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Energetics of Kinetic Reconnection in a Three-Dimensional Null-Point Cluster

Physical Review Letters 2013年第4期111卷 045002-045002页

作者： V. Olshevsky G. Lapenta S. Markidis Center for mathematical Plasma Astrophysics (CmPA) Department of Mathematics KU Leuven Celestijnenlaan 200B bus 2400 B-3001 Leuven Belgium Main Astronomical Observatory of NAS Akademika Zabolotnoho 27 03680 Kyiv Ukraine High Performance Computing and Visualization (HPCViz) KTH Royal Institute of Technology SE-100 44 Stockholm Sweden

We perform three-dimensional particle-in-cell simulations of magnetic reconnection with multiple magnetic null points. Magnetic field energy conversion into kinetic energy is about five times higher than in traditional Harris sheet configuration. More than 85% of initial magnetic field energy is transferred to particle energy during 25 reversed ion cyclofrequencies. Magnetic reconnection in the cluster of null points evolves in three phases. During the first phase, ion beams are excited, then give part of their energy back to the magnetic field in the second phase. In the third phase, magnetic reconnection occurs in many small patches around the current channels formed along the stripes of a low magnetic field. Magnetic reconnection in null points essentially presents three-dimensional features, with no two-dimensional symmetries or current sheets.

关键词： ION beams KINETIC energy MAGNETIC reconnection MAGNETIC field effects SYMMETRIES (Quantum mechanics)

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High Performance Solvers for Implicit Particle in Cell Simulation

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Procedia Computer Science 2013年 18卷 2251-2258页

作者： Pawan Kumar Stefano Markidis Giovanni Lapenta Karl Meerbergen Dirk Roose Department of Computer Science Celestijnenlaan 200A 3001 Heverlee Belgium Flanders Exascience Lab (Intel Labs Europe) Heverlee Belgium High Performance Computing and Visualization (HPCViz) Department KTH Royal Institute of Technology Stockholm Sweden Center for Plasma Astrophysics Department of Mathematics Celestijnenlaan 200B Heverlee Belgium

A three-dimensional implicit particle-in-cell (iPIC3D) method implemented by S. Markidis et. al. in [“Multiscale simulations of plasma with iPIC3D”, Mathematics and Computers in Simulation, 80(2010), 1509-1519] allows time steps at magnetohy- drodynamics time scale. The code requires the solution of two linear systems: a Poisson system related to divergence cleaning, and a system related to a second order formulation of Maxwell equation. In iPIC3D, the former is the most costly. To reduce the cost of solving the Poisson system, a parallel matrix assembly and partitioning method are implemented, and conjugate gradient and algebraic multigrid (AMG) solvers from the Hypre library are called. The scalability of AMG as a solver is studied for 1D and 3D partitionings and compared to that of CG.

关键词： Implicit PIC Algebraic multigrid Krylov solvers Distributed memory

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Topology exploration with hierarchical landscapes

Topology exploration with hierarchical landscapes

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Workshop at SIGGRAPH Asia 2012, WASA 2012

作者： Demir, Dogan Beketayev, Kenes Weber, Gunther H. Bremer, Peer-Timo Pascucci, Valerio Hamann, Bernd Scientific Computing and Imaging Institute School of Computing University of Utah United States Computational Research Divisition Lawrence Berkeley National Laboratory United States Center for Applied Scientific Computing Lawrence Livermore National Laboratory United States Institute for Data Analysis and Visualization Computer Science Department University of California Davis CA United States

ISBN: (纸本)9781450318358

Topological landscapes have been proposed as a visual metaphor for contour trees that does not require an understanding of the theory involved in defining contour trees. The idea is to create a representative terrain with the same topological structure as a given contour tree. This representation exploits the natural human ability to interpret topography and results in an intuitive visualization of otherwise abstract information. However, topological landscapes still suffer from some of the same limitations as traditional contour tree visualization. Most notable is the fact that for complex functions landscapes can quickly become highly complex, exceeding the limits of human comprehension as well as the available computing resources. To address this challenge, we propose a new framework for the dynamic creation and visualization of hierarchical topological landscapes. Our system provides an interactive visualization of complex functions by utilizing a hierarchical decomposition of the contour tree as well as focus+context type interactions. For three dimensional data, we link the landscape display to flexible isosurface extraction in order to correlate terrain features with their corresponding three dimensional counterparts. We demonstrate the utility and versatility of our approach on a variety of both low and high dimensional data sets. © 2012 ACM.

关键词： visualization

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Isosurface extraction from hybrid unstructured grids containing pentahedral elements

Isosurface extraction from hybrid unstructured grids contain...

