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See detailAn a posteriori error estimator for the spectral fractional power of the Laplacian
Bulle, Raphaël UL; Barrera, Olga; Bordas, Stéphane UL et al

E-print/Working paper (2022)

We develop a novel a posteriori error estimator for the L2 error committed by the finite ele- ment discretization of the solution of the fractional Laplacian. Our a posteriori error estimator takes ... [more ▼]

We develop a novel a posteriori error estimator for the L2 error committed by the finite ele- ment discretization of the solution of the fractional Laplacian. Our a posteriori error estimator takes advantage of the semi–discretization scheme using a rational approximation which allows to reformulate the fractional problem into a family of non–fractional parametric problems. The estimator involves applying the implicit Bank–Weiser error estimation strategy to each parametric non–fractional problem and reconstructing the fractional error through the same rational approximation used to compute the solution to the original fractional problem. We provide several numerical examples in both two and three-dimensions demonstrating the effectivity of our estimator for varying fractional powers and its ability to drive an adaptive mesh refinement strategy. [less ▲]

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See detailA hyper-reduction method using adaptivity to cut the assembly costs of reduced order models
Hale, Jack UL; Schenone, Elisa; Baroli, Davide UL et al

in Computer Methods in Applied Mechanics and Engineering (2021), 380

At every iteration or timestep of the online phase of some reduced-order modelling schemes, large linear systems must be assembled and then projected onto a reduced order basis of small dimension. The ... [more ▼]

At every iteration or timestep of the online phase of some reduced-order modelling schemes, large linear systems must be assembled and then projected onto a reduced order basis of small dimension. The projected small linear systems are cheap to solve, but assembly and projection are now the dominant computational cost. In this paper we introduce a new hyper-reduction strategy called reduced assembly (RA) that drastically cuts these costs. RA consists of a triangulation adaptation algorithm that uses a local error indicator to con- struct a reduced assembly triangulation specially suited to the reduced order basis. Crucially, this reduced assembly triangulation has fewer cells than the original one, resulting in lower assembly and projection costs. We demonstrate the efficacy of RA on a Galerkin-POD type reduced order model (RAPOD). We show performance increases of up to five times over the baseline Galerkin-POD method on a non-linear reaction-diffusion problem solved with a semi-implicit time-stepping scheme and up to seven times for a 3D hyperelasticity problem solved with a continuation Newton-Raphson algorithm. The examples are implemented in the DOLFIN finite element solver using PETSc and SLEPc for linear algebra. Full code and data files to produce the results in this paper are provided as supplementary material. [less ▲]

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See detailBubble-Enriched Smoothed Finite Element Methods for Nearly-Incompressible Solids
Lee, Changkye; Natarajan, Sundararajan; Hale, Jack UL et al

in Computer Modeling in Engineering and Sciences (2021), 127(2), 411-436

This work presents a locking-free smoothed finite element method (S-FEM) for the simulation of soft matter modelled by the equations of quasi-incompressible hyperelasticity. The proposed method overcomes ... [more ▼]

This work presents a locking-free smoothed finite element method (S-FEM) for the simulation of soft matter modelled by the equations of quasi-incompressible hyperelasticity. The proposed method overcomes well-known issues of standard finite element methods (FEM) in the incompressible limit: the over-estimation of stiffness and sensitivity to severely distorted meshes. The concepts of cell-based, edge-based and node-based S-FEMs are extended in this paper to three-dimensions. Additionally, a cubic bubble function is utilized to improve accuracy and stability. For the bubble function, an additional displacement degree of freedom is added at the centroid of the element. Several numerical studies are performed demonstrating the stability and validity of the proposed approach. The obtained results are compared with standard FEM and with analytical solutions to show the effectiveness of the method. [less ▲]

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See detailHierarchical a posteriori error estimation of Bank-Weiser type in the FEniCS Project
Bulle, Raphaël UL; Hale, Jack UL; Lozinski, Alexei et al

E-print/Working paper (2021)

In the seminal paper of Bank and Weiser [Math. Comp., 44 (1985), pp.283-301] a new a posteriori estimator was introduced. This estimator requires the solution of a local Neumann problem on every cell of ... [more ▼]

In the seminal paper of Bank and Weiser [Math. Comp., 44 (1985), pp.283-301] a new a posteriori estimator was introduced. This estimator requires the solution of a local Neumann problem on every cell of the finite element mesh. Despite the promise of Bank-Weiser type estimators, namely locality, computational efficiency, and asymptotic sharpness, they have seen little use in practical computational problems. The focus of this contribution is to describe a novel implementation of hierarchical estimators of the Bank-Weiser type in a modern high-level finite element software with automatic code generation capabilities. We show how to use the estimator to drive (goal-oriented) adaptive mesh refinement and to mixed approximations of the nearly-incompressible elasticity problems. We provide comparisons with various other used estimators. An open-source implementation based on the FEniCS Project finite element software is provided as supplementary material. [less ▲]

