We present a numerical approach to the solution of elastic phonon-interface and phonon-nanostructure scattering problems based on a frequency-domain decomposition of the atomistic equations of motion and the use of perfectly matched layer (PML) boundaries. Unlike molecular dynamic wavepacket analysis, the current approach provides the ability to simulate scattering from individual phonon modes, including wavevectors in highly dispersive regimes. Like the atomistic Green's function method, the technique reduces scattering problems to a system of linear algebraic equations via a sparse, tightly banded matrix regardless of dimensionality. However, the use of PML boundaries enables rapid absorption of scattered wave energies at the boundaries and provides a simple and inexpensive interpretation of the scattered phonon energy flux calculated from the energy dissipation rate in the PML. The accuracy of the method is demonstrated on connected monoatomic chains, for which an analytic solution is known. The parameters defining the PML are found to affect the performance and guidelines for selecting optimal parameters are given. The method is used to study the energy transmission coefficient for connected diatomic chains over all available wavevectors for both optical and longitudinal phonons; it is found that when there is discontinuity between sublattices, even connected chains of equivalent acoustic impedance have near-zero transmission coefficient for short wavelengths. The phonon scattering cross section of an embedded nanocylinder is calculated in 2D for a wide range of frequencies to demonstrate the extension of the method to high dimensions. The calculations match continuum theory for long-wavelength phonons and large cylinder radii, but otherwise show complex physics associated with discreteness of the lattice. Examples include Mie oscillations which terminate when incident phonon frequencies exceed the maximum available frequency in the embedded nanocylinder, and scattering efficiencies larger than two near the Brillouin zone edge.
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