34,554 research outputs found
Efficient Implementations of Molecular Dynamics Simulations for Lennard-Jones Systems
Efficient implementations of the classical molecular dynamics (MD) method for
Lennard-Jones particle systems are considered. Not only general algorithms but
also techniques that are efficient for some specific CPU architectures are also
explained. A simple spatial-decomposition-based strategy is adopted for
parallelization. By utilizing the developed code, benchmark simulations are
performed on a HITACHI SR16000/J2 system consisting of IBM POWER6 processors
which are 4.7 GHz at the National Institute for Fusion Science (NIFS) and an
SGI Altix ICE 8400EX system consisting of Intel Xeon processors which are 2.93
GHz at the Institute for Solid State Physics (ISSP), the University of Tokyo.
The parallelization efficiency of the largest run, consisting of 4.1 billion
particles with 8192 MPI processes, is about 73% relative to that of the
smallest run with 128 MPI processes at NIFS, and it is about 66% relative to
that of the smallest run with 4 MPI processes at ISSP. The factors causing the
parallel overhead are investigated. It is found that fluctuations of the
execution time of each process degrade the parallel efficiency. These
fluctuations may be due to the interference of the operating system, which is
known as OS Jitter.Comment: 33 pages, 19 figures, add references and figures are revise
Efficient method for simulating quantum electron dynamics under the time dependent Kohn-Sham equation
A numerical scheme for solving the time-evolution of wave functions under the
time dependent Kohn-Sham equation has been developed. Since the effective
Hamiltonian depends on the wave functions, the wave functions and the effective
Hamiltonian should evolve consistently with each other. For this purpose, a
self-consistent loop is required at every time-step for solving the
time-evolution numerically, which is computationally expensive. However, in
this paper, we develop a different approach expressing a formal solution of the
TD-KS equation, and prove that it is possible to solve the TD-KS equation
efficiently and accurately by means of a simple numerical scheme without the
use of any self-consistent loops.Comment: 5 pages, 3 figures. Physical Review E, 2002, in pres
Asymptotic Learning Curve and Renormalizable Condition in Statistical Learning Theory
Bayes statistics and statistical physics have the common mathematical
structure, where the log likelihood function corresponds to the random
Hamiltonian. Recently, it was discovered that the asymptotic learning curves in
Bayes estimation are subject to a universal law, even if the log likelihood
function can not be approximated by any quadratic form. However, it is left
unknown what mathematical property ensures such a universal law. In this paper,
we define a renormalizable condition of the statistical estimation problem, and
show that, under such a condition, the asymptotic learning curves are ensured
to be subject to the universal law, even if the true distribution is
unrealizable and singular for a statistical model. Also we study a
nonrenormalizable case, in which the learning curves have the different
asymptotic behaviors from the universal law
Rhythmic Motion of a Droplet under a DC Electric Field
The effect of a stationary electric field on a water droplet with a diameter
of several tens micrometers in oil was examined. Such a droplet exhibits
repetitive translational motion between the electrodes in a spontaneous manner.
The state diagram of this oscillatory motion was deduced; at 0-20 V the droplet
is fixed at the surface of the electrode, at 20-70 V the droplet exhibits
small-amplitude oscillatory motion between the electrodes, and at 70-100 V the
droplet shows large-amplitude periodic motion between the electrodes. The
observed rhythmic motion is explained in a semi-quantitative manner by using
differential equations, which includes the effect of charging the droplet under
an electric field. We also found that twin droplets exhibit synchronized
rhythmic motion between the electrodes
Formation of hydrogen peroxide and water from the reaction of cold hydrogen atoms with solid oxygen at 10K
The reactions of cold H atoms with solid O2 molecules were investigated at 10
K. The formation of H2O2 and H2O has been confirmed by in-situ infrared
spectroscopy. We found that the reaction proceeds very efficiently and obtained
the effective reaction rates. This is the first clear experimental evidence of
the formation of water molecules under conditions mimicking those found in cold
interstellar molecular clouds. Based on the experimental results, we discuss
the reaction mechanism and astrophysical implications.Comment: 12 pages, 3 Postscript figures, use package amsmath, amssymb,
graphic
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