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International Conference on Computer Graphics Theory and Applications, GRAPP 2012 and International Conference on Information visualization Theory and Applications, IVAPP 2012

作者： Narayan, Akshay Sreevalsan-Nair, Jaya Gaither, Kelly Hamann, Bernd International Institute of Information Technology - Bangalore 26/C Electronics City Hosur Road Bangalore 560100 India Texas Advanced Computing Center University of Texas at Austin 10100 Burnet Road Austin TX 78758 United States Institute for Data Analysis and Visualization Department of Computer Science University of California Davis One Shields Avenue Davis CA 95616 United States

ISBN: (纸本)9789898565020

Grid-based computational simulations often use hybrid unstructured grids consisting of various types of elements. Most commonly used elements are tetrahedral, pentahedral (namely, square pyramids and right triangular prisms) and hexahedral elements. Extracting isosurfaces of scalar fields defined on such hybrid unstructured grids is often done using indirect methods, such as, (a) subdividing all non-tetrahedral cells into tetrahedra and computing the triangulated isosurfaces using the marching tetrahedra algorithm, or (b) triangulating intersection points of edges of cells and computing the isosurface using a standard triangulation algorithm. Using the basic ideas underlying the well-established marching cubes and marching tetrahedra algorithms, which are applied to hexahedral and tetrahedral elements, respectively, we generate look-up tables for extracting isosurfaces directly from pentahedral elements. By using appropriate look-up tables, it is possible to process nearly all types of hybrid unstructured grids used in practical applications without the need for indirect methods. We construct look-up tables for square pyramidal and triangular prismatic cells with accurate topological considerations.

关键词： Table lookup

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Abstract: Exploring Performance Data with Boxfish

Abstract: Exploring Performance Data with Boxfish

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High Performance computing, Networking, Storage and Analysis (SCC), SC Companion:

作者： Katherine E. Isaacs Aaditya G. Landge Todd Gamblin Peer-Timo Bremer Valerio Pascucci Bernd Hamann Institute for Data Analysis and Visualization Department of Computer Science University of California Davis CA USA Scientific Computing and Imaging Institute University of Utah Salt Lake UT USA Center for Applied Scientific Computing Lawrence Livermore National Laboratories Livermore CA USA

The growth in size and complexity of scaling applications and the systems on which they run pose challenges in analyzing and improving their overall performance. With metrics coming from thousands or millions of processes, visualization techniques are necessary to make sense of the increasing amount of data. To aid the process of exploration and understanding, we announce the initial release of Boxfish, an extensible tool for manipulating and visualizing data pertaining to application behavior. Combining and visually presenting data and knowledge from multiple domains, such as the application's communication patterns and the hardware's network configuration and routing policies, can yield the insight necessary to discover the underlying causes of observed behavior. Boxfish allows users to query, filter and project data across these domains to create interactive, linked visualizations.

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Dynamic Fracture Mechanisms in Nanostructured and Amorphous Silica Glasses Million-Atom Molecular Dynamics Simulations

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MRS Online Proceedings Library 2011年第1期703卷 1-6页

作者： Laurent Van Brutzel Cindy L. Rountree Rajiv K. Kalia Aiichiro Nakano Priya Vashishta Concurrent Computing Laboratory for Materials Simulations Biological Computation and Visualization Center Department of Physics and Astronomy Department of Computer Science Louisiana State University Baton Rouge Louisiana USA

Parallel molecular dynamics simulations are performed to investigate dynamic fracture in bulk and nanostructured silica glasses at room temperature and 1000 K. In bulk silica the crack front develops multiple branches and nanoscale pores open up ahead of the crack tip. Pores coalesce and then they merge with the advancing crack-front to cause cleavage fracture. The calculated fracture toughness is in good agreement with experiments. In nanostrucutred silica the crack-front meanders along intercluster boundaries, merging with nanoscale pores in these regions to cause intergranular fracture. The failure strain in nanostructured silica is significantly larger than in the bulk systems.

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Topology-based visualization of transformation pathways in complex chemical systems

Topology-based visualization of transformation pathways in c...

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13th Eurographics / IEEE Symposium on visualization, EuroVis 2011

作者： Beketayev, K. Weber, G.H. Haranczyk, M. Bremer, P.-T. Hlawitschka, M. Hamann, B. Computational Research Division Lawrence Berkeley National Laboratory United States Center for Applied Scientific Computing Lawrence Livermore National Laboratory United States Institute for Data Analysis and Visualization Department of Computer Science University of California Davis CA United States

(Figure Presented) Studying transformation in a chemical system by considering its energy as a function of coordinates of the system's components provides insight and changes our understanding of this process. Currently, a lack of effective visualization techniques for high-dimensional energy functions limits chemists to plot energy with respect to one or two coordinates at a time. In some complex systems, developing a comprehensive understanding requires new visualization techniques that show relationships between all coordinates at the same time. We propose a new visualization technique that combines concepts from topological analysis, multi-dimensional scaling, and graph layout to enable the analysis of energy functions for a wide range of molecular structures. We demonstrate our technique by studying the energy function of a dimer of formic and acetic acids and a LTA zeolite structure, in which we consider diffusion of methane. © 2011 The Author(s) Journal compilation © 2011 The Eurographics Association and Blackwell Publishing Ltd. Published by Blackwell Publishing.

