126,564 research outputs found
Stochastic Speculative Computation Method and its Application to Monte Carlo Molecular Simulation
Monte Carlo (MC) molecular simulation has significant computational complexity, and parallel processing is considered effective for computation of problems with large complexity. In recent years, multicore or many-core processors have gained significant attention as they enable computation with a large degree of parallelism on desktop computers. However, in conventional parallel processing, processes must be synchronized frequently; thus, parallel computing is not necessarily efficient. In this study, we evaluate the effect of applying MultiStart-based speculative parallel computation to MC simulations. Using probability theory, we performed theoretical verification to determine if speculative computation is more effective than conventional parallel computation methods. The parameters obtained from the theoretical calculations were observed in experiments wherein the speculative method was applied to an MC molecular simulation. In this paper, we report the results of the theoretical verification and experiments, and we show that speculative computation can accelerate MC molecular simulations
Quantum computing of molecular magnet Mn
Quantum computation in molecular magnets is studied by solving the
time-dependent Schr\"{o}dinger equation numerically. Following Leuenberger and
Loss (Nature (London) 410, 789(2001)), an external oscillating magnetic field
is applied to populate and manipulate the spin coherent states in molecular
magnet Mn. The conditions to realize parallel recording and reading data
bases of Grover algorithsm in molecular magnets are discussed in details. It is
found that an accurate duration time of magnetic pulse as well as the
amplitudes are required to design the device of quantum computing.Comment: 3 pages, 1 figur
An Efficient Cell List Implementation for Monte Carlo Simulation on GPUs
Maximizing the performance potential of the modern day GPU architecture
requires judicious utilization of available parallel resources. Although
dramatic reductions can often be obtained through straightforward mappings,
further performance improvements often require algorithmic redesigns to more
closely exploit the target architecture. In this paper, we focus on efficient
molecular simulations for the GPU and propose a novel cell list algorithm that
better utilizes its parallel resources. Our goal is an efficient GPU
implementation of large-scale Monte Carlo simulations for the grand canonical
ensemble. This is a particularly challenging application because there is
inherently less computation and parallelism than in similar applications with
molecular dynamics. Consistent with the results of prior researchers, our
simulation results show traditional cell list implementations for Monte Carlo
simulations of molecular systems offer effectively no performance improvement
for small systems [5, 14], even when porting to the GPU. However for larger
systems, the cell list implementation offers significant gains in performance.
Furthermore, our novel cell list approach results in better performance for all
problem sizes when compared with other GPU implementations with or without cell
lists.Comment: 30 page
Million-atom molecular dynamics simulation by order-N electronic structure theory and parallel computation
Parallelism of tight-binding molecular dynamics simulations is presented by
means of the order-N electronic structure theory with the Wannier states,
recently developed (J. Phys. Soc. Jpn. 69,3773 (2000)). An application is
tested for silicon nanocrystals of more than millions atoms with the
transferable tight-binding Hamiltonian. The efficiency of parallelism is
perfect, 98.8 %, and the method is the most suitable to parallel computation.
The elapse time for a system of atoms is 3.0 minutes by a
computer system of 64 processors of SGI Origin 3800. The calculated results are
in good agreement with the results of the exact diagonalization, with an error
of 2 % for the lattice constant and errors less than 10 % for elastic
constants.Comment: 5 pages, 3 figure
Accurate Reaction-Diffusion Operator Splitting on Tetrahedral Meshes for Parallel Stochastic Molecular Simulations
Spatial stochastic molecular simulations in biology are limited by the
intense computation required to track molecules in space either in a discrete
time or discrete space framework, meaning that the serial limit has already
been reached in sub-cellular models. This calls for parallel simulations that
can take advantage of the power of modern supercomputers; however exact methods
are known to be inherently serial. We introduce an operator splitting
implementation for irregular grids with a novel method to improve accuracy, and
demonstrate potential for scalable parallel simulations in an initial MPI
version. We foresee that this groundwork will enable larger scale, whole-cell
stochastic simulations in the near future.Comment: 33 pages, 10 figure
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