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Journal Articles

Molecular dynamic simulations evaluating the effect of the stacking fault energy on defect formations in face-centered cubic metals subjected to high-energy particle irradiation

Terayama, Satoshi*; Iwase, Yuki*; Hayakawa, Sho*; Okita, Taira*; Itakura, Mitsuhiro; Suzuki, Katsuyuki*

Computational Materials Science, 195, p.110479_1 - 110479_12, 2021/07

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

Journal Articles

Self-learning hybrid Monte Carlo method for isothermal-isobaric ensemble; Application to liquid silica

Kobayashi, Keita; Nagai, Yuki; Itakura, Mitsuhiro; Shiga, Motoyuki

Journal of Chemical Physics, 155(3), p.034106_1 - 034106_9, 2021/07

 Times Cited Count:0 Percentile:0.01(Chemistry, Physical)

no abstracts in English

Journal Articles

Investigation of Cu diffusivity in Fe by a combination of atom probe experiments and kinetic Monte Carlo simulation

Zhao, C.*; Suzudo, Tomoaki; Toyama, Takeshi*; Nishitani, Shigeto*; Inoue, Koji*; Nagai, Yasuyoshi*

Materials Transactions, 62(7), p.929 - 934, 2021/07

 Times Cited Count:0 Percentile:0.01(Materials Science, Multidisciplinary)

We succeeded in measuring the diffusion coefficient of Cu in Fe in a low temperature range that had not been measured so far. Since the diffusion couple, which is a general method for measuring the diffusion coefficient, can be applied only at high temperature, atom probe tomography and Cu precipitation rate theory were used in this study. The estimated diffusion coefficient was found to be more reliable than that obtained in previous studies. Therefore, it is considered that the estimation by the atom probe provided higher accuracy. Furthermore, the kinetic Monte Carlo simulation revealed that the diffusion coefficient estimated by this method tends to be slightly overestimated as the temperature decreases.

Journal Articles

Inclination of self-interstitial dumbbells in molybdenum and tungsten; A First-principles study

Suzudo, Tomoaki; Tsuru, Tomohito

AIP Advances (Internet), 11(6), p.065012_1 - 065012_7, 2021/06

In the current study, we analyzed the self-interstitial atoms (SIAs) in BCC molybdenum (Mo) and tungsten (W) in comparison with other BCC transition metals utilizing first-principles method; particularly, we focused on uncommon dumbbells, whose direction are inclined from $$<$$111$$>$$ toward $$<$$110$$>$$ on the {110} plane. Such a direction is not stable neither in the group 5 BCC metals (i.e., vanadium, niobium, and tantalum) nor in $$alpha$$-iron. Our first-principles relaxation simulations indicated that inclined dumbbells were more energetically-favored than common $$<$$111$$>$$ dumbbells in Mo, while this is not necessarily the case for W. However, under a certain degree of lattice strain, such as shear or expansive strain, could make inclined dumbbells more favored also in W, suggesting that the lattice strain can substantially influence the migration barrier of SIAs in these metals because inclined dumbbells generally have a larger migration barrier than $$<$$111$$>$$ dumbbells.

Journal Articles

Neoclassical transport simulations with an improved model collision operator

Matsuoka, Seikichi*; Sugama, Hideo*; Idomura, Yasuhiro

Physics of Plasmas, 28(6), p.064501_1 - 064501_5, 2021/06

 Times Cited Count:0

The improved model collision operator proposed by Sugama et al., which can recover the friction-flow relation of the linearized Landau collision operator, is newly implemented in a global full- f gyrokinetic simulation code, GT5D, and collisional transport simulations of a single ion species plasma in a tokamak are performed over the wide collisionality regime. The improved operator is verified to reproduce the theoretical collisional thermal diffusivity precisely in the high collisionality regime, where the friction-flow relation of higher accuracy is required than in the lower collisional regime. In addition, it is found in all collisionality regimes that the higher accuracy of the collisional thermal diffusivity and the parallel flow coefficient is obtained by the improved operator, demonstrating that collisional processes described by the linearized Landau collision operator is correctly retained.

Journal Articles

Real-time tracer dispersion simulations in Oklahoma City using the locally mesh-refined lattice Boltzmann method

Onodera, Naoyuki; Idomura, Yasuhiro; Hasegawa, Yuta; Nakayama, Hiromasa; Shimokawabe, Takashi*; Aoki, Takayuki*

Boundary-Layer Meteorology, 179(2), p.187 - 208, 2021/05

 Times Cited Count:2 Percentile:89.67(Meteorology & Atmospheric Sciences)

A plume dispersion simulation code named CityLBM enables a real time simulation for ~several km by applying adaptive mesh refinement (AMR) method on GPU supercomputers. We assess plume dispersion problems in the complex urban environment of Oklahoma City (JU2003). Realistic mesoscale wind boundary conditions of JU2003 produced by a Weather Research and Forecasting Model (WRF), building structures, and a plant canopy model are introduced to CityLBM. Ensemble calculations are performed to reduce turbulence uncertainties. The statistics of the plume dispersion field, mean and max concentrations show that ensemble calculations improve the accuracy of the estimation, and the ensemble-averaged concentration values in the simulations over 4 km areas with 2-m resolution satisfied factor 2 agreements for 70% of 24 target measurement points and periods in JU2003.

