Journal of Advanced Simulation in Science and Engineering
Online ISSN : 2188-5303
ISSN-L : 2188-5303
Volume 6, Issue 1
Displaying 1-25 of 25 articles from this issue
Special Issue on Recent Advances in Simulation in Science and Engineering
Preface
Special Issue on Recent Advances in Simulation in Science and Engineering
  • Yoshiaki Yamaoka, Kengo Hayashi, Naohisa Sakamoto, Jorji Nonaka
    2019 Volume 6 Issue 1 Pages 1-10
    Published: 2019
    Released on J-STAGE: March 15, 2019
    JOURNAL FREE ACCESS

    Large-scale simulations have widely been conducted on modern High-Performance Computing (HPC) systems in a variety of scientific and engineering fields, and scientific visualization has been a popular approach for analyzing and extracting meaningful information from the simulation results. In this work, we focused on Particle Based Volume Rendering (PBVR) method because of its proven effectiveness for handling non-trivial unstructured volume data, which is still commonly used on numerical simulations in the engineering fields. PBVR possesses a visibility sorting-free characteristics thanks to its use of small and opaque particles as the rendering primitives. However, there is a memory cost and image quality trade-off because of the necessity of storing the entire sets of generated particle data before starting the rendering process. In this paper, we present a memory cost efficient parallel PBVR approach for enabling high-quality and high-resolution PBVR of large-scale numerical simulation results. For this purpose, we focused on the image data gathering and processing instead of traditional particle data gathering and processing by using the sort-last parallel image composition approach. We evaluated its effectiveness on the K computer by using the Binary-Swap-based 234Compositor library, and verified its potential for reducing the memory cost while generating high-quality and high-resolution image data.

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  • Daisuke Toriu, Satoru Ushijima
    2019 Volume 6 Issue 1 Pages 11-20
    Published: 2019
    Released on J-STAGE: March 15, 2019
    JOURNAL FREE ACCESS

    In this study, we propose a new fully explicit scheme for non-isothermal and compressible low Mach number gas flows based on a fractional step method and a control method for the speed of sound. Since the Courant-Friedrichs-Lewy (CFL) condition based on the speed of sound is improved according to an artificial coefficient for pressure fluctuation terms, the time increment in the proposed method can be set on the same order as that of a conventional semi-implicit method which treats pressure terms in momentum and energy equations implicitly. As a result of the application to the natural convection in a square cavity, it is demonstrated that the proposed fully explicit method enables to conduct computations reasonably about 6 ~ 8 times faster than the conventional semi-implicit method by setting the appropriate value of the artificial coefficient for pressure fluctuation terms.

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  • Nizam Ahmad, Hideyuki Usui, Yohei Miyake
    2019 Volume 6 Issue 1 Pages 21-31
    Published: 2019
    Released on J-STAGE: March 15, 2019
    JOURNAL FREE ACCESS

    The spacecraft in space is exposed to charged particle bombardment leading to significant charging and distorting the wake structure. The complexity of interaction between spacecraft and particle is difficult to assess, thus needs to be resolved numerically using appropriate method. Electro Magnetic Spacecraft Environment Simulator (EMSES) was developed based on Particle-in-Cell (PIC) which treated not only electro-static phenomena but also self-consistent analysis of electromagnetic effects on the spacecraft surfaces. We employed EMSES to simulate the charging of ERS-1 spacecraft and its influence on the vicinity of the spacecraft in low Earth orbit (LEO) environment. We focused on the floating potential of the spacecraft and the wake structure in the downstream region of the spacecraft. We also present the contribution of electric field to drive the ion trajectory passing through the sheath edge of the spacecraft.

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  • Taishi Matsumura, Tetsuya Yuasa, Siu Kang
    2019 Volume 6 Issue 1 Pages 32-42
    Published: 2019
    Released on J-STAGE: March 15, 2019
    JOURNAL FREE ACCESS

    Cortical neurons exhibit membrane fluctuations and spontaneous transitions between distinct different two states characterized by subthreshold level of membrane potential. It has been known by modeling study that the mechanism of the spontaneous fluctuation originates from not only reverberation in a cortical circuit but intrinsic factor at a single neuron level. The two-state transitions are widely found in many brain regions and these transitions typically occurred spontaneously and synchronously. However, its computational advantage is still unclear. In this study, we investigated synaptic learning for external inputs in a model neuron whose dynamics of membrane potential fluctuation was modulated through the modification of ionic channel dynamics. It was observed that the membrane fluctuation could modulate the learning property to sequential inputs through the spike-timing-dependent plasticity.

