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To achieve high quality localization of nodes, a smart-mesh strategy is employed in the discontinuous Galerkin time-domain (DGTD) simulation. The strategy is able to adjust adaptively the nodes defined on the unstructured triangular element in real-time simulation, thus an arbitrary or uncertain shaped object can be modeled accurately. The benefits of smart-mesh strategy are demonstrated for a partially dielectric filled cavity with microscale random material height and uncertain rough interface. Numerical experiments show that the smart-mesh approach can capture fine structural information and achieve more effective positions to match variable shapes.