arXiv subjects

Jack S. Hale

Publications and source records attributed to Jack S. Hale.

11 recordsLinked to original sources

arXiv2025

FEniCSx-pctools: Tools for PETSc block linear algebra preconditioning in FEniCSx

Solving partial differential equations with the finite element method leads to large linear systems of equations that must be solved. When these systems have a natural block structure due to multiple field variables, using iterative solvers with carefully designed preconditioning strategies that exploit the underlying physical structure becomes necessary for an efficient and scalable solution process. FEniCSx Preconditioning Tools (FEniCSx-pctools) is a software package that eases the specification of PETSc (Portable, Extensible Toolkit for Scientific Computation) block preconditioning strategies on linear systems assembled using the DOLFINx finite element solver of the FEniCS Project. The package automatically attaches all necessary metadata so that preconditioning strategies can be applied via PETSc's standard options database to monolithic and block assembled systems. The documented examples include a simple mixed Poisson system and more complex pressure convection-diffusion approach to preconditioning the Navier-Stokes equations. We show weak parallel scaling on a fully coupled temperature-Navier-Stokes system up to 8192 MPI (Message Passing Interface) processes, demonstrating the applicability of the approach to large-scale problems.

cs.MS↗

arXiv2024

Formulae and transformations for simplicial tensorial finite elements via polytopal templates

We introduce a unified method for constructing the basis functions of a wide variety of partially continuous tensor-valued finite elements on simplices using polytopal templates. These finite element spaces are essential for achieving well-posed discretisations of mixed formulations of partial differential equations that involve tensor-valued functions, such as the Hellinger-Reissner formulation of linear elasticity. In our proposed polytopal template method, the basis functions are constructed from template tensors associated with the geometric polytopes (vertices, edges, faces etc.) of the reference simplex and any scalar-valued $H^1$-conforming finite element space. From this starting point we can construct the Regge, Hellan-Herrmann-Johnson, Pechstein-Schöberl, Hu-Zhang, Hu-Ma-Sun and Gopalakrishnan-Lederer-Schöberl elements. Because the Hu-Zhang element and the Hu-Ma-Sun element cannot be mapped from the reference simplex to a physical simplex via standard double Piola mappings, we also demonstrate that the polytopal template tensors can be used to define a consistent mapping from a reference simplex even to a non-affine simplex in the physical mesh. Finally, we discuss the implications of element regularity with two numerical examples for the Reissner-Mindlin plate problem.

math.NA↗

arXiv2024

Intrinsic mixed-dimensional beam-shell-solid couplings in linear Cosserat continua via tangential differential calculus

We present an approach to the coupling of mixed-dimensional continua by employing the mathematically enriched linear Cosserat micropolar model. The kinematical reduction of the model to lower dimensional domains leaves its fundamental degrees of freedom intact. Consequently, the degrees of freedom intrinsically agree even at the interface with a domain of a different dimensionality. Thus, this approach circumvents the need for intermediate finite elements or mortar methods. We introduce the derivations of all models of various dimensions using tangential differential calculus. The coupling itself is then achieved by defining a mixed-dimensional action functional with consistent Sobolev trace operators. Finally, we present numerical examples involving a three-dimensional silicone-rubber block reinforced with a curved graphite shell on its lower surface, a three-dimensional silver block reinforced with a graphite plate and beams, and lastly, intersecting silver shells reinforced with graphite beams.

math.NA↗

arXiv2023

A Reissner-Mindlin plate formulation using symmetric Hu-Zhang elements via polytopal transformations

In this work we develop new finite element discretisations of the shear-deformable Reissner--Mindlin plate problem based on the Hellinger-Reissner principle of symmetric stresses. Specifically, we use conforming Hu-Zhang elements to discretise the bending moments in the space of symmetric square integrable fields with a square integrable divergence $\boldsymbol{M} \in \mathcal{HZ} \subset H^{\mathrm{sym}}(\mathrm{Div})$. The latter results in highly accurate approximations of the bending moments $\boldsymbol{M}$ and in the rotation field being in the discontinuous Lebesgue space $\boldsymbolϕ \in [L]^2$, such that the Kirchhoff-Love constraint can be satisfied for $t \to 0$. In order to preserve optimal convergence rates across all variables for the case $t \to 0$, we present an extension of the formulation using Raviart-Thomas elements for the shear stress $\mathbf{q} \in \mathcal{RT} \subset H(\mathrm{div})$. We prove existence and uniqueness in the continuous setting and rely on exact complexes for inheritance of well-posedness in the discrete setting. This work introduces an efficient construction of the Hu-Zhang base functions on the reference element via the polytopal template methodology and Legendre polynomials, making it applicable to hp-FEM. The base functions on the reference element are then mapped to the physical element using novel polytopal transformations, which are suitable also for curved geometries. The robustness of the formulations and the construction of the Hu-Zhang element are tested for shear-locking, curved geometries and an L-shaped domain with a singularity in the bending moments $\boldsymbol{M}$. Further, we compare the performance of the novel formulations with the primal-, MITC- and recently introduced TDNNS methods.

