Publications
401 results found
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
High-order methods are becoming increasingly attractive in both academia and industry, especially in the context of computational fluid dynamics. However, before they can be more widely adopted, issues such as lack of robustness in terms of numerical stability need to be addressed, particularly when treating industrial-type problems where challenging geometries and a wide range of physical scales, typically due to high Reynolds numbers, need to be taken into account. One source of instability is aliasing effects which arise from the nonlinearity of the underlying problem. In this work we detail two dealiasing strategies based on the concept of consistent integration. The first uses a localised approach, which is useful when the nonlinearities only arise in parts of the problem. The second is based on the more traditional approach of using a higher quadrature. The main goal of both dealiasing techniques is to improve the robustness of high order spectral element methods, thereby reducing aliasing-driven instabilities. We demonstrate how these two strategies can be effectively applied to both continuous and discontinuous discretisations, where, in the latter, both volumetric and interface approximations must be considered. We show the key features of each dealiasing technique applied to the scalar conservation law with numerical examples and we highlight the main differences in terms of implementation between continuous and discontinuous spatial discretisations.
Moxey D, Ekelschot D, Keskin U, et al., 2015, High-order curvilinear meshing using a thermo-elastic analogy, Computer Aided Design, Vol: 72, Pages: 130-139, ISSN: 0010-4485
With high-order methods becoming increasingly popular in both academia and industry, generating curvilinear meshes that align with the boundaries of complex geometries continues to present a significant challenge. Whereas traditional low-order methods use planar-faced elements, high-order methods introduce curvature into elements that may, if added naively, cause the element to self-intersect. Over the last few years, several curvilinear mesh generation techniques have been designed to tackle this issue, utilising mesh deformation to move the interior nodes of the mesh in order to accommodate curvature at the boundary. Many of these are based on elastic models, where the mesh is treated as a solid body and deformed according to a linear or non-linear stress tensor. However, such methods typically have no explicit control over the validity of the elements in the resulting mesh. In this article, we present an extension of this elastic formulation, whereby a thermal stress term is introduced to 'heat' or 'cool' elements as they deform. We outline a proof-of-concept implementation and show that the adoption of a thermo-elastic analogy leads to an additional degree of robustness, by considering examples in both two and three dimensions.
Cantwell CD, Roney CH, Ng FS, et al., 2015, Techniques for automated local activation time annotation and conduction velocity estimation in cardiac mapping, Computers in Biology and Medicine, Vol: 65, Pages: 229-242, ISSN: 0010-4825
Measurements of cardiac conduction velocity provide valuable functional and structural insight into the initiation and perpetuation of cardiac arrhythmias, in both a clinical and laboratory context. The interpretation of activation wavefronts and their propagation can identify mechanistic properties of a broad range of electrophysiological pathologies. However, the sparsity, distribution and uncertainty of recorded data make accurate conduction velocity calculation difficult. A wide range of mathematical approaches have been proposed for addressing this challenge, often targeted towards specific data modalities, species or recording environments. Many of these algorithms require identification of activation times from electrogram recordings which themselves may have complex morphology or low signal-to-noise ratio. This paper surveys algorithms designed for identifying local activation times and computing conduction direction and speed. Their suitability for use in different recording contexts and applications is assessed.
Moura RC, Sherwin SJ, Peiro J, 2015, Linear dispersion-diffusion analysis and its application to under-resolved turbulence simulations using discontinuous Galerkin spectral/hp methods, Journal of Computational Physics, Vol: 298, Pages: 695-710, ISSN: 0021-9991
We investigate the potential of linear dispersion–diffusion analysis in providing direct guidelines for turbulence simulations through the under-resolved DNS (sometimes called implicit LES) approach via spectral/hp methods. The discontinuous Galerkin (DG) formulation is assessed in particular as a representative of these methods. We revisit the eigensolutions technique as applied to linear advection and suggest a new perspective to the role of multiple numerical modes, peculiar to spectral/hp methods. From this new perspective, “secondary” eigenmodes are seen to replicate the propagation behaviour of a “primary” mode, so that DG's propagation characteristics can be obtained directly from the dispersion–diffusion curves of the primary mode. Numerical dissipation is then appraised from these primary eigencurves and its effect over poorly-resolved scales is quantified. Within this scenario, a simple criterion is proposed to estimate DG's effective resolution in terms of the largest wavenumber it can accurately resolve in a given hp approximation space, also allowing us to present points per wavelength estimates typically used in spectral and finite difference methods. Although strictly valid for linear advection, the devised criterion is tested against (1D) Burgers turbulence and found to predict with good accuracy the beginning of the dissipation range on the energy spectra of under-resolved simulations. The analysis of these test cases through the proposed methodology clarifies why and how the DG formulation can be used for under-resolved turbulence simulations without explicit subgrid-scale modelling. In particular, when dealing with communication limited hardware which forces one to consider the performance for a fixed number of degrees of freedom, the use of higher polynomial orders along with moderately coarser meshes is shown to be the best way to translate available degrees of freedom into resolution power.
