Preconditioned IDR(s) iterative solver for non‐symmetric linear system associated with FEM analysis of shallow foundation

Non‐associated flow rule is essential when the popular Mohr–Coulomb model is used to model nonlinear behavior of soil. The global tangent stiffness matrix in nonlinear finite element analysis becomes non‐symmetric when this non‐associated flow rule is applied. Efficient solution of this large‐scale non‐symmetric linear system is of practical importance. The standard Krylov solver for a non‐symmetric solver is Bi‐CGSTAB. The Induced Dimension Reduction [IDR(s)] solver was proposed in the scientific computing literature relatively recently. Numerical studies of a drained strip footing problem on homogenous soil layer show that IDR(s = 6) is more efficient than Bi‐CGSTAB when the preconditioner is the incomplete factorization with zero fill‐in of global stiffness matrix K_ep (ILU(0)‐K_ep). Iteration time is reduced by 40% by using IDR(s = 6) with ILU(0)‐K_ep. To further reduce computational cost, the global stiffness matrix K_ep is divided into two parts. The first part is the linear elastic stiffness matrix K_e, which is formed only once at the beginning of solution step. The second part is a low‐rank matrix Δ, which is re‐formed at each Newton–Raphson iteration. Numerical studies show that IDR(s = 6) with this ILU(0)‐K_e preconditioner is more time effective than IDR(s = 6) with ILU(0)‐K_ep when the percentage of yielded Gauss points in the mesh is less than 15%. The total computation time is reduced by 60% when all the recommended optimizing methods are used. Copyright © 2013 John Wiley & Sons, Ltd.     

An interactive system to assist mineral identification in ore microscopy

An interactive computer system has been developed to assist the mineral identification in ore microscopy. The reference file of the system consists of optical, mechanical, and chemical properties of about 130 ore minerals. The properties are name, chemical formula, color, bireflectance, anisotropism, internal reflection, reflectance at wavelengths of 470, 546, 589, and 650 nm, and polishing hardness and micro-indentation hardness. All the properties except reflectance and microindentation hardness are qualitative or semi-qualitative. Most of the properties are given as characters relative to the more common minerals. This implies that most of the identification processes advance on the basis of the comparison between a subject mineral and coexisting minerals. For this reason, the system asks a user at first to input already identified mineral names. This is quite different from the mineral identification procedures used in petrographic microscopy. To reduce the number of possible minerals, the system presents a series of questions to a user, and the user selects any of the prepared answers according to his observation. The user can also choose any desired question independently of the sequence. The user is expected to be able to recognize some common minerals, such as pyrite, chalcopyrite, galena, and hematite, without the assistance of the system.     

Phase relation of CaSO<Subscript>4</Subscript> at high pressure and temperature up to 90 GPa and 2300 K

Calcium sulfate (CaSO₄), one of the major sulfate minerals in the Earth’s crust, is expected to play a major role in sulfur recycling into the deep mantle. Here, we investigated the crystal structure and phase relation of CaSO₄ up to ~90 GPa and 2300 K through a series of high-pressure experiments combined with in situ X-ray diffraction. CaSO₄ forms three thermodynamically stable polymorphs: anhydrite (stable below 3 GPa), monazite-type phase (stable between 3 and ~13 GPa) and barite-type phase (stable up to at least 93 GPa). Anhydrite to monazite-type phase transition is induced by pressure even at room temperature, while monazite- to barite-type transition requires heating at least to 1500 K at ~20 GPa. The barite-type phase cannot always be quenched from high temperature and is distorted to metastable AgMnO₄-type structure or another modified barite structure depending on pressure. We obtained the pressure–volume data and density of anhydrite, monazite- and barite-type phases and found that their densities are lower than those calculated from the PREM model in the studied P–T conditions. This suggests that CaSO₄ is gravitationally unstable in the mantle and fluid/melt phase into which sulfur dissolves and/or sulfate–sulfide speciation may play a major role in the sulfur recycling into the deep Earth.     

