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arXiv 2018年

作者： Dombrowski, Thomas Jones, Shannon K. Katsikis, Georgios Bhalla, Amneet Pal Singh Griffith, Boyce E. Klotsa, Daphne Department of Physics University of North Carolina at Chapel Hill Chapel HillNC United States Department of Applied Physical Sciences University of North Carolina at Chapel Hill Chapel HillNC United States Koch Institute for Integrative Cancer Research Massachusetts Institute of Technology CambridgeMA United States Applied Numerical Algorithms Group Lawrence Berkeley National Laboratory BerkeleyCA United States Mechanical Engineering San Diego State University CA United States Departments of Mathematics Applied Physical Sciences and Biomedical Engineering University of North Carolina at Chapel Hill Chapel HillNC United States

We propose a reciprocal, self-propelled model swimmer at intermediate Reynolds numbers (Re). Our swimmer consists of two unequal spheres that oscillate in antiphase generating nonlinear steady streaming (SS) flows. We show computationally that the SS flows enable the swimmer to propel itself, and also switch direction as Re increases. We quantify the transition in the swimming direction by collapsing our data on a critical Re and show that the transition in swimming directions corresponds to the reversal of the SS flows. Based on our findings, we propose that SS can be an important physical mechanism for motility at intermediate Re. Copyright © 2018, The Authors. All rights reserved.

关键词： Reynolds number

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Ten simple rules for measuring the impact of workshops

arXiv

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arXiv 2018年

作者： Sufi, Shoaib Duckles, Beth Simera, Iveta Nurmikko-Fuller, Terhi Bellis, Louisa Miah, Wadud Wilde, Adriana Nenadic, Aleksandra Silva, Raniere de Beyer, Jennifer A. Struthers, Caroline Emsley, Iain Philippe, Olivier Balzano, Melissa Coelho, Sara Ford, Heather Jones, Catherine Higgins, Vanessa School of Computer Science University of Manchester Manchester United Kingdom Portland State University PortlandOR United States UK EQUATOR Centre Centre for Statistics in Medicine NDORMS University of Oxford Oxford United Kingdom College of Arts and Social Sciences Australian National University Canberra Australia Cancer Research UK Cambridge Centre University of Cambridge Cambridge United Kingdom Numerical Algorithms Group Oxford United Kingdom School of Computer Science University of St Andrews St Andrews United Kingdom Oxford e-Research Centre University of Oxford Oxford United Kingdom Electronics and Computer Science University of Southampton Southampton United Kingdom ELIXIR Hub Wellcome Genome Campus Cambridge United Kingdom EGI Foundation Amsterdam Netherlands School of Media and Communication University of Leeds Leeds United Kingdom Scientific Computing Department Science and Technology Facilities Council Rutherford Appleton Laboratory Didcot United Kingdom School of Social Sciences University of Manchester Manchester United Kingdom

Workshops are used to explore a specific topic, transfer knowledge, solve identified problems or create something new. In funded research projects and other research endeavours, workshops are the mechanism to gather the wider project, community or interested people together around a particular topic. However, natural questions arise: how do we measure the impact of these workshops? Do we know whether they are meeting the goals and objectives we set for them? What indicators should we use? In response to these questions, this paper will outline rules that will improve the measurement of the impact of workshops. Copyright © 2018, The Authors. All rights reserved.

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High-order Discretization of a Gyrokinetic Vlasov Model in Edge Plasma Geometry

arXiv

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arXiv 2017年

作者： Dorr, Milo R. Colella, Phillip Dorf, Mikhail A. Ghosh, Debojyoti Hittinger, Jeffrey A.F. Schwartz, Peter O. Center for Applied Scientific Computing Lawrence Livermore National Laboratory 7000 East Avenue L-561 LivermoreCA94550 United States Fusion Energy Program Lawrence Livermore National Laboratory 7000 East Avenue L-630 LivermoreCA94550 United States Applied Numerical Algorithms Group Lawrence Berkeley National Laboratory One Cyclotron Road Mail Stop 50A-1148 BerkeleyCA94720 United States

