Domain-Based Decomposition Parallel Molecular Dynamics Algorithm on Computer Clusters

Abstract

With MPI and C/C++, a parallel algorithm of molecular dynamics based on octal-tree domain decomposition method was implemented for micro canonical system (NVE), and run the code on a small cluster. The code speed-up was examined for a number of particles ranging from N = 192 to 10800 and for number of processors from P = 2 up to 8. As a result, the computing performance has been improved obviously, that is the computing speedup of the system can be three times or more than those computing on the single computer.