A Comparison of Numerical Methods used for\ud Finite Element Modelling of Soft Tissue\ud Deformation

Soft tissue deformation is often modelled using incompressible nonlinear elasticity, with solutions computed using the finite element method. There are a range of options available when using the finite element method, in particular, the polynomial degree of the basis functions used for interpolating position and pressure, and the type of element making up the mesh. We investigate the effect of these choices on the accuracy of the computed solution, using a selection of model problems motivated by typical deformations seen in soft tissue modelling. We set up model problems with discontinuous material properties (as is the case for the breast), steeply changing gradients in the body force (as found in contracting cardiac tissue), and discontinuous first derivatives in the solution at the boundary, caused by a discontinuous applied force (as in the breast during mammography). We find that the choice of pressure basis functions are vital in the presence of a material interface, higher-order schemes do not perform as well as may be expected when there are sharp gradients, and in general that it is important to take the expected regularity of the solution into account when choosing a numerical scheme

Two fluid space-time discontinuous Galerkin finite element method. Part I: numerical algorithm

A novel numerical method for two fluid flow computations is presented, which combines the space-time discontinuous Galerkin finite element discretization with the level set method and cut-cell based interface tracking. The space-time discontinuous Galerkin (STDG) finite element method offers high accuracy, an inherent ability to handle discontinuities and a very local stencil, making it relatively easy to combine with local {\it hp}-refinement. The front tracking is incorporated via cut-cell mesh refinement to ensure a sharp interface between the fluids. To compute the interface dynamics the level set method (LSM) is used because of its ability to deal with merging and breakup. Also, the LSM is easy to extend to higher dimensions. Small cells arising from the cut-cell refinement are merged to improve the stability and performance. The interface conditions are incorporated in the numerical flux at the interface and the STDG discretization ensures that the scheme is conservative as long as the numerical fluxes are conservative

Grid generation for the solution of partial differential equations

A general survey of grid generators is presented with a concern for understanding why grids are necessary, how they are applied, and how they are generated. After an examination of the need for meshes, the overall applications setting is established with a categorization of the various connectivity patterns. This is split between structured grids and unstructured meshes. Altogether, the categorization establishes the foundation upon which grid generation techniques are developed. The two primary categories are algebraic techniques and partial differential equation techniques. These are each split into basic parts, and accordingly are individually examined in some detail. In the process, the interrelations between the various parts are accented. From the established background in the primary techniques, consideration is shifted to the topic of interactive grid generation and then to adaptive meshes. The setting for adaptivity is established with a suitable means to monitor severe solution behavior. Adaptive grids are considered first and are followed by adaptive triangular meshes. Then the consideration shifts to the temporal coupling between grid generators and PDE-solvers. To conclude, a reflection upon the discussion, herein, is given

An Accurate and Robust Numerical Scheme for Transport Equations

En esta tesis se presenta una nueva técnica de discretización para ecuaciones de transporte en problemas de convección-difusión para el rango completo de números de Péclet. La discretización emplea el flujo exacto de una ecuación de transporte unidimensional en estado estacionario para deducir una ecuación discreta de tres puntos en problemas unidimensionales y cinco puntos en problemas bidimensionales. Con "flujo exacto" se entiende que se puede obtener la solución exacta en función de integrales de algunos parámetros del fluido y flujo, incluso si estos parámetros son vari- ables en un volumen de control. Las cuadraturas de alto orden se utilizan para lograr resultados numéricos cercanos a la precisión de la máquina, incluso con mallas bastas.Como la discretización es esencialmente unidimensional, no está garantizada una solución con precisión de máquina para problemas multidimensionales, incluso en los casos en que las integrales a lo largo de cada coordenada cartesiana tienen una primitiva. En este sentido, la contribución principal de esta tesis consiste en una forma simple y elegante de obtener soluciones en problemas multidimensionales sin dejar de utilizar la formulación unidimensional. Además, si el problema es tal que la solución tiene precisión de máquina en el problema unidimensional a lo largo de las líneas coordenadas, también la tendrá para el dominio multidimensional.In this thesis, we present a novel discretization technique for transport equations in convection-diffusion problems across the whole range of Péclet numbers. The discretization employs the exact flux of a steady-state one-dimensional transport equation to derive a discrete equation with a three-point stencil in one-dimensional problems and a five-point stencil in two-dimensional ones. With "exact flux" it is meant that the exact solution can be obtained as a function of integrals of some fluid and flow parameters, even if these parameters are variable across a control volume. High-order quadratures are used to achieve numerical results close to machine- accuracy even with coarse grids. As the discretization is essentially one-dimensional, getting the machine- accurate solution of multidimensional problems is not guaranteed even in cases where the integrals along each Cartesian coordinate have a primitive. In this regard, the main contribution of this thesis consists in a simple and elegant way of getting solutions in multidimensional problems while still using the one-dimensional formulation. Moreover, if the problem is such that the solution is machine-accurate in the one-dimensional problem along coordinate lines, it will also be for the multidimensional domain.<br /

Atomic electronic structure calculations with Hermite interpolating polynomials

We have recently described the implementation of atomic electronic structure calculations within the finite element method with numerical radial basis functions of the form $\chi_{\mu}(r)=r^{-1}B_{\mu}(r)$, where high-order Lagrange interpolating polynomials (LIPs) were used as the shape functions $B_{\mu}(r)$ [S. Lehtola, Int. J. Quantum Chem. 119, e25945 (2019)]. In this work, we discuss how $\chi_{\mu}(r)$ can be evaluated in a stable manner at small $r$ and also revisit the choice of the shape functions $B_{\mu}(r)$. Three kinds of shape functions are considered: in addition to the $\mathcal{C}^{0}$ continuous LIPs, we consider the analytical implementation of first-order Hermite interpolating polynomials (HIPs) that are $\mathcal{C}^{1}$ continuous, as well as numerical implementations of $n$-th order ($\mathcal{C}^{n}$ continuous) HIPs that are expressed in terms of an underlying high-order LIP basis. Furnished with the new implementation, we demonstrate that the first-order HIPs are reliable even with large numbers of nodes and that they also work with non-uniform element grids, affording even better results in atomic electronic structure calculations than LIPs with the same total number of basis functions. We demonstrate that discontinuities can be observed in the spin-$\sigma$ local kinetic energy $\tau_{\sigma}$ in small LIP basis sets, while HIP basis sets do not suffer from such issues; however, either set can be used to reach the complete basis set limit with smooth $\tau_{\sigma}$. Moreover, we discuss the implications of HIPs on calculations with meta-GGA functionals with a number of recent meta-GGA functionals, and find most Minnesota functionals to be ill-behaved. We also examine the potential usefulness of the explicit control over the derivative in HIPs for forming numerical atomic orbital basis sets, but find that confining potentials are still likely a better option.Comment: 25 pages, 9 figure