**DynaPhoPy: A code for extracting phonon quasiparticles from molecular
dynamics simulations**

A Carreras and A Togo and I Tanaka, COMPUTER PHYSICS COMMUNICATIONS, 221, 221-234 (2017).

DOI: 10.1016/j.cpc.2017.08.017

We have developed a computational code, DYNAPHOPY, that allows us to
extract the microscopic anharmonic phonon properties from molecular
dynamics (MD) simulations using the normal-mode decomposition technique
as presented by Sun et al. (2014). Using this code we calculated the
quasiparticle phonon frequencies and linewidths of crystalline silicon
at different temperatures using both of first principles and the Tersoff
empirical potential approaches. In this work we show the dependence of
these properties on the temperature using both approaches and compare
them with reported experimental data obtained by Raman spectroscopy
(Balkanski et al., 1983; Tsu and Hernandez, 1982). Program summary
Manuscript Title: DynaPhoPy: A code for extracting phonon quasiparticles
from molecular dynamics simulations Authors: Abel Carreras, Atsushi Togo
and Isao Tanaka Program Title: DynaPhoPy Journal Reference: Catalogue
identifier: Licensing provisions: MIT License Programming language:
Python and C Computer: PC and cluster computers Operating system:
UNIX/OSX RAM: Depends strongly on number of input data (several Gb)
Number of processors used: 1-16 Supplementary material: Keywords:
anharmonicity, phonon, linewidth, frequency shift, molecular dynamics
Classification: 7.8 Structure and Lattice Dynamics External
routines/libraries: phonopy, numpy, matplotlib, scipy and h5py python
modules. Optional: FFTW and Cuda Subprograms used: Catalogue identifier
of previous version:* Journal reference of previous version:* Does the
new version supersede the previous version?:* Nature of problem:
Increasing temperature, a crystal potential starts to deviate from the
harmonic regime and anharmonicity is getting to be evident **1**. To treat
anharmonicity, perturbation approach often describes successfully
phenomena such as phonon lifetime and lattice thermal conductivity.
However it fails when the system contains large atomic displacements.
Solution method: Extracting the phonon quasiparticles from molecular
dynamics (MD) simulations using the normal mode-decomposition technique.
Reasons for the new version:* Summary of revisions:* Restrictions:
Quantum effects of lattice dynamics are not considered. Unusual
features: Additional comments: Running time: It is highly dependent on
the type of calculation requested. It depends mainly on the number of
atoms in the primitive cell, the number of time steps of the MD
simulation and the method employed to calculate the power spectra.
Currently two methods are implemented in DyaPhoPy: The Fourier transform
and the maximum entropy methods. The Fourier transform method scales to
O **N-2** and the maximum entropy method scales to O **N x M** where N is
the number of time steps and M is the number of coefficients. (C) 2017
Elsevier B.V. All rights reserved.

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