45 results found
Corbett RW, Grechy L, Iori F, et al., 2018, Heterogeneity in the nonplanarity and arterial curvature of arteriovenous fistulas in vivo., J Vasc Surg
OBJECTIVE: Native arteriovenous fistulas (AVFs) for hemodialysis are susceptible to nonmaturation. Adverse features of local blood flow have been implicated in the formation of perianastomotic neointimal hyperplasia that may underpin nonmaturation. Whereas computational fluid dynamic simulations of idealized models highlight the importance of geometry on fluid and vessel wall interactions, little is known in vivo about AVF geometry and its role in adverse clinical outcomes. This study set out to examine the three-dimensional geometry of native AVFs and the geometric correlates of AVF failure. METHODS: As part of an observational study between 2013 and 2016, patients underwent creation of an upper limb AVF according to current surgical best practice. Phase-contrast magnetic resonance imaging was performed on the day of surgery to obtain luminal geometry along with ultrasound measurements of flow. Magnetic resonance imaging data sets were segmented and reconstructed for quantitative and qualitative analysis of local geometry. Clinical maturation was evaluated at 6 weeks. RESULTS: There were 60 patients who were successfully imaged on the day of surgery. Radiocephalic (n = 17), brachiocephalic (n = 40), and brachiobasilic (n = 3) fistulas were included in the study. Centerlines extracted from segmented vessel lumen exhibited significant heterogeneity in arterial nonplanarity and curvature. Furthermore, these features are more marked in brachiocephalic than in radiocephalic fistulas. Across the cohort, the projected bifurcation angle was 73 ± 16 degrees (mean ± standard deviation). Geometry was preserved at 2 weeks in 20 patients who underwent repeated imaging. A greater degree of arterial nonplanarity (log odds ratio [logOR], 0.95 per 0.1/vessel diameter; 95% confidence interval [CI], 0.22-1.90; P = .03) and a larger bifurcation angle (logOR, 0.05 per degree; 95% CI, 0.01-0.09; P = .02) are assoc
Loppi NA, Witherden FD, Jameson A, et al., 2018, A high-order cross-platform incompressible Navier–Stokes solver via artificial compressibility with application to a turbulent jet, Computer Physics Communications, Vol: 233, Pages: 193-205, ISSN: 0010-4655
© 2018 The Authors Modern hardware architectures such as GPUs and manycore processors are characterised by an abundance of compute capability relative to memory bandwidth. This makes them well-suited to solving temporally explicit and spatially compact discretisations of hyperbolic conservation laws. However, classical pressure-projection-based incompressible Navier–Stokes formulations do not fall into this category. One attractive formulation for solving incompressible problems on modern hardware is the method of artificial compressibility. When combined with explicit dual time stepping and a high-order Flux Reconstruction discretisation, the majority of operations can be cast as compute bound matrix–matrix multiplications that are well-suited for GPU acceleration and manycore processing. In this work, we develop a high-order cross-platform incompressible Navier–Stokes solver, via artificial compressibility and dual time stepping, in the PyFR framework. The solver runs on a range of computer architectures, from laptops to the largest supercomputers, via a platform-unified templating approach that can generate/compile CUDA, OpenCL and C/OpenMP code at runtime. The extensibility of the cross-platform templating framework defined within PyFR is clearly demonstrated, as is the utility of P-multigrid for convergence acceleration. The platform independence of the solver is verified on Nvidia Tesla P100 GPUs and Intel Xeon Phi 7210 KNL manycore processors with a 3D Taylor–Green vortex test case. Additionally, the solver is applied to a 3D turbulent jet test case at Re=10,000, and strong scaling is reported up to 144 GPUs. The new software constitutes the first high-order accurate cross-platform implementation of an incompressible Navier–Stokes solver via artificial compressibility and P-multigrid accelerated dual time stepping to be published in the literature. The technology has applications in a range of sectors, including the maritime
