Questions tagged [vibrations]

Questions concerning molecular and solid vibrational modes.

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Algorithm for finding the v=1 state of an H2O molecule

In the context of simulating the dissociation dynamics of an H₂O molecule on a metal surface, what algorithm is employed for generating the initial state of a tri-atomic non-linear molecule, such as H₂...
6 votes
2 answers
393 views

How may I solve the radial Schrödinger equation?

I want to solve the radial Schrodinger equation for a Carbon atom with all six electrons. The equation I want to solve is for $r>0$: $$[\frac{-\hbar^2}{2m}\frac{\partial^2}{\partial r^2}+ \frac{\...
5 votes
0 answers
47 views

How does dimer and monomer zero point energy affect dissociation energy?

This paper by Xinchuan Huang et al. gives a calculation for the dissociation energy of a water dimer. The electronic dissociation energy (what they call $D_e$) is around 21 kJ/mol, and this is ...
4 votes
0 answers
41 views

Carbon Capture Research - Force Constants & Basis Sets

Greetings Matter Modeling, I'm researching carbon capture dynamics in the context of sorbent regeneration. The UN IPCC Net-Zero goal requires 75 Mt-CO₂/year captured by 2030. According to the IEA, we ...
7 votes
0 answers
159 views

How do you calculate a full quartic force field for anharmonic frequencies?

I am an experimental chemist interested in anharmonicity—I am particularly interested in how to calculate anharmonic frequencies. The method I have the most experience with is (generalised) second ...
6 votes
1 answer
141 views

Do conformations arise from vibrations?

Cross-posted on Chemistry SE. I was wondering how a molecule transforms from one conformation into another. Surely, since the conformations are separated by a potential barrier, some activation energy ...
10 votes
3 answers
513 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, ...
5 votes
1 answer
35 views

Database on calculated molecular vibrations including coordination complexes?

Related to the question Are there dashboards displaying experimental properties of molecular materials? My question is: Are there any good, free, online databases on calculated vibrational modes of ...
7 votes
1 answer
103 views

How many non-redundant internal coordinates are needed for optimisation of linear molecule?

I have been working to implement optimisation in internal coordinates (for a transition state search software I am working on). However, the implementation details are almost always glossed over in ...
2 votes
1 answer
148 views

Helmholtz vibrational energy from VASP calculations

I would like to calculate the Helmholtz vibrational energy. I have done the phonon calculations. My question is how to extract the vibrational energy from the output of the Vasp calculation. A source ...
3 votes
1 answer
138 views

Script to draw one-dimensional PES comparing harmonic and anharmonic vibrational modes

This is an extension of a question I asked a little while ago: Software to draw one-dimensional PES including vibrational energy levels. I am asking the followup here based on advice received after ...
5 votes
0 answers
48 views

2D Infrared spectroscopy for bulk systems using molecular dynamics

There are some questions and answers (1,2) on this site regarding simple infrared and vibrational density of states calculations with molecular dynamics and there any simple algorithmic descriptions ...
6 votes
1 answer
159 views

Is it possible to restrict the calculation of frequencies in ORCA program?

I looked in the orca manual but didn't find anything, but in the case of having a molecule adsorbed in a cluster, is it possible to perform the frequency calculation only on the molecule and not on ...
2 votes
1 answer
881 views

How to generate k-point grid using Quantum ESPRESSO?

I am doing an exercise to calculate silicon crystal mobility using quantum ESPRESSO. I'm in a step where i should do a non self-consistent calculation on a 6x6x6 uniform and Γ-centered k-point grid ...
6 votes
1 answer
119 views

Are there packages which calculate normal modes for ML potentials?

While I'm primarily interested in molecular normal modes, the question could also apply to calculating phonon spectra / vibrations in solids. There are many machine learning approaches to calculate ...
5 votes
1 answer
156 views

Can a material have negative phonon modes in the phonon spectrum but still exist?

I came across a paper which talks about $Cs_2SnI_6$ the material is well researched and there are dozens of experimental papers which say that the material exists in Fm3m space group(FCC), the ...
5 votes
1 answer
234 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
397 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
2k 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 ...
3 votes
1 answer
866 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 ...
3 votes
0 answers
101 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?
19 votes
0 answers
229 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 ...
5 votes
0 answers
55 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 ...
27 votes
2 answers
2k 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 ...
5 votes
0 answers
108 views

How does the VIBRA module of SIESTA compute IR intensities? [closed]

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 ...
7 votes
1 answer
229 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.
7 votes
1 answer
223 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 ...
4 votes
1 answer
421 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 ...
7 votes
1 answer
651 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 ...
10 votes
1 answer
1k 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 ...
6 votes
0 answers
251 views

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

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 ...
10 votes
1 answer
280 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
1 answer
244 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 votes
0 answers
244 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 votes
1 answer
118 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
1 answer
256 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 ...
19 votes
1 answer
4k 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
2 answers
231 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
311 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 votes
1 answer
146 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 votes
1 answer
277 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 votes
1 answer
796 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 votes
5 answers
3k 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 ...
12 votes
1 answer
593 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
2 answers
439 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
83 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
989 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
1 answer
1k 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?
14 votes
2 answers
671 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
2 answers
608 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?