An analysis of thermal transients from non-equilibrium 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, modelled 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.