A Simple Single-Layer Urban Canopy Model For Atmospheric Models: Comparison With Multi-Layer And Slab Models

We developed a simple, single-layer urban canopy model, and comparedit to both multi-layer and slab models. Our single-layer model has thefollowing features: (a) It is a column model of energy and momentumexchange between an urban surface and the atmosphere, (b) it includesthe influence of street canyons, which are parameterized to representthe urban geometry, (c) it includes shadowing from buildings andreflection of radiation, and (d) it estimates both the surfacetemperatures of, and heat fluxes from, three surface types: roof, wall,and road. In the simulation of the single-layer model, the roof washottest during the daytime, but coolest from midnight to early morning.This is consistent with output from the multi-layer model and fieldobservations at a residential area on a clear, summer day. The diurnalvariation of the energy budget from the single-layer model agrees wellwith that from the multi-layer model. Our single-layer model'sperformance is nearly that of a multi-layer model for studyingmesoscale heat islands. Nevertheless, it is simply parameterized,and thus easily included in larger-scale atmospheric models. The slabmodel has the largest nighttime cooling rate of the three models. Toovercome this, it needs more adjustments than for the canopy models.     

Disturbance of recruitment success of mantis shrimp in Tokyo Bay associated with effects of hypoxia on the early life history

We investigated effects of severe hypoxia (dissolved oxygen <1 ml l⁻¹) on recruitment of mantis shrimp Oratosquilla oratoria in Tokyo Bay. Ten-year field surveys were conducted to examine quantitative relationships in annual mean densities of larvae and juveniles, and spatial distribution of juveniles and severe hypoxia. There was no significant correlation between annual mean densities of larvae and juveniles, suggesting that mortality during larval or juvenile stages varies among years, which might have regulated abundance of young-of-the-year juveniles. Juvenile density was low in the severely hypoxic area, implying that hypoxia could affect survivals and spatial distribution of juveniles. Meanwhile, there are yearly fluctuations in juvenile density in normoxic areas of both northern and southern part of the bay. This evidence suggests that abundance of post-settled juveniles might have been determined by not only effects of hypoxia, but also other factors influencing mortality during the early life stages.     

The succession of microbial community in the organic rich fish-farm sediment during bioremediation by introducing artificially mass-cultured colonies of a small polychaete, Capitella sp. I

We monitored seasonal changes of the abundance and composition of microorganisms in the fish-farm sediment in Kusuura Bay, Amakusa, Japan, using the quinone profiling technique, during bioremediation by introducing cultured colonies of polychaete, Capitella sp. I. In November 2004, approximately 9.2 million cultured worms were transferred to the fish-farm sediment, which increased rapidly, and reached 458.5 gWW/m(2) (528,000 indiv./m(2)) in March 2005. During this fast-increasing period of Capitella, the microbial quinone content of the surface sediment (0-2 cm) also increased markedly, and reached 237 micromol/m(2) in January 2005, although the water temperature decreased to the lowest levels in the year. Particularly, the mole fraction of ubiquinone-10 in total quinones in the sediment, indicating the presence of alpha subclass of Proteobacteria, increased by 9.3%. These facts suggest that the bacterial growth was enhanced markedly by the biological activities of worms in the sediment, and the bacteria played an important role in the decomposition of the organic matter in the sediment.     

Gonadal histology and serum vitellogenin levels of bigeye tuna Thunnus obesus from the Northern Pacific Ocean--absence of endocrine disruption bio-indicators

Endocrine disrupting chemicals such as organochlorines have been detected in a large number of marine fish. Histological observation of the gonads, measurement of serum vitellogenin (VTG) level and of liver polychlorinated biphenyl (PCB) content were performed to evaluate the reproductive health and the contamination with endocrine disruptors in bigeye tuna Thunnus obesus, collected in the northern Pacific Ocean in 1999 and 2000. Abnormalities commonly found in species affected by endocrine disruptors such as the presence of oocytes in the testis or elevated serum VTG levels were not found in any of males examined. Both males and females had only small amounts of liver PCB content. The results suggest that currently there is little if any risk of organochlorine contamination or endocrine disruption of gonadal function in bigeye tuna from the northern Pacific Ocean. However, further studies are necessary to evaluate the health status of the open sea fishery resources.     

