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Journal Articles

Machine learning potentials for tobermorite minerals

Kobayashi, Keita; Nakamura, Hiroki; Yamaguchi, Akiko; Itakura, Mitsuhiro; Machida, Masahiko; Okumura, Masahiko

Computational Materials Science, 188, p.110173_1 - 110173_14, 2021/02

no abstracts in English

Journal Articles

Calculations for ambient dose equivalent rates in nine forests in eastern Japan from $$^{134}$$Cs and $$^{137}$$Cs radioactivity measurements

Malins, A.; Imamura, Naohiro*; Niizato, Tadafumi; Takahashi, Junko*; Kim, M.; Sakuma, Kazuyuki; Shinomiya, Yoshiki*; Miura, Satoru*; Machida, Masahiko

Journal of Environmental Radioactivity, 226, p.106456_1 - 106456_12, 2021/01

Journal Articles

Numerical interpretation of hydrogen thermal desorption spectra for iron with hydrogen-enhanced strain-induced vacancies

Ebihara, Kenichi; Sugiyama, Yuri*; Matsumoto, Ryosuke*; Takai, Kenichi*; Suzudo, Tomoaki

Metallurgical and Materials Transactions A, 52(1), p.257 - 269, 2021/01

We simulated the thermal desorption spectra of a small-size iron specimen to which was applied during charging with hydrogen atoms using a model incorporating the behavior of vacancies and vacancy clusters. The model considered up to vacancy clusters $$V_9$$, which is composed of nine vacancies and employed the parameters based on atomistic calculations, including the H trapping energy of vacancies and vacancy clusters that we estimated using the molecular static calculation. As a result, we revealed that the model could, on the whole, reproduced the experimental spectra except two characteristic differences, and also the dependence of the spectra on the aging temperature. By examining the cause of the differences, the possibilities that the diffusion of clusters of $$V_2$$ and $$V_3$$ is slower than the model and that vacancy clusters are generated by applying strain and H charging concurrently were indicated.

Journal Articles

Dynamics of enhanced neoclassical particle transport of tracer impurity ions in ion temperature gradient driven turbulence

Idomura, Yasuhiro; Obrejan, K.*; Asahi, Yuichi; Honda, Mitsuru*

Physics of Plasmas, 28(1), p.012501_1 - 012501_11, 2021/01

Tracer impurity transport in ion temperature gradient driven (ITG) turbulence is investigated using a global full-$$f$$ gyrokinetic simulation including kinetic electrons, bulk ions, and low to medium $$Z$$ tracer impurities, where $$Z$$ is the charge number. It is found that in addition to turbulent particle transport, enhanced neoclassical particle transport due to a new synergy effect between turbulent and neoclassical transports makes a significant contribution to tracer impurity transport. Bursty excitation of the ITG mode generates non-ambipolar turbulent particle fluxes of electrons and bulk ions, leading to a fast growth of the radial electric field following the ambipolar condition. The divergence of $$Etimes B$$ flows compresses up-down asymmetric density perturbations, which are subject to transport induced by the magnetic drift. The enhanced neoclassical particle transport depends on the ion mass, because the magnitude of up-down asymmetric density perturbation is determined by a competition between the $$Etimes B$$ compression effect and the return current given by the parallel streaming motion. This mechanism does not work for the temperature, and thus, selectively enhances only particle transport.

JAEA Reports

Review of research on advanced computational science in FY2019

Center for Computational Science & e-Systems

JAEA-Evaluation 2020-002, 37 Pages, 2020/12

JAEA-Evaluation-2020-002.pdf:1.59MB

Research on advanced computational science for nuclear applications, based on "the plan to achieve the mid and long term goal of the Japan Atomic Energy Agency", has been performed at Center for Computational Science & e-Systems (CCSE), Japan Atomic Energy Agency. CCSE established a committee consisting of outside experts and authorities which does research evaluation and advice for the assistance of the future research and development. This report summarizes the results of the R&D performed at CCSE in FY2019 (April 1st, 2019 - March 31st, 2020) and the evaluation by the committee on them.

