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A highly parallel multilevel Newton-Krylov-Schwarz method with subspace-based coarsening and partition-based balancing for the multigroup neutron transport equations on 3D unstructured meshes

arXiv

引用

arXiv 2019年

作者： Kong, Fande Wang, Yaqi Gaston, Derek R. Permann, Cody J. Slaughter, Andrew E. Lindsay, Alexander D. Martineau, Richard C. Computational Frameworks Idaho National Laboratory Idaho FallsID83415 United States Nuclear Engineering Methods Development Idaho National Laboratory Idaho FallsID83415 United States

The multigroup neutron transport equations have been widely used to study the motion of neutrons and their interactions with the background materials. Numerical simulation of the multigroup neutron transport equations is computationally challenging because the equations is defined on a high dimensional phase space (1D in energy, 2D in angle, and 3D in spatial space), and furthermore, for realistic applications, the computational spatial domain is complex and the materials are heterogeneous. The multilevel domain decomposition methods is one of the most popular algorithms for solving the multigroup neutron transport equations, but the construction of coarse spaces is expensive and often not strongly scalable when the number of processor cores is large. A scalable algorithm has to be designed in such a way that the compute time is almost halved without any comprise on the solution accuracy when the number of processor cores is doubled. In this paper, we study a highly parallel multilevel Newton-Krylov-Schwarz method equipped with several novel components, such as subspace-based coarsening, partition-based balancing and hierarchical mesh partitioning, that enable the overall simulation strongly scalable in terms of the compute time. Compared with the traditional coarsening method, the subspace-based coarsening algorithm significantly reduces the cost of the preconditioner setup that is often unscalable. In addition, the partition-based balancing strategy enhances the parallel efficiency of the overall solver by assigning a nearly-equal amount of work to each processor core. The hierarchical mesh partitioning is able to generate a large number of subdomains and meanwhile minimizes the off-node communication. We numerically show that the proposed algorithm is scalable with more than 10,000 processor cores for a realistic application with a few billions unknowns on 3D unstructured meshes. Copyright © 2019, The Authors. All rights reserved.

关键词： Ostwald ripening

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Bump-on-tail instability across coupling and interaction-range regimes

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Physical Review Research 2019年第3期1卷 033166-033166页

作者： Joseph J. Williams Gautham Dharuman Mathieu Marciante James Hamilton Cooley Michael S. Murillo Department of Aerospace Engineering and Department of Mathematics University of Texas Austin Texas 78705 USA Department of Computational Mathematics Science and Engineering Michigan State University East Lansing Michigan 48824 USA Computational Physics and Methods Group Los Alamos National Laboratory Los Alamos New Mexico 87545 USA

The impact of collisionality and the range of the interparticle interaction on the bump-on-tail instability is examined both computationally and theoretically. Using three-dimensional, nonequilibrium molecular dynamics with a force law that varies continuously from long range (pure 1/r Coulomb limit) to short range and across coupling regimes from weakly to strongly collisional, we examine properties of the instability; unlike other computational methods, molecular dynamics includes large-angle scattering, including the extreme limit of caging, and dynamical nonlinear screening across length scales as small as the interparticle spacing. A simpler theoretical model is also developed for comparison to the molecular dynamics results; we find that the two methods agree well in the appropriate limit, revealing that molecular dynamics is an accurate tool for the exploration of plasma instabilities. Our results reveal that the bump-on-tail instability exists only for long-range interactions.

关键词： Beam-plasma instability Plasma instabilities Two-stream instability Hamiltonian systems Single-component plasmas Molecular dynamics

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EGADSlite: A lightweight geometry kernel for HPC

EGADSlite: A lightweight geometry kernel for HPC

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AIAA Aerospace Sciences Meeting, 2018

作者： Haimes, Robert Dannenhoffer, John F. Department of Aeronautics and Astronautics Aerospace Computational Design Laboratory Massachusetts Institute of Technology CambridgeMA02139 United States Mechanical and Aerospace Engineering Aerospace Computational Methods Laboratory Syracuse University SyracuseNY13244 United States

ISBN: (数字)9781624105241

ISBN: (纸本)9781624105241

As attention is focused upon the "time to solution", it becomes obvious that the entire process must be taken into account – not just the cost and efficiency of the solver. Amdahl’s Law tells us that any serial portion of the application will be the limiting factor in scalability. Therefore it does not matter how efficient a solver is if both the pre- and post-processing have not been given the same focus towards scalability. The most obvious way to insure that a scalable process exists is to view the process as an integrated whole and remove any serial portions. The work discussed in this paper makes geometry available in a parallel environment to support parallel mesh generation, solver-based grid adaptation, and the curving of linear meshes to support high(er) order spacial discretizations. © 2018, American Institute of Aeronautics and Astronautics Inc, AIAA. All rights reserved.

