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Project
Automatic, or algorithmic, differentiation addresses the need for the accurate
and efficient calculation of derivative values in scientific computing. To this
end procedural programs for the evaluation of problem-specific functions are
transformed into programs that also compute the required derivative values
at the same numerical arguments in floating point arithmetic. Disregarding
many important implementation issues, we examine in this article complexity
bounds and other more mathematical aspects of the program transformation
task sketched above.
Quasi-Newton methods based on least change secant updating
formulas that solve linear equations $Ax=b$ in $n=\dim(x)=\dim(b)$ steps
can be expected to solve corresponding smooth nonlinear
systems $n$-step quadratically, i.e. with an $r$-order
of $\rho = 2^{1/n} = 1 + 1/n +O(1/n^2)$. The best rate one can
possibly expect on general problems is given by the positive root
$\rho_n$ of $\rho^n(\rho -1)=1$, for which
$\rho_n-1 = \ln(n)/n + O(1/n^2)$. To show that this upper bound is
actually achieved one usually has to impose a priori some kind of
linear independence condition on the sequence of steps taken by the
quasi-Newton iteration in question. Without any such assumptions we
establish in this paper the convergence order $\rho_n$ for the
two-sided rank one formula proposed by Schlenkrich et al in \cite{SGW06}.
It requires the evaluation of adjoint vectors, is invariant with respect
to linear transformations on the variable domain and combines the
properties of bounded deterioration and heredity.
We present a new extension of the well-known
Perron-Frobenius theorem to regular matrix pairs $(E,A)$.
The new extension is based on projector chains and is motivated from
the solution of positive differential-algebraic systems or descriptor
systems. We present several examples where the new condition holds, whereas conditions
in previous literature are not satisfied.
We present globally convergent multigrid methods for the nonsymmetric
obstacle problems as arising from the discretization of Black–Scholes models of
American options with local volatilities and discrete data. No tuning or regularization
parameters occur. Our approach relies on symmetrization by transformation
and data recovery by superconvergence.
We present a domain decomposition approach for the computation of the
electromagnetic field within periodic structures. We use a
Schwarz method with transparent boundary conditions at the interfaces of
the domains. Transparent boundary conditions are approximated by the
perfectly matched layer method (PML). To cope with Wood anomalies
appearing in periodic structures an adaptive strategy to determine
optimal PML parameters is developed. \\ We focus on the application to
typical EUV lithography line masks. Light propagation within the
multi-layer stack of the EUV mask is treated analytically. This results
in a drastic reduction of the computational costs and allows for the
simulation of next generation lithography masks
on a standard personal computer.
We present a new solver for large-scale two-body contact problems in nonlinear elasticity. It is based on an SQP-trust-region approach.
This guarantees global convergence to a first-order critical point of
the energy functional. The linearized contact conditions are
discretized using mortar elements. A
special basis transformation known from linear contact problems
allows to use a monotone multigrid solver for the inner quadratic programs.
They can thus be solved with multigrid complexity. Our algorithm
does not contain any regularization or penalization parameters,
and can be used for all hyperelastic material models.
The purpose of the paper is to apply monotone multigrid methods
to static and dynamic biomechanical contact problems.
In space, a finite element method involving a mortar
discretization of the contact conditions is used.
In time, a new contact--stabilized Newmark scheme is presented.
Numerical experiments for a two body Hertzian contact problem
and a biomechanical knee problem are reported.
For the solution of nonlinear equation systems
quasi-Newton methods based on low-rank updates are of particular interest. We analyze a class
of TR1 update formulas to approximate the system Jacobian. The local q-superlinear convergence for nonlinear problems is proved for a particular subclass of updates. Moreover, we give an estimate of the r-order of convergence. Numerical results comparing the TR1 method to Newton's and other quasi-Newton methods atr presented.
A new concept is introduced for the adaptive finite element discretization of partial differential equations that have a sparsely
representable solution. Motivated by recent work on compressed sensing, a recursive mesh refinement procedure is presented that uses linear programming to find a good approximation to the sparse solution on a given refinement level. Then only those parts of the mesh are refined that belong to nonzero expansion coefficients. Error estimates for this procedure are refined and the behavior of the procedure is demonstrated via some simple elliptic model problems.
