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At least 55 records · Page 3

Nonlinear optimization for a tumor invasion PDE model

In this work, we introduce a methodology to approximate unknown parameters that appear on a non-linear reaction–diffusion model of tumor invasion. These equations consider that tumor-induced alteration of micro-environmental pH furnishes a mechanism for cancer invasion. A coupled system reaction–diffusion explaining this model is given by three partial differential equations for the non-dimensional spatial distribution and temporal evolution of the density of normal tissue, the neoplastic tissue growth and the excess concentration of H{sup +} ions. The tumor model parameters have a corresponding biological meaning: the reabsorption rate, the destructive influence of H{sup +} ions in the healthy tissue, the growth rate of tumor tissue and the diffusion coefficient. We propose to solve the direct problem using the Finite Element Method (FEM) and minimize an appropriate functional including both the real data (obtained via in-vitro experiments and fluorescence ratio imaging microscopy) and the numerical solution. The gradient of the functional is computed by the adjoint method.

60 APPLIED LIFE SCIENCES↗

Parallel Ellipsoidal Perfectly Matched Layers for Acoustic Helmholtz Problems on Exterior Domains

Exterior acoustic problems occur in a wide range of applications, making the finite element analysis of such problems a common practice in the engineering community. Various methods for truncating infinite exterior domains have been developed, including absorbing boundary conditions, infinite elements, and more recently, perfectly matched layers (PML). PML are gaining popularity due to their generality, ease of implementation, and effectiveness as an absorbing boundary condition. PML formulations have been developed in Cartesian, cylindrical, and spherical geometries, but not ellipsoidal. In addition, the parallel solution of PML formulations with iterative solvers for the solution of the Helmholtz equation, and how this compares with more traditional strategies such as infinite elements, has not been adequately investigated. In this study, we present a parallel, ellipsoidal PML formulation for acoustic Helmholtz problems. To faciliate the meshing process, the ellipsoidal PML layer is generated with an on-the-fly mesh extrusion. Though the complex stretching is defined along ellipsoidal contours, we modify the Jacobian to include an additional mapping back to Cartesian coordinates in the weak formulation of the finite element equations. This allows the equations to be solved in Cartesian coordinates, which is more compatible with existing finite element software, but without the necessity of dealing with corners in the PML formulation. Herein we also compare the conditioning and performance of the PML Helmholtz problem with infinite element approach that is based on high order basis functions. On a set of representative exterior acoustic examples, we show that high order infinite element basis functions lead to an increasing number of Helmholtz solver iterations, whereas for PML the number of iterations remains constant for the same level of accuracy. Finally, this provides an additional advantage of PML over the infinite element approach.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

The second-generation Shifted Boundary Method and its numerical analysis

Recently, the Shifted Boundary Method (SBM) was proposed within the class of unfitted (or immersed, or embedded) finite element methods. By reformulating the original boundary value problem over a surrogate (approximate) computational domain, the SBM avoids integration over cut cells and the associated problematic issues regarding numerical stability and matrix conditioning. Accuracy is maintained by modifying the original boundary conditions using Taylor expansions. Hence the name of the method, that shifts the location and values of the boundary conditions. In this article, we present enhanced variational SBM formulations for the Poisson and Stokes problems with improved flexibility and robustness. These simplified variational forms allow to relax some of the assumptions required by the mathematical proofs of stability and convergence of earlier implementations. First, we show that these new SBM implementations can be proved asymptotically stable and convergent even without the rather restrictive assumption that the inner product between the normals to the true and surrogate boundaries is positive. Second, we show that it is not necessary to introduce a stabilization term involving the tangential derivatives of the solution at Dirichlet boundaries, therefore avoiding the calibration of an additional stabilization parameter. Finally, we prove enhanced L 2 -estimates without the cumbersome assumption – of earlier proofs – that the surrogate domain is convex. Instead we rely on a conventional assumption that the boundary of the true domain is smooth, which can also be replaced by requiring convexity of the true domain. The aforementioned improvements open the way to a more general and efficient implementation of the Shifted Boundary Method, particularly in complex three-dimensional geometries. We complement these theoretical developments with numerical experiments in two and three dimensions.

42 ENGINEERING↗

Calibration of elastoplastic constitutive model parameters from full-field data with automatic differentiation-based sensitivities

Here, we present a framework for calibration of parameters in elastoplastic constitutive models that is based on the use of automatic differentiation (AD). The model calibration problem is posed as a partial differential equation-constrained optimization problem where a finite element (FE) model of the coupled equilibrium equation and constitutive model evolution equations serves as the constraint. The objective function quantifies the mismatch between the displacement predicted by the FE model and full-field digital image correlation data, and the optimization problem is solved using gradient-based optimization algorithms. Forward and adjoint sensitivities are used to compute the gradient at considerably less cost than its calculation from finite difference approximations. Through the use of AD, we need only to write the constraints in terms of AD objects, where all of the derivatives required for the forward and inverse problems are obtained by appropriately seeding and evaluating these quantities. We present three numerical examples that verify the correctness of the gradient, demonstrate the AD approach's parallel computation capabilities via application to a large-scale FE model, and highlight the formulation's ease of extensibility to other classes of constitutive models.