Journal Articles

Improved domain partitioning on tree-based mesh-refined lattice Boltzmann method

Hasegawa, Yuta; Aoki, Takayuki*; Kobayashi, Hiromichi*; Idomura, Yasuhiro; Onodera, Naoyuki

Keisan Kogaku Koenkai Rombunshu (CD-ROM), 26, 6 Pages, 2021/05

We introduce an improved domain partitioning method called "tree cutting approach" for the aerodynamics simulation code based on the lattice Boltzmann method (LBM) with the forest-of-octrees-based local mesh refinement (LMR). The conventional domain partitioning algorithm based on the space-filling curve (SFC), which is widely used in LMR, caused a costly halo data communication which became a bottleneck of our aerodynamics simulation on the GPU-based supercomputers. Our tree cutting approach adopts a hybrid domain partitioning with the coarse structured block decomposition and the SFC partitioning in each block. This hybrid approach improved the locality and the topology of the partitioned sub-domains and reduced the amount of the halo communication to one-third of the original SFC approach. The code achieved $$times 1.23$$ speedup on 8 GPUs, and achieved $$times 1.82$$ speedup at the performance of 2207 MLUPS (mega-lattice update per second) on 128 GPUs with strong scaling test.

Journal Articles

Acceleration of locally mesh allocated Poisson solver using mixed precision

Onodera, Naoyuki; Idomura, Yasuhiro; Hasegawa, Yuta; Shimokawabe, Takashi*; Aoki, Takayuki*

Keisan Kogaku Koenkai Rombunshu (CD-ROM), 26, 3 Pages, 2021/05

We develop a mixed-precision preconditioner for the pressure Poisson equation in a two-phase flow CFD code JUPITER-AMR. The multi-grid (MG) preconditioner is constructed based on the geometric MG method with a three- stage V-cycle, and a cache-reuse SOR (CR-SOR) method at each stage. The numerical experiments are conducted for two-phase flows in a fuel bundle of a nuclear reactor. The MG-CG solver in single-precision shows the same convergence histories as double-precision, which is about 75% of the computational time in double-precision. In the strong scaling test, the MG-CG solver in single-precision is accelerated by 1.88 times between 32 and 96 GPUs.

Journal Articles

Multi-resolution steady flow prediction with convolutional neural networks

Asahi, Yuichi; Hatayama, Sora*; Shimokawabe, Takashi*; Onodera, Naoyuki; Hasegawa, Yuta; Idomura, Yasuhiro

Keisan Kogaku Koenkai Rombunshu (CD-ROM), 26, 4 Pages, 2021/05

We develop a convolutional neural network model to predict the multi-resolution steady flow. Based on the state-of-the-art image-to-image translation model Pix2PixHD, our model can predict the high resolution flow field from the signed distance function. By patching the high resolution data, the memory requirements in our model is suppressed compared to Pix2PixHD.

Journal Articles

Hydrogen-trapping energy in screw and edge dislocations in aluminum; First-principles calculations

Yamaguchi, Masatake; Itakura, Mitsuhiro; Tsuru, Tomohito; Ebihara, Kenichi

Materials Transactions, 62(5), p.582 - 589, 2021/05

 Times Cited Count:0 Percentile:0.01(Materials Science, Multidisciplinary)

no abstracts in English

Journal Articles

Data-driven derivation of partial differential equations using neural network model

Koyamada, Koji*; Yu, L.*; Kawamura, Takuma; Konishi, Katsumi*

International Journal of Modeling, Simulation, and Scientific Computing, 12(2), p.2140001_1 - 2140001_19, 2021/04

With the improvement of sensors technologies in various fields such as fluid dynamics, meteorology, and space observation, it is an important issue to derive explanatory models using partial differential equations (PDEs) for the big data obtained from them. In this paper, we propose a technique for estimating linear PDEs with higher-order derivatives for spatiotemporally discrete point cloud data. The technique calculates the time and space derivatives from a neural network (NN) trained on the point cloud data, and estimates the derivative term of the PDE using regression analysis techniques. In the experiment, we computed the error of the estimated PDEs for various meta-parameters for the PDEs with exact solutions. As a result, we found that increasing the hierarchy of NNs to match the order of the derivative terms in the exact solution PDEs and adopting L1 regularization with LASSO as the method of regression analysis increased the accuracy of the model.