math.NA↗

arXiv2023

An a posteriori error estimator for the spectral fractional power of the Laplacian

We develop a novel a posteriori error estimator for the $L^2$ error committed by the finite element discretization of the solution of the fractional Laplacian. Our a posteriori error estimator takes advantage of the semi-discretization scheme using rational approximations which allow 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. In addition we propose an algorithm to adapt both the finite element mesh and the rational scheme in order to balance the discretization errors. 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.

math.NA↗

arXiv2022

SOniCS: Develop intuition on biomechanical systems through interactive error controlled simulations

This new approach allows the user to experiment with model choices easily and quickly without requiring in-depth expertise, as constitutive models can be modified by one line of code only. This ease in building new models makes SOniCS ideal to develop surrogate, reduced order models and to train machine learning algorithms for uncertainty quantification or to enable patient-specific simulations. SOniCS is thus not only a tool that facilitates the development of surgical training simulations but also, and perhaps more importantly, paves the way to increase the intuition of users or otherwise non-intuitive behaviors of (bio)mechanical systems. The plugin uses new developments of the FEniCSx project enabling automatic generation with FFCx of finite element tensors such as the local residual vector and Jacobian matrix. We validate our approach with numerical simulations such as manufactured solutions, cantilever beams, and benchmarks provided by FEBio. We reach machine precision accuracy and demonstrate the use of the plugin for a real-time haptic simulation involving a surgical tool controlled by the user in contact with a hyperelastic liver. We include complete examples showing the use of our plugin for simulations involving Saint Venant-Kirchhoff, Neo-Hookean, Mooney-Rivlin, and Holzapfel Ogden anisotropic models as supplementary material.

cs.MS↗

arXiv2022

Hierarchical a posteriori error estimation of Bank-Weiser type in the FEniCS Project

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.

math.NA↗

arXiv2021

Inverse deformation analysis: an experimental and numerical assessment using the FEniCS Project

In this paper, we develop a framework for solving inverse deformation problems using the FEniCS Project finite element software. We validate our approach with experimental imaging data acquired from a soft silicone beam under gravity. In contrast with inverse iterative algorithms that require multiple solutions of a standard elasticity problem, the proposed method can compute the undeformed configuration by solving only one modified elasticity problem. This modified problem has a complexity comparable to the standard one. The framework is implemented within an open-source pipeline enabling the direct and inverse deformation simulation directly from imaging data. We use the high-level Unified Form Language (UFL) of the FEniCS Project to express the finite element model in variational form and to automatically derive the consistent Jacobian. Consequently, the design of the pipeline is flexible: for example, it allows the modification of the constitutive models by changing a single line of code. We include a complete working example showing the inverse deformation of a beam deformed by gravity as supplementary material.

cs.CE↗

arXiv2018

A volume-averaged nodal projection method for the Reissner-Mindlin plate model

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.

math.NA↗

arXiv2017

Bayesian inference for the stochastic identification of elastoplastic material parameters: Introduction, misconceptions and insights

We discuss Bayesian inference (BI) for the probabilistic identification of material parameters. This contribution aims to shed light on the use of BI for the identification of elastoplastic material parameters. For this purpose a single spring is considered, for which the stress-strain curves are artificially created. Besides offering a didactic introduction to BI, this paper proposes an approach to incorporate statistical errors both in the measured stresses, and in the measured strains. It is assumed that the uncertainty is only due to measurement errors and the material is homogeneous. Furthermore, a number of possible misconceptions on BI are highlighted based on the purely elastic case.

cs.CE↗

arXiv2016

Containers for portable, productive and performant scientific computing

Containers are an emerging technology that hold promise for improving productivity and code portability in scientific computing. We examine Linux container technology for the distribution of a non-trivial scientific computing software stack and its execution on a spectrum of platforms from laptop computers through to high performance computing (HPC) systems. We show on a workstation and a leadership-class HPC system that when deployed appropriately there are no performance penalties running scientific programs inside containers. For Python code run on large parallel computers, the run time is reduced inside a container due to faster library imports. The software distribution approach and data that we present will help developers and users decide on whether container technology is appropriate for them. We also provide guidance for the vendors of HPC systems that rely on proprietary libraries for performance on what they can do to make containers work seamlessly and without performance penalty.

cs.DC↗