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See detailRemoving the saturation assumption in Bank-Weiser error estimator analysis in dimension three
Bulle, Raphaël UL; Chouly, Franz; Hale, Jack UL et al

in Applied Mathematics Letters (2020), 107

We provide a new argument proving the reliability of the Bank-Weiser estimator for Lagrange piecewise linear finite elements in both dimension two and three. The extension to dimension three constitutes ... [more ▼]

We provide a new argument proving the reliability of the Bank-Weiser estimator for Lagrange piecewise linear finite elements in both dimension two and three. The extension to dimension three constitutes the main novelty of our study. In addition, we present a numerical comparison of the Bank-Weiser and residual estimators for a three-dimensional test case. [less ▲]

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See detailA Tutorial on Bayesian Inference to Identify Material Parameters in Solid Mechanics
Rappel, Hussein UL; Beex, Lars UL; Hale, Jack UL et al

in Archives of Computational Methods in Engineering (2019)

The aim of this contribution is to explain in a straightforward manner how Bayesian inference can be used to identify material parameters of material models for solids. Bayesian approaches have already ... [more ▼]

The aim of this contribution is to explain in a straightforward manner how Bayesian inference can be used to identify material parameters of material models for solids. Bayesian approaches have already been used for this purpose, but most of the literature is not necessarily easy to understand for those new to the field. The reason for this is that most literature focuses either on complex statistical and machine learning concepts and/or on relatively complex mechanical models. In order to introduce the approach as gently as possible, we only focus on stress–strain measurements coming from uniaxial tensile tests and we only treat elastic and elastoplastic material models. Furthermore, the stress–strain measurements are created artificially in order to allow a one-to-one comparison between the true parameter values and the identified parameter distributions. [less ▲]

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See detailA volume-averaged nodal projection method for the Reissner-Mindlin plate model
Ortiz-Bernardin, Alejandro; Köbrich, Philip; Hale, Jack UL et al

in Computer Methods in Applied Mechanics and Engineering (2018), 341

We introduce a novel meshfree Galerkin method for the solution of Reissner-Mindlin plate problems that is written in terms of the primitive variables only (i.e., rotations and transverse displacement) and ... [more ▼]

We introduce a novel meshfree Galerkin method for the solution of Reissner-Mindlin plate problems that is written in terms of the primitive variables only (i.e., rotations and transverse displacement) and is devoid of shear-locking. The proposed approach uses linear maximum-entropy approximations and is built variationally on a two-field potential energy functional wherein the shear strain, written in terms of the primitive variables, is computed via a volume-averaged nodal projection operator that is constructed from the Kirchhoff constraint of the three-field mixed weak form. The stability of the method is rendered by adding bubble-like enrichment to the rotation degrees of freedom. Some benchmark problems are presented to demonstrate the accuracy and performance of the proposed method for a wide range of plate thicknesses. [less ▲]

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See detailSimple and extensible plate and shell finite element models through automatic code generation tools
Hale, Jack UL; Brunetti, Matteo; Bordas, Stéphane UL et al

in Computers and Structures (2018), 209

A large number of advanced finite element shell formulations have been developed, but their adoption is hindered by complexities of transforming mathematical formulations into computer code. Furthermore ... [more ▼]

A large number of advanced finite element shell formulations have been developed, but their adoption is hindered by complexities of transforming mathematical formulations into computer code. Furthermore, it is often not straightforward to adapt existing implementations to emerging frontier problems in thin structural mechanics including nonlinear material behaviour, complex microstructures, multi-physical couplings, or active materials. We show that by using a high-level mathematical modelling strategy and automatic code generation tools, a wide range of advanced plate and shell finite element models can be generated easily and efficiently, including: the linear and non-linear geometrically exact Naghdi shell models, the Marguerre-von K ́arm ́an shallow shell model, and the Reissner-Mindlin plate model. To solve shear and membrane-locking issues, we use: a novel re-interpretation of the Mixed Interpolation of Tensorial Component (MITC) procedure as a mixed-hybridisable finite element method, and a high polynomial order Partial Selective Reduced Integration (PSRI) method. The effectiveness of these approaches and the ease of writing solvers is illustrated through a large set of verification tests and demo codes, collected in an open-source library, FEniCS-Shells, that extends the FEniCS Project finite element problem solving environment. [less ▲]

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See detailCalculating the Malliavin derivative of some stochastic mechanics problems
Hauseux, Paul UL; Hale, Jack UL; Bordas, Stéphane UL

in PLoS ONE (2017), 12(12), 0189994

The Malliavin calculus is an extension of the classical calculus of variations from deterministic functions to stochastic processes. In this paper we aim to show in a practical and didactic way how to ... [more ▼]