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  • Akira Matsumoto, Yoshihisa Fujita, Taku Itoh, Kuniyoshi Abe, Soichiro ...
    2019 Volume 6 Issue 1 Pages 43-55
    Published: 2019
    Released on J-STAGE: March 15, 2019
    JOURNAL FREE ACCESS

    An improvement strategy of a convergence property of a communication-avoiding Krylov subspace method is numerically investigated, and the method is adopted for a linear system obtained from the Element-Free Galerkin (EFG) method. Although a communication-avoiding Krylov subspace method such as k-skip Conjugate Gradient (k-skip CG) improves parallelization efficiency, a convergence property of the method is degraded. To improve this degradation, we propose two improvement techniques, calculating a true residual vector once in several iterations and adopting weighted average of the a true residual and a numerical residual. As the result, the convergence of k-skip CG becomes more stabilized and faster.

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  • Tomio Petrosky
    2019 Volume 6 Issue 1 Pages 56-66
    Published: 2019
    Released on J-STAGE: March 15, 2019
    JOURNAL FREE ACCESS

    Radiation damping process by a charged particle in classical dynamics is discussed in terms of a complex spectral analysis of the Liouville operator in an extended function space outside the Hilbert space. The complex spectral analysis has been introduced to describe irreversible process with a broken time-symmetry on a rigorous dynamical basis starting from the fundamental laws of physics. Thanks to this analysis, we show that the long-standing difficulty of that leads to non-dynamical behaviors such as non-causal behavior and the existence of a runaway solution of the charged particle has been resolve. The propagation of the optical vertex inside a waveguide is also discussed.

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  • Daisuke Ishihara, Atsushi Goto, Minato Onishi, Tomoya Niho, Tomoyoshi ...
    2019 Volume 6 Issue 1 Pages 67-74
    Published: 2019
    Released on J-STAGE: March 15, 2019
    JOURNAL FREE ACCESS

    The selective mesh stiffening in this study changes the stiffness of the element based on both the element area and shape. It includes the stiffening in the previous studies as a specific case, and leads to a general scenario in the pseudoelastic mesh–moving. This scenario gives better mesh quality in the mesh-moving of a rectangular domain with a structure consisting of a square and a fin undergoes large rotations. This is because the shear deformation of the element is adaptively considered.

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  • Masahito Hosaka
    2019 Volume 6 Issue 1 Pages 75-79
    Published: 2019
    Released on J-STAGE: March 15, 2019
    JOURNAL FREE ACCESS

    It was theoretically shown that a single free electron in circular/spiral motion emits optical vortex. Such process can be found in relativistic electron beam crossing a helical undulator and the emitted radiation is known as undulator radiation. We have carried out experimental studies to characterize the synchrotron radiation at the UVSOR-III electron storage ring. We also have performed numerical simulations of the radiation process using a code Synchrotron Radiation Workshop (SRW), widely used in the synchrotron radiation community. The simulation reproduces the radiation properties very well. The simulation is expected to predict further characteristics of undulator radiation as optical vortex.

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  • Tomotaka Kobayashi, Ken Naitoh
    2019 Volume 6 Issue 1 Pages 80-93
    Published: 2019
    Released on J-STAGE: March 15, 2019
    JOURNAL FREE ACCESS

    Quasi-stable ratios are defined as making stability which weaker than neutral stability. Various quasi-stable ratios including new ones are quantitatively revealed by performing multi-dimensional Taylor approximation for the momentum equation describing deformation and translational motions of connected flexible particles, although our previous reports based on one-dimensional Taylor approximation cannot. Quasi-stable ratios including about 2:3 which close to golden and silver ratios and 1:1 are identical to size ratios seen in replication of biological molecules (e.g. nitrogenous base pairs and amino acids) and fission of uranium atoms.

