Unsteady processes in the solar wind - magnetosphere interaction, such as vortices developed at the magnetopause boundary by the Kelvin-Helmholtz instability, may contribute to the process of mass, momentum and energy transfer into the Earth's magnetosphere. The research described in this paper validates an algorithm to automatically detect and characterize vortices based on velocity data from simulations. The Vortex Identification Algorithm (VIA) systematically searches the 3-dimensional velocity fields to identify critical points where the magnitude of the velocity vector vanishes. The velocity gradient tensor is computed and its invariants are used to assess vortex structure in the flow field. We use the Community Coordinated Modeling Center (CCMC) Runs on Request capability to create a series of model runs initialized from the conditions observed by the Cluster mission in the Hwang et. al., (2011) analysis of Kelvin-Helmholtz vortices observed during southward Interplanetary Magnetic Field (IMF) conditions. We analyze further the properties of the vortices found in the runs, including the velocity changes within their motion across the magnetosheath. We also demonstrate the potential of our tool to identify and characterize other transient features (e.g. Flux Transfer Event (FTEs)) with vortical internal structures. We find that the vortices are associated with flows on the magnetosheath side of the magnetopause that reach speeds greater than the solar wind speed at the bowshock.