The Malliavin calculus is an extension of the classical calculus of variations from deterministic functions to stochastic processes. In this paper we aim to show in a practical and didactic way how to calculate the Malliavin derivative, the derivative of the expectation of a quantity of interest of a model with respect to its underlying stochastic parameters, for four problems found in mechanics. The non-intrusive approach uses the Malliavin Weight Sampling (MWS) method in conjunction with a standard Monte Carlo method. The models are expressed as ODEs or PDEs and discretised using the finite difference or finite element methods. Specifically, we consider stochastic extensions of; a 1D Kelvin-Voigt viscoelastic model discretised with finite differences, a 1D linear elastic bar, a hyperelastic bar undergoing buckling, and incompressible Navier-Stokes flow around a cylinder, all discretised with finite elements. A further contribution of this paper is an extension of the MWS method to the more difficult case of non-Gaussian random variables and the calculation of second-order derivatives. We provide open-source code for the numerical examples in this paper. [less ▲]

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See detailMicro-structured materials: inhomogeneities and imperfect interfaces in plane micropolar elasticity, a boundary element approach
Atroshchenko, Elena; Hale, Jack UL; Videla, Javier A. et al

in Engineering Analysis with Boundary Elements (2017), 83

In this paper we tackle the simulation of microstructured materials modelled as heterogeneous Cosserat media with both perfect and imperfect interfaces. We formulate a boundary value problem for an ... [more ▼]

In this paper we tackle the simulation of microstructured materials modelled as heterogeneous Cosserat media with both perfect and imperfect interfaces. We formulate a boundary value problem for an inclusion of one plane strain micropolar phase into another micropolar phase and reduce the problem to a system of boundary integral equations, which is subsequently solved by the boundary element method. The inclusion interface condition is assumed to be imperfect, which permits jumps in both displacements/microrotations and tractions/couple tractions, as well as a linear dependence of jumps in displacements/microrotations on continuous across the interface tractions/couple traction (model known in elasticity as homogeneously imperfect interface). These features can be directly incorporated into the boundary element formulation. The BEM-results for a circular inclusion in an in finite plate are shown to be in excellent agreement with the analytical solutions. The BEM-results for inclusions in finite plates are compared with the FEM-results obtained with FEniCS. [less ▲]

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See detailReduced basis Nitsche-based domain decomposition: a biomedical application
Baroli, Davide UL; Beex, Lars UL; Hale, Jack UL et al

Scientific Conference (2017, March 10)

Nowadays, the personalized biomedical simulations demand real-time efficient and reliable method to alleviate the computational complexity of high-fidelity simulation. In such applications, the necessity ... [more ▼]

Nowadays, the personalized biomedical simulations demand real-time efficient and reliable method to alleviate the computational complexity of high-fidelity simulation. In such applications, the necessity of solving different substructure, e.g. tissues or organs, with different numbers of the degrees of freedom and of coupling the reduced order spaces for each substructure poses a challenge in the on-fly simulation. In this talk, this challenge is taken into account employing the Nitsche-based domain decomposition technique inside the reduced order model [1]. This technique with respect to other domain decomposition approach allows obtaining a solution with the same accuracy of underlying finite element formulation and to flexibly treat interface with non-matching mesh. The robustness of the coupling is determined by the penalty coefficients that is chosen using ghost penalty technique [2]. Furthermore, to reduce the computational complexity of the on-fly assembling it is employed the empirical interpolation approach proposed in [3]. The numerical tests, performed using FEniCS[4], petsc4py and slepc4py [5], shows the good performance of the method and the reduction of computation cost. [1] Baroli, D., Beex L. and Bordas, S. Reduced basis Nitsche-based domain decomposition. In preparation. [2] Burman, E., Claus, S., Hansbo, P., Larson, M. G., & Massing, A. (2015). CutFEM: Discretizing geometry and partial differential equations. International Journal for Numerical Methods in Engineering, 104(7), 472-501. [3] E. Schenone, E., Beex,L., Hale, J.S., Bordas S. Proper Orthogonal Decomposition with reduced integration method. Application to nonlinear problems. In preparation. [4] A. Logg, K.-A. Mardal, G. N. Wells et al. Automated Solution of Differential Equations by the Finite Element Method, Springer 2012. [5] L. Dalcin, P. Kler, R. Paz, and A. Cosimo, Parallel Distributed Computing using Python, Advances in Water Resources, 34(9):1124-1139, 2011. http://dx.doi.org/10.1016/j.advwatres.2011.04.013 [less ▲]

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See detailImage to analysis pipeline: single and double balloons kyphoplasty
Baroli, Davide UL; Hauseux, Paul UL; Hale, Jack UL et al

