Data-parallel molecular dynamics with neighbor-lists

Abstract

We report on a data-parallel classical molecular dynamics algorithm and its implementation on Connection Machines CM-5 and CM-200 using CM-Fortran, a Fortran-90 dialect. A grid-based spatial decomposition of the atomic system is used for parallelization. Our previous algorithm on the CM's calculated all forces in the nearby region. A different algorithm using classical Verlet neighbor lists is more efficient, when implemented on the CM-5 with its indirect addressing hardware. The code has been used for extensive simulations on a 128-node CM-5E, and performance measurements are reported.