TY - JOUR

T1 - Algorithm optimization in molecular dynamics simulation

AU - Wang, Di Bao

AU - Hsiao, Fei Bin

AU - Chuang, Cheng Hsin

AU - Lee, Yung Chun

N1 - Funding Information:
This research was partially supported by the National Science Council of Taiwan through Grant NSC 95-2120-M-006-002.

PY - 2007/10/1

Y1 - 2007/10/1

N2 - Establishing the neighbor list to efficiently calculate the inter-atomic forces consumes the majority of computation time in molecular dynamics (MD) simulation. Several algorithms have been proposed to improve the computation efficiency for short-range interaction in recent years, although an optimized numerical algorithm has not been provided. Based on a rigorous definition of Verlet radius with respect to temperature and list-updating interval in MD simulation, this paper has successfully developed an estimation formula of the computation time for each MD algorithm calculation so as to find an optimized performance for each algorithm. With the formula proposed here, the best algorithm can be chosen based on different total number of atoms, system average density and system average temperature for the MD simulation. It has been shown that the Verlet Cell-linked List (VCL) algorithm is better than other algorithms for a system with a large number of atoms. Furthermore, a generalized VCL algorithm optimized with a list-updating interval and cell-dividing number is analyzed and has been verified to reduce the computation time by 30 ∼ 60 % in a MD simulation for a two-dimensional lattice system. Due to similarity, the analysis in this study can be extended to other many-particle systems.

AB - Establishing the neighbor list to efficiently calculate the inter-atomic forces consumes the majority of computation time in molecular dynamics (MD) simulation. Several algorithms have been proposed to improve the computation efficiency for short-range interaction in recent years, although an optimized numerical algorithm has not been provided. Based on a rigorous definition of Verlet radius with respect to temperature and list-updating interval in MD simulation, this paper has successfully developed an estimation formula of the computation time for each MD algorithm calculation so as to find an optimized performance for each algorithm. With the formula proposed here, the best algorithm can be chosen based on different total number of atoms, system average density and system average temperature for the MD simulation. It has been shown that the Verlet Cell-linked List (VCL) algorithm is better than other algorithms for a system with a large number of atoms. Furthermore, a generalized VCL algorithm optimized with a list-updating interval and cell-dividing number is analyzed and has been verified to reduce the computation time by 30 ∼ 60 % in a MD simulation for a two-dimensional lattice system. Due to similarity, the analysis in this study can be extended to other many-particle systems.

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U2 - 10.1016/j.cpc.2007.05.009

DO - 10.1016/j.cpc.2007.05.009

M3 - Article

AN - SCOPUS:34548311853

VL - 177

SP - 551

EP - 559

JO - Computer Physics Communications

JF - Computer Physics Communications

SN - 0010-4655

IS - 7

ER -