42 ENGINEERING↗

Finite Volume Discretization of the Euler Equations in Pronghorn

Modeling flow and heat transfer in high temperature gas reactors (HTGR) requires the ability to model a wide range of flow speeds from slow (natural convection), to intermediate (forced-flow conditions), to supersonic regimes (depressurization) for a wide range of geometries including the pebble bed, upper and lower plenum, and risers. In previous work, Pronghorn has effectively modeled low-to-medium speed flows in scenarios such as the one described in the two-dimensional PBMR-400 benchmark, using its finite-element-based streamline-upwind Petrov-Galerkin (SUPG) stabilized implementation of the Euler equations. However, limitations of this method become apparent when dealing with more complicated geometries (e.g. imposing slip boundary conditions at nodes belonging to two different boundaries) and when gas speeds are fast enough for shocks and supersonic flow to occur. For these problems, the finite-element-based solver lacks robustness and is plagued by slow iterative convergence or even divergence. In order to address these challenges, the Pronghorn code at INL has been updated with new, modified versions of its original equations. The new Pronghorn models are built on the finite volume method with a Harten-Lax-van Leer-Contact (HLLC) Riemann solver based numerical flux method, which (1) allows imposing slip boundary conditions much more robustly and (2) performs well for a wide range of flow speeds. The finite-volume-based flow solver will form the basis for a robust coarse-mesh thermal-hydraulics capability in Pronghorn.

97 MATHEMATICS AND COMPUTING↗

Modeling and simulation of Ultrasonic Guided Waves propagation in the fluid-structure domain by a monolithic approach

The present study introduces the coupled multiphysics model as part of the structural health monitoring (SHM) system. In particular, the Ultrasonic Guided Waves (UGWs) propagation is tracked in order to identify the damage to the structure. For this purpose, a multiphysics mathematical model is proposed. The model constitutes a monolithically coupled system of acoustic and elastic wave equations (WpFSI problem) where the wave signal displacement measurements are analyzed as the UGWs propagates in the solid, fluid and their interface. The ultimate goal of this paper is to explore and develop the efficient numerical solution of the WpFSI problem using the finite element method. A detailed description of the modeling framework and conditions that facilitate the coupling is provided. To couple the displacement-based acoustic wave equations for the isothermal fluid with elastic wave equations for the Saint Venant-Kirchhoff material model, the present study uses a monolithic solution algorithm. In particular, at each time step, wave equations are transformed to a fixed reference configuration via the arbitrary Lagrangian-Eulerian (ALE) mapping and automatically adopt the boundary conditions from the previous time step. The implementation is accomplished via the finite element library deal.II (Goll et al., 2017) based software toolbox DOpElib (Bangerth et al., 2007) which provides modularized higher level algorithms. Beyond SHM systems, the model is relevant for problems from biomechanics and biomedicine, vibromechanics, poroelasticity as well as subsurface and porous media flow. Here, the model developed here serves as a first step towards the on-line SHM system modeling, where structural dynamics are accounted for.

42 ENGINEERING↗

Crank–Nicolson WSGI difference scheme with finite element method for multi-dimensional time-fractional wave problem

In this article, a second-order Crank–Nicolson weighted and shifted Grünwald integral (WSGI) time-discrete scheme combined with finite element method is studied for finding the numerical solution of the multi-dimensional time-fractional wave equation. The time-fractional wave equation with Caputo-fractional derivative is transformed into the time-fractional integral equation by integral technique, then the second-order Crank–Nicolson finite element scheme with a time second-order WSGI discrete approximation for fractional integral is formulated. The analysis of stability is made, then a priori error estimate is given by making use of the conversion technique between the WSGI formula and fractional integral. At the end of the article, some numerical examples covering two two-dimensional cases with rectangular element and triangular element and a three-dimensional case with tetrahedral element are shown to test and verify our theoretical results.

97 MATHEMATICS AND COMPUTING↗

Thermal Test Suite for Code Maintenance and Validation of Diablo

This document describes a series of test problems that ensure that the Thermal capabilities of Diablo are working correctly. Diablo utilizes the Finite Element Method to discretize the problem in space and a trapezoidal rule finite difference scheme to discretize the problem in time. This suite will test the codes capabilities to handle various boundary conditions, source terms, and initial conditions. It will also test the coupling between thermal and solid effects, and the use of various linear and nonlinear solvers.

