FPGA-based three-body molecular dynamics simulator

The computer simulation of three-body potentials using the Stillinger-Weber method has been extensively used in the study of three-body molecular forces between partially rigid molecules such as silicon. The Stillinger-Weber method of computing three-body interactions is generally computationally intense. This paper presents a FPGA-based framework that is designed and implemented on a Virtex 4 that can be used to compute Stillinger-Weber potential. This framework extends the PowerPC instruction set to include vector operations and a custom datapath. Design details of the framework along with initial performance results with two well-known data sets are also presented. The results show that FPGA design is competitive with current microprocessors on small problems sizes and with only half of the algorithm implemented. As the problem size increases, the results suggest the FPGA-based design will gain a significant performance advantage. Coding the second half of the algorithm will increase the on-chip parallelism as well.