Interior Point Methods in Function Space for State Constraints - Inexact Newton and Adaptivity
(2009)
We consider an interior point method in function space for PDE constrained optimal control problems with state constraints. Our emphasis is on the construction and analysis of an algorithm that integrates a Newton path-following method with adaptive grid refinement. This is done in the framework of inexact Newton methods in function space, where the discretization error of each Newton step is controlled by adaptive grid refinement in the innermost loop. This allows to perform most of the required Newton steps on coarse grids, such that the overall computational time is dominated by the last few steps. For this purpose we propose an a-posteriori error estimator for a problem suited norm.
A continuity result for Nemyckii Operators and some applications in PDE constrained optimal control
(2008)
This work explores two applications of a classical result on the continuity of Nemyckii operators to optimal control with PDEs. First, we present an alternative approach to the analysis of Newton's method for function space problems involving semi-smooth Nemyckii operators. A concise proof for superlinear convergence is presented, and sharpened bounds on the rate of convergence are derived. Second, we derive second order sufficient conditions for problems, where the underlying PDE has poor regularity properties. We point out that the analytical structure in both topics is essentially the same.
We propose and analyse an interior point path-following method in function space
for state constrained optimal control. Our emphasis is on proving convergence in
function space and on constructing a practical path-following algorithm. In particular, the introduction of a pointwise damping step leads to a very efficient method, as verified by numerical experiments.
We consider hybrid systems of differential-algebraic equations and present
a general framework for general nonlinear over- and underdetermined hybrid
systems that allows the
analysis of existence and uniqueness and the application of index reduction
methods for hybrid differential-algebraic systems.
A particular difficulty in the numerical simulation of hybrid systems is
(numerical) chattering, i.e., fast oscillations between modes of operations.
A regularization technique using sliding modes allows to regularize the
system behavior in the case of chattering.
Further, we show how chattering behavior during the numerical solution can
be prevented using sliding mode simulation. The advantage of the sliding mode
simulation is illustrated by numerical examples.
A generalization of the method of Chu, Liu and Mehrmann
for the computation of the Hamiltonian real Schur form is presented.
The new method avoids some of the difficulties that may arise when
a Hamiltonian matrix has tightly clustered groups of eigenvalues.
A detailed analysis of the method is presented and several numerical examples demonstrate the superior behavior of the method.
We present and analyze novel hierarchical a posteriori error estimates
for self-adjoint elliptic obstacle problems.
Our approach differs from straightforward, but non-reliable estimators~\cite{RHWHoppe_RKornhuber_1994a}
by an additional extra term accounting for the deviation
of the discrete free boundary in the localization step.
We prove efficiency and reliability
on a saturation assumption and a regularity condition on the underlying grid.
Heuristic arguments suggest
that the extra term is of higher order and preserves full locality.
Numerical computations confirm our theoretical findings.
The main focus of this paper is on an a-posteriori analysis for the method of proper orthogonal decomposition (POD) applied to optimal control problems governed by
parabolic and elliptic PDEs. Based on a perturbation method it is deduced how far the suboptimal
control, computed on the basis of the POD model, is from the (unknown)
exact one. Numerical examples illustrate the realization of the proposed approach for linear-quadratic problems governed by parabolic and elliptic partial differential equations.
The complexity of molecular kinetics can be reduced significantly by a restriction to metastable conformations which are almost invariant sets of molecular dynamical systems. With the Robust Perron Cl uster Analysis PCCA+, developed by Weber and Deuflhard, we have a tool available which can be used to identify these conformations from a transition probability matrix. This method can also be applied to the corresponding transition rate matrix which provides important information concerning transition pathways of single molecules. In the present paper, we explain the relationship between these tw o concepts and the extraction of conformation kinetics from transition rates. Moreover, we show how transition rates can be approximated and conclude with numerical examples.
Wigner functions are functions on classical phase space, which are in one-to-one correspondence to square integrable functions on configuration space. For molecular quantum systems, classical transport of Wigner functions provides the basis of asymptotic approximation methods in the high energy regime. The article addresses the sampling of Wigner functions by Monte Carlo techniques. The approximation step is realized by an adaption of the Metropolis algorithm for real-valued functions with disconnected support. The quadrature, which computes values of the Wigner function, uses importance sampling with a Gaussian weight function. The numerical experiments combine the sampling with a surface hopping algorithm for non-adiabatic quantum dynamics. In agreement with theoretical considerations, the obtained results show an accuracy of two to four percent.