Jordi BE, Cotter CJ, Sherwin SJ, 2015, An adaptive selective frequency damping method, Physics of Fluids, Vol: 27, ISSN: 1089-7666
The selective frequency damping (SFD) method is an alternative to classical Newton’smethod to obtain unstable steady-state solutions of dynamical systems. However, thismethod has two main limitations: it does not converge for arbitrary control parameters,and when it does converge, the time necessary to reach a steady-state solution may bevery long. In this paper, we present an adaptive algorithm to address these two issues.We show that by evaluating the dominant eigenvalue of a “partially converged” steadyflow, we can select a control coefficient and a filter width that ensure an optimumconvergence of the SFD method. We apply this adaptive method to several classicaltest cases of computational fluid dynamics and we show that a steady-state solution canbe obtained with a very limited (or without any) a priori knowledge of the flow stabilityproperties
Cantwell C, Sherwin SJ, Moxey D, 2015, Nektar++
Nektar++ is a tensor product based finite element package designed to allow one to construct efficient classical low polynomial order h-type solvers (where h is the size of the finite element) as well as higher p-order piecewise polynomial order solvers.
Tzortzis KN, Roney CH, Qureshi NA, et al., 2015, Influence of left atrial geometry on rotor core trajectories in a model of atrial fibrillation, Computing in Cardiology, Publisher: IEEE, Pages: 481-484, ISSN: 2325-8861
Left atrial anatomy and myocardial architecture areknown to influence rotor initiation and maintenance.However, identifying their relative contribution clinicallyis challenging. The present study aims to investigate insilico the effect of left atrial geometry in isolation onrotor generation and evolution through thespatiotemporal tracking of phase singularities. Aftermeandering for a short period of time, rotors areattracted to specific areas of the chamber where there ishigh curvature, primarily near the base of the left atrialappendage and the junctions of the pulmonary veins. Thissuggests that the left atrial anatomy could play a key rolein the perpetuation of fibrillatory activity.
Ali RL, Cantwell CD, Qureshi NA, et al., 2015, Automated fiducial point selection for reducing registration error in the co-localisation of left atrium electroanatomic and imaging data., 2015 37th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC), Publisher: IEEE, Pages: 1989-1992, ISSN: 1557-170X
Registration of electroanatomic surfaces and segmented images for the co-localisation of structural and functional data typically requires the manual selection of fiducial points, which are used to initialise automated surface registration. The identification of equivalent points on geometric features by the human eye is heavily subjective, and error in their selection may lead to distortion of the transformed surface and subsequently limit the accuracy of data co-localisation. We propose that the manual trimming of the pulmonary veins through the region of greatest geometrical curvature, coupled with an automated angle-based fiducial-point selection algorithm, significantly reduces target registration error compared with direct manual selection of fiducial points.
Cantwell C, sherwin SJ, moxey DM, 2015, Nektar++
Nektar++ is a tensor product based finite element package designed to allow one to construct efficient classical low polynomial order h-type solvers (where h is the size of the finite element) as well as higher p-order piecewise polynomial order solvers.
Yakovlev S, Moxey D, Kirby RM, et al., 2015, To CG or to HDG: A Comparative Study in 3D, Journal of Scientific Computing, Vol: 67, Pages: 192-220, ISSN: 0885-7474
Since the inception of discontinuous Galerkin (DG) methods for elliptic problems, there has existed a question of whether DG methods can be made more computationally efficient than continuous Galerkin (CG) methods. Fewer degrees of freedom, approximation properties for elliptic problems together with the number of optimization techniques, such as static condensation, available within CG framework made it challenging for DG methods to be competitive until recently. However, with the introduction of a static-condensation-amenable DG method—the hybridizable discontinuous Galerkin (HDG) method—it has become possible to perform a realistic comparison of CG and HDG methods when applied to elliptic problems. In this work, we extend upon an earlier 2D comparative study, providing numerical results and discussion of the CG and HDG method performance in three dimensions. The comparison categories covered include steady-state elliptic and time-dependent parabolic problems, various element types and serial and parallel performance. The postprocessing technique, which allows for superconvergence in the HDG case, is also discussed. Depending on the direct linear system solver used and the type of the problem (steady-state vs. time-dependent) in question the HDG method either outperforms or demonstrates a comparable performance when compared with the CG method. The HDG method however falls behind performance-wise when the iterative solver is used, which indicates the need for an effective preconditioning strategy for the method.
