论文信息 - Large Scale Molecular Dynamics on Parallel Computers using the Link-cell Algorithm

Large Scale Molecular Dynamics on Parallel Computers using the Link-cell Algorithm

Abstract Parallel computers offer a more cost-effective route to high performance computing than traditional single processor machines. Software for such machines is still in its infancy and they are often much more difficult to program than sequential machines. In addition many of the algorithms which are successful with sequential and vector processors are no longer appropriate. Both the force calculation and integration steps of molecular dynamics are parallel in nature and for that reason we have developed a parallel algorithm based on the link cell technique. This method is particularly efficient when the range of intermolecular potential is much smaller than the dimensions of the simulation box. The details of the algorithm are presented for systems of atoms in two and three dimensions using a number of decompositions into sub-units. The algorithm has been tested on an Intel iPSC/2 and a Cray X-MP/416 and the results are presented for simulations of up to 2 · 106 atoms.

[1] David Fincham,et al. Systolic loop methods for molecular dynamics simulation using multiple transputers , 1989 .

[2] Stephan W Koch,et al. Molecular-dynamics simulations of the incommensurate phase of krypton on graphite using more than 100 000 atoms , 1984 .

[3] D. C. Rapaport,et al. Large-scale molecular dynamics simulation using vector and parallel computers , 1988 .

[4] N. Metropolis,et al. Equation of State Calculations by Fast Computing Machines , 1953, Resonance.

[5] Rapaport. Microscale hydrodynamics: Discrete-particle simulation of evolving flow patterns. , 1987, Physical review. A, General physics.

[6] H. G. Petersen,et al. Molecular dynamics on transputer arrays. I: Algorithm design, programming issues, timing experiments and scaling projections , 1989 .

[7] J. Banavar,et al. Computer Simulation of Liquids , 1988 .