Well-Centered Triangulation

Meshes composed of well-centered simplices have nice orthogonal dual meshes (the dual Voronoi diagram). This is useful for certain numerical algorithms that prefer such primal-dual mesh pairs. We prove that well-centered meshes also have optimality properties and relationships to Delaunay and minmax angle triangulations. We present an iterative algorithm that seeks to transform a given triangulation in two or three dimensions into a well-centered one by minimizing a cost function and moving the interior vertices while keeping the mesh connectivity and boundary vertices fixed. The cost function is a direct result of a new characterization of well-centeredness in arbitrary dimensions that we present. Ours is the first optimization-based heuristic for well-centeredness, and the first one that applies in both two and three dimensions. We show the results of applying our algorithm to small and large two-dimensional meshes, some with a complex boundary, and obtain a well-centered tetrahedralization of the cube. We also show numerical evidence that our algorithm preserves gradation and that it improves the maximum and minimum angles of acute triangulations created by the best known previous method.Comment: Content has been added to experimental results section. Significant edits in introduction and in summary of current and previous results. Minor edits elsewher

Tetrahedral mesh improvement using moving mesh smoothing, lazy searching flips, and RBF surface reconstruction

Given a tetrahedral mesh and objective functionals measuring the mesh quality which take into account the shape, size, and orientation of the mesh elements, our aim is to improve the mesh quality as much as possible. In this paper, we combine the moving mesh smoothing, based on the integration of an ordinary differential equation coming from a given functional, with the lazy flip technique, a reversible edge removal algorithm to modify the mesh connectivity. Moreover, we utilize radial basis function (RBF) surface reconstruction to improve tetrahedral meshes with curved boundary surfaces. Numerical tests show that the combination of these techniques into a mesh improvement framework achieves results which are comparable and even better than the previously reported ones.Comment: Revised and improved versio

Parallel implementation of an optimal two level additive Schwarz preconditioner for the 3-D finite element solution of elliptic partial differential equations

This paper presents a description of the extension and parallel implementation of a new two level additive Schwarz (AS) preconditioner for the solution of 3-D elliptic partial differential equations (PDEs). This preconditioner, introduced in Bank et al. (SIAM J. Sci. Comput. 2002; 23: 1818), is based upon the use of a novel form of overlap between the subdomains which makes use of a hierarchy of meshes: with just a single layer of overlapping elements at each level of the hierarchy. The generalization considered here is based upon the restricted AS approach reported in (SIAM J. Sci. Comput. 1999; 21: 792) and the parallel implementation is an extension of work in two dimensions (Concurrency Comput. Practice Experience 2001; 13: 327)

3D mesh processing using GAMer 2 to enable reaction-diffusion simulations in realistic cellular geometries

Recent advances in electron microscopy have enabled the imaging of single cells in 3D at nanometer length scale resolutions. An uncharted frontier for in silico biology is the ability to simulate cellular processes using these observed geometries. Enabling such simulations requires watertight meshing of electron micrograph images into 3D volume meshes, which can then form the basis of computer simulations of such processes using numerical techniques such as the Finite Element Method. In this paper, we describe the use of our recently rewritten mesh processing software, GAMer 2, to bridge the gap between poorly conditioned meshes generated from segmented micrographs and boundary marked tetrahedral meshes which are compatible with simulation. We demonstrate the application of a workflow using GAMer 2 to a series of electron micrographs of neuronal dendrite morphology explored at three different length scales and show that the resulting meshes are suitable for finite element simulations. This work is an important step towards making physical simulations of biological processes in realistic geometries routine. Innovations in algorithms to reconstruct and simulate cellular length scale phenomena based on emerging structural data will enable realistic physical models and advance discovery at the interface of geometry and cellular processes. We posit that a new frontier at the intersection of computational technologies and single cell biology is now open.Comment: 39 pages, 14 figures. High resolution figures and supplemental movies available upon reques