Journal Articles

Plume dispersion simulation based on ensemble simulation with lattice Boltzmann method

Hasegawa, Yuta; Onodera, Naoyuki; Idomura, Yasuhiro

Dai-34-Kai Suchi Ryutai Rikigaku Shimpojiumu Koen Rombunshu (Internet), 3 Pages, 2020/12

We developed a real-time ensemble simulation code for analyzing urban wind conditions and plume dispersion using a locally mesh-refined lattice Boltzmann method. We validated the developed code against the wind tunnel experiment by AIST, and against the field experiment JU2003 in Oklahoma City. In the case of the wind tunnel experiment, the wind condition showed a good agreement with the experiment, and 61.2% of the tracer gas concentration data observed on the ground satisfied the FACTOR2 condition, that is an accuracy criterion given by the environmental assessment guideline. In the case of the field experiment JU2003, the instantaneous wind speed showed a good agreement with the experiment, while the wind direction showed a difference up to 100$$^{circ}$$. The means of the tracer gas concentration satisfied the FACTOR2 condition at all observation interval. These results demonstrate that the developed code is accurate enough for the environmental assessment.

Journal Articles

Acceleration of fusion plasma turbulence simulation on Fugaku and Summit

Idomura, Yasuhiro; Ina, Takuya*; Ali, Y.*; Imamura, Toshiyuki*

Dai-34-Kai Suchi Ryutai Rikigaku Shimpojiumu Koen Rombunshu (Internet), 6 Pages, 2020/12

A new communication avoiding (CA) Krylov solver with a FP16 (half precision) preconditioner is developed for a semi-implicit finite difference solver in the Gyrokinetic Toroidal 5D full-f Eulerian code GT5D. In the solver, the bottleneck of global collective communication is resolved using a CA-Krylov subspace method, and halo data communication is reduced by the FP16 preconditioner, which improves the convergence property. The FP16 preconditioner is designed based on the physics properties of the operator and is implemented using the new support for FP16 SIMD operations on A64FX. The solver is ported also on GPUs, and the performance of ITER size simulations with $$sim 0.1$$ trillion grids is measured on Fugaku (A64FX) and Summit (V100). The new solver accelerates GT5D by $$2 sim3times$$ from the conventional non-CA solver, and excellent strong scaling is obtained up to 5,760 CPUs/GPUs both on Fugaku and Summit.

Journal Articles

Brittle-fracture simulations of curved cleavage cracks in $$alpha$$-iron; A Molecular dynamics study

Suzudo, Tomoaki; Ebihara, Kenichi; Tsuru, Tomohito

AIP Advances (Internet), 10(11), p.115209_1 - 115209_8, 2020/11

The mechanism of their brittle fracture of BCC metals is not fully understood. In this study, we conduct a series of three-dimensional molecular dynamics simulations of cleavage fracture of $$alpha$$-iron. In particular, we focus on mode-I loading starting from curved crack fronts. In the simulations, brittle fractures are observed at cleavages on the {100} plane, while the initial cracks become blunted on other planes as a result of dislocation emissions. Our modeling results agreed with a common experimental observation, that is, {100} is the preferential cleavage plane in bcc transition metals.

Journal Articles

Atomistic modeling of hardening in spinodally-decomposed Fe-Cr binary alloys

Suzudo, Tomoaki; Takamizawa, Hisashi; Nishiyama, Yutaka; Caro, A.*; Toyama, Takeshi*; Nagai, Yasuyoshi*

Journal of Nuclear Materials, 540, p.152306_1 - 152306_10, 2020/11

 Times Cited Count:0 Percentile:100(Materials Science, Multidisciplinary)

Spinodal decomposition in thermally aged Fe-Cr alloys leads to significant hardening, which is the direct cause of the so-called 475C-embrittlement. To illustrate how spinodal decomposition induces hardening by atomistic interactions, we conducted a series of numerical simulations as well as reference experiments. The numerical results indicated that the hardness scales linearly with the short-range order (SRO) parameter, while the experimental result reproduced this relationship within statistical error. Both seemingly suggest that neighboring Cr-Cr atomic pairs essentially cause hardening, because SRO is by definition uniquely dependent on the appearance probability of such pairs. A further numerical investigation supported this notion, as it suggests that the dominant cause of hardening is the pinning effect of dislocations passing over such Cr-Cr pairs.

