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

Electron screening in the liquid-gas mixed phases of nuclear matter

Screening effects of electrons on inhomogeneous nuclear matter, which includes spherical, slablike, and rodlike nuclei as well as spherical and rodlike nuclear bubbles, are investigated in view of possible application to cold neutron star matter and supernova matter at subnuclear densities. Using a compressible liquid-drop model incorporating uncertainties in the surface tension, we find that the energy change due to the screening effects broadens the density region in which bubbles and nonspherical nuclei appear in the phase diagram delineating the energetically favorable shape of inhomogeneous nuclear matter. This conclusion is considered to be general since it stems from a model-independent feature that the electron screening acts to decrease the density at which spherical nuclei become unstable against fission and to increase the density at which uniform matter becomes unstable against proton clustering.Comment: 12 pages, 8 figures, accepted for publication in Physical Review

Delayed particles in EAS at Akeno

Using two 2.25 square meter fast scintillation detectors, delayed particles in cosmic ray showers (CRS) have been observed at Akeno Observatory. These are set under 1 m concrete and 2.5 cm lead plates respectively. About 2500 CRS are analyzed. The lateral distribution of delayed particles for the CRS size 10 to the 7th power is flatter than that for to the 7th power. The lateral density of delayed particles is almost constant for the size range 2.2 X 10 to the 5th power approx. 10 to the 7th power and increases rapidly above 10 to the 7th power. These facts may suggest change of nuclear interaction at 10 to the 7th power and substantially the existence of heavy particles with long life

An infrared measurement of chemical desorption from interstellar ice analogues

In molecular clouds at temperatures as low as 10 K, all species except hydrogen and helium should be locked in the heterogeneous ice on dust grain surfaces. Nevertheless, astronomical observations have detected over 150 different species in the gas phase in these clouds. The mechanism by which molecules are released from the dust surface below thermal desorption temperatures to be detectable in the gas phase is crucial for understanding the chemical evolution in such cold clouds. Chemical desorption, caused by the excess energy of an exothermic reaction, was first proposed as a key molecular release mechanism almost 50 years ago. Chemical desorption can, in principle, take place at any temperature, even below the thermal desorption temperature. Therefore, astrochemical net- work models commonly include this process. Although there have been a few previous experimental efforts, no infrared measurement of the surface (which has a strong advantage to quantify chemical desorption) has been performed. Here, we report the first infrared in situ measurement of chemical desorption during the reactions H + H2S -> HS + H2 (reaction 1) and HS + H -> H2S (reaction 2), which are key to interstellar sulphur chemistry. The present study clearly demonstrates that chemical desorption is a more efficient process for releasing H2S into the gas phase than was previously believed. The obtained effective cross-section for chemical desorption indicates that the chemical desorption rate exceeds the photodesorption rate in typical interstellar environments

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