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KARDOS - User"s Guide
(2002)
The adaptive finite element code {\sc Kardos} solves nonlinear parabolic systems of partial differential equations. It is applied to a wide range of problems from physics, chemistry, and engineering in one, two, or three space dimensions. The implementation is based on the programming language C. Adaptive finite element techniques are employed to provide solvers of optimal complexity. This implies a posteriori error estimation, local mesh refinement, and preconditioning of linear systems. Linearely implicit time integrators of {\em Rosenbrock} type allow for controlling the time steps adaptively and for solving nonlinear problems without using {\em Newton's} iterations. The program has proved to be robust and reliable. The user's guide explains all details a user of {\sc Kardos} has to consider: the description of the partial differential equations with their boundary and initial conditions, the triangulation of the domain, and the setting of parameters controlling the numerical algorithm. A couple of examples makes familiar to problems which were treated with {\sc Kardos}. We are extending this guide continuously. The latest version is available by network: {\begin{rawhtml} <A href="http://www.zib.de/Numerik/software/kardos/"> <i> Downloads.</i></a> \end{rawhtml}}
By computed tomography data (CT), the individual geometry of the mandible is quite well reproduced, also the separation between cortical and trabecular bone. Using anatomical knowledge about the architecture and the functional potential of the masticatory muscles, realistic situations were approximated. The solution of the underlying partial differential equations describing linear elastic material behaviour is provided by an adaptive finite element method. Estimations of the discretization error, local grid refinement, and multilevel techniques guarantee the reliability and efficiency of the method.
The correlation of the inner architecture of bone and its functional loading was already stated by Wolff in 1892. Our objective is to demonstrate this interdependence in the case of the human mandible. For this purpose, stress/strain profiles occuring at a human lateral bite were simulated. Additionally, by a combination of computer graphics modules, a three--dimensional volumetric visualization of bone mineral density could be given. Qualitative correspondences between the density profile of the jaw and the simulated stress/strain profiles could be pointed out. In the long run, this might enable the use of the simulation for diagnosis and prognosis. The solution of the underlying partial differential equations describing linear elastic material behaviour was provided by an adaptive finite element method. Estimates of the discretization errors, local grid refinement, and multilevel techniques guaranteed the reliability and efficiency of the method.
Structural mechanics simulation of bony organs is of general medical and biomechanical interest, because of the interdependence of the inner architecture of bone and its functional loading already stated by Wolff in 1892. This work is part of a detailed research project concerning the human mandible. By adaptive finite element techniques, stress/strain profiles occurring in the bony structure under biting were simulated. Estimates of the discretization errors, local grid refinement, and multilevel techniques guarantee the reliability and efficiency of the method. In general, our simulation requires a representation of the organ's geometry, an appropriate material description, and the load case due to teeth, muscle, or joint forces. In this paper, we want to focus on the influence of the masticatory system. Our goal is to capture the physiological situation as far as possible. By means of visualization techniques developed by the group, we are able to extract individual muscle fibres from computed tomography data. By a special algorithm, the fibres are expanded to fanlike (esp. for the musc. temporalis) coherent vector fields similar to the anatomical reality. The activity of the fibres can be adapted according to compartmentalisation of the muscles as measured by electromyological experiments. A refined sensitivity analysis proved remarkable impact of the presented approach on the simulation results.
We focus on the role of anisotropic elasticity in the simulation of the load distribution in a human mandible due to a lateral bite on the leftmost premolar. Based on experimental evidence, we adopt ``local''" orthotropy of the elastic properties of the bone tissue. Since the trajectories of anisotropic elasticity are not accessible from Computer Tomographic (CT) data, they will be reconstructed from (i) the organ's geometry and (ii) from coherent structures which can be recognized from the spatial distribution of the CT values. A sensitivity analysis comprising various 3D FE simulations reveals the relevance of elastic anisotropy for the load carrying behavior of a human mandible: Comparison of the load distributions in isotropic and anisotropic simulations indicates that anisotropy seems to ``spare''" the mandible from loading. Moreover, a maximum degree of anisotropy leads to kind of an load minimization of the mandible, expressed by a minimum of different norms of local strain, evaluated throughout the organ. Thus, we may suggest that anisotropy is not only relevant, but also in some sense ``optimal''.
The paper extends affine conjugate Newton methods from convex to nonconvex minimization, with particular emphasis on PDE problems originating from compressible hyperelasticity. Based on well-known schemes from finite dimensional nonlinear optimization, three different algorithmic variants are worked out in a function space setting, which permits an adaptive multilevel finite element implementation. These algorithms are tested on two well-known 3D test problems and a real-life example from surgical operation planning.
Reasons for the failure of adaptive methods to deliver improved efficiency when integrating monodomain models for myocardiac excitation are discussed. Two closely related techniques for reducing the computational complexity of linearly implicit integrators, deliberate sparsing and splitting, are investigated with respect to their impact on computing time and accuracy.