Rocco G, Zaki TA, Mao X, et al., 2015, Floquet and transient growth stability analysis of a flow through a compressor passage, AEROSPACE SCIENCE AND TECHNOLOGY, Vol: 44, Pages: 116-124, ISSN: 1270-9638
Cantwell CD, Moxey D, Comerford A, et al., 2015, Nektar++: an open-source spectral/hp element framework, Computer Physics Communications, Vol: 192, Pages: 205-219, ISSN: 0010-4655
Nektar++ is an open-source software framework designed to support the development of high-performance scalable solvers for partial differential equations using the spectral/hphp element method. High-order methods are gaining prominence in several engineering and biomedical applications due to their improved accuracy over low-order techniques at reduced computational cost for a given number of degrees of freedom. However, their proliferation is often limited by their complexity, which makes these methods challenging to implement and use. Nektar++ is an initiative to overcome this limitation by encapsulating the mathematical complexities of the underlying method within an efficient C++ framework, making the techniques more accessible to the broader scientific and industrial communities. The software supports a variety of discretisation techniques and implementation strategies, supporting methods research as well as application-focused computation, and the multi-layered structure of the framework allows the user to embrace as much or as little of the complexity as they need. The libraries capture the mathematical constructs of spectral/hphp element methods, while the associated collection of pre-written PDE solvers provides out-of-the-box application-level functionality and a template for users who wish to develop solutions for addressing questions in their own scientific domains.
Mao X, Blackburn HM, Sherwin SJ, 2015, Nonlinear optimal suppression of vortex shedding from a circular cylinder, Journal of Fluid Mechanics, Vol: 775, Pages: 241-265, ISSN: 1469-7645
This study is focused on two- and three-dimensional incompressible flow pasta circular cylinder for Reynolds number Re 6 1000. To gain insight into themechanisms underlying the suppression of unsteadiness for this flow we determinethe nonlinear optimal open-loop control driven by surface-normal wall transpiration.The spanwise-constant wall transpiration is allowed to oscillate in time, althoughsteady forcing is determined to be most effective. At low levels of control cost,defined as the square integration of the control, the sensitivity of unsteadiness withrespect to wall transpiration is a good approximation of the optimal control. Thedistribution of this sensitivity suggests that the optimal control at small magnitude isachieved by applying suction upstream of the upper and lower separation points andblowing at the trailing edge. At high levels of wall transpiration, the assumptionsunderlying the linearized sensitivity calculation become invalid since the base flowis eventually altered by the size of the control forcing. The large-magnitude optimalcontrol is observed to spread downstream of the separation point and draw the shearlayer separation towards the rear of the cylinder through suction, while blowingalong the centreline eliminates the recirculation bubble in the wake. We furtherdemonstrate that it is possible to completely suppress vortex shedding in two- andthree-dimensional flow past a circular cylinder up to Re = 1000, accompanied by70 % drag reduction when a nonlinear optimal control of moderate magnitude (withroot-mean-square value 8 % of the free-stream velocity) is applied. This is confirmedthrough linearized stability analysis about the steady-state solution when the nonlinearoptimal wall transpiration is applied. While continuously distributed wall transpirationis not physically realizable, the study highlights localized regions where discretecontrol strategies could be further developed. It also highlights the appropriate rangeof application of
Mengaldo G, Kravtsova M, Ruban A, et al., 2015, Triple-deck and direct numerical simulation analyses high-speed subsonic flows past a roughness element, Journal of Fluid Mechanics, Vol: 774, Pages: 311-323, ISSN: 1469-7645
This paper is concerned with the boundary-layer separation in subsonic and transonic flows caused by a two-dimensional isolated wall roughness. The process of the separation is analysed by means of two approaches: the direct numerical simulation (DNS) of the flow using the Navier–Stokes equations, and the numerical solution of the triple-deck equations. Since the triple-deck theory relies on the assumption that the Reynolds number ( ) is large, we performed the Navier–Stokes calculations at Re = 4 x 10^5 based on the distance of the roughness element from the leading edge of the flat plate. This Re is also relevant for aeronautical applications. Two sets of calculation were conducted with the free-stream Mach number Ma_∞ = 0.5 and Ma_∞ = 0.87 . We used different roughness element heights, some of which were large enough to cause a well-developed separation region behind the roughness. We found that the two approaches generally compare well with one another in terms of wall shear stress, longitudinal pressure gradient and detachment/reattachment points of the separation bubbles (when present). The main differences were found in proximity to the centre of the roughness element, where the wall shear stress and longitudinal pressure gradient predicted by the triple-deck theory are noticeably different from those predicted by DNS. In addition, DNS predicts slightly longer separation regions.
