DynamO

a free O(N) general event-driven molecular dynamics simulator

Research output: Contribution to journalArticle

81 Citations (Scopus)

Abstract

Molecular dynamics algorithms for systems of particles interacting through discrete or “hard” potentials are fundamentally different to the methods for continuous or “soft” potential systems. Although many software packages have been developed for continuous potential systems, software for discrete potential systems based on event-driven algorithms are relatively scarce and specialized. We present DynamO, a general event-driven simulation package, which displays the optimal O(N) asymptotic scaling of the computational cost with the number of particles N, rather than the O(N log N) scaling found in most standard algorithms. DynamO provides reference implementations of the best available event-driven algorithms. These techniques allow the rapid simulation of both complex and large (>10^6 particles) systems for long times. The performance of the program is benchmarked for elastic hard sphere systems, homogeneous cooling and sheared inelastic hard spheres, and equilibrium Lennard–Jones fluids. This software and its documentation are distributed under the GNU General Public license and can be freely downloaded from http://marcusbannerman.co.uk/dynamo
Original languageEnglish
Pages (from-to)3329-3338
Number of pages10
JournalJournal of Computational Chemistry
Volume32
Issue number15
Early online date29 Aug 2011
DOIs
Publication statusPublished - 30 Oct 2011

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Event-driven
Molecular Dynamics
Molecular dynamics
Simulator
Simulators
Hard Spheres
Scaling
Dynamic Algorithms
Particle System
Cooling systems
Software Package
Software packages
Software System
Cooling
Computational Cost
Simulation
Fluid
Software
Fluids
Costs

Keywords

  • molecular dynamics
  • square-well potential
  • hard spheres
  • event-driven simulation
  • discontinuous potentials

Cite this

DynamO : a free O(N) general event-driven molecular dynamics simulator. / Campbell Bannerman, Marcus Nigel; Sargant, R.; Lue, L.

In: Journal of Computational Chemistry, Vol. 32, No. 15, 30.10.2011, p. 3329-3338.

Research output: Contribution to journalArticle

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AB - Molecular dynamics algorithms for systems of particles interacting through discrete or “hard” potentials are fundamentally different to the methods for continuous or “soft” potential systems. Although many software packages have been developed for continuous potential systems, software for discrete potential systems based on event-driven algorithms are relatively scarce and specialized. We present DynamO, a general event-driven simulation package, which displays the optimal O(N) asymptotic scaling of the computational cost with the number of particles N, rather than the O(N log N) scaling found in most standard algorithms. DynamO provides reference implementations of the best available event-driven algorithms. These techniques allow the rapid simulation of both complex and large (>10^6 particles) systems for long times. The performance of the program is benchmarked for elastic hard sphere systems, homogeneous cooling and sheared inelastic hard spheres, and equilibrium Lennard–Jones fluids. This software and its documentation are distributed under the GNU General Public license and can be freely downloaded from http://marcusbannerman.co.uk/dynamo

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