A domain is conventionally defined as a stationary sub-region of the simulated system in a domain-decomposition scheme for molecular dynamics (MD) simulations on parallel computers. We proposed an algorithm where all domains pre-assigned to processors are shifted to a particular direction, beyond the 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 partners in the particle re-allocation procedure. We also proposed a systematic 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 parallel MD simulation program implemented via a MPI-based message-passing interface on several parallel computers. A result on a 16-CPU parallel computer system shows that the new scheme allows us to achieve a high parallel efficiency (over 75 %) for MD simulations of a system with relatively small number of particles per processor (N/P < 500).
ASJC Scopus subject areas
- Physics and Astronomy (miscellaneous)