In this review, we intend to clarify the underlying ideas and the relations
between various multigrid methods ranging from subset decomposition,
to projected subspace decomposition and truncated multigrid.
In addition, we present a novel globally convergent inexact active set method
which is closely related to truncated multigrid. The numerical properties
of algorithms are carefully assessed by means of a degenerate problem and
a problem with a complicated coincidence set.
We present a new inexact nonsmooth Newton method for the solution
of convex minimization problems with piecewise smooth, pointwise
nonlinearities. The algorithm consists of a nonlinear smoothing
step on the fine level and a linear coarse correction.
Suitable postprocessing guarantees global convergence
even in the case of a single multigrid step for each linear subproblem.
Numerical examples show that the overall efficiency
is comparable to multigrid for similar linear problems.
In this paper, we propose and investigate numerical methods based on QR factorization for computing all or some Lyapunov or Sacker-Sell spectral intervals for
linear differential-algebraic equations.
Furthermore, a perturbation and error analysis for these methods is presented. We
investigate how errors in the data and in the numerical integration affect the
accuracy of the approximate spectral intervals. Although we need to integrate
numerically some differential-algebraic systems on usually very long
time-intervals, under certain assumptions, it is shown that the error of the
computed spectral intervals can be controlled by the local error of numerical
integration and the error in solving the algebraic constraint.
Some numerical examples are presented to illustrate the theoretical results.
Motivated by the analysis of passive control systems, we undertake a detailed perturbation analysis of Hamiltonian matrices that have eigenvalues on the imaginary axis. We construct minimal Hamiltonian perturbations that move and coalesce eigenvalues of opposite sign characteristic to form multiple eigenvalues with mixed sign characteristics, which are then moved from the imaginary axis to specific locations in the complex plane by small Hamiltonian perturbations. We also present a numerical method to compute upper bounds for the minimal perturbations that move all eigenvalues of a given Hamiltonian matrix outside a vertical strip along the imaginary axis.
The PSurface Library
(2010)
We describe psurface, a C++ library that allows to store and access piecewise linear mappings between simplicial surfaces in $\R^2$ and $\R^3$. These mappings are stored in a graph data structure and can be constructed explicitly, by projection, or by surface simplification. Piecewise linear maps can be used, e.g., to construct boundary
approximations for finite element grids, and grid intersections for domain decomposition methods. In computer graphics the mappings allow to build level-of-detail representations as well as texture- and bump maps. We document the data structures and algorithms used and show how \psurface is used in the numerical analysis framework Dune
and the visualization software Amira.
This paper is devoted to the numerical approximation of Lyapunov and Sacker-Sell spectral intervals for linear differential-algebraic equations (DAEs). The spectral analysis for DAEs is improved and the concepts of leading directions and solution subspaces associated with spectral intervals are extended to DAEs. Numerical methods
based on smooth singular value decompositions are introduced for computing all or only some spectral intervals and their associated leading directions. The numerical algorithms as well as implementation issues are discussed in detail and numerical examples are presented to illustrate the theoretical results.
This paper presents three different adaptive algorithms for eigenvalue problems
associated with non-selfadjoint partial differential
operators. The basis for the developed algorithms is a homotopy method.
The homotopy method starts from a well-understood selfadjoint problem,
for which well-established adaptive methods are available.
Apart from the adaptive grid refinement, the progress of the homotopy as
well as the solution of the iterative method are adapted to balance the contributions
of the different error sources.
The first algorithm balances the homotopy, discretization and approximation errors with respect
to a fixed step-size $\tau$ in the homotopy.
The second algorithm combines the adaptive step-size control for the homotopy
with an adaptation in space that ensures an error below a fixed tolerance $\varepsilon$.
The third algorithm allows the complete adaptivity in space,
homotopy step-size as well as the iterative algebraic eigenvalue solver.
All three algorithms are compared in numerical examples.
