Domain-shifting algorithm: A new domain-decomposition scheme for moleculardynamics simulations on parallel computers

A domain is conventionally defined as a stationary sub-region of the simula ted system in a domain-decomposition scheme for molecular dynamics (MD) sim ulations on parallel computers. We proposed an algorithm where all domains pre-assigned to processors are shifted to a particular direction, beyond th e displacement of particles in the system during a time-step or a period of small time-steps; as a result, it allows us to reduce the data transfer pa rtners in the particle re-allocation procedure. We also proposed a systemat ic link-cell method that allows us to make use of small domain and reduces the amount of data to be transferred for updating the positions and forces of particles, in comparison to the conventional schemes. Benchmark studies of a three-dimensional Lennard-Jones system have been carried out using a p arallel MD simulation program implemented via a MPI-based message-passing i nterface on several parallel computers. A result on a 16-CPU parallel compu ter system shows that the new scheme allows us to achieve a high parallel e fficiency (over 75%) for MD simulations of a system with relatively small n umber of particles per processor (N/P < 500).