We present a new algorithm, called linked neighbour list (LNL), useful to substantially speed up off lattice Monte Carlo simulations of fluids by avoiding the computation of the molecular energy before every attempted move. We introduce a few variants of the LNL method targeted to minimise memory footprint or augment memory coherence and cache utilisation. Additionally, we present a few algorithms which drastically accelerate neighbour finding. We test our methods on the simulation of a dense offlattice Gay–Berne fluid subjected to periodic boundary conditions observing a speedup factor of about 2.5 with respect to a well-coded implementation based on a conventional link-cell. We provide several implementation details of the different key data structures and algorithms used in this work.
M. Mazzeo , M. Ricci , C. Zannoni (2010). The Linked Neighbour List (LNL) method for fast off-lattice Monte Carlo simulations of fluids. COMPUTER PHYSICS COMMUNICATIONS, 181, 569-581 [10.1016/j.cpc.2009.11.006].
The Linked Neighbour List (LNL) method for fast off-lattice Monte Carlo simulations of fluids
ZANNONI, CLAUDIO
2010
Abstract
We present a new algorithm, called linked neighbour list (LNL), useful to substantially speed up off lattice Monte Carlo simulations of fluids by avoiding the computation of the molecular energy before every attempted move. We introduce a few variants of the LNL method targeted to minimise memory footprint or augment memory coherence and cache utilisation. Additionally, we present a few algorithms which drastically accelerate neighbour finding. We test our methods on the simulation of a dense offlattice Gay–Berne fluid subjected to periodic boundary conditions observing a speedup factor of about 2.5 with respect to a well-coded implementation based on a conventional link-cell. We provide several implementation details of the different key data structures and algorithms used in this work.I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.