We present a high-order spatial discretization of a continuum gyrokinetic Vlasov model in axisymmetric tokamak edge plasma geometries. Such models describe the phase space advection of plasma species distribution functions in the absence of collisions. The gyrokinetic model is posed in a four-dimensional phase space, upon which a grid is imposed when discretized. To mitigate the computational cost associated with high-dimensional grids, we employ a high-order discretization to reduce the grid size needed to achieve a given level of accuracy relative to lower-order methods. Strong anisotropy induced by the magnetic field motivates the use of mapped coordinate grids aligned with magnetic flux surfaces. The natural partitioning of the edge geometry by the separatrix between the closed and open field line regions leads to the consideration of multiple mapped blocks, in what is known as a mapped multiblock (MMB) approach. We describe the specialization of a more general formalism that we have developed for the construction of high-order, finite-volume discretizations on MMB grids, yielding the accurate evaluation of the gyrokinetic Vlasov operator, the metric factors resulting from the MMB coordinate mappings, and the interaction of blocks at adjacent boundaries. Our conservative formulation of the gyrokinetic Vlasov model incorporates the fact that the phase space velocity has zero divergence, which must be preserved discretely to avoid truncation error accumulation. We describe an approach for the discrete evaluation of the gyrokinetic phase space velocity that preserves the divergence-free property to machine precision. A distinguishing feature of an edge geometry is the X point, where the poloidal field component vanishes. The inability to construct fully flux-surface aligned MMB coordinate systems that are smooth up to and through the X point requires the relaxation of alignment in the vicinity of this point. We therefore describe an approach for the generation of s

关键词： Finite volume method

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Modeling Coronal Mass Ejections with the Multi-Scale Fluid-Kinetic Simulation Suite

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Journal of Physics: Conference Series 2017年第1期837卷

作者： N. V. Pogorelov S. N. Borovikov I. A. Kryukov S. T. Wu M. S. Yalim P. C. Colella B. Van Straalen Department of Space Science University of Alabama in Huntsville Huntsville AL 35805 U.S.A. Center for Space Plasma and Aeronomic Research University of Alabama in Huntsville Huntsville AL 35805 U.S.A. Institute for Problems in Mechanics Russian Academy of Sciences Moscow Russia Applied Numerical Algorithms Group Lawrence Berkeley National Laboratory MS 50A-1148 Berkeley CA 94720 U.S.A.

The solar eruptions and interacting solar wind streams are key drivers of geomagnetic storms and various related space weather disturbances that may have hazardous effects on the space-borne and ground-based technological systems as well as on human health. Coronal mass ejections (CMEs) and their interplanetary counterparts, interplanetary CMEs (ICMEs), belong to the strongest disturbances and therefore are of great importance for the space weather predictions. In this paper we show a few examples of how adaptive mesh refinement makes it possible to resolve the complex CME structure and its evolution in time while a CME propagates from the inner boundary to Earth. Simulations are performed with the Multi-Scale Fluid-Kinetic Simulation Suite (MS-FLUKSS).

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A fourth-order boundary treatment for viscous fluxes on Cartesian grid finite-volume methods 52

A fourth-order boundary treatment for viscous fluxes on Cart...

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52nd AIAA Aerospace Sciences Meeting - AIAA Science and Technology Forum and Exposition, SciTech 2014

作者： Gao, Xinfeng Guzik, Stephen Colella, Phillip Computational Fluid Dynamics and Propulsion Laboratory Colorado State University United States Appied Numerical Algorithms Group Lawrence Berkeley National Laboratory United States

ISBN: (数字)9781624102561

ISBN: (纸本)9781624102561

This study focuses on a fourth-order boundary treatment for finite-volume schemes to solve the compressible Navier-Stokes equations on a Cartesian grid. A fourth-order finite-volume stencil is derived for the viscous stress tensor operator and the modified fourth-order stencil near the physical boundary is developed. Fourier error analysis and stability analysis are performed for the fourth-order elliptic operator. For time integration, we use the fourth-order Runge-Kutta method. The fourth-order scheme was applied to the transient Couette flow and the solution accuracy was verified.

关键词： Finite volume method

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Solving the Klein-Gordon equation using Fourier spectral methods: A benchmark test for computer performance 23

Solving the Klein-Gordon equation using Fourier spectral met...

