Parallel multiple-time-step molecular dynamics with three-body interaction

Abstract For particles interacting via two- and three-body potentials, a domain-decomposition algorithm is used to implement molecular dynamics (MD) on distributed memory MIMD (multiple-instruction multiple-data) computers. The algorithm employs the linked-cell-list method and separable three-body force calculation. The force calculation is accelerated by the multiple-time-step (MTS) method. For a 1.54 million particle SiO 2 system, the MD program runs at a speed of 660 time steps per hour (1100 steps/h without the three-body interaction) on a 64-node Intel iPSC/860. The parallel algorithm is highly efficient (parallel efficiency = 0.973), as it involves only 3% communication overhead. Utilizing the second derivatives of the potential energy, the conjugate-gradient search for a local minimum underlying an MD configuration is accelerated by a factor of 13.

[1]  L. h. Yang,et al.  A Linked-Cell Domain Decomposition Method for Molecular Dynamics Simulation on a Scalable Multiprocessor , 1992, Sci. Program..

[2]  David Brown,et al.  MOLECULAR-DYNAMICS SIMULATIONS ON DISTRIBUTED MEMORY MACHINES , 1991 .

[3]  D. C. Rapaport,et al.  Multi-million particle molecular dynamics: II. Design considerations for distributed processing , 1991 .

[4]  C. W. Gear,et al.  Numerical initial value problem~ in ordinary differential eqttations , 1971 .

[5]  D. Tildesley,et al.  Multiple time-step methods in molecular dynamics , 1978 .

[6]  D. Brandt,et al.  Multi-level adaptive solutions to boundary-value problems math comptr , 1977 .

[7]  Leon Cohen,et al.  A numerical integration scheme for the N-body gravitational problem , 1973 .

[8]  Rino,et al.  Interaction potential for SiO2: A molecular-dynamics study of structural correlations. , 1990, Physical review. B, Condensed matter.

[9]  William Smith,et al.  Molecular dynamics on hypercube parallel computers , 1991 .

[10]  Leslie Greengard,et al.  A fast algorithm for particle simulations , 1987 .

[11]  Kawai,et al.  Large-scale elastic-plastic indentation simulations via nonequilibrium molecular dynamics. , 1990, Physical review. A, Atomic, molecular, and optical physics.

[12]  Nakano,et al.  Structural correlations in porous silica: Molecular dynamics simulation on a parallel computer. , 1993, Physical review letters.

[13]  J. Banavar,et al.  Computer Simulation of Liquids , 1988 .

[14]  Rajiv K. Kalia,et al.  Molecular dynamics simu-lations of Coulombic systems on ditributed-memory MIMD machines , 1993 .