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We provide a primer to numerical methods based on Taylor series expansions such as generalized finite difference methods and collocation methods. We provide a detailed benchmarking strategy for these methods as well as all data files including input files, boundary conditions, point distribution and solution fields, so as to facilitate future benchmarking of new methods. We review traditional methods and recent ones which appeared in the last decade. We aim to help newcomers to the field understand the main characteristics of these methods and to provide sufficient information to both simplify implementation and benchmarking of new methods. Some of the examples are chosen within a subset of problems where collocation is traditionally known to perform sub-par, namely when the solution sought is non-smooth, i.e. contains discontinuities, singularities or sharp gradients. For such problems and other simpler ones with smooth solutions, we study in depth the influence of the weight function, correction function, and the number of nodes in a given support. We also propose new stabilization approaches to improve the accuracy of the numerical methods. In particular, we experiment with the use of a Voronoi diagram for weight computation, collocation method stabilization approaches, and support node selection for problems with singular solutions. With an appropriate selection of the above-mentioned parameters, the resulting collocation methods are compared to the moving least-squares method (and variations thereof), the radial basis function finite difference method and the finite element method. Extensive tests involving two and three dimensional problems indicate that the methods perform well in terms of efficiency (accuracy versus computational time), even for non-smooth solutions., Comment: Arch Computat Methods Eng (2019)

Errors in biomechanics simulations arise from modeling and discretization. Modeling errors are due to the choice of the mathematical model whilst discretization errors measure the impact of the choice of the numerical method on the accuracy of the approximated solution to this specific mathematical model. A major source of discretization errors is mesh generation from medical images, that remains one of the major bottlenecks in the development of reliable, accurate, automatic and efficient personalized, clinically-relevant Finite Element (FE) models in biomechanics. The impact of mesh quality and density on the accuracy of the FE solution can be quantified with \emph{a posteriori} error estimates. Yet, to our knowledge, the relevance of such error estimates for practical biomechanics problems has seldom been addressed, see [25]. In this contribution, we propose an implementation of some a posteriori error estimates to quantify the discretization errors and to optimize the mesh. More precisely, we focus on error estimation for a user-defined quantity of interest with the Dual Weighted Residual (DWR) technique. We test its applicability and relevance in two situations, corresponding to computations for a tongue and an artery, using a simplified setting, i.e., plane linearized elasticity with contractility of the soft-tissue modeled as a pre-stress. Our results demonstrate the feasibility of such methodology to estimate the actual solution errors and to reduce them economically through mesh refinement., Comment: 35 pages, 10 figures

This paper presents a novel methodology of local adaptivity for the frequency-domain analysis of the vibrations of Reissner-Mindlin plates. The adaptive discretization is based on the recently developed Geometry Independent Field approximaTion (GIFT) framework, which may be seen as a generalisation of the Iso-Geometric Analysis (IGA). Within the GIFT framework, we describe the geometry of the structure exactly with NURBS (Non-Uniform Rational B-Splines), whilst independently employing Polynomial splines over Hierarchical T-meshes (PHT)-splines to represent the solution field. The proposed strategy of local adaptivity, wherein a posteriori error estimators are computed based on inexpensive hierarchical $h-$refinement, aims to control the discretisation error within a frequency band. The approach sweeps from lower to higher frequencies, refining the mesh appropriately so that each of the free vibration mode within the targeted frequency band is sufficiently resolved. Through several numerical examples, we show that the GIFT framework is a powerful and versatile tool to perform local adaptivity in structural dynamics. We also show that the proposed adaptive local $h-$refinement scheme allows us to achieve significantly faster convergence rates than when using a uniform $h-$refinement.

This paper describes the use of the corotational cut Finite Element Method (FEM) for real-time surgical simulation. Users only need to provide a background mesh which is not necessarily conforming to the boundaries/interfaces of the simulated object. The details of the surface, which can be directly obtained from binary images, are taken into account by a multilevel embedding algorithm applied to elements of the background mesh that cut by the surface. Boundary conditions can be implicitly imposed on the surface using Lagrange multipliers. The implementation is verified by convergence studies with optimal rates. The algorithm is applied to various needle insertion simulations (e.g. for biopsy or brachytherapy) into brain and liver to verify the reliability of method, and numerical results show that the present method can make the discretisation independent from geometric description, and can avoid the complexity of mesh generation of complex geometries while retaining the accuracy of the standard FEM. Using the proposed approach is very suitable for real-time and patient specific simulations as it improves the simulation accuracy by taking into account automatically and properly the simulated geometry., Comment: 25 pages, 25 figures

