Mesh generation for voxel -based objects

A new physically-based approach to unstructured mesh generation via Monte-Carlo simulation is proposed. Geometrical objects to be meshed are represented by systems of interacting particles with a given interaction potential. A new way of distributing nodes in complex domains is proposed based on a concept of dynamic equilibrium ensemble, which represents a liquid state of matter. The algorithm is simple, numerically stable and produces uniform node distributions in domains of complex geometries and different dimensions. Well-shaped triangles or tetrahedra can be created by connecting a set of uniformly-spaced nodes. The proposed method has many advantages and potential applications.;The new method is applied to the problem of meshing of voxel-based objects. By customizing system potential energy function to reflect surface features, particles can be distributed into desired locations, such as sharp corners and edges. Feature-preserved surface mesh can then be constructed by connecting the node set.;A heuristic algorithm using an advancing front approach is proposed to generate triangulated surface meshes on voxel-based objects. The resultant surface meshes do not inherit the anisotropy of the underlying hexagonal grid. However, the important surface features, such as edges and corners may not be preserved in the mesh.;To overcome this problem, surface features such as edges, corners need to be detected. A new approach of edge capturing is proposed and demonstrated. The approach is based on a Laplace solver with incomplete Jacobi iterations, and as such is very simple and efficient. This edge capturing approach combined with the mesh generation methods above forms a simple and robust technique of unstructured mesh generation on voxel-based objects.;A graphical user interface (GUI) capable of complex geometric design and remote simulation control was implemented. The GUI was used in simulations of large fuel-cell stacks. It enables one to setup, run and monitor simulations remotely through secure shell (SSH2) connections. A voxel-based 3D geometrical modeling module is built along with the GUI. The flexibility of voxel-based geometry representation enables one to use this technique for both geometric design and visualization of volume data

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

Curvature bounds for surfaces in hyperbolic 3-manifolds

We prove existence of thick geodesic triangulations of hyperbolic 3-manifolds and use this to prove existence of universal bounds on the principal curvatures of surfaces embedded in hyperbolic 3-manifolds.Comment: 21 pages, 9 figures, published version, added figures, fixed typo

Real-Time High-Quality Image to Mesh Conversion for Finite Element Simulations

Technological Advances in Medical Imaging have enabled the acquisition of images accurately describing biological tissues. Finite Element (FE) methods on these images provide the means to simulate biological phenomena such as brain shift registration, respiratory organ motion, blood flow pressure in vessels, etc. FE methods require the domain of tissues be discretized by simpler geometric elements, such as triangles in two dimensions, tetrahedra in three, and pentatopes in four. This exact discretization is called a mesh . The accuracy and speed of FE methods depend on the quality and fidelity of the mesh used to describe the biological object. Elements with bad quality introduce numerical errors and slower solver convergence. Also, analysis based on poor fidelity meshes do not yield accurate results specially near the surface. In this dissertation, we present the theory and the implementation of both a sequential and a parallel Delaunay meshing technique for 3D and ---for the first time--- 4D space-time domains. Our method provably guarantees that the mesh is a faithful representation of the multi-tissue domain in topological and geometric sense. Moreover, we show that our method generates graded elements of bounded radius-edge and aspect ratio, which renders our technique suitable for Finite Element analysis. A notable feature of our implementation is speed and scalability. The single-threaded performance of our 3D code is faster than the state of the art open source meshing tools. Experimental evaluation shows a more than 82% weak scaling efficiency for up to 144 cores, reaching a rate of more than 14.3 million elements per second. This is the first 3D parallel Delaunay refinement method to achieve such a performance, on either distributed or shared-memory architectures. Lastly, this dissertation is the first to develop and examine the sequential and parallel high-quality and fidelity meshing of general space-time 4D multi-tissue domains

Geometry Modeling for Unstructured Mesh Adaptation

The quantification and control of discretization error is critical to obtaining reliable simulation results. Adaptive mesh techniques have the potential to automate discretization error control, but have made limited impact on production analysis workflow. Recent progress has matured a number of independent implementations of flow solvers, error estimation methods, and anisotropic mesh adaptation mechanics. However, the poor integration of initial mesh generation and adaptive mesh mechanics to typical sources of geometry has hindered adoption of adaptive mesh techniques, where these geometries are often created in Mechanical Computer- Aided Design (MCAD) systems. The difficulty of this coupling is compounded by two factors: the inherent complexity of the model (e.g., large range of scales, bodies in proximity, details not required for analysis) and unintended geometry construction artifacts (e.g., translation, uneven parameterization, degeneracy, self-intersection, sliver faces, gaps, large tolerances be- tween topological elements, local high curvature to enforce continuity). Manual preparation of geometry is commonly employed to enable fixed-grid and adaptive-grid workflows by reducing the severity and negative impacts of these construction artifacts, but manual process interaction inhibits workflow automation. Techniques to permit the use of complex geometry models and reduce the impact of geometry construction artifacts on unstructured grid workflows are models from the AIAA Sonic Boom and High Lift Prediction are shown to demonstrate the utility of the current approach

