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Different molecular dynamics methods like the direct method, the Green–Kubo (GK) method and homogeneous non-equilibrium molecular dynamics (HNEMD) method have been widely used to calculate lattice thermal conductivity (${kappa }_{{ell }}$). While the first two methods have been used and compared quite extensively, there is a lack of comparison of these methods with the HNEMD method. Focusing on the underlying computational parameters, we present a detailed comparison of the GK and HNEMD methods for both bulk and vacancy Si using the Stillinger–Weber potential. For the bulk calculations, we find both methods to perform well and yield ${kappa }_{{ell }}$ within acceptable uncertainties. In case of the vacancy calculations, HNEMD method has a slight advantage over the GK method as it becomes computationally cheaper for lower ${kappa }_{{ell }}$ values. This study could promote the application of HNEMD method in ${kappa }_{{ell }}$ calculations involving other lattice defects like nanovoids, dislocations, interfaces.