Pulse thermography of concrete structures is used in civil engineering for detecting voids, honeycombing and delamination. The physical situation is readily modeled by Fourier's law. Despite the simplicity of the PDE structure, quantitatively realistic numerical 3D simulation faces two major obstacles. First, the short heating pulse induces a thin boundary layer at the heated surface which encapsulates all information and therefore has to be resolved faithfully. Even with adaptive mesh refinement techniques, obtaining useful accuracies requires an unsatisfactorily fine discretization. Second, bulk material parameters and boundary conditions are barely known exactly. We address both issues by a semi-analytic reformulation of the heat transport problem and by parameter identification. Numerical results are compared with measurements of test specimens.
In this paper we present a self--adaptive finite element method to solve flame propagation problems in 3D. An implicit time integrator of Rosenbrock type is coupled with a multilevel approach in space. The proposed method is applied to an unsteady thermo--diffusive combustion model to demonstrate its potential for the solution of complicated problems.
The KASKADE toolbox defines an interface to a set of C subroutines which can be used to implement adaptive multilevel Finite Element Methods solving systems of elliptic equations in two and three space dimensions. The manual contains the description of the data structures and subroutines. The main modules of the toolbox are a runtime environment, triangulation and node handling, assembling, direct and iterative solvers for the linear systems, error estimators, refinement strategies, and graphic utilities. Additionally, we included appendices on the basic command language interface, on file formats, and on the definition of the partial differential equations which can be solved. The software is available on the ZIB ftp--server {\tt elib} in the directory {\tt pub/kaskade}. TR 93--5 supersedes TR 89--4 and TR 89--05.
KASKADE 3.0 User's Guide
(1995)
KASKADE 3.x was developed for the solution of partial differential equations in one, two, or three space dimensions. Its object-oriented implementation concept is based on the programming language C++$\,$.~Adaptive finite element techniques are employed to provide solution procedures of optimal computational complexity. This implies a posteriori error estimation, local mesh refinement and multilevel preconditioning. The program was designed both as a platform for further developments of adaptive multilevel codes and as a tool to tackle practical problems. Up to now we have implemented scalar problem types like stationary or transient heat conduction. The latter one is solved with the Rothe method, enabling adaptivity both in space and time. Some nonlinear phenomena like obstacle problems or two-phase Stefan problems are incorporated as well. Extensions to vector-valued functions and complex arithmetic are provided. This report helps to work with KASKADE Especially we \begin{itemize} \setlength{\parskip}{0ex} \item [{\bf --}] study a set of examples, \item [{\bf --}] explain how to define a user's problem and \item [{\bf --}] introduce a graphical user interface. \end{itemize} We are extending this guide continuously. The latest version is available by network.
KASKADE 3.0 was developed for the solution of partial differential equations in one, two, or three space dimensions. Its object-oriented implementation concept is based on the programming language C++$\,$.~Adaptive finite element techniques are employed to provide solution procedures of optimal computational complexity. This implies a posteriori error estimation, local mesh refinement and multilevel preconditioning. The program was designed both as a platform for further developments of adaptive multilevel codes and as a tool to tackle practical problems. Up to now we have implemented scalar problem types like stationary or transient heat conduction. The latter one is solved with the Rothe method, enabling adaptivity both in space and time. Some nonlinear phenomena like obstacle problems or two-phase Stefan problems are incorporated as well. Extensions to vector-valued functions and complex arithmetic are provided. %Such free boundary problems ... We have implemented several iterative solvers for both symmetric and unsymmetric systems together with multiplicative and additive multilevel preconditioners. Systems arising from the nonlinear problems can be solved with lately developed monotone multigrid methods. %An object-oriented concept was chosen for KASKADE~3.0, based on the programming %language C++$\,$. This should provide the desired extensibilty and clearly %reflect the structure of the code. %A direct sparse matrix solver (Harwell MA28) is included.
The C-implementation of KASKADE, an adaptive solver for linear elliptic differential equations in 2D, is object of a set of numerical experiments to analyze the use of resources (time and memory) with respect to numerical accuracy. We study the dependency of the reliability, robustness, and efficiency of the program from the parameters controlling the algorithm.
Adaptive Solutions of Nonlinear Parabolic Equations with Application to Hyperthermia Treatments
(1997)
We present a self-adaptive finite element method to solve nonlinear evolution problems in 3D. An implicit time integrator of Rosenbrock type is coupled with a multilevel approach in space. The proposed method is applied to hyperthermia treatments to demonstrate its potential for the solving of complicated problems.
The transient heating in an unsymmetrical coated hot--strip sensor was simulated with a self--adaptive finite element method. The first tests of this model show that it can determine with a small error the thermal conductivity of liquids, from the transient temperature rise in the hot--strip, deposited in a substrate and coated by an alumina spray.
We present a self--adaptive finite element method to solve combustion problems in 1D, 2D, and 3D. An implicit time integrator of Rosenbrock type is coupled with a multilevel approach in space. A posteriori error estimates are obtained by constructing locally higher order solutions involving all variables of the problem. Adaptive strategies such as step size control, spatial refinement and coarsening allow us to get economically an accurate solution. Various examples are presented to demonstrate practical applications of the proposed method.
