Massively parallel molecular dynamics simulations with EAM potentials
CS Becquart and KM Decker and C Domain and J Ruste and Y Souffez and JC Turbatte and JC Van Duysen, RADIATION EFFECTS AND DEFECTS IN SOLIDS, 142, 9-21 (1997).
Molecular dynamics of cascades in pure iron and iron-copper alloys using embedded atom method type of interatomic potentials are presented. Reliable simulations of radiation damage at the atomic scale with high energy Primary Knocked Atoms (PKA) need systems with large numbers of particles and very long computational time. To perform the simulation in a reasonable amount of time high-performance computer systems such as massively parallel machines need to be used. This paper presents the parallelisation strategy applied to a serial classical Molecular Dynamics code: DYMOKA. The original sequential Fortran code CDCMD from the University of Connecticut was first improved algorithmically by applying a link cell method for the neighbour list construction of the Verlet list, resulting in a fully linear algorithm. The parallelisation strategy adopted is a multidimensional domain decomposition of the simulation box using a link cell method and a Verlet list method for each subdomain independently. The program paradigm is based on explicit message passing, and the standard Message-Passing Interface (MPI) was chosen in order to achieve portability. First measurements have demonstrated that the simulation of a system of 2.000.000 (750.000) atoms on 128 (32) processors costs 2.5 (10.) mu s per atom per step. The current implementation has proven good scalability up to 32 processors on a NEC Cenju-3 machine. To study the effects of irradiation on copper segregation, simulations with up to 1.000.000 atoms in iron and iron- copper were performed with PKA energies up to 20 keV.
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