12,124 research outputs found
DynamO: A free O(N) general event-driven molecular-dynamics simulator
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
Enhanced molecular dynamics performance with a programmable graphics processor
Design considerations for molecular dynamics algorithms capable of taking
advantage of the computational power of a graphics processing unit (GPU) are
described. Accommodating the constraints of scalable streaming-multiprocessor
hardware necessitates a reformulation of the underlying algorithm. Performance
measurements demonstrate the considerable benefit and cost-effectiveness of
such an approach, which produces a factor of 2.5 speed improvement over
previous work for the case of the soft-sphere potential.Comment: 20 pages (v2: minor additions and changes; v3: corrected typos
Efficient Parallelization of Short-Range Molecular Dynamics Simulations on Many-Core Systems
This article introduces a highly parallel algorithm for molecular dynamics
simulations with short-range forces on single node multi- and many-core
systems. The algorithm is designed to achieve high parallel speedups for
strongly inhomogeneous systems like nanodevices or nanostructured materials. In
the proposed scheme the calculation of the forces and the generation of
neighbor lists is divided into small tasks. The tasks are then executed by a
thread pool according to a dependent task schedule. This schedule is
constructed in such a way that a particle is never accessed by two threads at
the same time.Benchmark simulations on a typical 12 core machine show that the
described algorithm achieves excellent parallel efficiencies above 80 % for
different kinds of systems and all numbers of cores. For inhomogeneous systems
the speedups are strongly superior to those obtained with spatial
decomposition. Further benchmarks were performed on an Intel Xeon Phi
coprocessor. These simulations demonstrate that the algorithm scales well to
large numbers of cores.Comment: 12 pages, 8 figure
Improved neighbor list algorithm in molecular simulations using cell decomposition and data sorting method
An improved neighbor list algorithm is proposed to reduce unnecessary
interatomic distance calculations in molecular simulations. It combines the
advantages of Verlet table and cell linked list algorithms by using cell
decomposition approach to accelerate the neighbor list construction speed, and
data sorting method to lower the CPU data cache miss rate, as well as partial
updating method to minimize the unnecessary reconstruction of the neighbor
list. Both serial and parallel performance of molecular dynamics simulation are
evaluated using the proposed algorithm and compared with those using
conventional Verlet table and cell linked list algorithms. Results show that
the new algorithm outperforms the conventional algorithms by a factor of 2~3 in
cases of both small and large number of atoms.Comment: 14 pages, 7 figures. Submitted to Computer Physics Communication
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