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  • Susumu Fujiwara, Hiroaki Nakamura, Haolun Li, Hisanori Miyanishi, Tomo ...
    2019 Volume 6 Issue 1 Pages 94-99
    Published: 2019
    Released on J-STAGE: March 15, 2019
    JOURNAL FREE ACCESS

    We propose a computational strategy for investigating structural change of tritium-substituted macromolecules. Effects of radiation on macromolecules such as polymeric materials and DNA are classified into three categories: (1) direct action, (2) indirect action, and (3) decay effect. In this study, we focus on the decay effect exclusively. After a beta decay of substituted tritium in macromolecules to helium-3, the generated inert helium-3 is assumed to be deleted quickly. To get an insight into the decay effect to the damage of macromolecules, we perform molecular dynamics simulations of tritium-deleted macromolecules and analyze their structural change. Preliminary simulation results of decay effect on polymeric materials and DNA are presented.

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  • Hiroto Tadano, Ryosei Kuramoto
    2019 Volume 6 Issue 1 Pages 100-117
    Published: 2019
    Released on J-STAGE: March 15, 2019
    JOURNAL FREE ACCESS

    The Block BiCGSTAB method is an efficient method for solving linear systems with multiple right-hand sides. However, when the number of right-hand sides is large, this method may not generate high accuracyapproximate solution due to an error in the computation of matrix-matrix multiplication. In this paper, in order to improve the accuracy of the approximate solution, the recursions of the Block BiCGSTAB method are reconstructed by using the group-wise updating technique. Moreover, the convergence property of the proposed method is also improved when the number of right-hand sides is large.

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  • Yuta Nakagawa, Naobumi Michishita, Hisashi Morishita
    2019 Volume 6 Issue 1 Pages 118-127
    Published: 2019
    Released on J-STAGE: March 15, 2019
    JOURNAL FREE ACCESS

    In order to achieve a near-metal-insensitive antenna for closed space wireless communications, the impedance characteristics of folded monopole antennas (FMA) are of intense interest. The characteristics of a near-metal-insensitive antenna are basically not influenced by proximate objects, especially metal. This paper investigates the antenna characteristics when the antenna approaches metal plates in multiple directions to replicate an actual use environment. The results allow us to develop a higher impedance model that yields greater antenna performance than the conventional middle impedance model.

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  • Kuniyoshi Abe, Seiji Fujino, Soichiro Ikuno
    2019 Volume 6 Issue 1 Pages 128-140
    Published: 2019
    Released on J-STAGE: March 15, 2019
    JOURNAL FREE ACCESS

    We treat with Krylov subspace methods for efficiently solving linear equations. AZMJ variant of Orthomin(2) [1, 2] (abbreviated as AZMJ) has been proposed for solving the linear equations. In this paper, we redesign an alternative AZMJ variant, i.e., propose an alternative minimum residual method for symmetric matrices using the coupled twoterm recurrences formulated by Rutishauser. The recurrence coefficients are determined by imposing the A-orthogonality on the residuals as well as the Conjugate Residual (CR) method. The proposed variant is referred to as MrR. It is mathematically equivalent to CR and AZMJ, but the implementations are different; the recurrence formulas contain alternative expressions for the auxiliary vector and the recurrence coefficients. Moreover, we derive a preconditioned MrR algorithm. By numerical experiments on the linear equations with real symmetric matrices, we demonstrate that the residual norms of MrR converge faster than those of CG and AZMJ, and the preconditioned MrR algorithm is effective.

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  • Shun Tomioka, Tomohiro Tanaka, Koyo Mori, Yasuhide Tsuji
    2019 Volume 6 Issue 1 Pages 141-148
    Published: 2019
    Released on J-STAGE: March 15, 2019
    JOURNAL FREE ACCESS

    Function expansion based topology optimization method for optical waveguide devices has been proposed as an automatic design method which can produce an optimal device structure having an arbitrary topology. In this paper, we aim to extend the function expansion based topology optimization method to the design problems of three-dimensional photonic devices with structural variation in the depth direction. We confirm the effectiveness of our approach through the design example of the polarization splitter and rotator which utilizes structural asymmetry in the depth direction.

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  • Ye Fangzhou, Hajime Igarashi
    2019 Volume 6 Issue 1 Pages 149-156
    Published: 2019
    Released on J-STAGE: March 15, 2019
    JOURNAL FREE ACCESS

    This paper presents topology optimization of electromagnetic metamaterial using the on/off method based on the Normalized Gaussian network (NGnet). In this work, the conductor shape printed on a dielectric slab of fixed dimensions is optimized to have a negative macroscopic permeability at a prescribed frequency band for realization of metamaterial. It is shown that the proposed method successfully provides the metamaterial that works at any desired operating frequency.

