Questions tagged [vibrations]

Questions concerning molecular and solid vibrational modes.

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5
votes
1answer
63 views

Numerical Frequency Parallelization in ORCA

In orca it is possible to use NumFreq and AnFreq to get the numerical and analytical frequencies, but the analytical frequencies take a large amount of memory and computing time compared to numerical ...
8
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1answer
96 views

How to eliminate imaginary frequencies during a Gaussian geometry optimization?

When conducting a minimization on Gaussian software, What are the procedures used to eliminate imaginary frequencies if we have already found a stationary point? Are there any keywords that would help ...
5
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0answers
62 views

How do you Select a Time Step for Molecular Dynamics Simulations?

It seems there is a general agreement among the practitioners of Molecular Dynamics that 1fs is a fairly reasonable time step, with shorter time steps being required for materials with higher ...
9
votes
2answers
164 views

Transformation between two different sets of molecular vibrational normal coordinate systems

Lets assume we have $N$ Atoms and we treat them within the Born-Oppenheimer Approximation. We can calculate the adiabatic electronic groundstate potential. Lets assume we observe two local minima, ...
9
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1answer
116 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: ...
5
votes
1answer
73 views

GAMESS(US) Hessian calculation sometimes does not produce the IR intensities

I have noticed that for certain Hessian calculations that I run with GAMESS(US), the IR intensities are not produced in the log file. Below I have an example input card (without the molecule $DATA ...
5
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0answers
92 views

Q-Chem gives "Hessian Appears to have all zero or negative eigenvalues" error when calculating Frequencies [closed]

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 ...
9
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1answer
64 views

Package for computing properties of excited vibrational states

We're starting to develop some calculations of the hyperfine parameters (electric field gradient, spin-rotation coupling, spin-spin coupling) with CFOUR, and we reached a limitation of the public ...
10
votes
1answer
129 views

How to generate accurate displacements along normal modes?

How can i displace my structure along a particular normal mode, without coupling to other modes ? Rather than a exact mathematical procedure, I am more interested in a software/script/package that can ...
16
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1answer
2k 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
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2answers
194 views

Excited state normal mode frequency doesn't match for NH3

I am trying to optimize the geometry of excited state NH3 and get the corresponding normal modes for excited states. I am trying to get the frequencies as mentioned in this reference. They claim to ...
8
votes
1answer
104 views

Optimization and vibrational analysis of excited state CO using GAMESS

I am facing some problems in performing HESSIAN analysis on excited states of molecules: I am testing it out with CO. My input file to GAMESS is pasted below. Could ...
7
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1answer
79 views

Can we translate vibrational frequencies at q-points to vibrational frequencies of atoms?

Lattice dynamics codes like phonopy output vibrational frequencies at q-points. Can we get data of vibrational frequencies for each of the atoms in the supercell? (...
9
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1answer
193 views

Mismatched number of normal modes calculation in GAMESS

I am trying to calculate normal modes frequency matrix using HESSIAN calculation in GAMESS. Since we know that number of normal modes for a non-linear molecule is 3N-5 where N is the number of atoms. ...
17
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1answer
395 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. “...
7
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5answers
1k 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 ...
15
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1answer
267 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 ...
15
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0answers
129 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 ...
12
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1answer
202 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{...
10
votes
2answers
273 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 ...
8
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0answers
70 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
938 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
361 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
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2answers
613 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
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2answers
168 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?
8
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1answer
87 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 ...
19
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1answer
165 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
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1answer
102 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,...
26
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1answer
178 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 ...
14
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2answers
120 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 ...