关键词： Dimers

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Coupling of Length Scales: Hybrid Molecular Dynamics and Finite Element Approach for Multiscale Nanodevice Simulations

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MRS Online Proceedings Library 2011年第1期653卷 1-6页

作者： Elefterios Lidorikis Martina E. Bachlechner Rajiv K. Kalia George Z. Voyiadjis Aiichiro Nakano Priya Vashishta Concurrent Computing Laboratory for Materials Simulations and Biological Computation & Visualization Center Department of Physics & Astronomy and Department of Computer Science Louisiana State University Baton Rouge USA Advanced Computational Solid Mechanics Laboratory Department of Civil and Environmental Engineering Louisiana State University Baton Rouge USA

A hybrid molecular-dynamics/finite-element simulation scheme is applied to describe multiscale phenomena in nanodevices. The quality of both static and dynamic coupling between atomistic and continuum regions is studied. The hybrid scheme is used for the Si/Si3N4 interface problem (static coupling), and for the projectile impact on Si problem (dynamic coupling). Excellent agreement is found between hybrid and full molecular dynamics simulation results in the static case, and no wave reflections are found at the atomistic/continuum hand-shake in the dynamic case. The hybrid scheme is thus validated a powerful and cost effective method for performing multiscale simulations of nanodevices.

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A general approach to model biomedical data from 3D unorganised point clouds with Medial Scaffolds

A general approach to model biomedical data from 3D unorgani...

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2nd Eurographics Workshop on Visualcomputing in Biology and Medicine, EG VCBM 2010

作者： Leymarie, Frederic Fol Chang, Ming-Ching Imielinska, Celina Kimia, Benjamin B. Computing Dept. Goldsmiths College University of London United Kingdom Visualization and Computer Vision Lab. General Electric Global Research Center Niskayuna NY United States Department of Biomedical Informatics Columbia University United States Division of Engineering Brown University United States

ISBN: (纸本)9783905674286

We present the latest developments in modeling 3D biomedical data via the Medial Scaffold (MS), a 3D acyclic oriented graph representation of the Medial Axis (MA) [LK07, SP08]. TheMS (and associated 3DMA) can be computed as the result of the singularities of a geometric wave propagation simulation. We consider here some of the potential applications of this shape model in the realm of biomedical imaging. We can reconstruct complex object surfaces and make explicit the coarse-scale structures, which are ready-to-use in a number of practical applications, including: morphological measurement for cortex or bone thickness, centerline extraction (curve skeleton) for tracheotomy or colonoscopy, surface partitioning for cortical or anatomical surface classification, as well as registration and matching of shapes of tumors or carpal bones. TheMS permits to automatically and efficiently map an unorganised point cloud, i.e., simple 3D coordinates of point samples, to a coherent surface set and associated approximateMA. The derivedMS is used to further recover significant medium and large scale features, such as surface ridges and main axial symmetries. The radius field of theMS provides an intuitive definition for morphological measurements, while the graph structure made explicit by theMS is useful for shape registration and matching applications. © The Eurographics Association 2010.

关键词： Wave propagation

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Fast estimation of the vascular cooling in RFA based on numerical simulation

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Open Biomedical Engineering Journal 2010年第SPEC. ISSUE 1期4卷 16-26页

作者： Kröger, T. Pätz, T. Altrogge, I. Schenk, A. Lehmann, K.S. Frericks, B.B. Ritz, J.-P. Peitgen, H.-O. Preusser, T. Fraunhofer MEVIS Institute for Medical Image Computing Bremen Germany CeVis Center of Complex Systems and Visualization University of Bremen Germany Chirurgische Klinik I Charité - Campus Benjamin Franklin Berlin Germany Jacobs University Bremen Germany

We present a novel technique to predict the outcome of an RF ablation, including the vascular cooling effect. The main idea is to separate the problem into a patient independent part, which has to be performed only once for every applicator model and generator setting, and a patient dependent part, which can be performed very fast. The patient independent part fills a look-up table of the cooling effects of blood vessels, depending on the vessel radius and the distance of the RF applicator from the vessel, using a numerical simulation of the ablation process. The patient dependent part, on the other hand, only consists of a number of table look-up processes. The paper presents this main idea, along with the required steps for its implementation. First results of the computation and the related ex-vivo evaluation are presented and discussed. The paper concludes with future extensions and improvements of the approach. © Kröger et al.

关键词： Cooling

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