Chooi KY, Comerford A, Sherwin S, et al., 2015, SMOOTH MUSCLE TONE-DEPENDENT HYDRAULIC CONDUCTANCE OF AORTIC MEDIA TO WATER FILTRATION, British-Cardiac-Society (BCS) Annual Conference on Hearts and Genes, Publisher: BMJ PUBLISHING GROUP, Pages: A106-A107, ISSN: 1355-6037
Peiro J, Moxey D, Hazan M, et al., 2015, On the generation of curvilinear meshes through subdivision of isoparametric elements, New Challenges in Grid Generation and Adaptivity for Scientific Computing, Editors: Perotto, Formaggia, Publisher: Springer, ISBN: 9783319060538
This volume collects selected contributions from the “Fourth Tetrahedron Workshop on Grid Generation for Numerical Computations”, which was held in Verbania, Italy in July 2013.
Xu H, lombard J, sherwin S, 2015, Delaying natural transition of a boundary layer using smooth steps, Sixth International Symposium on Bifurcations and Instabilities in Fluid Dynamics
Xu H, Sherwin SJ, 2015, On a mechanism of delaying laminar-turbulent transition
© TU Delft. In this paper we investigate the boundary layer flows over a flat plate on which smooth localized imperfections are located. The localized imperfections have the width scale (d) comparable with the wavelength (λTS) of the Tollmien-Schlichting (T-S) waves and the height scale (h) less than the boundary layer thickness δ99. The existence of the localized imperfection gives rise to the change of the instability property of the boundary layer. The investigations are focused on the interaction between the T-S waves and the base flows distorted by smooth forward-facing steps and aim to forge links between the localized imperfections and the mechanisms of stabilizing the T-S waves. Numerical investigations show that isolated smooth forward-facing steps can perform as a robust strategy of delaying laminar-turbulent transition. Finally, direct numerical simulations are implemented to validate the strategy.
Mohamied Y, Rowland EM, Bailey EL, et al., 2015, Change of direction in the biomechanics of atherosclerosis, Annals of Biomedical Engineering, Vol: 43, Pages: 16-25, ISSN: 0090-6964
The non-uniform distribution of atherosclerosis within the arterial system has been attributed to pro-atherogenic influences of low, oscillatory haemodynamic wall shear stress (WSS) on endothelial cells (EC). This theory is challenged by the changes in lesion location that occur with age in human and rabbit aortas. Furthermore, a number of point-wise comparisons of lesion prevalence and WSS have failed to support it. Here we investigate the hypothesis that multidirectional flow—characterized as the average magnitude of WSS components acting transversely to the mean vector (transWSS)—plays a key role. Maps of lesion prevalence around aortic branch ostia in immature and mature rabbits were compared with equivalent maps of time average WSS, the OSI (an index characterizing oscillatory flow) and transWSS, obtained from computational simulations; Spearman’s rank correlation coefficients were calculated for aggregated data and 95% confidence intervals were obtained by bootstrapping methods. Lesion prevalence correlated positively, strongly and significantly with transWSS at both ages. Correlations of lesion prevalence with the other shear metrics were not significant or were significantly lower than those obtained for transWSS. No correlation supported the low, oscillatory WSS theory. The data are consistent with the view that multidirectional near-wall flow is highly pro-atherogenic. Effects of multidirectional flow on EC, and methods for investigating them, are reviewed. The finding that oscillatory flow has pro-inflammatory effects when acting perpendicularly to the long axis of EC but anti-inflammatory effects when acting parallel to it may explain the stronger correlation of lesion prevalence with transWSS than with the OSI.
Moxey D, Feldman Y, Perdikaris P, et al., 2015, Proper orthogonal decomposition analysis of a puff in a pipe
We have performed direct numerical simulations of transitional turbulence in pipe flow for Re=2,250. The results confirm the existence of a spatio-temporal intermittency when turbulence is localized in a puff convected downstream. To analyze the turbulence, we follow a turbulent puff by a 3D moving-window centered at the location of the maximum total energy of transverse (turbulent) motion. The flow field data collected over 6,000 time instances (snapshots) have been analyzed by Proper Orthogonal Decomposition (POD) and used for identifying vortical structures. The presence of large-scale structures in a puff has been found by time-averaging of the cross-sectional turbulent velocity field and confirmed by POD analysis and by applying the Q- and λ2-criteria.