Journal Articles

Quantum chemical calculation studies toward microscopic understanding of retention mechanism of Cs radioisotopes and other alkali metals in lichens

Suno, Hiroya; Machida, Masahiko; Dohi, Terumi; Omura, Yoshihito*

Scientific Reports (Internet), 11(1), p.8228_1 - 8228_13, 2021/04

 Times Cited Count:1 Percentile:66.59(Multidisciplinary Sciences)

We evaluate stability of caesium (Cs) and other alkali-metal cation complexes of lichen metabolites in both gas and aqueous phases to discuss why lichens can retain radioactive Cs in the thalli over several years. We focus on oxalic acid, (+)-usnic acid, atranorin, lecanoric acid, and protocetraric acid, which are common metabolite substances in various lichens including, e.g., $textit{Flavoparmelia caperata}$ and $textit{Parmotrema tinctorum}$ retaining Cs in Fukushima, Japan. By performing quantum chemical calculations, their gas-phase complexation energies and aqueous-solution complexation free energies with alkali-metal cations are computed for their neutral and deprotonated cases. Consequently, all the molecules are found to energetically favor cation complexations and the preference order is Li$$^+>$$Na$$^+>$$K$$^+>$$Rb$$^+>$$Cs$$^+$$ for all conditions, indicating no specific Cs selectivity but strong binding with all alkali cations. Comparing complexation stabilities among these metabolites, lecanoric and protocetraric acids seen in medullary layer are found to keep higher affinity in their neutral case, while (+)-usnic acid and atranorin in upper cortex exhibit rather strong affinity only in deprotonated cases through forming stable six atoms' ring containing alkali cation chelated by two oxygens. These results suggest that the medullary layer can catch all alkali cations in a wide pH range around the physiological one, while the upper cortex can effectively block penetration of metal ions when the metal stress grows. Such insights highlight a physiological role of metabolites like blocking of metal-cation migrations into intracellular tissues, and explain long-term retention of alkali cations including Cs in lichens containing enough such metabolites to bind them.

Journal Articles

Computational study of solute effects in tungsten under irradiation

Suzudo, Tomoaki

Materials Science Forum, 1024, p.87 - 94, 2021/03

Tungsten (W) is suitable for solid targets of spallation neutron source due to its high neutron yield. The prediction of radiation effects of W is, therefore, of importance; especially, the influence of solute elements are complex and are not clearly known to date. We discuss here the solute effects using the first principles and kinetic Monte Carlo calculations and show that rhenium (Re) and osmium (Os), which are nuclear transmutation products of W, can largely change the stability and mobility of radiation defects. Such influences of the solute elements seem to explain the unsolved mechanism of the microstructural evolution of W-based materials under irradiation.

JAEA Reports

Summaries of research and development activities by using supercomputer system of JAEA in FY2019 (April 1, 2019 - March 31, 2020)

HPC Technology Promotion Office

JAEA-Review 2020-021, 215 Pages, 2021/02


Japan Atomic Energy Agency (JAEA) conducts research and development (R&D) in various fields related to nuclear power as a comprehensive institution of nuclear energy R&Ds, and utilizes computational science and technology in many activities. As shown in the fact that about 20 percent of papers published by JAEA are concerned with R&D using computational science, the supercomputer system of JAEA has become an important infrastructure to support computational science and technology. In FY2019, the system was used for R&D aiming to restore Fukushima (environmental recovery and nuclear installation decommissioning) as a priority issue, as well as for JAEA's major projects such as research and development of fast reactor cycle technology, research for safety improvement in the field of nuclear energy, and basic nuclear science and engineering research. This report presents a great number of R&D results accomplished by using the system in FY2019, as well as user support, operational records and overviews of the system, and so on.

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

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

no abstracts in English

Journal Articles

Nuclear quantum effects on autoionization of water isotopologs studied by ${it ab initio}$ path integral molecular dynamics

Thomsen, B.; Shiga, Motoyuki

Journal of Chemical Physics, 154(8), p.084117_1 - 084117_10, 2021/02

 Times Cited Count:0 Percentile:0.01(Chemistry, Physical)

In this study we investigate the nuclear quantum effects on the acidity constant of liquid water isotopologues at the ambient condition by ${it ab initio}$ path integral molecular dynamics simulations. This technique not only reproduces the acidity constants of liquid D$$_{2}$$O experimentally measured but also allows for a theoretical prediction of the acidity constants of liquid T$$_{2}$$O, aqueous HDO and HTO, which are unknown due to its scarcity. The results indicate that the nuclear quantum effects play an indispensable role in the absolute determination of acidity constants.