42 ENGINEERING↗

Peri-Net-Pro: the neural processes with quantified uncertainty for crack patterns

Abstract This paper develops a deep learning tool based on neural processes (NPs) called the Peri-Net-Pro, to predict the crack patterns in a moving disk and classifies them according to the classification modes with quantified uncertainties. In particular, image classification and regression studies are conducted by means of convolutional neural networks (CNNs) and NPs. First, the amount and quality of the data are enhanced by using peridynamics to theoretically compensate for the problems of the finite element method (FEM) in generating crack pattern images. Second, case studies are conducted with the prototype microelastic brittle (PMB), linear peridynamic solid (LPS), and viscoelastic solid (VES) models obtained by using the peridynamic theory. The case studies are performed to classify the images by using CNNs and determine the suitability of the PMB, LBS, and VES models. Finally, a regression analysis is performed on the crack pattern images with NPs to predict the crack patterns. The regression analysis results confirm that the variance decreases when the number of epochs increases by using the NPs. The training results gradually improve, and the variance ranges decrease to less than 0.035. The main finding of this study is that the NPs enable accurate predictions, even with missing or insufficient training data. The results demonstrate that if the context points are set to the 10th, 100th, 300th, and 784th, the training information is deliberately omitted for the context points of the 10th, 100th, and 300th, and the predictions are different when the context points are significantly lower. However, the comparison of the results of the 100th and 784th context points shows that the predicted results are similar because of the Gaussian processes in the NPs. Therefore, if the NPs are employed for training, the missing information of the training data can be supplemented to predict the results.

Mathematics↗

Active learning with multifidelity modeling for efficient rare event simulation

Here, while multifidelity modeling provides a cost-effective way to conduct uncertainty quantification with computationally expensive models, much greater efficiency can be achieved by adaptively deciding the number of required high-fidelity (HF) simulations, depending on the type and complexity of the problem and the desired accuracy in the results. We propose a framework for active learning with multifidelity modeling emphasizing the efficient estimation of rare events. Our framework works by fusing a low-fidelity (LF) prediction with an HF-inferred correction, filtering the corrected LF prediction to decide whether to call the high-fidelity model, and for enhanced subsequent accuracy, adapting the correction for the LF prediction after every HF model call. The framework does not make any assumptions as to the LF model type or its correlations with the HF model. In addition, for improved robustness when estimating smaller failure probabilities, we propose using dynamic active learning functions that decide when to call the HF model. We demonstrate our framework using several academic case studies (including some high-dimensional problems) and two finite element model case studies: estimating Navier-Stokes velocities using the Stokes approximation and estimating stresses in a transversely isotropic model subjected to displacements via a coarsely meshed isotropic model. Across these case studies, not only did the proposed framework estimate the failure probabilities accurately, but compared with either Monte Carlo or a standard variance reduction method, it also required only a small fraction of the calls to the HF model.

42 ENGINEERING↗

Effects of strain-dependent surface stress on the adhesive contact of a rigid sphere to a compliant substrate

Recent experiments have reported that the surface stress of soft elastic solids can increase rapidly with surface strain. For example, when a small hard sphere in adhesive contact with a soft silicone gel is slowly retracted from its rest position, it was found that the retraction force versus displacement relation cannot be explained either by the Johnson–Kendall–Roberts (JKR) theory or a recent indentation theory based on an isotropic surface stress that is independent of surface strain. In this paper, we address this problem using a finite element method to simulate the retraction process. Our numerical model does not have the restrictions of the aforementioned theories; that is, it can handle large nonlinear elastic deformation as well as a surface-strain-dependent surface stress. Our simulation is in good agreement with experimental force versus displacement data with no fitting parameters. Therefore, our results lend further support to the claim that significant strain-dependent surface stresses can occur in simple soft elastic gels. However, significant challenges remain in the reconciliation of theory and experiments, particularly regarding the geometry of the contact and substrate deformation.

36 MATERIALS SCIENCE↗

Statistics of internal stress fluctuations in dislocated crystals and relevance to density-based dislocation dynamics models

A statistical analysis of internal stress fluctuations, defined as the difference between the local mean stress and stress on dislocations, is presented for deforming crystals with 3D discrete dislocation systems. Dislocation realizations are generated using dislocation dynamics simulations and the associated stress field is computed as a superposition of a regularized stress field of dislocation lines within the domain of the solution and a complementary stress field computed via a finite-element boundary value problem. The internal stress fluctuations of interest are defined by an ensemble of the difference between the stress on dislocation lines and the local mean field stress in the crystal. The latter is established in a piecewise fashion over small voxels in the crystal thus allowing the difference between the local average stress and stress on segments to be easily estimated. The results show that the Schmid stress (resolved shear stress) and Escaig stress fluctuations on various slip systems sampled over a random set of points follow a Cauchy (Lorentz) distribution at all strain levels, with the amplitude and width of the distribution being dependent on the strain. Finally, the implications of the Schmid and Escaig internal stress fluctuations are discussed from the points of view of dislocation cross-slip and the dislocation motion in continuum dislocation dynamics.