In this work we propose a general framework for the structured perturbation
analysis of several classes of structured matrix polynomials in homogeneous
form, including complex symmetric, skew-symmetric, even and odd matrix polynomials. We introduce structured backward errors for approximate eigenvalues and eigenvectors and we construct minimal structured perturbations such that an approximate eigenpair is an exact eigenpair of an appropriately perturbed matrix polynomial. This work extends previous work for the non-homogeneous case (we include infinite eigenvalues) and we show that the structured backward errors improve the known unstructured backward errors.
The paper proposes goal-oriented error estimation and mesh refinement
for optimal control problems with elliptic PDE constraints using the value
of the reduced cost functional as quantity of interest. Error representation,
hierarchical error estimators, and greedy-style error indicators are derived and
compared to their counterparts when using the all-at-once cost functional as
quantity of interest. Finally, the efficiency of the error estimator and generated
meshes are demonstrated on numerical examples.
We investigate geodesic finite elements for functions with values in a space of zero curvature, like a torus or the M\"obius strip. Unlike in the general case, a closed-form expression for geodesic finite element functions is then available. This simplifies computations, and allows us to prove optimal estimates for the interpolation error in 1d and 2d. We also show the somewhat surprising result that the discretization by Kirchhoff transformation of the Richards equation proposed by Berninger et al. is a discretization by geodesic finite elements in the manifold $\mathbb{R}$ with a special metric.
We propose a generalization of the Structured Doubling Algorithm (SDA) to compute invariant subspaces
of structured matrix pencils
that arise in the context of solving linear quadratic optimal control problems.
The new algorithm is
designed to attain better accuracy when the classical Riccati equation approach for the solution of the optimal control problem is not well suited because
the stable and unstable invariant subspaces are not well separated (due to eigenvalues near or on the imaginary
axis) or in the case when the Riccati solution does not exist at all. We analyze the convergence
of the method and compare the new method with the classical SDA algorithm as well as some recent structured QR-methods.
This paper presents concepts and implementation of the finite element toolbox Kaskade 7, a flexible C++ code for solving elliptic and parabolic PDE systems. Issues such as problem formulation, assembly and adaptivity are discussed at the example of optimal control problems. Trajectory compression for parabolic optimization problems is considered as a case study.
Deflated and augmented Krylov subspace methods: Basic Facts and a Breakdown-free deflated MINRES
(2011)
In this paper we consider deflation and augmentation techniques for accelerating
the convergence of Krylov subspace methods for the solution of nonsingular linear
algebraic systems. The two techniques are conceptually different from
preconditioning. Deflation "removes" certain parts from the operator, while
augmentation adds a subspace to the Krylov subspace. Both approaches have been
used in a variety of methods and settings. For Krylov subspace methods that
satisfy a (Petrov-) Galerkin condition we show that augmentation can in general
be achieved implicitly by projecting the residuals appropriately and correcting
the approximate solutions in a final step. In this context, we analyze known
methods to deflate CG, GMRes and MinRes. Our analysis reveals that the recently
proposed RMinRes method can break down. We show how such breakdowns can be
avoided by choosing a special initial guess, and we derive a breakdown-free
deflated MinRes method. In numerical experiments we study the properties of
different variants of MinRes analyzed in this paper.
One of the most challenging problems in dynamic concurrent multiscale
simulations is the reflectionless transfer of physical quantities between the
different scales. In particular, when coupling molecular dynamics and finite
element discretizations in solid body mechanics, often spurious wave reflections
are introduced by the applied coupling technique. The reflected waves are
typically of high frequency and are arguably of little importance in the domain
where the finite element discretization drives the simulation.
In this work, we provide an analysis of this phenomenon.
Based on the gained
insight, we derive a new coupling approach, which neatly separates high and low
frequency waves. Whereas low frequency waves are permitted to
bridge the scales, high frequency waves can be removed by applying damping techniques without affecting the coupled share of the solution. As a consequence, our new method almost completely eliminates unphysical wave reflections and deals in a consistent way with waves of arbitrary frequencies. The separation of
wavelengths is achieved by employing a discrete $L^2$-projection, which acts as a
low pass filter. Our coupling constraints enforce matching in the range of this projection. With respect to the numerical realization this approach
has the advantage of a small number of constraints, which is computationally
efficient. Numerical results in one and two dimensions confirm our theoretical
findings and illustrate the performance of our new weak coupling approach.
