Sampling phonon spectra from molecular-dynamics simulations: Difference between revisions

Revision as of 11:49, 15 October 2025

Sampling phonon DOS from molecular dynamics simulation

The phonon density of states can be obtained as the power spectrum from the normalized velocity auto correlation function. The normalized velocity auto correlation function for a $N$-particle system is given by \begin{equation} A = B +c \end{equation}

Further information can be found on the following page. External tools as for example phonopy may also be considered. To compute the power spectra of the Fourier transformed projected velocity autocorrelations

[math]\displaystyle{ |G_{\nu}(\mathbf{q},\omega)|^{2}=\sum_{I,\alpha}\sum_{J,\beta} \int\left( \varepsilon_{I\nu}^{\beta}(\mathbf{q}) \sqrt{M_{I}}v_{I}^{\alpha}(t') \right )\left( \varepsilon_{J\nu}^{\beta}(\mathbf{q}) \sqrt{M_{J}}v_{J}^{\beta}(t'') \right )e^{i\mathbf{q} \cdot (\mathbf{R}_{I}(t')-\mathbf{R}_{J}(t''))}e^{-i\omega (t'-t'')}d(t'-t'') }[/math]

external tools are required. The following table summarizes a small list of codes which can compute projected velocity correlation functions from VASP output.

code	publication
DSLEAP	Lahnsteiner et.al.
phq	Zhang et.al.
DynaPhoPy	Carreras et.al.

@@ Line 1: / Line 1: @@
-== Finite temperature phonon renormalization with velocity correlation functions  ==
+== Sampling phonon DOS from molecular dynamics simulation  ==
-To account for finite temperature phonon renormalization, finite temperature molecular dynamics (MD) trajectories of the system under consideration are required. Additionally, harmonic phonon eigenvectors are necessary, as the velocities obtained from the MD simulations must be projected onto these eigenvectors. The molecular dynamics simulations should be conducted in the [[NVE ensemble]], which can be set up using the following example [[INCAR]]-file.
+The phonon density of states can be obtained as the power spectrum from the normalized velocity auto correlation function. The normalized velocity auto correlation function for a $N$-particle system is given by
-=== [[INCAR]] ===
+\begin{equation}
- #INCAR molecular-dynamics tags NVE ensemble
+A = B +c
- IBRION = 0                   # choose molecular-dynamics
+\end{equation}
- MDALGO = 1                   # using Andersen thermostat
- ISIF = 2                     # compute stress tensor but do not change box volume/shape
- TEBEG = 300                  # set temperature
- NSW = 10000                  # number of time steps
- POTIM = 1.0                  # time step in femto seconds
- ANDERSEN_PROB = 0.0          # setting Andersen collision probability to zero to get NVE enseble
-The forces during the molecular dynamics run can be either obtained by DFT or by [[Machine learning force field: Theory|machine learning force fields]].
-The trajectories of the molecular dynamics have to be started from structures which were equilibrated for the conditions of interest. The harmonic phonon eigenvectors can be computed with VASP by performing a 3 step procedure
-* Step 1: Compute the force constants
-# Using [[Phonons_from_finite_differences|finite differences]] with {{TAGO|IBRION|5, 6}}.
-# Using [[Phonons_from_density-functional-perturbation_theory|DFPT]] with {{TAGO|IBRION|7, 8}}.
-* Step 2: Provide '''q'''-points file for which the projected velocity correlation functions should be computed.
-* Step 3: Compute the eigenvectors by setting {{TAGO|LPHON_DISPERSION|True}} and {{TAGO|PHON_NWRITE|-3}}.
 Further information can be found on the following [[Computing the phonon dispersion and DOS|page]]. External tools as for example [https://phonopy.github.io/phonopy/ phonopy] may also be considered. To compute the power spectra of the Fourier transformed projected velocity autocorrelations

Revision as of 11:49, 15 October 2025

Sampling phonon DOS from molecular dynamics simulation

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