README.md

phonon-dos-matlab

A 20-line MATLAB function for calculating phonon density of states from velocity data

This code can be used to obtain the phonon density of states (PDOS) from velocity data obtained from molecular dynamics simulation:
- First, the normalized velocity autocorrelation function (VACF) is calculated from the velocity data.
- Then, the PDOS is calculated from the normalized VACF by discrete cosine tranform.
The orignianl reference for this method is
- [1] J. M. Dickey and A. Paskin, Computer Simulation of the Lattice Dynamics of Solids, Phys. Rev. 188, 1407 (1969).
For more backgrounds, see section 3.8 of the manual of the GPUMD code (https://github.com/brucefan1983/GPUMD).

There is a single Matlab function in the find_pdos.m file:
- [vacf_output,pdos]=find_pdos(v_all,Nc,dt,omega)
Inputs of the function
- v_all: all the velocity data, which is an N*3*Nf matlab array. Here, N is the number of atoms, 3 refers to the space dimension, and Nf is the number of velocity frames. The units of the velocity data are not important.
- Nc: number of correlation steps.
- dt: time interval between two velocity frames, in units of ps. The maximum correlation time is then dt*Nc.
- omega: the Nw phonon angular frequency points you want to consider in units of THz, which can be a 1*Nw or Nw*1 array.
Outputs of the function
- vacf_output: the normalized (dimensionless) VACF, which is a 1*Nc array
- pdos: the PDOS in units of 1/THz, which is a Nw*1 array.

Zheyong Fan: brucenju(at)gmail.com; zheyong.fan(at)aalto.fi; zheyongfan(at)163.com