关键词： Scalability

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Persistent meanders and eddies lead to a quasi-steady lagrangian transport pattern in a weak western boundary current

arXiv

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arXiv 2020年

作者： Gouveia, Mainara Biazati Duran, Rodrigo Lorenzzetti, Joao Antonio Assireu, Arcilan Trevenzoli Toste, Raquel de Freitas Assad, Luiz Paulo Gherardi, Douglas Francisco Marcolino Division of Remote Sensing Brazilian National Institute for Space Research São José dos Campos12227-010 Brazil National Energy Technology Laboratory AlbanyOR97321 United States Theiss Research San diegoCA92037 United States Institute of Natural Resources Federal University of Itajubá Itajubá37500-015 Brazil Laboratory for Computational Methods in Engineering COPPE/UFRJ Rio de Janeiro21941-907 Brazil

The Brazil Current (BC) is a weak western boundary current flowing along the Southwestern Atlantic Ocean. It is frequently described as a flow with intense mesoscale activity and relatively low volume transport between 5.0 to 10.0 Sv. We use a 13-year eddy-resolving primitive-equation simulation to show that the presence of persistent meanders and eddies leads to characteristic quasi-steady Lagrangian transport patterns, aptly extracted through climatological Lagrangian Coherent Structures (cLCSs). The cLCSs position the surface expression of the BC core along the 2000 m isobath, in excellent agreement with high resolution satellite sea-surface temperature and the model Eulerian mean velocity. The cLCSs deformation pattern also responds to zonally persistent cross-shelf SSH transition from positive (high) values near coastline to low (negative) values between 200 and 2000 m and back to positive (high) offshore from the 2000 m isobath. Zonally-paired cyclonic and anticyclonic structures are embedded in this transition, also causing the cLCSs to deform into chevrons. An efficient transport barrier is identified close to the 200 m isobath confirmed by limited inshore movement of drogued buoys and accurately indicated by an along slope maxima of climatological strength of attraction. We also show that the persistent cyclonic and anticyclonic structures may induce localized cross-shelf transport. Regions of low climatological strength of attraction coincide with large shelves and with stagnant synthetic trajectories. We also show that cLCSs accurately depict trajectories initiated at the location of Chevron’s spill (November 2011) as compared to synthetic and satellite trajectories, and the outline of the oil from that accident. There is also an agreement between the large-scale oil slicks reaching the Brazilian beaches (from August 2019 to February 2020) and the strength of climatological attraction at the coast. The identification and quantitative description of climat

关键词： Trajectories

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A scalable multilevel domain decomposition preconditioner with a subspace-based coarsening algorithm for the neutron transport calculations

arXiv

引用

arXiv 2019年

作者： Kong, Fande Wang, Yaqi Gaston, Derek R. Lindsay, Alexander D. Permann, Cody J. Martineau, Richard C. Computational Frameworks Idaho National Laboratory P.O. Box 1625 Idaho FallsID83415-3840 United States Nuclear Engineering Methods Development Idaho National Laboratory P.O. Box 1625 Idaho FallsID83415 United States

The multigroup neutron transport equations has been widely used to study the interactions of neutrons with their background materials in nuclear reactors. High-resolution simulations of the multigroup neutron transport equations using modern supercomputers require the development of scalable parallel solving techniques. In this paper, we study a scalable transport method for solving the algebraic system arising from the discretization of the multigroup neutron transport equations. The proposed transport method consists of a fully coupled Newton solver for the generalized eigenvalue problems and GMRES together with a novel multilevel domain decomposition preconditioner for the Jacobian system. The multilevel preconditioner has been successfully used for many problems, but the construction of coarse spaces for certain problems, especially for unstructured mesh problems, is expensive and often *** introduce a new subspace-based coarsening algorithm to address this issue by exploring the structure of the matrix in the discretized version of the neutron transport *** numerically demonstrate that the proposed transport method is highly scalable with more than 10,000 processor cores for the 3D C5G7 benchmark problem on unstructured meshes with billions of unknowns. Compared with the traditional multilevel domain decomposition method, the new approach equipped with the subspace-based coarsening algorithm is much faster on the construction of coarse spaces. Copyright © 2019, The Authors. All rights reserved.

