jats:pAn analysis of thermal transients from nonequilibrium ab initio molecular-dynamics simulations can be used to calculate the thermal conductivity of materials with a short phonon mean-free path. We adapt the approach-to-equilibrium methodology to the three-dimensional case of a simulation that consists of a cubic core region at higher temperature approaching thermal equilibrium with a thermostatted boundary. This leads to estimates of the lattice thermal conductivity for the glassy state of the phase-change memory material, Ge2Sb2Te5, which are close to previously reported experimental measurements. Self-atom irradiation of the material, modeled using thermal spikes and stochastic-boundary conditions, results in glassy models with a significant reduction of diffusive thermal transport compared to the pristine glassy structure. This approach may prove to be useful in technological applications, e.g., for the suppression of thermal cross talk in phase-change memory and data-storage devices.</jats:p>