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