC 2020
Dear Patrick,
Thank you for your input. The point is, in some cases (e.g. unstable
initial gas phase reactants like radicals) I can't get convergence for
CI-NEB with the criteria tighter than:
RMS_DR : 0.0002
MAX_DR : 0.002
RMS_FORCE: 0.0003
MAX_FORCE: 0.004
Even with this level of accuracy convergence is not possible if I use line
search (which again I have no clue what I'm loosing by deactivating it).
The main goal is to get a reaction barrier that makes sense. As long as I
somehow reach this goal and get a "reliable" barrier for a difficult
reaction containing/ending to gas phase reactants/products, I'm happy.
One may suggest using DIMER method for transition state optimization, and
then doing the vibrational analysis to see whether I can get an imaginary
frequency or not, but still some points are not clear to me.
If I use DIMER method for a TS corresponding to a BAND which is very hard
to converge, how can I get the "correct" reaction barrier considering that
the minimas achieved from NEB are not at the same accuracy level of the
DIMER method? specially considering that the GEO_OPT gives different total
energies than the BAND calculation does for the two minima.
Kind regards,
Jacob
On Tuesday, March 3, 2020 at 1:31:09 PM UTC+1, Patrick Gono wrote:
>
> 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 <pa... at gmail.com
> <javascript:>> 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 <ne... at gmail.com
>> <javascript:>> 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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