Stratified spin-up experiments in enclosed cylinders have reported the presence of small pockets of well-mixed fluids but quantitative measurements of the mixedness of the fluid has been lacking. Previous numerical simulations have not addressed these measurements. Here we present numerical simulations that address how the combined effect of spin-up and thermal boundary conditions enhances or hinders mixing of a fluid in a cylinder. Measurements of efficiency of mixing are based on the variance of temperature and explained in terms of the potential energy available. The numerical simulations of the Navier-Stokes equations for the problem with different sets of thermal boundary conditions at the horizontal walls helped shed some light on the physical mechanisms of mixing, for which a clear explanation was lacking.