We compare two methods for the calculation of mode dependent ballistic phonon transmission in nanoscale waveguides. The first method is based on continuum acoustic waveguide theory and uses an eigenmode expansion to solve for phonon transmission coefficients. The second method uses lattice dynamics (LD)-computed mode shapes to excite guided phonon wavepackets in a nonequilibrium molecular dynamics (MD) simulation and calculates phonon transmission from the final distribution of system energy. The two methods are compared for the case of shear-horizontal (SH) phonons propagating in a planar waveguide with a T-stub irregularity, a geometry which has been proposed for the tuning of phonon transmission and nanostructure thermal conductance. Our comparison highlights advantages and disadvantages of the two methods and illustrates regimes when atomistic effects are prominent and continuum approaches are not appropriate.

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