Fast Parallel Algorithms for Short-Range Molecular Dynamics-英文文献.pdf

Journal of Computational Physics vol p March originally Sandia Technical Rep ort SAND May June Fast Parallel Algorithms for ShortRange Molecular Dynamics Steve Plimpton Parallel Computational Sciences Department MS Sandia National Lab oratories Albuquerque NM sjplimpcssandiagov Keywords molecular dynamics parallel computing Nb o dy problem Abstract Three parallel algorithms for classical molecular dynamics are presented The rst assigns each pro cessor a xed subset of atoms the second assigns each a xed subset of interatomic forces to compute the third assigns each a xed spatial region The algorithms are suitable for molecular dynamics mo dels which can b e dicult to paralleli ze eciently those with shortrange forces where the neighb ors of each atom change rapidly They can b e implemented on any distributedmemo ry parallel machine which allows for messagepassing of data b etween indep endently executing pro cessors The algorithms are tested on a standard LennardJones b enchmark problem for system sizes ranging from to atoms on several parallel sup ercomputers the nCUBE Intel iPSC and Paragon and Cray TD Comparing the results to the fastest rep orted vectorized Cray YMP and C algorithm shows that the current generation of parallel machines is comp etitive with conventional vector sup ercomputers even for small problems For large problems the spatial algorithm achie