36 MATERIALS SCIENCE↗

Efficient Low-Order Refined Preconditioners for High-Order Matrix-Free Continuous and Discontinuous Galerkin Methods

In this paper, we design preconditioners for the matrix-free solution of high-order continuous and discontinuous Galerkin discretizations of elliptic problems based on finite element method--spectral element method (FEM-SEM) equivalence and additive Schwarz methods. The high-order operators are applied without forming the system matrix, making use of sum factorization for efficient evaluation. The system is preconditioned using a spectrally equivalent low-order (p = 1) finite element operator discretization on a refined mesh. The low-order refined mesh is anisotropic and not shape regular in the polynomial degree of the high-order operator, requiring specialized solvers to treat the anisotropy. We make use of an element-structured, geometric multigrid V-cycle with ordered ILU(0) smoothing. The preconditioner is parallelized through an overlapping additive Schwarz method that is robust in h and p. The method is extended to interior penalty and Bassi and Rebay (BR2) discontinuous Galerkin discretizations, for which it is also robust in the size of the penalty parameter. Finally, numerical results are presented on a variety of examples, verifying the uniformity of the preconditioner.

97 MATHEMATICS AND COMPUTING↗

On a nonlocal Cahn–Hilliard model permitting sharp interfaces

A nonlocal Cahn–Hilliard model with a non-smooth potential of double-well obstacle type that promotes sharp interfaces in the solution is presented. To capture long-range interactions between particles, a nonlocal Ginzburg–Landau energy functional is defined which recovers the classical (local) model as the extent of nonlocal interactions vanish. In contrast to the local Cahn–Hilliard problem that always leads to diffuse interfaces, the proposed nonlocal model can lead to a strict separation into pure phases of the substance. In this work, the lack of smoothness of the potential is essential to guarantee the aforementioned sharp-interface property. Mathematically, this introduces additional inequality constraints that, in a weak formulation, lead to a coupled system of variational inequalities which at each time instance can be restated as a constrained optimization problem. We prove the well-posedness and regularity of the semi-discrete and continuous in time weak solutions, and derive the conditions under which pure phases are admitted. Moreover, we develop discretizations of the problem based on finite element methods and implicit–explicit time-stepping methods that can be realized efficiently. Finally, we illustrate our theoretical findings through several numerical experiments in one and two spatial dimensions that highlight the differences in features of local and nonlocal solutions and also the sharp interface properties of the nonlocal model.

97 MATHEMATICS AND COMPUTING↗

OpenFUSIONToolkit

The Open FUSION Toolkit (OFT) is a suite of modeling tools, and their underlying finite element framework, for problems in plasma and fusion research and engineering in arbitrary 2D and 3D geometries.

Hansen, Chris [Columbia Univ., New York, NY (Unite↗

Matrix-free preconditioning for high-order H (curl) discretizations

The greater arithmetic intensity of high-order finite element discretizations makes them attractive for implementation on next-generation hardware, but assembly of high-order finite element operators as matrices is prohibitively expensive. As a result, the development of general algebraic solvers for such operators has been an open research challenge. Fast matrix-free application of high-order operators has received significant attention in the literature in the context of Poisson-type problems, but preconditioners and solvers for inverting more general operators are not very well-developed. In this paper, we consider the problem of preconditioning a definite Maxwell operator at high polynomial order without assembling a matrix. We show that given efficient preconditioners for high-order H 1 finite element problems on the same mesh, efficient H(curl) preconditioners can be constructed in an auxiliary space framework. We demonstrate the resulting preconditioners in a practical setting with tensor-product basis functions on an unstructured mesh of quadrilaterals. Overall, our approach uses a sparsified H 1 solver constructed on a low-order mesh of the nodal points of the underlying high-order space, and we show that the resulting H(curl) preconditioner is effective at very high polynomial orders for two-dimensional model problems with complicated geometry, varying piecewise constant coefficients, and curved elements. The resulting preconditioner scales with nearly optimal O(p d+1 ) floating point operation count and optimal O(p d ) memory transfer requirements, outperforming existing Maxwell preconditioners in the high-order regime.

97 MATHEMATICS AND COMPUTING↗