An improved neighbor list algorithm is proposed to reduce unnecessaryinteratomic distance calculations in molecular simulations. It combines theadvantages of Verlet table and cell linked list algorithms by using celldecomposition approach to accelerate the neighbor list construction speed, anddata sorting method to lower the CPU data cache miss rate, as well as partialupdating method to minimize the unnecessary reconstruction of the neighborlist. Both serial and parallel performance of molecular dynamics simulation areevaluated using the proposed algorithm and compared with those usingconventional Verlet table and cell linked list algorithms. Results show thatthe new algorithm outperforms the conventional algorithms by a factor of 2~3 incases of both small and large number of atoms.
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