Multi-Processor Molecular Dynamics Using The Brenner Potential: Parallelization Of An Implicit Multi-Body Potential

We present computational aspects of Molecular Dynamics calculations of thermal properties of diamond using the Brenner potential. Parallelization was essential in order to carry out these calculations on samples of suitable sizes. Our implementation uses MPI on a multi-processor machine such as the IBM SP2. Three aspects of parallelization of the Brenner potential are discussed in depth. These are its long-range nature, the need for different parallelization algorithms for forces and neighbors, and the relative expense of force calculations compared to that of data communication. The efficiency of parallelization is presented as a function of different approaches to these issues as well as of cell size and number of processors employed in the calculation. In the calculations presented here, information from almost half of the atoms were needed by each processor even when 16 processors were used. This made it worthwhile to avoid unnecessary complications by making data from all atoms available to all processors. Superlinear speedup was achieved for four processors (by avoiding paging) with 512 atom samples, and 5ps long trajectories were calculated (for 5120 atom samples) in 53 hours using 16 processors; 514 hours would have been needed to complete this calculation using a serial program. Finally, we discuss and make available a set of routines that enable MPI-based codes such as ours to be debugged on scalar machines.