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35 votes

How big should a supercell be in phonon calculations?

Quick Summary: There's no way around performing a convergence test. However, it is possible to obtain convergence much faster than the Phonopy approach by using nondiagonal supercells [1]. The basic ...
ProfM's user avatar
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What do negative phonon frequencies signify?

Phonons are a measure of the curvature of the potential energy surface about a stationary point. In particular, the matrix of force constants is calculated as: $$ D_{i\alpha,i^{\prime}\alpha^{\prime}}(...
ProfM's user avatar
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21 votes
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Are there differences in accuracy and reliability between the frozen phonon method and Density Functional Perturbation Theory?

Short answer: Modern implementations of these two methods lead to similar accuracies. Longer answer: The calculation of phonons requires the calculation of the Hessian of the potential energy surface ...
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How to deduce phase transitions from a phonon calculation?

Background theory. In the harmonic approximation, the potential energy surface (PES) is expanded about an equilibrium point to second order, to obtain the Hamiltonian: $$ \hat{H}=\sum_{p,\alpha}-\frac{...
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17 votes

How big should a supercell be in phonon calculations?

Ideally, a convergence test would be the best way to decide the required size of the supercell, but it can get expensive. When phonopy (or any similar calculation technique) finds displacements in the ...
Hitanshu Sachania's user avatar
15 votes
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Computing phonon dispersion from molecular dynamics simulations?

You are basically looking for finding phonon frequencies with respect to $\mathbf{q}$ the scattering vector in reciprocal space. From fluctuation-dissipation theory, the force constants of the system ...
Mithridates the Great's user avatar
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Ab initio molecular dynamics to check material stability at finite temperature

This is a description of some methods available to study dynamical and chemical stability, not limited to MD: Dynamical stability. The question here is: given a compound in a particular structure, is ...
ProfM's user avatar
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15 votes

How big should a supercell be in phonon calculations?

Considering this in terms of a 2x2x2 supercell matrix is the wrong way to think about this, as choice depends on the cell length and bonding type. Given that rigorous convergence testing is near-...
Keith Refson's user avatar
15 votes

What does it mean to say a material is 'anharmonic'?

This is a difficult question without a straight-forward answer. In general you have to perform a test to decide whether the harmonic approximation is sufficient or whether you need to include higher ...
ProfM's user avatar
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14 votes

Logic of published geometry optimization results without checking phonons

In general it is not justified to published the geometry of a system without performing a phonon calculation. This is where you may end up in the potential energy surface depending on which type of ...
ProfM's user avatar
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14 votes

Logic of published geometry optimization results without checking phonons

Phonon calculations tend to be very expensive to run. That being said, for gas phase molecules it is very common and expected that frequency calculations are run to ensure the molecule is not on a ...
Tristan Maxson's user avatar
14 votes

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

Assuming that all calculation parameters associated with the electronic structure are properly converged, then obtaining imaginary frequencies can mean one of two things. Physical imaginary ...
ProfM's user avatar
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How can I scan the whole PES of a bulk structure?

The potential energy surface (PES) is a 3N-dimensional function for a bulk system containing N atoms (in reality 3N-3 to account for the trivial translational degrees of freedom). For a bulk structure,...
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Phonon dispersion and phonon DOS

The phonon dispersion relates the phonon frequencies $\omega_{\mathbf{q}\nu}$ for each branch $\nu$ with the phonon wave vector $\mathbf{q}$, typically along a path in the Brillouin zone joining high-...
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How to determine LA/TA, ZA/ZO and LO/TO by PHONOPY

There are two major techniques used to model phonon interactions - The frozen phonon method and density functional perturbation theory (DFPT). Phonopy is used to carry out calculations in the frozen ...
Xivi76's user avatar
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Morse potential for phonons in solids instead of the harmonic potential approximation?

Some people do: In this paper there is a system coupled to a bath of Morse oscillators rather than a bath of harmonic oscillators, but it is not exactly solvable, they used a numerical approach called ...
Nike Dattani - No Free Time's user avatar
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What are the methods that can be used to ensure that an optimized geometry is a local minimum?

This depends on what you are studying. For molecular systems without periodicity, the simplest approach is to carry out a vibrational frequency analysis and confirm that there are no imaginary modes. ...
Andrew Rosen's user avatar
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10 votes

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

The zero-point energy is of no importance here, since you can always choose your reference energy freely you can energy-shift your hamiltonian by $\frac{1}{2}\hbar\omega$ $$ H = \frac{p^2}{2m}+\frac{1}...
lepmueller's user avatar
9 votes

How to map molecular vibrations into lattice phonons?

If you index the molecule and the atoms in the crystallographic unit cell the same, you could extract the displacement from the phonon eigenvectors and the displacement from the normal modes. By ...
Phil Maffettone's user avatar
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How to improve a phonon spectrum calculation for a monolayer material?

This is actually an important question regardless of the code you're using (I use SIESTA and NWChem). To obtain a good phonon spectrum, the first thing you need is a truly relaxed/optimized structure. ...
Elie H's user avatar
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9 votes

Should one perform geometry optimisation before calculating electronic/phonon band structures via DFT?

For the electronic band structure, I'd say it's debatable. For consistency reasons, it would make sense for example to perform a geometry optimization with PBE and calculate its PBE band structure. ...
CW Tan's user avatar
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8 votes

Phonon Calculations for Bilayer 2D systems

The presence of imaginary frequencies in a phonon dispersion can have two sources: Physical origin. If the imaginary frequency appears at a $\mathbf{q}$-point in the Brillouin zone that is included ...
ProfM's user avatar
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8 votes

How to calculate temperature dependent phonon band structure in VASP

There are two main contributions that can be included in the DFT context when calculating phonons at finite temperature: Thermal expansion. As temperature increases, the volume of materials changes (...
ProfM's user avatar
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8 votes
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The Appearance of Imaginary Frequencies in Lattice Vibration Calculations with Increasing KPOINTS

In the usual perturbation theory approach, we optimise a structure to minimise the forces (to zero, within some small tolerance) and obtain the ground state structure (or a local energy minimum). ...
Phil Hasnip's user avatar
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7 votes

"Input forces are not enough to calculate force constants" Phonopy error?

I have never used Phonopy, so we will have to wait for an actual user for a full answer. However, I can make some general statements about phonon calculations that could plausibly explain your error. ...
ProfM's user avatar
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7 votes

What is a "Charge Density Wave" and how is it related to the imaginary frequencies on phonon dispersion bandstructures?

Charge density waves (CDW's) exist in a few circumstances that I know of. The simplest example I can think of is the CDW due to nesting of the Fermi surface. This can be discussed in the context of ...
Tyler Sterling's user avatar
7 votes

How to simulate atomic scattering from solid walls at finite temperature for a particles in a box simulation?

Whatever scattering mechanism you choose must respect detailed balance in equilibrium: on average, the number of particles hitting a patch of the wall at a given angle and velocity must equal the ...
lnmaurer's user avatar
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7 votes

Can we do anything to reduce the number of displacements in a frozen phonon lattice dynamics study?

ProfM's answer gets the core idea perfectly right: Symmetry really is your best friend here. However, symmetry analysis is often quite involved, especially for larger unit cells. I recently ...
Anubhab Haldar's user avatar
7 votes

Stability using Phonon Calculation

The basic quantity you build when performing a phonon calculation is the matrix of force constants, given by: $$ D_{i\alpha,i^{\prime}\alpha^{\prime}}(\mathbf{R}_p,\mathbf{R}_{p^{\prime}})=\frac{\...
ProfM's user avatar
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