Journal Articles

Acceleration of fusion plasma turbulence simulations using the mixed-precision communication-avoiding Krylov method

Idomura, Yasuhiro; Ina, Takuya*; Ali, Y.*; Imamura, Toshiyuki*

Proceedings of International Conference on High Performance Computing, Networking, Storage, and Analysis (SC 2020) (Internet), p.1318 - 1330, 2020/11

The multi-scale full-$$f$$ simulation of the next generation experimental fusion reactor ITER based on a five dimensional (5D) gyrokinetic model is one of the most computationally demanding problems in fusion science. In this work, a Gyrokinetic Toroidal 5D Eulerian code (GT5D) is accelerated by a new mixed-precision communication-avoiding (CA) Krylov method. The bottleneck of global collective communication on accelerated computing platforms is resolved using a CA Krylov method. In addition, a new FP16 preconditioner, which is designed using the new support for FP16 SIMD operations on A64FX, reduces both the number of iterations (halo data communication) and the computational cost. The performance of the proposed method for ITER size simulations with 0.1 trillion grids on 1,440 CPUs/GPUs on Fugaku and Summit shows 2.8x and 1.9x speedups respectively from the conventional non-CA Krylov method, and excellent strong scaling is obtained up to 5,760 CPUs/GPUs.

Journal Articles

Hydrogen trapping in Mg$$_2$$Si and Al$$_7$$FeCu$$_2$$ intermetallic compounds in aluminum alloy; First-principles calculations

Yamaguchi, Masatake; Tsuru, Tomohito; Ebihara, Kenichi; Itakura, Mitsuhiro; Matsuda, Kenji*; Shimizu, Kazuyuki*; Toda, Hiroyuki*

Materials Transactions, 61(10), p.1907 - 1911, 2020/10

 Times Cited Count:0

no abstracts in English

Journal Articles

Applications of radiocesium migration models to Fukushima environmental issues: Numerical analysis of radiocesium transport in temperature-stratified reservoirs by 3D-Sea-SPEC

Yamada, Susumu; Machida, Masahiko; Kurikami, Hiroshi

Proceedings of Joint International Conference on Supercomputing in Nuclear Applications + Monte Carlo 2020 (SNA + MC 2020), p.140 - 146, 2020/10

no abstracts in English

Journal Articles

Interactive in-situ steering and visualization of GPU-accelerated simulations using particle-based volume rendering

Kawamura, Takuma; Hasegawa, Yuta; Idomura, Yasuhiro

Proceedings of Joint International Conference on Supercomputing in Nuclear Applications + Monte Carlo 2020 (SNA + MC 2020), p.187 - 192, 2020/10

In order to realize the atmospheric dispersion prediction of pollutants, a fluid simulation by adaptive mesh refinement (AMR) optimized for GPU supercomputer has been developed, and interactive visualization and parameter steering of the simulation results are needed. In this study, we extend particle-based in-situ visualization method for structured grids into AMR, and enables in-situ steering of the simulation parameters by utilizing an in-situ control mechanism via files. By combining the developed method with plume dispersion simulation in urban areas running on a GPU platform, it was shown that human-in-the-loop pollution source search is possible without enormous parameter scanning.

