Questions tagged [vibrations]

Questions concerning molecular and solid vibrational modes.

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6
votes
5answers
630 views

Quantum harmonic oscillator, zero-point energy, and the quantum number n

The energy of a quantum harmonic oscillator is given as, \begin{equation} E_{qho} = \left(n + \frac{1}{2}\right)\hbar\omega,\;\;\;\;\;\; n = 0,1,2,3,... \tag{1} \end{equation} I understand the ...
9
votes
1answer
64 views

Where did the “Computational Chemistry Comparison and Benchmark DataBase” find its scaling factors for vibrational specra?

I worked with gaussian to simulate vibrational IR and Raman spectra. For that purpose, I scaled the vibrational frequencies from my gaussian calculation with the scaling factors from this website: ...
16
votes
1answer
144 views

Is it right to neglect very small imaginary frequencies?

I'm running a DFT optimization (B3LYP/def2-TZVP) and frequencies in ORCA for a molecule. And I get one or two very small (1-6 cm^-1) imaginary frequencies which corresponds to a slight bend of the ...
12
votes
1answer
131 views

Geometric optimization taking a long time. Are my convergence criteria too tight in CP2K?

I have been having trouble with the VIBRATIONAL_ANALYSIS routine. Namely, the routine keeps timing out. I am trying to find the vibrational modes of Pyridine in a non periodic system, as well as $\ce{...
14
votes
1answer
801 views

What do negative phonon frequencies signify?

Negative frequencies "in general" mean the direction of displacement is reverse to that in positive frequencies. Does it mean two frequencies with opposite signs but the same magnitude give ...
6
votes
0answers
45 views

Q-Chem gives “Hessian Appears to have all zero or negative eigenvalues” error when calculating Frequencies

I have troubles with obtaining spectra for selected molecules in different DFT functionals. I calculate IR spectra for my target molecules (gold complexes with C/H/N/O/S/Au composition) to find how ...
11
votes
2answers
237 views

Morse potential for phonons in solids instead of the harmonic potential approximation?

As the title says, the Morse potential (https://en.wikipedia.org/wiki/Morse_potential) is an exactly solvable model in quantum mechanics, just like the quantum harmonic oscillator. Extensions of it ...
9
votes
0answers
64 views

Equilibration of normal modes in water molecule [closed]

When running a molecular dynamics simulation on a singular water molecule in vacuum to analyze its normal modes of vibration from the NVE (microcanonical) ensemble, the bending mode frequency is ...
17
votes
2answers
921 views

Logic of published geometry optimization results without checking phonons

I see that in many papers where optimization results presented, they do not mention phonons and their force convergence criterion is 0.01 eV/A. Can you publish a result like that? And is not this ...
7
votes
1answer
124 views

DFPT vs Finite Difference Method [duplicate]

Which one is better in case of a phonon calculation and does DFPT also have small negative frequencies near Gamma due to the numerical noise? What are their advantages and disadvantages?
13
votes
2answers
583 views

What does it mean if a strictly optimized experimental geometry presents imaginary frequencies?

Let's say you optimize an experimental geometry of a structure with very large basis sets, strict optimization settings with different XC functionals and after calculating phonons of this structure ...
10
votes
2answers
128 views

What are the methods that can be used to ensure that an optimized geometry is a local minimum?

Usually it is suggested to do a phonon calculation. What are the other ways?
9
votes
1answer
60 views

Phonon Calculations and Vibrational Modes

The Raman spectrum of a material shows certain 'active' modes for which we get experimental signatures. Phonon calculations are mostly used to calculate vibrational modes. How can we determine the ...
17
votes
1answer
89 views

Discrepancy between numerical and transformed derivatives

This is related to a prior question of mine Derivatives with respect to user defined vibrational modes. While that one focuses on potential software to use for derivatives with respect to normal modes,...
16
votes
0answers
125 views

Is there a software that can do derivatives with respect to user defined vibrational modes? [closed]

I'm doing some property calculations that depend on a sum of derivatives of some quantity with respect to normal vibrational modes. I was hoping to find some physical intuition relating the type of ...
14
votes
2answers
111 views

What is the largest system for which vibrationally resolved electronic spectra have been simulated using ML-MCTDH?

Multi-layer Multi-configuration time-dependent Hartree (ML-MCTDH) is a method widely used for simulation of vibrationally resolved electronic spectra that incorporate the coupling between vibrational ...
18
votes
1answer
97 views

Retrieving Translational and Rotational Modes

I'm doing some post-processing using the vibrational modes of a molecule to solve a linear system of equations, but I believe I need all the modes in order to have a single, well-determined solution. ...
17
votes
1answer
212 views

Alternatives to VEDA 4 vibrational energy distribution analysis software?

Said software is useful when you need to assign the peaks in vibrational spectra to different vibrational modes found in a hessian calculation for a given molecule, as described in Jamróz, Michał H. “...
26
votes
1answer
157 views

How to map molecular vibrations into lattice phonons?

Let's assume I have already relaxed a molecular structure for a non-trivial molecule and obtained a geometry that is close to the one resulting from X-ray crystallography. This can be achieved in a ...