Meyer, Ralf

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Browsing Meyer, Ralf by Subject "molecular dynamics simulations"

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    Efficient parallelization of molecular dynamics simulations with short-ranged forces
    (IOP Publishing Ltd., 2014) Meyer, Ralf
    Recently, an alternative strategy for the parallelization of molecular dynamics simulations with short-ranged forces has been proposed. In this work, this algorithm is tested on a variety of multi-core systems using three types of benchmark simulations. The results show that the new algorithm gives consistent speedups which are depending on the properties of the simulated system either comparable or superior to those obtained with spatial decomposition. Comparisons of the parallel speedup on different systems indicates that on multi-core machines the parallel efficiency of the method is mainly limited by memory access speed.
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    Efficient parallelization of short-range molecular dynamics simulations on many-core systems
    (American Physical Society, 2013-11) Meyer, Ralf
    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 are 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.
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    Parallelization of Molecular-Dynamics Simulations Using Tasks
    (Cambridge University Press, 2015-02) Meyer, Ralf; Mangiardi, Chris M.
    This article discusses novel algorithms for molecular-dynamics (MD) simulations with short-ranged forces on modern multi- and many-core processors like the Intel Xeon Phi. A task-based approach to the parallelization of MD on shared-memory computers and a tiling scheme to facilitate the SIMD vectorization of the force calculations is described. The algorithms have been tested with three different potentials and the resulting speed-ups on Intel Xeon Phi coprocessors are shown.
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    Vibrational band structure of nanoscale phononic crystals
    (Wiley, 2016-11) Meyer, Ralf
    The vibrational properties of two-dimensional phononic crystals are studied with large-scale molecular dynamics simulations and finite element method calculation. The vibrational band structure derived from the molecular dynamics simulations shows the existence of partial acoustic band gaps along the Γ-M direction. The band structure is in excellent agreement with the results from the finite element model, proving that molecular dynamics simulations can be used to study the vibrational properties of such complex systems. An analysis of the structure of the vibrational modes reveals how the acoustic modes deviate from the homogeneous bulk behaviour for shorter wavelengths and hints towards a decoupling of vibrations in the phononic crystal.
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    Vibrational density of states of silicon nanoparticles
    (American Physical Society, 2011-01) Meyer, Ralf; Comtesse, Denis
    The vibrational density of states of silicon nanoparticles in the range from 2.3 to 10.3 nm is studied with the help of molecular-dynamics simulations. From these simulations the vibrational density of states and frequencies of bulklike vibrational modes at high-symmetry points of the Brillouin zone have been derived. The results show an increase of the density of states at low frequencies and a transfer of modes from the high-frequency end of the spectrum to the intermediate range. At the same time the peak of transverse optical modes is shifted to higher frequencies. These observations are in line with previous simulation studies of metallic nanoparticles and they provide an explanation for a previously observed discrepancy between experimental and theoretical data [C. Meier, S. Lu ̈ttjohann, V. G. Kravets, H. Nienhaus, A. Lorke, and H. Wiggers, Physica E 32, 155 (2006).].