Grechy L, Iori F, Corbett RW, et al., 2017, The Effect of Arterial Curvature on Blood Flow in Arterio-Venous Fistulae: Realistic Geometries and Pulsatile Flow, CARDIOVASCULAR ENGINEERING AND TECHNOLOGY, Vol: 8, Pages: 313-329, ISSN: 1869-408X
Grechy L, Iori F, Corbett RW, et al., 2017, Suppressing unsteady flow in arterio-venous fistulae, PHYSICS OF FLUIDS, Vol: 29, ISSN: 1070-6631
Park JS, Witherden FD, Vincent PE, 2017, High-order accurate implicit Large Eddy Simulations of flow over a NACA0021 aerofoil in deep stall, AIAA Journal, ISSN: 1533-385X
In this study the GPU-accelerated solver PyFR is used to simu-late flow over a NACA0021 aerofoil in deep stall at a Reynolds numberof 270, 000 using the high-order Flux Reconstruction (FR) approach.Wall-resolved Implicit Large Eddy Simulations (ILES) are undertakenon unstructured hexahedral meshes at fourth- and fifth-order accuracyin space. It was found that either modal filtering, or anti-aliasing viaan approximate L2 projection, is required in order to stabilise simu-lations. Time-span averaged pressure coefficient distributions on theaerofoil, and associated lift and drag coefficients, are seen to converge towards experimental data as the simulation setup is made more realis-tic by increasing the aerofoil span. Indeed, the lift and drag coefficientsobtained by fifth-order ILES with anti-aliasing via an approximateL2projection agree better with experimental data than a wide range ofprevious studies. Stabilisation via modal filtering, however, is foundto reduce solution accuracy. Finally, performance of various PyFRsimulations is compared, and it is found that fifth-order simulationswith anti-aliasing via an L2 projection are the most efficient. Resultsindicate that high-order FR schemes with anti-aliasing via anL2 projection are a good candidate for underpinning accurate wall-resolved ILES of separated, turbulent flows over complex engineering geometries.
Park JS, Witherden FD, Vincent PE, 2017, High-Order Implicit Large-Eddy Simulations of Flow over a NACA0021 Aerofoil, AIAA JOURNAL, Vol: 55, Pages: 2186-2197, ISSN: 0001-1452
Vermeire BC, Vincent PE, 2017, On the behaviour of fully-discrete flux reconstruction schemes, COMPUTER METHODS IN APPLIED MECHANICS AND ENGINEERING, Vol: 315, Pages: 1053-1079, ISSN: 0045-7825
Vermeire BC, Witherden FD, Vincent PE, 2017, On the utility of GPU accelerated high-order methods for unsteady flow simulations: A comparison with industry-standard tools, JOURNAL OF COMPUTATIONAL PHYSICS, Vol: 334, Pages: 497-521, ISSN: 0021-9991
Vincent P, Grechy L, Corbett R, 2017, A device for maintaining vascular connections
There is provided a device for maintaining a vascular connection comprising a vein- supporting section and an artery-supporting section. The centreline of the vein-supporting section and the centreline of the artery-supporting section meet at an intersection point which defines the origin of a right-handed Cartesian coordinate system. The centreline of the artery-supporting section is arcuate and lies in the region y<=0 and has a tangent parallel to the x axis at the origin and wherein the artery-supporting section is configured to carry blood flow in a direction from negative x towards positive x. A tangent of the centreline of the vein-supporting section at the origin has direction [cos (Θ) sin (Φ), sin (Θ) sin (Φ), ± cos (Φ)], where Φ is in the range 225 to 270 degrees and Θ is in the range 200 to 300 degrees.