Large-eddy simulations of convection-driven dynamos using a dynamic scale-similarity model

Dynamo simulations require sub-grid scale (SGS) models for the momentum and heat flux, the Lorentz force, and the magnetic induction. Previous large eddy simulations (LES) using the scale similarity model have represented many aspects of the SGS motion. However, discrepancies are observed due to interchanging the order of filtering operation and spatial differentiation. In this study, we implement a correction term for this commutation error specifically for the scale-similarity model. Furthermore, we implement a dynamic scheme to evaluate time-dependent coefficients for the SGS models. We perform dynamo simulations in a rotating plane layer with different spatial resolutions, and compare results for the time dependence of the large-scale magnetic field. Simulations are performed at two different Rayleigh numbers, using constant values for the other dimensionless numbers (Ekman, Prandtl, and magnetic Prandtl numbers). Both cases show that the dynamic LES can accurately represent the large-scale magnetic field, whereas the dynamo failed in the direct simulations without the SGS terms at the same spatial resolutions. We conclude that the dynamic versions of the SGS and commutation error correction are essential for successful dynamos on coarser grids.     

Three-dimensional distributions of sewage markers in Tokyo Bay water--fluorescent whitening agents (FWAs)

Three-dimensional distributions of fluorescent whitening agents (FWAs: more specifically, DSBP and DAS1), which are sewage-derived water-soluble markers, were observed in Tokyo Bay water through multi-layer sampling of water at 20 locations. In summer, FWAs predominated in the surface layers, with trace but significant concentration of FWAs in bottom water due to stratification of seawater. In winter, on the other hand, FWAs were extensively mixed into the bottom layers because of the vertical mixing of seawater. In the surface layer, FWA concentrations and the DSBP/DAS1 ratio (the concentration ratio of DSBP to DAS1) were lower in summer than in winter, suggesting more efficient photodegradation of FWAs in euphotic zones during the summer due to stronger solar radiation. Horizontally, FWAs were widely distributed over the surface layer of Tokyo Bay. Surface water with DSBP concentrations above 50ng/L, corresponding to <200 times dilution of sewage effluent, was found to have spread up to 10km from the coastline. In addition, an offshore decline in FWA concentrations was observed, showing a half-distance of 10-20km. The decrease was caused by dilution by seawater of fresh water containing FWAs. The eastern part of the bay was different with respect to surface layers, with higher concentrations seen in northeastern parts. Furthermore, dispersion of combined sewer overflow (CSO)-derived water mass was observed in Tokyo Bay after heavy rain.     

Heat influx and exhumation of the Shimanto accretionary complex: Miocene fission track ages from the Kii Peninsula, southwest Japan

Abstract   To determine how local geological events contributed to the evolution of accretionary complexes and eventual exposure of rocks with different structural levels, geochronological mapping was carried out using fission track (FT) analysis at the Kii Peninsula, southwest Japan. At this site, the original zonal structure of Cretaceous accretionary complexes parallel to the subduction zone is disturbed by the northward projection of the Shimanto accretionary complex. Twenty-six zircon FT ages were obtained from an area of ∼12 km in an east–west direction and ∼15 km in a north–south direction, and classified into three groups: (i) ages ∼15 Ma (range ∼10–20 Ma), which are distributed along the northwest–southeast valley; (ii) ages of ∼50 Ma in the northwest of the study area; and (iii) ages older than those in Groups 1 and 2. Based on results from eight zircon FT length distributions, the Miocene ages appear to be the result of spatial variations in heat influx and cooling after the regional exhumation of the area, as recorded by FT ages of ∼50 Ma.