关键词： Finite element method

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Ion friction at small values of the Coulomb logarithm

arXiv

引用

arXiv 2019年

作者： Sprenkle, Tucker Dodson, Adam McKnight, Quinton Spencer, Ross Bergeson, Scott Diaw, Abdourahmane Murillo, Michael S. Department of Physics and Astronomy Brigham Young University ProvoUT84602 United States Computational Physics and Methods Group Los Alamos National Laboratory Los AlamosNM87544 United States Department of Computational Mathematics Science and Engineering Michigan State University East LansingMI48824 United States

Transport properties of high-energy-density plasmas are influenced by the ion collision rate. Traditionally, this rate involves the Coulomb logarithm, ln Λ. Typical values of lnΛ are ≈ 10 to 20 in kinetic theories where transport properties are dominated by weak-scattering events caused by long-range forces. The validity of these theories breaks down for strongly-coupled plasmas, when lnΛ is of order one. We present measurements and simulations of collision data in strongly-coupled plasmas when lnΛ is small. Experiments are carried out in the first dual-species ultracold neutral plasma (UNP), using Ca+and Yb+ions. We find strong collisional coupling between the different ion species in the bulk of the plasma. We simulate the plasma using a two-species fluid code that includes Coulomb logarithms derived from either a screened Coulomb potential or a the potential of mean force. We find generally good agreement between the experimental measurements and the simulations. With some improvements, the mixed Ca+and Yb+dual-species UNP will be a promising platform for testing theoretical expressions for ln Λ and collision cross-sections from kinetic theories through measurements of energy relaxation, stopping power, two-stream instabilities, and the evolution of sculpted distribution functions in an idealized environment in which the initial temperatures, densities, and charge states are accurately known. Copyright © 2019, The Authors. All rights reserved.

关键词： Ions

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Asymptotic Dynamics of High Dynamic Range Stratified Turbulence

引用

Physical Review Letters 2019年第19期122卷 194504-194504页

作者： G. D. Portwood S. M. de Bruyn Kops C. P. Caulfield Department of Mechanical and Industrial Engineering University of Massachusetts Amherst Massachusetts 01003 USA Continuum Models and Numerical Methods (XCP-4) X-Computational Physics Division Los Alamos National Laboratory Los Alamos New Mexico 87545 USA BP Institute University of Cambridge Cambridge CB3 0EZ United Kingdom Department of Applied Mathematics and Theoretical Physics University of Cambridge Cambridge CB3 0WA United Kingdom

Direct numerical simulations of homogeneous sheared and stably stratified turbulence are considered to probe the asymptotic high dynamic range regime suggested by Gargett et al. J. Fluid Mech. 144, 231 (1984) and Shih et al. J. Fluid Mech. 525, 193 (1999). We consider statistically stationary configurations of the flow that span three decades in dynamic range defined by the separation between the Ozmidov length scale LO=ε/N3 and the Kolmogorov length scale LK=(ν3/ε)1/4, up to Reb≡(LO/LK)4/3=ε/(νN2)∼O(1000), where ε is the mean turbulent kinetic energy dissipation rate, ν is the kinematic viscosity, and N is the buoyancy frequency. We isolate the effects of Reb, particularly on irreversible mixing, from the effects of other flow parameters of stratified and sheared turbulence. Specifically, we evaluate the influence of dynamic range independent of initial conditions. We present evidence that the flow approaches an asymptotic state for Reb⪆300, characterized both by an asymptotic partitioning between the potential and kinetic energies and by the approach of components of the dissipation rate to their expected values under the assumption of isotropy. As Reb increases above 100, there is a slight decrease in the turbulent flux coefficient Γ=χ/ε, where χ is the dissipation rate of buoyancy variance, but, for this flow, there is no evidence of the commonly suggested Γ∝Reb−1/2 dependence when 100≤Reb≤1000.

关键词： Shear flows Stratified geophysical flows Turbulence

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The creation of a static BRep model given a cloud of points 55

The creation of a static BRep model given a cloud of points

引用

55th AIAA Aerospace Sciences Meeting

作者： Dannenhoffer, John F. Mechanical and Aerospace Engineering Aerospace Computational Methods Laboratory Syracuse University SyracuseNY13244 United States

ISBN: (数字)9781624104473

ISBN: (纸本)9781624104473

Modern high-fidelity aerospace analysis and design tools require watertight, analytically- smooth representations of the configuration under consideration. Most recently created geometric models have appropriate representations;unfortunately, legacy configurations often do not have a geometric representation commensurate with the analysis task at- hand. Either the analytic data has been lost and the remaining configuration is in a discrete setting, or the legacy analytic information is not smooth or is not closed at the required precision. In order to utilize high-fidelity analyses on these legacy configurations, it is necessary to have a tool through which a user can easily create the required smooth watertight geometric model. Described here is a new interactive system, named SLUGS (Static Legacy Unstructured Geometry System), which starts with a cloud of points (which may be fully- or partially- connected through a surface tessellation) and which “fits”: the cloud to a watertight set of B-spline surface patches driven by the user. The process for this conversion, as well as the key technologies that are used, are described in this paper. © 2017 by John F. Dannenhoffer, III.