We investigate optimal elliptic
regularity (within the scale of Sobolev spaces) of anisotropic
div--grad operators in three dimensions at a multi-material vertex on
the Neumann boundary part of a polyhedral spatial domain. The
gradient of a solution to the corresponding elliptic PDE (in a
neighbourhood of the vertex) is integrable to an index greater than
three.
We consider Large Deformation Diffeomorphic Metric Mapping of general $m$-currents. After stating an optimization algorithm in the function space of admissable morph generating velocity fields, two innovative aspects in this framework are presented and numerically investigated: First, we spatially discretize the velocity field with conforming adaptive finite elements and discuss advantages of this new approach. Second, we directly compute the temporal evolution of discrete $m$-current attributes.
We consider the mechanical coupling of a geometrically exact Cosserat rod to a linear elastic continuum. The coupling conditions are formulated in the nonlinear rod configuration space. We describe a Dirichlet--Neumann algorithm for the coupled system, and use it to simulate the static stresses in a human knee joint, where the Cosserat rods are models for the ligaments.
In optimal control problems with nonlinear time-dependent 3D PDEs, full 4D discretizations are usually prohibitive due to the storage requirement. For this reason gradient and Newton type methods working on the reduced functional are often employed. The computation of the reduced gradient requires one solve of the state equation forward in time, and one backward solve of the adjoint equation. The state enters into the adjoint equation, again requiring the storage of a full 4D data set. We propose a lossy compression algorithm using an inexact but cheap predictor for the state data, with additional entropy coding of prediction errors. As the data is used inside a discretized, iterative algorithm, lossy compression
maintaining a certain error bound turns out to be sufficient.
We introduce geodesic finite elements as a conforming way to discretize partial differential equations for functions $v : \Omega \to M$, where $\Omega$ is an open subset of $\R^d$ and $M$ is a Riemannian manifold. These geodesic finite elements naturally generalize standard first-order
finite elements for Euclidean spaces. They also generalize the geodesic finite elements proposed for $d=1$ by the author. Our formulation is equivariant under isometries of $M$, and hence preserves objectivity of continuous problem formulations. We concentrate on partial differential equations that can be formulated as minimization problems. Discretization leads to algebraic minimization problems on product manifolds $M^n$. These can be solved efficiently
using a Riemannian trust-region method. We propose a monotone multigrid method to solve the constrained inner problems with linear multigrid speed. As an example we numerically compute harmonic maps from a domain in $\R^3$
to $S^2$.
Logical modeling of biological regulatory networks gives rise to a representation of the system's dynamics as a so-called state transition graph. Analysis of such a graph in its entirety allows for a comprehensive understanding of the functionalities and behavior of the modeled system. However, the size of the vertex set of the graph is exponential in the number of the network components making analysis costly, motivating development of reduction methods. In this paper, we present results allowing for a complete description of an asynchronous state transition graph of a Thomas network solely based on the analysis of the subgraph induced by certain extremal states. Utilizing this notion, we compare the behavior of a simple multi-valued network and a corresponding Boolean network and analyze the conservation of dynamical properties between them. Understanding the relation between such coarser and finer models is a necessary step towards meaningful network reduction as well as model refinement methods.
Mathematical modeling often helps to provide a systems perspective on gene regulatory networks. In particular, qualitative approaches are useful when detailed kinetic information is lacking. Multiple methods have been developed that implement qualitative information in different ways, e.g., in purely discrete or hybrid discrete/continuous models. In this paper, we compare the discrete asynchronous logical modeling formalism for gene regulatory networks due to R. Thomas with piecewise affine differential equation models.
We provide a local characterization of the qualitative dynamics of a piecewise affine differential equation model using the discrete dynamics of a corresponding Thomas model. Based on this result, we investigate the consistency of higher-level dynamical properties such as attractor characteristics and reachability. We show that although the two approaches are based on equivalent information, the resulting qualitative dynamics are different. In particular, the dynamics of the piecewise affine differential equation model is not a simple refinement of the dynamics of the Thomas model.
The authors propose a recycling MINRES scheme for a solution of subsequent self-adjoint linear systems as appearing, for example, in the Newton process for solving nonlinear equations. Ritz vectors are automatically extracted from one MINRES run and then used for self-adjoint deflation in the next. The method is designed to work with a preconditioner and arbitrary inner products. Numerical experiments with nonlinear Schrödinger equations indicate a substantial decrease in computation time when recycling is used.