We consider the approximate solution of selfadjoint elliptic problems in three space dimensions by piecewise linear finite elements with respect to a highly non-uniform tetrahedral mesh which is generated adaptively. The arising linear systems are solved iteratively by the conjugate gradient method provided with a multilevel preconditioner. Here, the accuracy of the iterative solution is coupled with the discretization error. as the performance of hierarchical bases preconditioners deteriorate in three space dimensions, the BPX preconditioner is used, taking special care of an efficient implementation. Reliable a-posteriori estimates for the discretization error are derived from a local comparison with the approximation resulting from piecewise quadratic elements. To illustrate the theoretical results, we consider a familiar model problem involving reentrant corners and a real-life problem arising from hyperthermia, a recent clinical method for cancer therapy.
We consider the discretization of obstacle problems for second order elliptic differential operators in three space dimensions by piecewise linear finite elements. Linearizing the discrete problems by suitable active set strategies, the resulting linear sub--problems are solved iteratively by preconditioned cg--iterations. We propose a variant of the BPX preconditioner and prove an $O(j)$ estimate for the resulting condition number. To allow for local mesh refinement we derive semi--local and local a posteriori error estimates. The theoretical results are illustrated by numerical computations.
An error controlled finite elemente method (FEM) for solving stationary Schrödinger equations in three space dimensions is proposed. The method is based on an adaptive space discretization into tetrahedra and local polynomial basis functions of order $p=1$--$5$ defined on these tetrahedra. According to a local error estimator the triangulation is automatically adapted to the solution. Numerical results for standard problems appearing in vibrational motion and molecular structure calculations are presented and discussed. Relative precisions better than 1e-8 are obtained. For equilateral H$_3^{++}$ the adaptive FEM turns out to be superior to global basis set expansions in the literature. Our precise FEM results exclude in a definite manner the stability or metastability of equilateral H$_3^{++}$ in its groundstate.
{\def\enorm {\mathop{\mbox{\boldmath{$|\!|$}}}\nolimits} Let $u \in H$ be the exact solution of a given self--adjoint elliptic boundary value problem, which is approximated by some $\tilde{u} \in {\cal S}$, $\cal S$ being a suitable finite element space. Efficient and reliable a posteriori estimates of the error $\enorm u - \tilde{u}\enorm $, measuring the (local) quality of $\tilde{u}$, play a crucial role in termination criteria and in the adaptive refinement of the underlying mesh. A well--known class of error estimates can be derived systematically by localizing the discretized defect problem using domain decomposition techniques. In the present paper, we provide a guideline for the theoretical analysis of such error estimates. We further clarify the relation to other concepts. Our analysis leads to new error estimates, which are specially suited to three space dimensions. The theoretical results are illustrated by numerical computations.}
We describe an optimization process specially designed for regional hyperthermia of deep seated tumors in order to achieve desired steady--state temperature distributions. A nonlinear three--dimensional heat transfer model based on temperature--dependent blood perfusion is applied to predict the temperature. Using linearly implicit methods in time and adaptive multilevel finite elements in space, we are able to integrate efficiently the instationary nonlinear heat equation with high accuracy. Optimal heating is obtained by minimizing an integral object function which measures the distance between desired and model predicted temperatures. A sequence of minima is calculated from successively improved constant--rate perfusion models employing a damped Newton method in an inner iteration. We compare temperature distributions for two individual patients calculated on coarse and fine spatial grids and present numerical results of optimizations for a Sigma 60 Applicator of the BSD 2000 Hyperthermia System.
We describe an optimization process specially designed for regional hyperthermia of deap seated tumors in order to achieve desired steady--state temperature distributions. A nonlinear three--dimensional heat--transfer model based on temperature--dependent blood perfusion is applied to predict the temperature. Optimal heating is obtained by minimizing an integral object function which measures the distance between desired and model predicted temperatures. Sequential minima are calculated from successively improved constant--rate perfusion models employing a damped Newton method in an inner iteration. Numerical results for a Sigma 60 applicator are presented. This work has been supported by Deutsche Forschungsgemeinschaft (DFG) within the Sonderforschungsbereich 273 \glqq Hyperthermie: Methodik und Klinik \grqq .
Dynamical process simulation of complex real-life problems often requires the use of modern algorithms, which automatically adapt both the time and space discretization in order to get error-controlled approximations of the solution. In this paper, a combination of linearly implicit time integrators of Rosenbrock type and adaptive multilevel finite elements based on a posteriori error estimates is presented. This approach has proven to work quite satisfactorily for a wide range of challenging practical problems. We show the performance of our adaptive method for two applications that arise in the study of flame balls and brine transport in porous media.
Adaptive Solutions of Nonlinear Parabolic Equations with Application to Hyperthermia Treatments
(1997)
The Impact of a Nonlinear Heat Transfer Model for Temperature Control in Regional Hyperthermia
(1999)
Consideration of Bone Inhomogeneity and Anisotropy in Deformation Analysis of a Human Mandible
(2005)
Effiziente und zuverlässige Finite-Elemente-Methoden zur Simulation des menschlichen Unterkiefers
(2003)