Eur. Phys. J. D 41, 629-639 (2007)
https://doi.org/10.1140/epjd/e2006-00255-3

Modeling of clusters by a molecular dynamics model using a fast tree method

Naval Research Laboratory, Plasma Physics Division, 4555 Overlook Ave SW, Washington, DC, 20375, USA

Corresponding authors: ^a george.petrov@nrl.navy.mil - ^b jack.davis@nrl.navy.mil

Received: 19 May 2006
Revised: 29 September 2006
Published online: 22 November 2006

Abstract

The dynamics of clusters irradiated by a high-intensity ultrashort pulse laser has been studied using a fully relativistic three-dimensional Molecular Dynamics Model. A fast three-dimensional tree algorithm for computing the electrostatic force has been developed and compared with the conventional particle-particle method. The particle-particle method requires computation time, which scales as O(N_p²), and it is faster for small number of particles N_p <10³. In the opposite case of relatively large ensemble of particles N_p >10³, the preferred method is the tree algorithm whose computation time scales as O(N_p log N_p). The tree algorithm has been benchmarked against the particle-particle method for clusters composed of xenon and deuterium atoms and its accuracy and computation time have been analyzed. The optimum free parameter of the tree method has been determined to be θ≈0.5. We addressed the effects of boundary conditions by studying the contribution of adjacent clusters to the total electromagnetic force exerted on individual particles. We found that the adjacent clusters play a minor role in the overall cluster dynamics.