34
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 ...
- 10.9k
24
votes
Accepted
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:
$$
D_{i\alpha,i^{\prime}\alpha^{\prime}}(...
- 10.9k
20
votes
Accepted
Are there differences in accuracy and reliability between the frozen phonon method and Density Functional Perturbation Theory?
Short answer: Modern implementations of these two methods lead to similar accuracies.
Longer answer: The calculation of phonons requires the calculation of the Hessian of the potential energy surface ...
- 10.9k
20
votes
Accepted
How to deduce phase transitions from a phonon calculation?
Background theory. In the harmonic approximation, the potential energy surface (PES) is expanded about an equilibrium point to second order, to obtain the Hamiltonian:
$$
\hat{H}=\sum_{p,\alpha}-\frac{...
- 10.9k
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 ...
- 5,125
15
votes
Accepted
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 ...
- 2,934
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-...
- 546
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 ...
- 10.9k
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 ...
- 10.9k
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 ...
- 10.9k
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 ...
- 10.8k
13
votes
Accepted
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 ...
- 10.9k
12
votes
Accepted
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,...
- 10.9k
12
votes
Accepted
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-...
- 10.9k
10
votes
Accepted
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 ...
- 33.6k
10
votes
Accepted
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. ...
- 7,281
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}...
- 101
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 ...
- 271
9
votes
Accepted
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 ...
- 2,342
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. ...
- 1,099
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 ...
- 10.9k
8
votes
Accepted
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. ...
- 1,402
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 (...
- 10.9k
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 ...
- 171
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 ...
- 1,416
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. ...
- 10.9k
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{\...
- 10.9k
6
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 ...
- 534
6
votes
What does it mean if a strictly optimized experimental geometry presents imaginary frequencies?
You mention phonons, so I assume you are doing periodic structures which I am not entirely familiar with since I study mostly single molecules. Although, when I get imaginary frequencies from ...
- 1,222
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