Particle simulation is a powerful method to study the dynamic behavior of fluids. In this method, fluids are modeled as systems of small particles with the proper physical properties. Large-scale 3D point data are often obtained as a result of particle simulations. In this paper, we visualize the data using particle-based rendering, which we recently proposed. The idea is to utilize the 3D points directly as the rendering primitives, which we call ”particles”. Based on this scheme, we can generate quick and high-quality visualization of large-scale particle simulations. Moreover, we can easily fuse objects surrounding or underlying the simulated fluid. It is also possible to fuse multiple physical values, for example, the velocity and vorticity of the simulated fluid. We demonstrate our method by applying it to a large-scale tsunami run-up simulation for the Great East Japan Earthquake, which occurred in March 2011.

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In this research, a novel distributed memory parallel algorithm for the explicit moving particle simulation (MPS) method is presented. In this method, the analysis area is divided for distributed memory parallel computation using ParMETIS. The development offers two improved points from the distributed parallel explicit particle method of single bucket-based domain decomposition [1]. The first improved point is the hierarchical domain decomposition of two levels. The second improved point is that particle data are managed by buckets. Based on the improvements, we are efficiently able to run a large-scale run-up tsunami analysis.

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The aim of this study was to formulate a relationship between the total perceived discomfort of the upper limbs and the perceived discomforts of each degree of freedom (DOF). The biomechanical analysis was performed based on classifying the posture and load via rapid upper limb assessment (RULA). The summary scores of the RULA and the perceived discomforts of each DOF were the objective and explanatory variables, respectively. Four approximation models (average, maximum, hybrid, and radial basis function (RBF) network) were compared in terms of accuracy in predicting the total perceived discomfort. In conclusion, among the four models, the RBF network provided the highest accuracy, followed by the hybrid model.

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The Great East Japan Earthquake on Mar. 11, 2011 in Japan was extremely huge and brought us enormous damage. In that earthquake, a lot of faults north and south were destroyed successively. Though many numerical models of earthquakes have been proposed, they are all inappropriate for many faults breakdown. Thus in this paper, a simple but interactive coupled stick-slip model based on 2-dimensional Burridge-Knopoff model is proposed. The emergence of catastrophic earthquakes can be found in our simulation. In addition multifractal analysis of earthquake data gives us new interpretation of earthquakes and the possibility of the prediction of catastrophic earthquake.

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High speed Tsunami run-up simulation is achieved by using General Purpose Graphical Processing Unit(GPGPU) at Toyama-bay coastal region. The simulation includes 5[m] grid size geometry data and 3,341,250 (2,475×1,350) grid points are used. The simulation is calculated on the Graphics Processing Unit (GPU) named TESLA K20 (NVIDIA) in about 90.6 seconds and it is more than about 78 times as faster as the CPU calculation. The simulation realizes both the high resolutional calculation (5 [m] intervals) and the high performance calculation.

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A coupled fluid-structure-sediment interaction model is applied to laboratory experiments on wave-induced topographic changes in shallows composed of fine sand. It was found that considerable erosion was occurred over the shallows in the predicted results for the same still water depth as in the experimental condition, which was a different trend from the measured data. In contrast, the condition of a small increase in the still water depth on the crown improved the computational accuracy of water surface elevations, pore-water pressure and the topographic change in the shallows. These results suggest that a small mean water level rise occurred during the experiments, and induced the different topographic evolutions.

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In oder to realize the DFT simulations on large-scale complex systems, we have been developing a linear-scaling DFT code Conquest. In this paper, we report the parallel efficiency of the code on K-computer and show that it has almost ideal parallel efficiency even when we use more than 200,000 cores. Using the code on such large-scale parallel computers, we are now ready to do actual DFT study on million-atom systems. By showing our current study on the nucleation of Ge dimers on three-dimensional Ge nano-islands on Si(001), we demonstrate that accurate, efficient and robust structure relaxation based on the DFT is possible in the actual scientific research on complex nano-structured materials.

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We are developing a theoretical and computational method to describe interactions between an intense laser pulse and a solid. The laser-solid interactions are extensively investigated in current frontiers of optical sciences. There are two spatial scales in the problem: the scale of laser wavelength typically a μm and the scale of electron dynamics in a solid less than a nm. We have developed a multi-scale simulation for this problem, describing propagation of the electromagnetic fields by the Maxwell equations and the electron dynamics in a unit cell of a solid by the time-dependent density functional theory. In calculating the coupled dynamics, we employ a finite difference scheme for both space and time variables. Two kinds of grids with different grid spacings are used for space, while a single time step is used for time. We present our theoretical framework, numerical implementation, and parallelization of our multi-scale simulation. It will be shown that high parallel efficiency and computing performance are realized in our computational code.

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Interviews with scallop aquaculturists were conducted using the Grid Evaluation Method to evaluate the information most valuable to them. The interviews suggested that low-salinity nearshore water, which can increase the mortality of cultured scallop in the nursery stage, is a major concern in spring. Here, we show that a coupled land–ocean, high-resolution model predicted springtime maps of the low-salinity nearshore water and its interannual variations in the specific enclosed bay with aquafarms. The proposed visualization for simultaneous display of low-salinity water, snow cover, and river runoff may be preferable to provide helpful information. The predicted salinity around aquafarms can provide essential information to help reduce mortal risks.