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23rd High Performance Computing Symposium, HPC 2015, Part of the 2015 Spring Simulation Multi-Conference, SpringSim 2015

作者： Aseeri, S. Batrašev, O. Icardi, M. Leu, B. Liu, A. Li, N. Muite, B.K. Müller, E. Palen, B. Quell, M. Servat, H. Sheth, P. Speck, R. Van Moer, M. Vienne, J. KAUST Supcrcomputing Laboratory 4700 King Abdullah University of Science and Technology Thuwal23955-6900 Saudi Arabia Arvutitcaduse Instituut Tartu Ülikool Liivi 2 Tartu50409 Estonia Stochastic Numerics Group 4700 King Abdullah University of Science and Technology Thuwal23955-6900 Saudi Arabia Electrical and Computer Engineering University of Michigan Ann ArborMI48109-2122 United States Numerical Algorithms Group Wilkinson House Jordan Hill Road Oxford0X2 8DR United Kingdom Numerical Mathematics Group 4700 King Abdullah University of Science and Technology Thuwal23955-6900 Saudi Arabia Department of Mathematical Sciences University of Bath BathBA2 7 AY United Kingdom CAEN Advanced Computing University of Michigan Ann ArborMI48109-2094 United States Lnstitut für Analysis und Scientific Computing Technische Universität Wien Wiedner Haupstrasse 8-10 Wien1040 Austria Compulcr Sciences Department BSC UPC c/Jordi Girona Barcelona Calalunya08034 Spain Biomedical Engineering University of Michigan Ann ArborMI48109-2122 United States Jülich Supercomputing Centre Forschungszentrum Jülich GmbH Germany Germany National Center for Supercomputing Applications University of Illinois at Urbiina-Chanipaign UrbanaIL61801 United States Texas Advanced Computing Center University of Texas at Austin AustinTX78758-4497 United States

ISBN: (纸本)9781510810600

The cubic Klein-Gordon equation is a simple but non-trivial partial differential equation whose numerical solution has the main building blocks required for the solution of many other partial differential equations. In this study, the library 2DE-COMP&FFT is used in a Fourier spectral scheme to solve the Klein-Gordon equation and strong scaling of the code is examined on thirteen different machines for a problem size of 5123. The results are useful in assessing likely performance of other parallel fast Fourier transform based programs for solving partial differential equations. The problem is chosen to be large enough to solve on a workstation, yet also of interest to solve quickly on a supercomputer, in particular for parametric studies. Unlike the Linpack benchmark, a high ranking will not be obtained by simply building a bigger computer. © 2015 Aseeri et al.

关键词： Fast Fourier transforms

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Adding value to business applications with embedded advanced analytics

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Journal of Marketing Analytics 2013年第2期1卷 64-70页

作者： Leventhal, Barry Langdell, Stephen BarryAnalytics United Kingdom Numerical Algorithms Group United Kingdom

Advanced analytics methods, such as predictive modelling, are increasingly being deployed within business processes – helping companies to increase their revenues or reduce their costs. This article shows how advanced analytics may be embedded directly into business applications, through the use of software drawn from libraries of mathematical and statistical algorithms. We list examples of applications that may benefit from embedded algorithms and provide a case study example on the theme of propensity modelling for customer management. Finally, the article summarises the typical stages in building a business application containing embedded analytics, and the skill sets that are likely to be required. © 2013 Macmillan Publishers Ltd.

关键词： Advanced analytics algorithms library Business applications Data mining Embedded algorithms

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Solving the Klein-Gordon equation using fourier spectral methods: a benchmark test for computer performance 15

Solving the Klein-Gordon equation using fourier spectral met...