Xu H, Sherwin SJ, 2015, On a mechanism of delaying laminar-turbulent transition
In this paper we investigate the boundary layer flows over a flat plate on which smooth localized imperfections are located. The localized imperfections have the width scale (d) comparable with the wavelength (λTS) of the Tollmien-Schlichting (T-S) waves and the height scale (h) less than the boundary layer thickness δ99. The existence of the localized imperfection gives rise to the change of the instability property of the boundary layer. The investigations are focused on the interaction between the T-S waves and the base flows distorted by smooth forward-facing steps and aim to forge links between the localized imperfections and the mechanisms of stabilizing the T-S waves. Numerical investigations show that isolated smooth forward-facing steps can perform as a robust strategy of delaying laminar-turbulent transition. Finally, direct numerical simulations are implemented to validate the strategy.
Moxey D, Green MD, Sherwin SJ, et al., 2015, An isoparametric approach to high-order curvilinear boundary-layer meshing, Computer Methods in Applied Mechanics and Engineering, Vol: 283, Pages: 636-650, ISSN: 0045-7825
The generation of high-order curvilinear meshes for complex three-dimensional geometries is presently a challenging topic, particularly for meshes used in simulations at high Reynolds numbers where a thin boundary layer exists near walls and elements are highly stretched in the direction normal to flow. In this paper, we present a conceptually simple but very effective and modular method to address this issue. We propose an isoparametric approach, whereby a mesh containing a valid coarse discretization comprising of high-order triangular prisms near walls is refined to obtain a finer prismatic or tetrahedral boundary-layer mesh. The validity of the prismatic mesh provides a suitable mapping that allows one to obtain very fine mesh resolutions across the thickness of the boundary layer. We describe the method in detail for a high-order approximation using modal basis functions, discuss the requirements for the splitting method to produce valid prismatic and tetrahedral meshes and provide a sufficient criterion of validity in both cases. By considering two complex aeronautical configurations, we demonstrate how highly stretched meshes with sufficient resolution within the laminar sublayer can be generated to enable the simulation of flows with Reynolds numbers of and above.
Cohen J, Cantwell C, Moxey D, et al., 2015, TemPSS: A service providing software parameter templates and profiles for scientific HPC, IEEE International Conference On eScience, Publisher: IEEE, Pages: 78-87, ISSN: 2325-372X
Rocco G, Sherwin SJ, 2015, Stabilisation of the absolute instability of a flow past a cylinder via spanwise forcing at <i>Re</i>=180, IUTAM/ABCM Symposium on Laminar Turbulent Transition, Publisher: ELSEVIER SCIENCE BV, Pages: 115-121, ISSN: 2210-9838
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Burovskiy P, Grigoras P, Sherwin S, et al., 2015, Efficient Assembly for High Order Unstructured FEM Meshes, 25th International Conference on Field Programmable Logic and Applications, Publisher: IEEE, ISSN: 1946-1488
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Cohen J, Moxey D, Cantwell C, et al., 2015, POSITION PAPER: Ensuring an Effective User Experience when Managing and Running Scientific HPC Software, IEEE ACM 1st International Workshop on Software Engineering for High Performance Computing in Science (SE4HPCS), Publisher: IEEE, Pages: 56-59
Moura RC, Sherwin S, Peiro J, 2015, Modified Equation Analysis for the Discontinuous Galerkin Formulation, 10th International Conference on Spectral and High-Order Methods (ICOSAHOM), Publisher: SPRINGER-VERLAG BERLIN, Pages: 375-383, ISSN: 1439-7358
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- Citations: 8
Peiro J, Moxey D, Jordi B, et al., 2015, High-Order Visualization with ElVis, IDIHOM: INDUSTRIALIZATION OF HIGH-ORDER METHODS - A TOP-DOWN APPROACH, Vol: 128, Pages: 521-534, ISSN: 1612-2909
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Moxey D, Hazan M, Sherwin SJ, et al., 2015, Curvilinear Mesh Generation for Boundary Layer Problems, IDIHOM: INDUSTRIALIZATION OF HIGH-ORDER METHODS - A TOP-DOWN APPROACH, Vol: 128, Pages: 41-64, ISSN: 1612-2909
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Rocco G, Sherwin SJ, 2015, The Role of Spanwise Forcing on Vortex Shedding Suppression in a Flow Past a Cylinder, INSTABILITY AND CONTROL OF MASSIVELY SEPARATED FLOWS, Vol: 107, Pages: 105-110, ISSN: 0926-5112
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