Efficiency of linked cell algorithms
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Abstract: The linked cell list algorithm is an essential part of molecular simulation software, both molecular dynamics and Monte Carlo. Though it scales linearly with the number of particles, there has been a constant interest in increasing its efficiency, because a large part of CPU time is spent to identify the interacting particles. Several recent publications proposed improvements to the algorithm and investigated their efficiency by applying them to particular setups. In this publication we develop a general method to evaluate the efficiency of these algorithms, which is mostly independent of the parameters of the simulation, and test it for a number of linked cell list algorithms. We also propose a combination of linked cell reordering and interaction sorting that shows a good efficiency for a broad range of simulation setups.
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- Algorithm optimization in molecular dynamics simulation
- Fast parallel algorithms for short-range molecular dynamics
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- General purpose molecular dynamics simulations fully implemented on graphics processing units
- Parallel atomistic simulations
Cited in
(10)- A multilevel-skin neighbor list algorithm for molecular dynamics simulation
- Approximating the dynamical evolution of systems of strongly interacting overdamped particles
- Cell List algorithms for nonequilibrium molecular dynamics
- Efficiency of classical molecular dynamics algorithms on supercomputing hardware
- An efficient linked list for molecular simulations on a spherical surface
- Spectral accuracy in fast Ewald-based methods for particle simulations
- The linked neighbour list (LNL) method for fast off-lattice Monte Carlo simulations of fluids
- Fast neighbor lists for adaptive-resolution particle simulations
- Body fitted link-cell algorithm for particulate flow simulation in curved pipeline domain
- Comparison research on the neighbor list algorithms: Verlet table and linked-cell
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