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This paper describes large-scale full-wave analyses of electromagnetic fields using numerical human body models. This is achieved by the use of the parallel finite element method with iterative domain decomposition. Numerical examples of FDTD analysis using numerical human model by a High Performance Computing (HPC) are shown in previous researches. However, numerical examples and performance evaluation of the finite element method hardly exists. Therefore, we perform a feasibility study and a detailed performance evaluation of the high-frequency electromagnetic field analysis using the numerical human model on a super computer constituting Japan’s High Performance Computing Infrastructure (HPCI) as a numerical simulation infrastructure so as to extract problems for advancement of the future analysis. The numerical human body models provided by the National Institute of Information and Communications Technology (NICT) in Japan are composed of voxel data with all sides of 2mm and include skin layers, blood vessels, bones, internal organs, etc. distinguished by material properties. By using HPC, the user can evaluate the electromagnetic filed distribution inside the whole body model.

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We have performed the molecular dynamics (MD) and the fragment molecular orbital (FMO) calculations on the complexes of Burkholderia cepacia lipase (BCL) with alcohol esters toward the prediction of lipase enantioselectivity. The MD computations show that for esters of high enantioselectivity, the difference in the C-O interatomic distance between (R)- and (S)-enantiomer complexes is more than 9.0Å, while for esters of low enantioselectivity, the difference is less than 3.0Å. In addition, the FMO computations indicate that for the esters with high enantioselectivity, each fast reacting enantiomer shows strong interactions with some particular amino acids including HIS286 in BCL, whereas for esters with low enantioselectivity, both (R)- and (S)-enantiomers interact with the identical amino acids including HIS286.

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The adoption of Hermite elements with complete cubic polynomials is one way to apply the constrained interpolation profile (CIP) scheme to unstructured elements. Apart from its ability to describe complicated boundary shapes, this scheme is expected to show enhanced accuracy in the way it interpolates independent variables. In this study, although limited to two-dimensional cases, the numerical error of advection calculations with Hermite triangular elements was compared with that of the A-type CIP scheme by numerical tests and Von Neumann stability analysis. The numerical error of Hermite triangular element calculations was revealed to depend on the flow direction.

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Data compression is always required in large-scale time-varying volume visualization. In some recent application cases, the compression method is also required to include a low-cost decompression process. In this paper, we propose a compression scheme for large-scale time-varying volume data using spatio-temporal features. With this compression scheme, we can provide a proper compression ratio to satisfy many system environments by setting proper compression parameters. After the compression, we can also provide a low-cost and fast decompression process for the compressed data. Furthermore, we also achieve an accelerated rendering process for the decompressed data.

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Virtual reality (VR) technology can be used to simulate environments of historical sites in virtual spaces. In fact, many VR reproductions of historical sites have already been studied and developed. For users, the quality of the visual experience largely determines the authenticity of a VR space. However, when developing a VR space, it is difficult and time-consuming to significantly improve visual quality while maintaining real-time rendering speed, which is the primary requirement of an effective user interface. For this reason, there have been few genuinely photorealistic VR spaces created for historical sites. However, this has begun to change due to the arrival of next-generation three-dimensional (3D) game engines. In this paper, we report on our recent development of photorealistic VR spaces for historical Kyoto sites created using the UDK 3D Game Engine. Specifically, we describe our VR reproduction of Reizei-ke, which consists of the Japanese court noble residence (kuge-yashiki), and Funehoko-cho, which is an important site for Japan's Gion Festival. Through the fabrication of these VR spaces, we could also extract a workflow that allows us to realize photorealistic and read-time VR contents of other cultural assets based on the abovementioned next-generation 3D game engine.

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Magnetic granular systems have been applied to many fields of study, e.g. spin glass properties or magnetic resistance phenomena. These magnetic granular systems have homogeneous densities of magnetic granules and there physical properties changes depending on its densities. In this study, to investigate magnetic properties of such granular systems, minor hysteresis loops analysis was performed using Monte Carlo simulation. As the granular systems, clusters with various magnetic site densities were prepared by simple diffusion model. Moreover, these clusters were analyzed from new point of view which is a concept of a ``colony''. The results of minor loop analysis were considered associating with colony.

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The deflated conjugate gradient (CG) method which can improve the convergence of CG is discussed. The distorted finite element mesh produces the system matrix with a large condition number, which results in poor convergence of CG method. The deflation technique replaces small eigenvalues with zeros in the system matrix. Therefore the deflated CG method is a useful solver for such ill-conditioned finite element analyses. However, the computational cost to obtain the eigenvectors is significantly high. To solve this problem, quasi eigenvectors which can be obtained with low cost are used in this paper. Moreover, the robustness of deflated CG method against distorted finite mesh with flat elements which bring ill-condition is presented.

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