Mengaldo G, De Grazia D, Vincent PE, et al., 2016, On the Connections Between Discontinuous Galerkin and Flux Reconstruction Schemes: Extension to Curvilinear Meshes, JOURNAL OF SCIENTIFIC COMPUTING, Vol: 67, Pages: 1272-1292, ISSN: 0885-7474
Vermeire BC, Vincent PE, 2016, On the properties of energy stable flux reconstruction schemes for implicit large eddy simulation, JOURNAL OF COMPUTATIONAL PHYSICS, Vol: 327, Pages: 368-388, ISSN: 0021-9991
Vincent P, Witherden F, Vermeire B, et al., 2016, Towards Green Aviation with Python at Petascale, International Conference on High Performance Computing, Networking, Storage and Analysis (SC), Publisher: IEEE, Pages: 1-11
Witherden FD, Park JS, Vincent PE, 2016, An Analysis of Solution Point Coordinates for Flux Reconstruction Schemes on Tetrahedral Elements, JOURNAL OF SCIENTIFIC COMPUTING, Vol: 69, Pages: 905-920, ISSN: 0885-7474
Witherden FD, Vincent PE, Jameson A, 2016, High-Order Flux Reconstruction Schemes, Handbook of Numerical Analysis, Pages: 227-263
© 2016 Elsevier B.V. There is an increasing desire among industrial practitioners of computational fluid dynamics to undertake high-fidelity scale-resolving simulations of unsteady flows within the vicinity of complex geometries. Such simulations require numerical methods that can operate on unstructured meshes with low numerical dissipation. The flux reconstruction (FR) approach describes one such family of numerical methods, which includes a particular type of collocation-based nodal discontinuous Galerkin method, and spectral difference methods, as special cases. In this chapter we describe the current state-of-the-art surrounding research into FR methods. To begin, FR is described in one dimension for both advection and advection–diffusion problems. This is followed by a description of its extension to multidimensional tensor product and simplex elements. Stability and accuracy issues are then discussed, including an overview of energy-stability proofs, von Neumann analysis results, and stability characteristics when the flux function of the governing system is nonlinear. Finally, implementation aspects are outlined in the context of modern hardware platforms, and three example applications of FR are presented, demonstrating the potential utility of FR schemes for scale resolving simulation of unsteady flow problems.
Wozniak BD, Witherden FD, Russell FP, et al., 2016, GiMMiK-Generating bespoke matrix multiplication kernels for accelerators: Application to high-order Computational Fluid Dynamics, COMPUTER PHYSICS COMMUNICATIONS, Vol: 202, Pages: 12-22, ISSN: 0010-4655
Iori F, Grechy L, Corbett RW, et al., 2015, The effect of in-plane arterial curvature on blood flow and oxygen transport in arterio-venous fistulae, PHYSICS OF FLUIDS, Vol: 27, ISSN: 1070-6631
Kahk JM, Villar-Garcia IJ, Grechy L, et al., 2015, A study of the pressure profiles near the first pumping aperture in a high pressure photoelectron spectrometer, JOURNAL OF ELECTRON SPECTROSCOPY AND RELATED PHENOMENA, Vol: 205, Pages: 57-65, ISSN: 0368-2048
Leow CH, Iori F, Corbett R, et al., 2015, MICROBUBBLE VOID IMAGING: A NON-INVASIVE TECHNIQUE FOR FLOW VISUALISATION AND QUANTIFICATION OF MIXING IN LARGE VESSELS USING PLANE WAVE ULTRASOUND AND CONTROLLED MICROBUBBLE CONTRAST AGENT DESTRUCTION, ULTRASOUND IN MEDICINE AND BIOLOGY, Vol: 41, Pages: 2926-2937, ISSN: 0301-5629
Mengaldo G, De Grazia D, Moxey D, et al., 2015, Dealiasing techniques for high-order spectral element methods on regular and irregular grids, JOURNAL OF COMPUTATIONAL PHYSICS, Vol: 299, Pages: 56-81, ISSN: 0021-9991
Vincent PE, Farrington AM, Witherden FD, et al., 2015, An extended range of stable-symmetric-conservative Flux Reconstruction correction functions, COMPUTER METHODS IN APPLIED MECHANICS AND ENGINEERING, Vol: 296, Pages: 248-272, ISSN: 0045-7825
Vincent PE, Witherden FD, Farrington AM, et al., 2015, PyFR: Next-generation high-order computational fluid dynamics on many-core hardware
© 2015, American Institute of Aeronautics and Astronautics Inc, AIAA. All rights reserved. High-order numerical methods for unstructured grids combine the superior accuracy of high-order spectral or finite difference methods with the geometric flexibility of low-order finite volume or finite element schemes. The Flux Reconstruction (FR) approach unifles various high-order schemes for unstructured grids within a single framework. Additionally, the FR approach exhibits a signiflcant degree of element locality, and is thus able to run efflciently on modern many-core hardware platforms, such as Graphical Processing Units (GPUs). The aforementioned properties of FR mean it offers a promising route to per-forming affordable, and hence industrially relevant, scale-resolving simulations of hitherto intractable unsteady flows within the vicinity of real-world engineering geometries. Here we present PyFR, an open-source Python based framework for solving advection-diffusion type problems using the FR approach. The framework is designed to solve a range of governing systems on mixed unstructured grids containing various element types. It is also designed to target a range of hardware platforms via use of a custom Mako-derived domain specific language. Specifically, the current release of PyFR is able to solve the compressible Euler and Navier-Stokes equations on grids of quadrilateral and triangular elements in two dimensions, and hexahedral, tetrahedral, prismatic, and pyramidal elements in three dimensions, targeting clusters of multi-core CPUs, NVIDIA GPUs (K20, K40 etc.), AMD GPUs (S10000, W9100 etc.), and heterogeneous mixtures thereof. Results will be presented for various benchmark and real-world' flow problems. PyFR is freely available under an open-source 3-Clause New-Style BSD license (www.pyfr.org).