Journal Articles

Image-based view selection for shape comparison of mode water regions in virtual reality spaces

Yano, Midori; Ito, Takayuki*; Tanaka, Yusuke*; Matsuoka, Daisuke*; Araki, Fumiaki*; Czauderna, T.*; Stephens, K.*

Proceedings of Joint International Conference on Supercomputing in Nuclear Applications + Monte Carlo 2020 (SNA + MC 2020), p.201 - 208, 2020/10

Visual analysis plays an important role in understanding and evaluating the climate models, their variables, and their outputs because complex processes are required for the tuning of the climate models. Virtual Reality (VR) technologies are effective for 3D visualization and have been recently employed for visual analysis of more various scientific data. However, researchers may have some problematic situations while using VR space depending on user operations and target geometries. Here, we propose an image-based view selection method to solve these situations and understand differences in ocean states between simulations and observations based on shapes of mode water regions. This view selection takes evaluation criteria for shape comparison of mode water regions generated from simulations and observations into account. This paper introduces two example cases applying this view selection and discusses on a degree of shape matching of mode water regions of each case.

Journal Articles

Communication-avoiding Krylov solvers for extreme scale nuclear CFD simulations

Idomura, Yasuhiro; Ina, Takuya*; Ali, Y.*; Imamura, Toshiyuki*

Proceedings of Joint International Conference on Supercomputing in Nuclear Applications + Monte Carlo 2020 (SNA + MC 2020), p.225 - 230, 2020/10

A new communication avoiding (CA) Krylov solver with a FP16 (half precision) preconditioner is developed for a semi-implicit finite difference solver in the Gyrokinetic Toroidal 5D full-f Eulerian code GT5D. In the solver, the bottleneck of global collective communication is resolved using a CA-Krylov subspace method, while the number of halo data communication is reduced by improving the convergence property using the FP16 preconditioner. The FP16 preconditioner is designed based on the physics properties of the operator and is implemented using the new support for FP16 SIMD operations on A64FX. The solver is ported on Fugaku (A64FX) and Summit (V100), which respectively show $$sim$$63x and $$sim$$29x speedups in socket performance compared to the conventional non-CA Krylov solver on JAEA-ICEX (Haswell).

Journal Articles

Intuitive interactions for immersive data exploration of numerical simulation results

Tabata, Ginga*; Sakamoto, Naohisa*; Kawamura, Takuma

Proceedings of Joint International Conference on Supercomputing in Nuclear Applications + Monte Carlo 2020 (SNA + MC 2020), p.193 - 200, 2020/10

In interactive visualization/analysis, interactive operation of visualization results on the screen is an important technology that is directly linked to knowledge extraction. On the conventional 2D display, interactive operations such as moving the viewpoint and adjusting the visualization parameters were performed using the mouse. Then, the virtual reality (VR) technology such as CAVE system and head mounted display (HMD) is used for visualization and analysis, and the development of technology for interactively operating visualization result data in VR space has become one of the important issues in the visualization field. In this paper, we propose a technique to capture a real hand gesture by Leap Motion and intuitively change the viewpoint movement and visualization parameters in VR space by HMD. We asked four people to test the developed technology, and obtained a result that it was easy to change the viewpoint from the questionnaire on the operation feeling.

Journal Articles

Performance portable implementation of a kinetic plasma simulation mini-app with a higher level abstraction and directives

Asahi, Yuichi; Latu, G.*; Bigot, J.*; Grandgirard, V.*

Proceedings of Joint International Conference on Supercomputing in Nuclear Applications + Monte Carlo 2020 (SNA + MC 2020), p.218 - 224, 2020/10

Performance portability is expected to be a critical issue in the upcoming exascale era. We explore a performance portable approach for a fusion plasma turbulence simulation code employing the kinetic model, namely the GYSELA code. For this purpose, we extract the key features of GYSELA such as the high dimensionality (more than 4D) and the semi-Lagrangian scheme, and encapsulate them into a mini-application which solves the similar but a simplified Vlasov-Poisson system as GYSELA. We implement the mini-app with OpenACC, OpenMP4.5 and Kokkos, where we suppress unnecessary duplications of code lines. Based on our experience, we discuss the advantages and disadvantages of OpenACC, OpenMP4.5 and Kokkos, from the view point of performance portability, readability and productivity.

