Questions tagged [vibrations]

Questions concerning molecular and solid vibrational modes.

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5 votes
1 answer
65 views

Finding normal mode vectors vs. vibrational frequencies?

For a given molecule, we can determine the normal modes of vibration and the corresponding vibrational frequencies by calculating the molecular Hessian of second-order energy derivatives, and finding ...
8 votes
1 answer
374 views

How much does it cost (RAM and CPU) to calculate the energy of H2?

I have recently come across this very intriguing paper “The Fundamental Vibration of Molecular Hydrogen”. I have asked the authors the following naïve questions directly via email: What was the ...
15 votes
5 answers
1k views

What's the point of doing high accuracy spectroscopy calculations?

I am currently reading Dickenson et al. (2013) The Fundamental Vibration of Molecular Hydrogen. I am trying to understand why this calculation is important for the field beyond basic scientific ...
2 votes
1 answer
206 views

NCORE bigger than 1 when performing phonon/vibrational calculation(IBRION=5) in VASP?

When I try to calculate the vibration frequency of TiO2, I set IBRION=5 in VASP, but it turns out I couldn't use NCORE>1 in this situation, once I use NCORE>1, VASP would run for only one ionic ...
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3 votes
0 answers
54 views

Interpreting Phonon calculations for 2D materials [closed]

What is the meaning of phonon calculation in 2D materials? And is it enough to predict the stability of materials based on positive phonon only?
5 votes
0 answers
45 views

How to derive specific heat of a crystalline material from phonon density of states? [closed]

I have done a simulation of a crystalline material using DFT and have extracted its normal modes and its phonon density of states. Does anyone have an algorithm/code or a detailed resource that can ...
  • 1,266
5 votes
0 answers
40 views

How does the VIBRA module of SIESTA compute IR intensities?

I am working with Fluoro-Graphene (let's assume a fully relaxed monolayer on the XY plane with 16C-1F cell where the F is "covalently" bound to the graphene on top of it with respect to the ...
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7 votes
1 answer
135 views

LDA vs GGA for vibrational properties?

The question is pretty simple, is GGA better than LDA at predicting vibrational properties of molecules/materials ? What is the nuance and so forth.
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7 votes
1 answer
112 views

How to move atom coordinates along a normal mode given the eigenvector?

I need to displace atoms along a complicated normal mode involving many atoms. I have the normal mode eigenvector, I just don't know how to turn the eigenvector into an algorithm to translate the ...
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4 votes
1 answer
174 views

RAMAN calculation with SIESTA and ASE-SIESTA

I have been using the ASE-SIESTA-PyNAO module to attempt some RAMAN/IR mode calculations on graphene (if anyone has any experience with this please send me a message maybe we can chat about it). At no ...
  • 1,266
5 votes
1 answer
166 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 ...
9 votes
1 answer
319 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 ...
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6 votes
0 answers
100 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 ...
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9 votes
1 answer
75 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 ...
  • 99
10 votes
2 answers
241 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, ...
10 votes
1 answer
161 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 ...
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6 votes
2 answers
203 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
1 answer
182 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 ...
9 votes
1 answer
219 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. ...
5 votes
1 answer
140 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 ...
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7 votes
1 answer
102 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? (...
7 votes
5 answers
2k 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 ...
10 votes
1 answer
167 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: ...
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25 votes
2 answers
753 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 ...
  • 2,323
12 votes
1 answer
336 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{...
19 votes
1 answer
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 ...
5 votes
0 answers
143 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 ...
10 votes
2 answers
347 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 votes
0 answers
75 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 ...
18 votes
2 answers
952 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 ...
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7 votes
1 answer
755 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?
  • 791
13 votes
2 answers
630 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 ...
  • 1,869
10 votes
2 answers
304 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?
  • 1,869
9 votes
1 answer
163 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 ...
18 votes
1 answer
117 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,...
  • 14.3k
18 votes
0 answers
171 views

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

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 ...
  • 14.3k
15 votes
2 answers
129 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 ...
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19 votes
1 answer
238 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. ...
  • 14.3k
17 votes
1 answer
525 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. “...
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26 votes
1 answer
193 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 ...
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