Witherden FD, Vermeire BC, Vincent PE, 2015, Heterogeneous computing on mixed unstructured grids with PyFR, COMPUTERS & FLUIDS, Vol: 120, Pages: 173-186, ISSN: 0045-7930
Witherden FD, Vincent PE, 2015, On the identification of symmetric quadrature rules for finite element methods, COMPUTERS & MATHEMATICS WITH APPLICATIONS, Vol: 69, Pages: 1232-1241, ISSN: 0898-1221
De Grazia D, Mengaldo G, Moxey D, et al., 2014, Connections between the discontinuous Galerkin method and high-order flux reconstruction schemes, INTERNATIONAL JOURNAL FOR NUMERICAL METHODS IN FLUIDS, Vol: 75, Pages: 860-877, ISSN: 0271-2091
Huynh HT, Wang ZJ, Vincent PE, 2014, High-order methods for computational fluid dynamics: A brief review of compact differential formulations on unstructured grids, COMPUTERS & FLUIDS, Vol: 98, Pages: 209-220, ISSN: 0045-7930
Mengaldo G, De Grazia D, Peiro J, et al., 2014, A guide to the implementation of boundary conditions in compact high-order methods for compressible aerodynamics
The nature of boundary conditions, and how they are implemented, can have a significant impact on the stability and accuracy of a Computational Fluid Dynamics (CFD) solver. The objective of this paper is to assess how different boundary conditions impact the performance of compact discontinuous high-order spectral element methods (such as the discontinuous Galerkin method and the Flux Reconstruction approach), when these schemes are used to solve the Euler and compressible Navier-Stokes equations on unstructured grids. Specifically, the paper will investigate inflow/outflow and wall boundary conditions. In all studies the boundary conditions were enforced by modifying the boundary flux. For Riemann invariant (characteristic), slip and no-slip conditions we have considered a direct and an indirect enforcement of the boundary conditions, the first obtained by calculating the flux using the known solution at the given boundary while the second achieved by using a ghost state and by solving a Riemann problem. All computations were performed using the open-source software Nektar++ (www.nektar.info).
Vincent PE, Weinberg PD, 2014, Flow-dependent concentration polarization and the endothelial glycocalyx layer: multi-scale aspects of arterial mass transport and their implications for atherosclerosis, BIOMECHANICS AND MODELING IN MECHANOBIOLOGY, Vol: 13, Pages: 313-326, ISSN: 1617-7959
Witherden FD, Farrington AM, Vincent PE, 2014, PyFR: An open source framework for solving advection-diffusion type problems on streaming architectures using the flux reconstruction approach, COMPUTER PHYSICS COMMUNICATIONS, Vol: 185, Pages: 3028-3040, ISSN: 0010-4655
Witherden FD, Vincent PE, 2014, An Analysis of Solution Point Coordinates for Flux Reconstruction Schemes on Triangular Elements, JOURNAL OF SCIENTIFIC COMPUTING, Vol: 61, Pages: 398-423, ISSN: 0885-7474
Castonguay P, Williams DM, Vincent PE, et al., 2013, Energy stable flux reconstruction schemes for advection-diffusion problems, COMPUTER METHODS IN APPLIED MECHANICS AND ENGINEERING, Vol: 267, Pages: 400-417, ISSN: 0045-7825
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