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  • Takuma Nemoto, Rajesh Elara Mohan
    2019 Volume 6 Issue 1 Pages 157-176
    Published: 2019
    Released on J-STAGE: March 15, 2019
    JOURNAL FREE ACCESS

    This paper presents an approach to simultaneously estimating the state of a wheeled mobile robot for autonomous cleaning and parameters of dynamic friction model for describing its wheel slip. To this end, we develop a dynamic model of a wheeled mobile robot with slip, applying the LuGre dynamic friction model for describing longitudinal and lateral slip. The dynamic model is used in an unscented Kalman filter (UKF) framework. The effectiveness of the proposed method is demonstrated through simulations, whose results indicate precise estimates of the state and parameters of a wheeled mobile robot in the no-slip case.

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  • Shunsuke Nansai, Hiroshi Itoh
    2019 Volume 6 Issue 1 Pages 177-188
    Published: 2019
    Released on J-STAGE: March 15, 2019
    JOURNAL FREE ACCESS

    The purpose of this study is to propose a foot location algorithm for a glass façade cleaning robot. As an initial stage of this study, we set three assumptions regarding aimed module robot and window shape. These assumptions set the system some geometric constraint conditions: Right edge of the right cleaning unit moves along with the line of the right window frame. The cleaning area of right and left cleaning unit overlaps a little. The module robot walks with a step at a time. From the conditions, a foot location determination algorithm is constructed corresponding to four situations. The effectiveness of the algorithm is verified through a numerical simulation.

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  • Takahiro Kenmotsu, Yue Ma, Moe Usui, Yuko Yoshikawa, Kenichi Yoshikawa
    2019 Volume 6 Issue 1 Pages 189-194
    Published: 2019
    Released on J-STAGE: March 30, 2019
    JOURNAL FREE ACCESS

    We evaluated double-strand breaks (DSBs) in genome-sized DNA (T4 DNA; 166 kbp) caused by photo-irradiation, gamma-rays and ultrasound through a single DNA observation by fluorescence microscopy in a quantitative manner. Based on experimental results, DSBs were induced by two-step mechanism for the photo-irradiation. On the other hands, one-step mechanism led to DSBs for the irradiations of gamma-ray and ultrasound. Regarding the effect of ultrasound, it was found that DSBs were generated above a threshold power. It is suggested that the experimental methodology of single DNA observation serves as a useful tool for studying DSBs of genome-sized DNA.

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  • Yuya Hanaoka, Momoko Nojiri, Taku Itoh, Susumu Nakata, Keiko Watanabe
    2019 Volume 6 Issue 1 Pages 195-214
    Published: 2019
    Released on J-STAGE: May 30, 2019
    JOURNAL FREE ACCESS

    To construct a model of metal foam that has rounded cells such as a real one, an implicit surface based modelling method has been proposed. In this method, uniformed points are first generated randomly by Poisson-disk sampling, and a Voronoi diagram is constructed from the points. In addition, an implicit function f (x) is generated in each of Voronoi cells by setting some constraints appropriately. An implicit surface is represented as f (x) = 0, and the constraints are set so that f (x) = 0 is generated inside each of Voronoi cells. In this model, walls of metal foam are represented by space between implicit surfaces of adjacent Voronoi cells. Rounded walls that have various thicknesses can be constructed by adjusting the constraints. In addition, the walls can be converted to a solid model constructed as tetrahedra filling the space.

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  • Amane Takei, Isamu Higashi, Masaru Aikawa, Tomonori Yamada
    2019 Volume 6 Issue 1 Pages 215-233
    Published: 2019
    Released on J-STAGE: May 30, 2019
    JOURNAL FREE ACCESS

    With the expansion of electromagnetic field analysis using computers, large spaces that include complex shapes have also become an analysis target, and the development of a high-accuracy analysis is required for these problems. Therefore, in the present study, Berenger's PML, which is currently the most effective absorbing boundary condition, is applied to the parallel finite element method based on the domain decomposition method, which is an effective analysis method for the microwave band. As a basic study, we developed an analysis code using a parallel finite element method based on the iterative domain decomposition method. In verifying the accuracy of the analysis code, we analyzed TEAM Workshop Problem 29, which is a benchmark problem, and confirmed that a highly accurate solution is obtained. Next, a model with Berenger's PML added to the dipole antenna model is used as an analysis object, and the absorption performance of the PML is evaluated using a reflection coefficient based on the S parameter. Moreover, the accuracy of the antenna analysis is evaluated by comparing the directivity of the dipole antenna with the theoretical solution. As a result, the effectiveness of the proposed method for microwave analysis is confirmed.