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Proceedings of the Symposium on High Performance Computing

作者： S. Aseeri O. Batrasev M. Icardi B. Leu A. Liu N. Li B. K. Muite E. Müller B. Palen M. Quell H. Servat P. Sheth R. Speck M. Van Moer J. Vienne King Abdullah University of Science and Technology Thuwal Kingdom of Saudi Arabia Arvutiteaduse instituut Tartu Estonia and Tartu Ülikool University of Michigan Ann Arbor MI Numerical Algorithms Group Oxford United Kingdom Arvutiteaduse instituut Tartu Estonia and Tartu Ülikool and King Abdullah University of Science and Technology University of Bath Bath United Kingdom Technische Universität Wien Wien Austria Barcelona Supercomputer Center Polytechnic University of Catalonia (UPC) Jülich Supercomputing Centre Germany University of Illinois at Urbana-Champaign Urbana IL University of Texas at Austin Austin Texas

ISBN: (纸本)9781510801011

The cubic Klein-Gordon equation is a simple but non-trivial partial differential equation whose numerical solution has the main building blocks required for the solution of many other partial differential equations. In this study, the library 2DECOMP&FFT is used in a Fourier spectral scheme to solve the Klein-Gordon equation and strong scaling of the code is examined on thirteen different machines for a problem size of 5123. The results are useful in assessing likely performance of other parallel fast Fourier transform based programs for solving partial differential equations. The problem is chosen to be large enough to solve on a workstation, yet also of interest to solve quickly on a supercomputer, in particular for parametric studies. Unlike the Linpack benchmark, a high ranking will not be obtained by simply building a bigger computer.

关键词： benchmarks

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Continuum kinetic model for simulating low-collisionality regimes in plasmas

Continuum kinetic model for simulating low-collisionality re...

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2013 19th IEEE Pulsed Power Conference, PPC 2013

作者： Vogman, G.V. Colella, P. Applied Science and Technology Program University of California - Berkeley Berkeley CA 94704 United States Applied Numerical Algorithms Group Lawrence Berkeley National Laboratory 1 Cyclotron Road Berkeley CA 94720 United States

ISBN: (纸本)9781467351676

Continuum kinetic models, such as Maxwell-Boltzmann, present a viable alternative to particle-in-cell (PIC) models because they can be cast in conservation form and are not susceptible to noise. By treating the associated phase space distribution function as a continuous incompressible fluid occupying a volume of position-velocity space, evolution of the distribution function is determined by solving a 6-D advection equation. In cases where collision terms are negligible, the Boltzmann model is reduced to a Vlasov model. A 4th-order accurate continuum kinetic Vlasov model has been developed in one spatial and one velocity dimension to address the challenges associated with solving a hyperbolic governing equation in multidimensional phase space. The governing equation is cast in conservation law form and solved with a finite volume representation. Adaptive mesh refinement (AMR) is used to allow for efficient use of computational resources while maintaining desired levels of resolution. Consequently, with AMR the model is able to capture the fine structures that develop in the distribution function as it evolves in time, while using low resolution in the tail of the distribution function. The model is tested on several plasma phenomena including: weak and strong Landau damping and the two-stream instability. Conservation properties of the method are investigated. © 2013 IEEE.

关键词： Distribution functions

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An adaptive mesh refinement strategy with conservative space-time coupling for the lattice-Boltzmann method 51

An adaptive mesh refinement strategy with conservative space...

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51st AIAA Aerospace Sciences Meeting including the New Horizons Forum and Aerospace Exposition 2013

作者： Guzik, S.M.J. Gao, Xinfeng Weisgraber, Todd Alder, Berni Colella, Phillip Colorado State University Department of Mechanical Engineering Fort Collins CO 80523 United States Lawrence Livermore National Laboratory Engineering Technologies Division Livermore CA 94551 United States Lawrence Berkeley National Laboratory Applied Numerical Algorithms Group Berkeley CA 94720 United States Lawrence Livermore National Laboratory Physical and Life Sciences Livermore CA 94551 United States

ISBN: (数字)9781624101816

ISBN: (纸本)9781624101816

A conservative lattice-Boltzmann method is presented for solving the time-dependent Navier-Stokes equations at low Mach numbers on lattices that are adaptively refined in space and time. A method for coupling the interfaces between grids at different resolutions was constructed following techniques established for finite-volume computational fluid dynamics methods. The effectiveness of the new coupling method, which relies on a space-time interpolation and solving constrained least-squares problems to ensure conservation is compared against similar approaches relying only on spatial interpolation.

关键词： Least squares approximations

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