Questions tagged [vibrations]
Questions concerning molecular and solid vibrational modes.
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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2
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1
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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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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?
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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 ...
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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 ...
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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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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 ...
Daniel Konstantinovsky
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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 ...
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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 ...
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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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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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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 ...
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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, ...
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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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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 ...
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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 ...
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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. ...
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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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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? (...
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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 ...
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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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2
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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 ...
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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{...
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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 ...
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0
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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 ...
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10
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2
answers
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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 ...
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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 ...
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2
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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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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?
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2
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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 ...
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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?
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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 ...
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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,...
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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 ...
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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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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. ...
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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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