Journal Articles

Ensemble wind simulations using a mesh-refined lattice Boltzmann method on GPU-accelerated systems

Hasegawa, Yuta; Onodera, Naoyuki; Idomura, Yasuhiro

Proceedings of Joint International Conference on Supercomputing in Nuclear Applications + Monte Carlo 2020 (SNA + MC 2020), p.236 - 242, 2020/10

The wind condition and the plume dispersion in urban areas are strongly affected by buildings and plants, which are hardly described in the conventional mesoscale simulations. To resolve this issue, we developed a GPU-based CFD code using a mesh-refined lattice Boltzmann method (LBM), which enables real-time plume dispersion simulations with a resolution of several meters. However, such high resolution simulations are highly turbulent and the time histories of the results are sensitive to various simulations conditions. In order to improve the reliability of such chaotic simulations, we developed an ensemble simulation approach, which enables a statistical estimation of the uncertainty. We examined the developed code against the field experiment JU2003 in Oklahoma City. In the comparison, the wind conditions showed good agreements, and the average values of the tracer gas concentration satisfied the factor 2 agreements between the ensemble simulation data and the experiment.

Journal Articles

GPU-acceleration of locally mesh allocated two phase flow solver for nuclear reactors

Onodera, Naoyuki; Idomura, Yasuhiro; Ali, Y.*; Yamashita, Susumu; Shimokawabe, Takashi*; Aoki, Takayuki*

Proceedings of Joint International Conference on Supercomputing in Nuclear Applications + Monte Carlo 2020 (SNA + MC 2020), p.210 - 215, 2020/10

This paper presents a GPU-based Poisson solver on a block-based adaptive mesh refinement (block-AMR) framework. The block-AMR method is essential for GPU computation and efficient description of the nuclear reactor. In this paper, we successfully implement a conjugate gradient method with a state-of-the-art multi-grid preconditioner (MG-CG) on the block-AMR framework. GPU kernel performance was measured on the GPU-based supercomputer TSUBAME3.0. The bandwidth of a vector-vector sum, a matrix-vector product, and a dot product in the CG kernel gave good performance at about 60% of the peak performance. In the MG kernel, the smoothers in a three-stage V-cycle MG method are implemented using a mixed precision RB-SOR method, which also gave good performance. For a large-scale Poisson problem with $$453.0 times 10^6$$ cells, the developed MG-CG method reduced the number of iterations to less than 30% and achieved $$times$$ 2.5 speedup compared with the original preconditioned CG method.

Journal Articles

Molecular dynamics study of phosphorus migration in $$Sigma$$5 grain boundary of $$alpha$$-iron

Ebihara, Kenichi; Suzudo, Tomoaki

Proceedings of Joint International Conference on Supercomputing in Nuclear Applications + Monte Carlo 2020 (SNA + MC 2020), p.65 - 69, 2020/10

Phosphorus (P) is known as one of the elements which cause the grain boundary (GB) embrittlement in steels and its GB segregation is promoted by the increase of vacancies and self-interstitial atoms due to irradiation. Thus we have been developing the rate-theory model for estimating GB P segregation under several temperatures and irradiation conditions. Because the model does not include the trapping and de-trapping processes properly, however, the model cannot calculate GB P coverage which is measured by experiments. As for the de-trapping process, so far, we have considered the migration of a P atom in the GB region of $$Sigma$$3 symmetrical tilt GB using molecular dynamics (MD). In the current study, we also simulated the P migration in $$Sigma$$5 GB using MD and compared the result with that of $$Sigma$$3. As a result, at 800K, it was found that a P atom cannot migrate in $$Sigma$$5 without vacancies while a P atom can migrate between iron atoms in $$Sigma$$3.

2503 (Records 1-20 displayed on this page)