We consider a shape implant design problem that arises in the context of facial surgery. We introduce a reformulation as an optimal control problem, where the control acts as a boundary force. The state is modelled as a minimizer of a polyconvex hyperelastic energy functional. We show existence of optimal solutions and derive - on a formal level - first order optimality conditions. Finally, preliminary numerical results are presented.
The pole condition approach for deriving transparent boundary conditions is extended to the time-dependent, two-dimensional case. Non-physical modes of the solution are identified by the position of poles of the solution's spatial Laplace transform in the complex plane. By requiring the Laplace transform to be analytic on some
problem dependent complex half-plane, these modes can be
suppressed. The resulting algorithm computes a finite number of coefficients of a series expansion of the Laplace transform, thereby providing an approximation to the exact boundary condition. The resulting error decays super-algebraically with the number of coefficients, so relatively few additional degrees of freedom are
sufficient to reduce the error to the level of the discretization error in the interior of the computational domain. The approach shows good results for the Schroedinger and the drift-diffusion equation
but, in contrast to the one-dimensional case, exhibits instabilities for the wave and Klein-Gordon equation. Numerical examples are shown that demonstrate the good performance in the former and the instabilities in the latter case.
Flux variability analysis (FVA) is an important tool to further analyze the results obtained by flux balance analysis (FBA) on genome-scale metabolic networks. Standard FVA may predict unbounded fluxes through some reactions in the network even if the nutrient uptake rate is bounded. These fluxes violate the second law of thermodynamics. They may be eliminated by extending flux variability analysis with thermodynamic constraints.
We present a new algorithm for efficient flux variability (and flux balance) analysis with thermodynamic constraints, suitable for analyzing genome-scale metabolic networks. We first show that flux balance analysis with thermodynamic constraints is NP-hard. Then we derive a theoretical tractability result, which can be applied to metabolic networks in practice. We use this result to develop a new constraint programming algorithm Fast-tFVA for fast flux variability analysis with thermodynamic constraints (tFVA). Computational comparisons with previous methods demonstrate the efficiency of the new method. For tFVA, a speed-up of factor 30-300 is achieved.
In an analysis of genome-scale metabolic networks in the BioModels database, we found that in 485 out of 716 networks additional irreversible or fixed reactions could be detected.
This article describes Fortran 77 subroutines for computing eigenvalues and invariant subspaces
of Hamiltonian and skew-Hamiltonian matrices. The implemented algorithms are based on orthogonal
symplectic decompositions, implying numerical backward stability as well as symmetry
preservation for the computed eigenvalues. These algorithms are supplemented with balancing and
block algorithms, which can lead to considerable accuracy and performance improvements. As a
by-product, an efficient implementation for computing symplectic QR decompositions is provided.
We demonstrate the usefulness of the subroutines for several, practically relevant examples.
Stewart's recently introduced Krylov-Schur algorithm
is a modification of the implicitly restarted Arnoldi algorithm which
employs reordered Schur decompositions to perform restarts and de-
ations in a numerically reliable manner. This paper describes a variant
of the Krylov-Schur algorithm suitable for addressing eigenvalue
problems associated with products of large and sparse matrices. It
performs restarts and de
ations via reordered periodic Schur decompositions
and, by taking the product structure into account, it is
capable to achieve qualitatively better approximations to the eigenvalues
of small magnitude.
The role of larger bulges in the QR algorithm is controversial. Large bulges are infamous
for having a strong, negative influence on the convergence of the implicit shifted QR algorithm.
This paper provides a new explanation of this shift blurring effect by connecting the computation of
the first column of the shift polynomial to the notoriously ill-conditioned pole placement problem.
To avoid shift blurring, modern variants of the QR algorithm employ chains of tightly coupled tiny
bulges instead of one large bulge. It turns out that larger bulges still play a positive role in these
variants; a slight increase of the bulge sizes often results in considerable performance improvements.
We investigate the condition number for a complex eigenvalue of a real matrix under
real perturbations. Based on an explicit formula, it is shown that this number is never
smaller than 1/
p
2 times the corresponding condition number with respect to complex
perturbations. This result can be generalized to the condition number of an arbitrary
complex-valued function under real perturbations. This extends to related condition
numbers.