36
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 ...
- 11.2k
27
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}}(...
- 11.2k
21
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 ...
- 11.2k
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 ...
- 5,225
17
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-...
- 681
14
votes
Accepted
Reliability about the predicted two-dimensional crystal structures based on DFT high-throughput calculation?
[Disclaimer - I am one of the co-authors of the 2D database on Materials Cloud (What you call "2D structures and layered materials", publishing the data of this work: N. Mounet et al., ...
- 236
12
votes
Accepted
What do phonon dispersion (or lattice dynamics) studies include?
TLDR: When you calculate phonons, you can describe electrons at different levels of theory, typically semilocal DFT, but also hybrids or dynamical mean-field theory. Phonons do include zero-point ...
- 11.2k
12
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 ...
- 2,452
11
votes
Accepted
Why do we need to build a supercell to use the DFPT in Phonopy interfaced with VASP?
Disclaimer: I have never used Phonopy.
The advantage of using DFPT is that in principle it can be used to calculate a perturbation of finite wave vector $\mathbf{q}$ using the primitive cell. This ...
- 11.2k
7
votes
Accepted
Tools to Visualize Phonons
1. Interactive Phonon visualizer by Materials Cloud
https://interactivephonon.materialscloud.io/
This tool allows to visualize the phonon dispersion calculated with an external software and display ...
- 9,237
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. ...
- 11.2k
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 ...
- 1,436
7
votes
Phonon calculations using DFPT
WARNING
(added by T.S., see comments below) As of 4/17/2024, VASP DFPT only works for $q=\Gamma$, thus you must use a supercell even with VASP-DFPT + Phonopy. Even the phonopy documentation uses a ...
- 3,770
6
votes
Can we do anything to reduce the number of displacements in a frozen phonon lattice dynamics study?
You can (should) use symmetry to reduce the number of displacements needed to construct the matrix of force constants. A nice pratical description of how to do this can be found in the description of ...
- 11.2k
6
votes
Best practice(s) for q-points convergence in phonon density of states calculations
In a calculation of the phonon density of states, $\mathbf{q}$-points feature in two ways:
Explicitly calculated $\mathbf{q}$-points. These are the $\mathbf{q}$-points for which you explicitly ...
- 11.2k
6
votes
Calculation of linear coefficient of thermal expansion using VASP-Phonopy for Hexagonal material
You can minimize the free energy F(a,c) as a function of (a,c), which is simply high school math. An example is provided in the section III (A) of the Supplementary Material of Phys. Rev. B 100, ...
- 675
6
votes
Accepted
How to solve this Phonopy-related problem?
This is basic bash-script which will be quite useful, just start with scratch
...
- 4,396
6
votes
Accepted
Which IBRION tag should be used for finite displacement method in calculating Phonons spectrum?
Phonopy creates different POSCAR file in which atoms are perturbed, as you are running each ...
- 4,396
5
votes
Temperature effect on elastic constant using VASP
It is always better to write your own code to get elastic constants. For example , In case of cubic system, we need three types of distorsion to unit cell. Now elastic constant is simply slope of ...
- 4,396
5
votes
Phonon density of states in statistical thermodynamics
There are two possible things tripping you up here:
Phonons are collective oscillations: they involve the motion of all the atoms together. Therefore it only makes sense to talk about the phonons of ...
- 6,804
5
votes
Accepted
Thermal Properties Calculated with Phonopy
$N_A$ stands for Avogadro's number. Energies are reported in kJ/mol, so they are technically for a mole of unit cells. Conversion factors to other units (kcal/mol, eV, Hartree, etc.) can be found or ...
- 1,536
4
votes
Should all q-points in the first Brillouin zone be sampled in phonon density of states calculations?
Background. The phonon density of states $g$ is given by:
$$
\tag{1}
g(\omega)=\sum_{\nu}\int\frac{d\mathbf{q}}{(2\pi)^3}\delta(\omega-\omega_{\mathbf{q}\nu})\approx\frac{1}{N_{\mathbf{q}}}\sum_{\nu}\...
- 11.2k
4
votes
"Input forces are not enough to calculate force constants" Phonopy error?
This error (input forces are not enough to calculate force constants) may arise when you are trying to plot the band structure or the density of state plots for some systems. Sometimes setting a ...
- 916
4
votes
Lattice Thermal conductivity calculation error
Partial Answers
To remove this error
Error in routine cdiaghg (211):
S matrix not positive definite
Use PAW pseudopotential files instead of USPP. Make sure the exchange correlational functional are ...
- 1,542
4
votes
Causes of Straight Bands in Phonon Dispersion Calculations
Such bands are usually called 'flat bands'. The group velocity vanishes, signalling that such an excitation is non-dispersive, i.e. is localized. See here. Think 'molecular modes'. For an isolated ...
- 1,678
4
votes
Accepted
Do the bottom layers of the slab need to be fixed when we use DFPT or finite displacement methods to compute the phonon spectrum of a surface?
No you do not need to.
Fixing atoms during a finite displacement or a DFPT calculation is not a real thing. This is a huge approximation that will break the symmetry of the force constant matrix, ...
- 1,467
3
votes
Calculating lattice thermal conductivity using Quantum ESPRESSO and phonopy
Some years ago I found the following steps in ResearchGate:
You need:
QuantumEspresso (QE)
Phono3py
ShengBTE & thirdorder.py
First, you need to create a QE input file (...
- 24.2k
3
votes
Accepted
Getting the Phonon Dispersion Using fix phonon in LAMMPS
I was able to compile the phana code but fix phonon just gave a peak around zero. I raised an issue on the GitHub repository and ...
- 705
3
votes
Can we translate vibrational frequencies at q-points to vibrational frequencies of atoms?
As known [1], the eigenvalues of the dynamical Hessian matrix represent the phonon frequencies, whereas the eigenvectors represent the particular atomic displacement patterns contributing to the ...
- 346
3
votes
Exploring Phonon Dispersion in Two-Dimensional Materials: Analytical Techniques and Mode Identification
Do you know what longitudinal, transverse, acoustic, and optical mean in this context? Or you want a code that can tell you what they are?
If you know what they mean, you can plot the displacements ...
- 1,678
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