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  • Shintaro Kawahara, Akira Kageyama
    2019 Volume 6 Issue 1 Pages 234-248
    Published: 2019
    Released on J-STAGE: May 30, 2019
    JOURNAL FREE ACCESS

    Head-mounted display-type VR devices (HMDs) are becoming a practical platform for three-dimensional scientific visualization. To reuse software assets that have been developed for CAVE-type VR systems (CAVEs), this paper presents a C++ library for porting CAVE application software to HMDs. Our library emulates the function calls of CAVELib, which is a commercial library for developing application software executable on CAVEs, and it enables us to easily port CAVELib application software to HMDs with minor modifications to the original source code. Sharing the source code also leads to an improvement in the software development efficiency, which is executable on both CAVEs and HMDs.

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  • Masataka Fuchida, Shota Chikushi, Alessandro Moro, Atsushi Yamashita, ...
    2019 Volume 6 Issue 1 Pages 249-259
    Published: 2019
    Released on J-STAGE: May 30, 2019
    JOURNAL FREE ACCESS

    In this work, we propose an arbitrary viewpoint visualization system for disaster response robots. Robot operation from safety areas using teleoperation is highly desirable. To provide sufficient information, it is common to employ multiple displays, however, this often reduces operability. To avoid reduced operability we integrate all acquired images into a single bird eye view. The system is also capable of moving this viewpoint to any arbitrary position for ease of operation, and to overlay a computer-generated image of the robot that is synchronized to match the real robot pose onto the generated view when necessary. Experiments confirmed pose synchronization, generation of views from arbitrary positions, as well as improved operability.

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  • S. Ushijima, H. Tanaka, D. Toriu
    2019 Volume 6 Issue 1 Pages 260-272
    Published: 2019
    Released on J-STAGE: May 30, 2019
    JOURNAL FREE ACCESS

    In the computations of incompressible fluids, it is essentially important to obtain accurately the velocity components that satisfy the incompressible condition (∇・u = 0) as well as the pressure variables which are consistent with the velocity fields. For this purpose, a pressure-velocity correction method (C-HSMAC method) has been proposed by Ushijima et al. (2002) with a finite volume method (FVM) for incompressible fluids. The purpose of this paper is to estimate the effects of the unsatisfied incompressible condition on the passive scalar convection and to confirm that the C-HSMAC method is able to suppress them. The C-HSMAC and usual SMAC methods were applied to the passive scalar convection in the cavity having an oscillating top wall. It was concluded that the unsatisfied incompressible condition may cause the unphysical scalar overshoots in the SMAC method. In contrast, the C-HSMAC method enables us to control |∇・u| with the given threshold ϵD and to suppress such overshoots. In addition, it was demonstrated that the C-HSMAC method allows us to obtain reasonable results without overshoots even in combination with a higher-order scheme for convection terms with finer cell divisions.

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  • Tojoarisoa Rakotoaritina, Megumi Saito, Zhenni Pan, Jiang Liu, Shigeru ...
    2019 Volume 6 Issue 1 Pages 273-281
    Published: 2019
    Released on J-STAGE: August 10, 2019
    JOURNAL FREE ACCESS

    Nowadays, within the concept of Internet of Things (IoT), smart homes, smart factory, intelligent transportation among others are infrastructure systems that connect our world to the Internet. However, wireless communications technology are considerably constrained by complicated structures, and lossy media in complex environments. Fundamental limitations on the transmission range have been treated to connect IoT devices in such Radio Frequency (RF) challenging environments. In order to extend the transmission range in complex environments, Magnetic Induction (MI) communication has been proved to be an efficient solution. In this paper, a Multilayered Metamaterial low profile antenna (MMLPA) using Magnetic Induction communication scheme is proposed for IoT applications. The system model of the MMLPA is analyzed. Then an MMLPA system is designed by using a circular loop antenna backed with isotropic metamaterial which is considered as a Defected Ground Structure (DGS) as well as with anisotropic metamaterial for the purpose of a dielectric uniaxial metamaterial. By using a full-wave finite-element method, the proposed analysis is supported with simulation results where good agreement is achieved compared to the measurement results after realizing four prototypes of the MMLPA antennas. The effect of the presence of metal in the vicinity of the transceivers is also analyzed.

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