Journal Articles

Lattice Boltzmann modeling and simulation of forced-convection boiling on a cylinder

Saito, Shimpei*; De Rosis, A.*; Fei, L.*; Luo, K. H.*; Ebihara, Kenichi; Kaneko, Akiko*; Abe, Yutaka*

Physics of Fluids, 33(2), p.023307_1 - 023307_21, 2021/02

 Times Cited Count:2 Percentile:0.01(Mechanics)

A Boiling phenomenon in a liquid flow field is known as forced-convection boiling. We numerically investigated the boiling system on a cylinder in a flow at a saturated condition. To deal with such a phenomenon, we developed a numerical scheme based on the pseudopotential lattice Boltzmann method. The collision was performed in the space of central moments (CMs) to enhance stability for high Reynolds numbers. Furthermore, additional terms for thermodynamic consistency were derived in a CMs framework. The effectiveness of the model was tested against some boiling processes, including nucleation, growth, and departure of a vapor bubble for high Reynolds numbers. Our model can reproduce all the boiling regimes without the artificial initial vapor phase. We found that the Nukiyama curve appears even though the focused system is the forced-convection system. Also, our simulations support experimental observations of intermittent direct solid-liquid contact even in the film-boiling regime.

Journal Articles

Data-driven analyses of avalanche like turbulent transport phenomena

Asahi, Yuichi; Fujii, Keisuke*

Purazuma, Kaku Yugo Gakkai-Shi, 97(2), p.86 - 92, 2021/02

The 5D gyrokinetic simulation data has been analyzed with the data-driven analysis methods. By defining an entropy-like quantity with singular values, we have quantitatively evaluated the randomness of the plasma state. We found that the randomness of plasma increases after the avalanche like transport and then gradually decrease. Since the decrease of the randomness is expected to be relevant to the phase space structure formation, we have developed a method to extract the phase space structures from the time series of 5D data. The relationship between the avalanche-like transport and phase space structures is discussed based on the contribution of each principal component to the energy transport.

Journal Articles

Density functional theory study of solute cluster growth processes in Mg-Y-Zn LPSO alloys

Itakura, Mitsuhiro; Yamaguchi, Masatake; Egusa, Daisuke*; Abe, Eiji*

Acta Materialia, 203, p.116491_1 - 116491_9, 2021/01

 Times Cited Count:1 Percentile:73.72(Materials Science, Multidisciplinary)

Solute cluster in LPSO alloys plays a key role in their idiosyncratic plastic behavior such as kink formation and kink strengthening. Identifying the atomistic details of the cluster structure is a prerequisite for any atomistic modeling of LPSO alloys aiming for their improved strength and ductility, but there have been uncertainty about interstitial atom in the cluster. While density functional theory calculations have shown that inclusion of interstitial atom is energetically favorable, it has been unclear how the extra atom is provided, how much of the cluster have interstitial atoms, and what kind of element they are. In the present work we use density functional theory calculations to investigate the growth process of the solute cluster, specifically that of Mg-Y-Zn LPSO alloy, to determine the precise atomistic structure of solute cluster. We show that a pair of an interstitial atom and a vacancy is spontaneously created when a certain number of solute atoms are absorbed into the cluster, and all the full-grown cluster should include interstitial atom. We also show that interstitial atom is either Mg or Y atom, while Zn interstitial atom is extremely rare. These knowledge greatly simplifies atomistic modeling of solute clusters in Mg-Y-Zn alloy. Owing to the vacancies emitted from the cluster, vacancy density should be over-saturated in regions where solute clusters are growing, and the increased vacancy density accelerates cluster growth.

Journal Articles

Refined metadynamics through canonical sampling using time-invariant bias potential; A Study of polyalcohol dehydration in hot acidic solutions

Kondo, Tomomi; Sasaki, Takehiko*; Ruiz-Barragan, S.*; Ribas-Ari$~n$o, J.*; Shiga, Motoyuki; Ruiz-Barragan, S.*

Journal of Computational Chemistry, 42(3), p.156 - 165, 2021/01

 Times Cited Count:2 Percentile:42.55(Chemistry, Multidisciplinary)

We propose a canonical sampling method to refine metadynamics simulations a posteriori. This approach could be useful particularly when two or more free energy barriers are to be compared among chemical reactions in different or competing conditions. The method was then applied to study the acid dependence of polyalcohol dehydration reactions in high-temperature aqueous solutions. It was found that the reaction proceeds consistently via an S$$_{rm N}$$2 mechanism, whereby the free energy of protonation of the hydroxyl group created as an intermediate is affected significantly by the acidic species.

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