Poster (2016, December 12)

In this work, we present a semi-automatic pipeline from image to simulation of a patient fractured vertebra after the kyphoplastic augmentation with two balloons. In this procedure, the CT-scan medical ... [more ▼]

In this work, we present a semi-automatic pipeline from image to simulation of a patient fractured vertebra after the kyphoplastic augmentation with two balloons. In this procedure, the CT-scan medical image are pre-processed using open-source software Slice3D for segmentation and 3D reconstruction operation. Then, using geometric processing the 3D surface geometry is enhanced to avoid degenerate element and trigging phenomena on vertebra and cement area. We perform a finite element analysis to evaluate the risk of subsequent vertebral fracture. Finally using Monte-Carlo technique, we assess the propagation of uncertainty of material parameter on the evaluation of this risk. Based on the developed semi-automatic pipelines, it is possible to perform a patient-specific simulation that assesses the successful of kyphoplasty operation. [less ▲]

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See detailNumerical methods for fracture/cutting of heterogeneous materials
Sutula, Danas UL; Agathos, Konstantinos UL; Ziaei Rad, Vahid UL et al

Presentation (2016, December)

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See detailPOD-based reduction methods, the Quasicontinuum Method and their Resemblance
Beex, Lars UL; Schenone, Elisa; Hale, Jack UL

Scientific Conference (2016, June 27)

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See detailPOD-based Reduction Methods, the Quasicontinuum Method and their Resemblance
Schenone, Elisa; Hale, Jack UL; Beex, Lars UL

Scientific Conference (2016, June)

POD-based reduction methods and the quasicontinuum method share two similar reduction steps to increase the computational speed of large mechanical models. Here, they are compared with each other.

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See detailOrchestrating clinical simulations with FEniCS
Weir, Phil; Ellerweg, Roland; Hale, Jack UL

Scientific Conference (2016, May)

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See detailBayesian statistical inference on the material parameters of a hyperelastic body
Hale, Jack UL; Farrel, Patrick E.; Bordas, Stéphane UL

in Proceedings of the ACME-UK 2016 24th Conference on Computational Mechanics (2016, March 31)

We present a statistical method for recovering the material parameters of a heterogeneous hyperelastic body. Under the Bayesian methodology for statistical inverse problems, the posterior distribution ... [more ▼]

We present a statistical method for recovering the material parameters of a heterogeneous hyperelastic body. Under the Bayesian methodology for statistical inverse problems, the posterior distribution encodes the probability of the material parameters given the available displacement observations and can be calculated by combining prior knowledge with a finite element model of the likelihood. In this study we concentrate on a case study where the observations of the body are limited to the displacements on the surface of the domain. In this type of problem the Bayesian framework (in comparison with a classical PDE-constrained optimisation framework) can give not only a point estimate of the parameters but also quantify uncertainty on the parameter space induced by the limited observations and noisy measuring devices. There are significant computational and mathematical challenges when solving a Bayesian inference problem in the case that the parameter is a field (i.e. exists infinite-dimensional Banach space) and evaluating the likelihood involves the solution of a large-scale system of non-linear PDEs. To overcome these problems we use dolfin-adjoint to automatically derive adjoint and higher-order adjoint systems for efficient evaluation of gradients and Hessians, develop scalable maximum aposteriori estimates, and use efficient low-rank update methods to approximate posterior covariance matrices. [less ▲]

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See detailReducing non-linear PDEs using a reduced integration proper orthogonal decomposition method
Schenone, Elisa; Hale, Jack UL; Beex, Lars UL et al

Scientific Conference (2016)

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See detailUsing Bayesian inference to recover the material parameters of a heterogeneous hyperelastic body
Hale, Jack UL; Farrell, Patrick; Bordas, Stéphane UL

Scientific Conference (2016)

We present a method for calculating a Bayesian uncertainty estimate on the recovered material parameters of a heterogeneous geometrically non-linear hyperelastic body. We formulate the problem in the ... [more ▼]

We present a method for calculating a Bayesian uncertainty estimate on the recovered material parameters of a heterogeneous geometrically non-linear hyperelastic body. We formulate the problem in the Bayesian inference framework [1]; given noisy and sparse observations of a body, some prior knowledge on the parameters and a parameter-to-observable map the goal is to recover the posterior distribution of the parameters given the observations. In this work we primarily focus on the challenges of developing dimension-independent algorithms in the context of very large inverse problems (tens to hundreds of thousands of parameters). Critical to the success of the method is viewing the problem in the correct infinite- dimensional function space setting [2]. With this goal in mind, we show the use of automatic symbolic differentiation techniques to construct high-order adjoint models [3], scalable maximum a posteriori (MAP) estimators, and efficient low-rank update methods to calculate credible regions on the posterior distribution [4]. [less ▲]

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