3D Delaunay triangulation of non-uniform point distributions

In view of the simplicity and the linearity of regular grid insertion, a multi-grid insertion scheme is proposed for the three-dimensional Delaunay triangulation of non-uniform point distributions by recursive application of the regular grid insertion to an arbitrary subset of the original point set. The fundamentals and difficulties of three-dimensional Delaunay triangulation of highly non-uniformly distributed points by the insertion method are reviewed. Current strategies and methods of point insertions for non-uniformly distributed spatial points are discussed. An enhanced kd-tree insertion algorithm with a specified number of points in a cell and its natural sequence derived from a sandwich insertion scheme is also presented. The regular grid insertion, the enhanced kd-tree insertion and the multi-grid insertion have been rigorously studied with benchmark non-uniform distributions of 0.4–20 million points. It is found that the kd-tree insertion is more efficient in locating the base tetrahedron, but it is also more sensitive to the triangulation of non-uniform point distributions with a large amount of conflicting elongated tetrahedra. Including the grid construction time, multi-grid insertion is the most stable and efficient for all the uniform and non-uniform point distributions tested.postprin

Fully anisotropic split-tree adaptive refinement mesh generation using tetrahedral mesh stitching

Due to the myriad of geometric topologies that modern computational fluid dynamicists desire to mesh and run solutions on, the need for a robust Cartesian Mesh Generation algorithm is paramount. Not only do Cartesian meshes require less elements and often help resolve flow features but they also allow the grid generator to have a great deal of control in so far as element aspect ratio, size, and gradation. Fully Anisotropic Split-Tree Adaptive Refinement (FASTAR) is a code that allows the user to exert a great deal of control and ultimately generate a valid, geometry conforming mesh. Due to the split-tree nature and the use of volumetric pixels (voxels), non-unit aspect ratio meshing is easily achieved. Nodes are not generated until the end which mitigates tolerance issues. The tree is retained coherently, and viscous layers may be inserted in the space between the geometry and the Cartesian mesh before it is tetrahedralized. FASTAR uses tree traversal to determine neighbors robustly, and with the tetrahedralization of only a small amount of space around the geometry, sliver cells and inverted elements are avoided. The code uses Riemannian Metric Tensors to generate geometry-appropriate spacing and is capable of adaptive meshing from a spacing field generated either by the user or from solution data. FASTAR is a robust, general mesh generator that allows maximum flexibility with minimal post-processing

Parallelization of the Advancing Front Local Reconnection Mesh Generation Software Using a Pseudo-Constrained Parallel Data Refinement Method

Preliminary results of a long-term project entailing the parallelization of an industrial strength sequential mesh generator, called Advancing Front Local Reconnection (AFLR), are presented. AFLR has been under development for the last 25 years at the NSF/ERC center at Mississippi State University. The parallel procedure that is presented is called Pseudo-constrained (PsC) Parallel Data Refinement (PDR) and consists of the following steps: (i) use an octree data-decomposition scheme to divide the original geometry into subdomains (octree leaves), (ii) refine each subdomain with the proper adjustments of its neighbors using the given refinement code, and (iii) combine all subdomain data into a single, conforming mesh. Parallelism was achieved by implementing Pseudo-constrained Parallel Data Refinement AFLR (PsC.AFLR) on top of a runtime system called Parallel Runtime Environment for Multi-computer Applications (PREMA). During run time, the PsC.AFLR method exposes data decomposition information (number of subdomains waiting to be refined) to the underlying runtime system. In turn, this system facilitates work-load balancing and guides the program’s execution towards the most efficient utilization of hardware resources. Preliminary results, on the mesh refinement operation, show that the end-user productivity (measured in terms of elements refined per second) increases as the number of cores in use are increased. When using approximately 16 cores, PsC.AFLR outperforms the serial AFLR code by about 11 times. PsC.AFLR also maintains its stability by generating meshes of comparable quality. Although it offers good end-user productivity, PsC.AFLR suffers in its capability to generate meshes with the same level of density or quality as that of the serial AFLR software due to the constraints set by subdomain boundaries that are required to successfully execute AFLR. These constraints demonstrate that it is not ideal to use AFLR in a black box manner when parallelizing the software. Its source code must be modified to a non-trivial extent if one wishes to remove these constraints and maximize the end-user productivity and potential scalability