# SIMPLE AND EFFICIENT ALGORITHM FOR LARGE SCALE MOLECULAR DYNAMICS SIMULATION IN HARD DISK SYSTEM

@article{Isobe1999SIMPLEAE,
title={SIMPLE AND EFFICIENT ALGORITHM FOR LARGE SCALE MOLECULAR DYNAMICS SIMULATION IN HARD DISK SYSTEM},
author={Masaharu Isobe},
journal={International Journal of Modern Physics C},
year={1999},
volume={10},
pages={1281-1293}
}
• M. Isobe
• Published 17 July 1999
• Computer Science
• International Journal of Modern Physics C
A simple and efficient algorithm of the molecular-dynamics simulation of the hard disk system based on the Event-Driven method is developed. From the analysis of algorithm, the complexity is ${\mathcal O} (\log N)$ per 1 event, and the constant coefficient of the complexity is smaller than conventional efficient algorithm based on the concept of Cell-Crossing Event. The maximum performance of more than 460 millions of collisions per CPU-hour on the Alpha600 compatible in a 2500 particle system…

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## References

SHOWING 1-10 OF 53 REFERENCES

### Efficient algorithms for many-body hard particle molecular dynamics

• Computer Science
• 1993
This paper proposes a strategy--for the simulation of hard particle systems--that is efficient, memory saving, and easy to understand and to program, and it is seen that the proposed algorithm is efficient for a wide density range.

### A Vectorized Algorithm for Molecular Dynamics of Short Range Interacting Particles

• Computer Science
• 1993
A lattice based algorithm, completely vectorized for molecular dynamics simulations, that works very effectively when the particles have short range interaction, but it is applicable to each kind of interaction.

### VECTORIZED AND PARALLELIZED ALGORITHMS FOR MULTI-MILLION PARTICLE MD-SIMULATION

• Computer Science
• 1993
Results for the Cray YMP, JAERI/NEC MONTE-4 vector computers and the Intel Paragon XP/S and Thinking Machine CM-5 parallel computers are presented, making the simulation of million particle systems possible.

### Analysis of an efficient algorithm for the hard-sphere problem

Both an empirical and analytic analysis of HAD's performance are presented which show that HAD scales well and the design differences of these algorithms are compared to RAP, LUB and HYBRID.

### Studies in Molecular Dynamics. I. General Method

• Physics
• 1959
A method is outlined by which it is possible to calculate exactly the behavior of several hundred interacting classical particles so that the solution of many problems in both equilibrium and nonequilibrium statistical mechanics is discussed.

### Studies in Molecular Dynamics. II. Behavior of a Small Number of Elastic Spheres

• Physics
• 1960
The equation of state and the collision rate for systems ranging in size from four to 500 particles are described. The dependence of the results on the number of particles is qualitatively discussed

### The Art of Molecular Dynamics Simulation

From the Publisher: This book describes the extremely powerful technique of molecular dynamics simulation, which involves solving the classical many-body problem in contexts relevant to the study of