This paper presents an approach to generalize the concept of isogeometric analysis (IGA) by allowing different spaces for parameterization of the computational domain and for approximation of the solution field. The method inherits the main advantage of isogeometric analysis, i.e. preserves the original, exact CAD geometry (for example, given by NURBS), but allows pairing it with an approximation space which is more suitable/flexible for analysis, for example, T-splines, LR-splines, (truncated) hierarchical B-splines, and PHT-splines. This generalization offers the advantage of adaptive local refinement without the need to re-parameterize the domain, and therefore without weakening the link with the CAD model. We demonstrate the use of the method with different choices of the geometry and field splines, and show that, despite the failure of the standard patch test, the optimum convergence rate is achieved for non-nested spaces., Comment: 39 pages, 24 figures, 10 tables, 2 algorithms

We present an error-controlled mesh refinement procedure for needle insertion simulation and apply it to the simulation of electrode implantation for deep brain stimulation, including brain shift. Our approach enables to control the error in the computation of the displacement and stress fields around the needle tip and needle shaft by suitably refining the mesh, whilst maintaining a coarser mesh in other parts of the domain. We demonstrate through academic and practical examples that our approach increases the accuracy of the displacement and stress fields around the needle without increasing the computational expense. This enables real-time simulations. The proposed methodology has direct implications to increase the accuracy and control the computational expense of the simulation of percutaneous procedures such as biopsy, brachytherapy, regional anesthesia, or cryotherapy and can be essential to the development of robotic guidance., Comment: 21 pages, 14 figures

Objective: To present the first real-time a posteriori error-driven adaptive finite element approach for real-time simulation and to demonstrate the method on a needle insertion problem. Methods: We use corotational elasticity and a frictional needle/tissue interaction model. The problem is solved using finite elements within SOFA. The refinement strategy relies upon a hexahedron-based finite element method, combined with a posteriori error estimation driven local $h$-refinement, for simulating soft tissue deformation. Results: We control the local and global error level in the mechanical fields (e.g. displacement or stresses) during the simulation. We show the convergence of the algorithm on academic examples, and demonstrate its practical usability on a percutaneous procedure involving needle insertion in a liver. For the latter case, we compare the force displacement curves obtained from the proposed adaptive algorithm with that obtained from a uniform refinement approach. Conclusions: Error control guarantees that a tolerable error level is not exceeded during the simulations. Local mesh refinement accelerates simulations. Significance: Our work provides a first step to discriminate between discretization error and modeling error by providing a robust quantification of discretization error during simulations., Comment: 12 pages, 16 figures, change of the title, submitted to IEEE TBME

We derive bounds for the minimum and maximum eigenvalues and the spectral condition number of matrices for isogeometric discretizations of elliptic partial differential equations in an open, bounded, simply connected Lipschitz domain $\Omega\subset \mathbb{R}^d$, $d\in\{2,3\}$. We consider refinements based on mesh size $h$ and polynomial degree $p$ with maximum regularity of spline basis functions. For the $h$-refinement, the condition number of the stiffness matrix is bounded above by a constant times $ h^{-2}$ and the condition number of the mass matrix is uniformly bounded. For the $p$-refinement, the condition number grows exponentially and is bounded above by $p^{2d+2}4^{pd}$ and $p^{2d}4^{pd}$ for the stiffness and mass matrices, respectively. Rigorous theoretical proofs of these estimates and supporting numerical results are provided.

We present functional-type a posteriori error estimates in isogeometric analysis. These estimates, derived on functional grounds, provide guaranteed and sharp upper bounds of the exact error in the energy norm. {Moreover, since these estimates do not contain any unknown/generic constants, they are fully computable, and thus provide quantitative information on the error.} By exploiting the properties of non-uniform rational B-splines, we present efficient computation of these error estimates. The numerical realization and the quality of the computed error distribution are addressed. The potential and the limitations of the proposed approach are illustrated using several computational examples., Comment: 28 pages, 18 figures, 18 tables, 1 algorithm

We derive computable upper bounds for the difference between an exact solution of the evolutionary convection-diffusion problem and an approximation of this solution. The estimates are obtained by certain transformations of the integral identity that defines the generalized solution. These estimates depend on neither special properties of the exact solution nor its approximation, and involve only global constants coming from embedding inequalities. The estimates are first derived for functions in the corresponding energy space, and then possible extensions to classes of piecewise continuous approximations are discussed., Comment: 10 pages

In this paper we show that the h-p spectral element method developed in \cite{pdstrk1,tomar-01,tomar-dutt-kumar-02} applies to elliptic problems in curvilinear polygons with mixed Neumann and Dirichlet boundary conditions provided that the Babuska--Brezzi inf--sup conditions are satisfied., Comment: 35 pages, 6 figures