关键词： Fuselages Dijkstra's Algorithm Newton's Method Wing Body Configuration Computer Aided Design Software Tool

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Density effects on the flow structure in multi-fluid shock-turbulence interaction

Density effects on the flow structure in multi-fluid shock-t...

引用

AIAA Aerospace Sciences Meeting, 2018

作者： Tian, Yifeng Jaberi, Farhad A. Livescu, Daniel Department of Mechanical Engineering Michigan State University 428 S. Shaw Lane Room 4110 East LansingMI48910 United States CCS-2 Computational Physics and Methods Los Alamos National Laboratory Mail Stop D413 Los AlamosNM87545 United States

ISBN: (数字)9781624105241

ISBN: (纸本)9781624105241

Turbulence-resolving shock-capturing simulations of isotropic turbulence interaction with a normal shock wave are conducted for small (single-fluid) and large (multi-fluid) density variations. This is an extension of the canonical Shock-Turbulence Interaction (STI) problem, involving significant variable density effects. Numerical accuracy of simulations has been established using a series of grid and LIA convergence tests. Eulerian and Lagrangian analyses of numerical data reveal several important features of the post-shock turbulence structure. For example, results show that the increase in the post-shock correlation between rotation and strain is weakened in the multi-fluid case. Consistent with the previous single-fluid studies and LIA predictions, the shock wave significantly changes the topology of the turbulent velocity field, exhibiting a symmetrization of the joint PDF of second and third invariant of anisotropic velocity gradient tensor. In the multi-fluid case, this trend is more significant and mainly manifested in the heavy fluid regions. Such symmetrization is shown to be connected to the decreased vortex stretching rate across the shock wave. The residence times in each quadrant and their contributions to vortex stretching during post-shock return-to-isotropy process are studied vis Lagrangian/particle statistics. © 2018, American Institute of Aeronautics and Astronautics Inc, AIAA. All rights reserved.

关键词： Shock waves

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A dynamical model for the calcineurin-NFATc signaling pathway and muscle fiber shifting

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PAMM 2021年第1期20卷

作者： Yesid Villota-Narvaez Angélica Ramírez-Martínez Diego Garzón-Alvarado Oliver Röhrle Biomimetics Laboratory and Numerical Methods and Modeling Research Group (GNUM) Instituto de Biotecnología (IBUN) Universidad Nacional de Colombia Bogotá Colombia Stuttgart Centre for Simulation Sciences (SC SimTech) Pfaffenwaldring 5a 70569 Stuttgart Germany Computational modeling of natural systems Research Group (COMMONS) Mechanical Engineering Department Universidad Central Bogota Colombia Institute for Modeling and Simulation of Biomechanical Systems University of Stuttgart Pfaffenwaldring 5a 70569 Stuttgart Germany

Training exercise produces skeletal muscle adaptation: at the organ scale, as anatomical changes; and at the myofiber scale, as mitochondrial and protein type content. The protein content of a myofiber is controlled by the calcineurin-NFATc signaling pathway: exercise triggers the pathway, and its final product is the translocation of dephosphorylated NFATc to the nucleus. Once in the nucleus, NFATc controls the state of the gene program to encode the slow or the fast fiber type characteristics. In the long term, the adaptation of the fiber type characteristics produces a shift in muscle fiber type: an increase in the number of myofibers of the fast type (which means that myofibers of the slow type shift to fast type) is related to force production; and an increase in the number of myofibers of the slow type (myofibers of the fast type shift to slow type) is related to fatigue resistance. These macroscopic features, i.e. force production and fatigue resistance, are the main target of most training protocols; however, little attention is focused on the limitations imposed by the fiber distribution of muscles at the organ scale. Based on the calcineurin-NFATc signaling pathway, we represented an exercise stimulus by a cytosolic calcium signal, and simulated the dynamics of NFATc in the nucleus. In this contribution, we present a dynamical model for the calcineurin-NFATc signaling pathway to describe the time course of dephosphorilated NFATc in the nucleus. We used an experimental report of a continuous stimulation pattern for calibration, and an experimental report of a pulsed stimulation pattern for comparison; we obtained a good agreement between the simulations and the experimental measurements.

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