Finite Element Modeling Driven by Health Care and Aerospace Applications

This thesis concerns the development, analysis, and computer implementation of mesh generation algorithms encountered in finite element modeling in health care and aerospace. The finite element method can reduce a continuous system to a discrete idealization that can be solved in the same manner as a discrete system, provided the continuum is discretized into a finite number of simple geometric shapes (e.g., triangles in two dimensions or tetrahedrons in three dimensions). In health care, namely anatomic modeling, a discretization of the biological object is essential to compute tissue deformation for physics-based simulations. This thesis proposes an efficient procedure to convert 3-dimensional imaging data into adaptive lattice-based discretizations of well-shaped tetrahedra or mixed elements (i.e., tetrahedra, pentahedra and hexahedra). This method operates directly on segmented images, thus skipping a surface reconstruction that is required by traditional Computer-Aided Design (CAD)-based meshing techniques and is convoluted, especially in complex anatomic geometries. Our approach utilizes proper mesh gradation and tissue-specific multi-resolution, without sacrificing the fidelity and while maintaining a smooth surface to reflect a certain degree of visual reality. Image-to-mesh conversion can facilitate accurate computational modeling for biomechanical registration of Magnetic Resonance Imaging (MRI) in image-guided neurosurgery. Neuronavigation with deformable registration of preoperative MRI to intraoperative MRI allows the surgeon to view the location of surgical tools relative to the preoperative anatomical (MRI) or functional data (DT-MRI, fMRI), thereby avoiding damage to eloquent areas during tumor resection. This thesis presents a deformable registration framework that utilizes multi-tissue mesh adaptation to map preoperative MRI to intraoperative MRI of patients who have undergone a brain tumor resection. Our enhancements with mesh adaptation improve the accuracy of the registration by more than 5 times compared to rigid and traditional physics-based non-rigid registration, and by more than 4 times compared to publicly available B-Spline interpolation methods. The adaptive framework is parallelized for shared memory multiprocessor architectures. Performance analysis shows that this method could be applied, on average, in less than two minutes, achieving desirable speed for use in a clinical setting. The last part of this thesis focuses on finite element modeling of CAD data. This is an integral part of the design and optimization of components and assemblies in industry. We propose a new parallel mesh generator for efficient tetrahedralization of piecewise linear complex domains in aerospace. CAD-based meshing algorithms typically improve the shape of the elements in a post-processing step due to high complexity and cost of the operations involved. On the contrary, our method optimizes the shape of the elements throughout the generation process to obtain a maximum quality and utilizes high performance computing to reduce the overheads and improve end-user productivity. The proposed mesh generation technique is a combination of Advancing Front type point placement, direct point insertion, and parallel multi-threaded connectivity optimization schemes. The mesh optimization is based on a speculative (optimistic) approach that has been proven to perform well on hardware-shared memory. The experimental evaluation indicates that the high quality and performance attributes of this method see substantial improvement over existing state-of-the-art unstructured grid technology currently incorporated in several commercial systems. The proposed mesh generator will be part of an Extreme-Scale Anisotropic Mesh Generation Environment to meet industries expectations and NASA\u27s CFD visio

Anisotropic Quadrilateral Mesh Optimization

In order to determine the validity and the quality of meshes, mesh optimization methods have been formulated with quality measures. The basic idea of mesh optimization is to relocate the vertices to obtain a valid mesh (untangling) or improve the mesh quality (smoothing), or both. We will look at a new algebraic way of calculating quality measure on quadrilateral meshes, based on triangular meshes in 2D as well as new optimization methods for simultaneous untangling and smoothing for severely deformed meshes. An innovative anisotropic diffusion method will be introduced for consideration of inner boundary deformation movements for quadrangle meshes in 2D

Variational tetrahedral meshing

In this paper, a novel Delaunay-based variational approach to isotropic tetrahedral meshing is presented. To achieve both robustness and efficiency, we minimize a simple mesh-dependent energy through global updates of both vertex positions and connectivity. As this energy is known to be the ∠1 distance between an isotropic quadratic function and its linear interpolation on the mesh, our minimization procedure generates well-shaped tetrahedra. Mesh design is controlled through a gradation smoothness parameter and selection of the desired number of vertices. We provide the foundations of our approach by explaining both the underlying variational principle and its geometric interpretation. We demonstrate the quality of the resulting meshes through a series of examples