Quality mesh generation for molecular skin surfaces using restricted union of balls

Quality surface meshes for molecular models are desirable in the studies of protein shapes and functionalities. However, there is still no robust software that is capable to generate such meshes with good quality. In this paper, we present a Delaunay-based surface triangulation algorithm generating quality surface meshes for the molecular skin model. We expand the restricted union of balls along the surface and generate an ε-sampling of the skin surface incrementally. At the same time, a quality surface mesh is extracted from the Delaunay triangulation of the sample points. The algorithm supports robust and efficient implementation and guarantees the mesh quality and topology as well. Our results facilitate molecular visualization and have made a contribution towards generating quality volumetric tetrahedral meshes for the macromolecules.     

Generating realistic terrains with higher-order Delaunay triangulations

For hydrologic applications, terrain models should have few local minima, and drainage lines should coincide with edges. We show that triangulating a set of points with elevations such that the number of local minima of the resulting terrain is minimized is NP-hard for degenerate point sets. The same result applies when there are no degeneracies for higher-order Delaunay triangulations. Two heuristics are presented to reduce the number of local minima for higher-order Delaunay triangulations, which start out with the Delaunay triangulation. We give efficient algorithms for their implementation, and test on real-world data how well they perform. We also study another desirable drainage characteristic, few valley components, and how to obtain it for higher-order Delaunay triangulations. This gives rise to a third heuristic. Tables and visualizations show how the heuristics perform for the drainage characteristics on real-world data.     

Optimal Delaunay Triangulations

The Delaunay triangulation, in both classic and more generalized sense, is studied in this paper for minimizing the linear interpolation error (measure in L^P-norm) for a given function. The classic Delaunay triangulation can then be characterized as an optimal triangulation that minimizes the interpolation error for the isotropic function ‖x‖^2 among all the triangulations with a given set of vertices. For a more general function, a functiondependent Delaunay triangulation is then defined to be an optimal triangulation that minimizes the interpolation error for this function and its construction can be obtained by a simple lifting and projection procedure. The optimal Delaunay triangulation is the one that minimizes the interpolation error among all triangulations with the same number of vertices, i.e. the distribution of vertices are optimized in order to minimize the interpolation error. Such a function-depend entoptimal Delaunay triangulation is proved to exist for any given convex continuous function.On an optimal Delaunay triangulation associated with f, it is proved that △↓f at the interior vertices can be exactly recovered by the function values on its neighboring vertices.Since the optimal Delaunay triangulation is difficult to obtain in practice, the concept of nearly optimal triangulation is introduced and two sufficient conditions are presented for a triangulation to be nearly optimal.     

Lepp-bisection algorithms,applications and mathematical properties

Longest edge (nested) algorithms for triangulation refinement in two dimensions are able to produce hierarchies of quality and nested irregular triangulations as needed both for adaptive finite element methods and for multigrid methods for PDEs. In addition, right-triangle bintree triangulations are multiresolution algorithms used for terrain modeling and real time visualization of terrain applications. These algorithms are based on the properties of the consecutive bisection of a triangle by the median of the longest edge, and can be formulated in terms of the longest edge propagation path (Lepp) and terminal edge concepts, which implies the use of very local refinement operations over fully conforming meshes (where the intersection of pairs of neighbor triangles is either a common edge or a common vertex). In this paper we review the Lepp-bisection algorithms, their properties and applications. To the end we use recent simpler and stronger results on the complexity aspects of the bisection method and its geometrical properties. We discuss and analyze the computational costs of the algorithms. The generalization of the algorithms to 3-dimensions is also discussed. Applications of these methods are presented: for serial and parallel view dependent level of detail terrain rendering, and for the parallel refinement of tetrahedral meshes.     

Generalized delaunay triangulation for planar graphs

We introduce the notion of generalized Delaunay triangulation of a planar straight-line graphG=(V, E) in the Euclidean plane and present some characterizations of the triangulation. It is shown that the generalized Delaunay triangulation has the property that the minimum angle of the triangles in the triangulation is maximum among all possible triangulations of the graph. A general algorithm that runs inO(|V|²) time for computing the generalized Delaunay triangulation is presented. When the underlying graph is a simple polygon, a divide-and-conquer algorithm based on the polygon cutting theorem of Chazelle is given that runs inO(|V| log |V|) time.Supported in part by the National Science Foundation under Grants DCR 8420814 and ECS 8340031.     

Constrained CVT meshes and a comparison of triangular mesh generators

Mesh generation in regions in Euclidean space is a central task in computational science, and especially for commonly used numerical methods for the solution of partial differential equations, e.g., finite element and finite volume methods. We focus on the uniform Delaunay triangulation of planar regions and, in particular, on how one selects the positions of the vertices of the triangulation. We discuss a recently developed method, based on the centroidal Voronoi tessellation (CVT) concept, for effecting such triangulations and present two algorithms, including one new one, for CVT-based grid generation. We also compare several methods, including CVT-based methods, for triangulating planar domains. To this end, we define several quantitative measures of the quality of uniform grids. We then generate triangulations of several planar regions, including some having complexities that are representative of what one may encounter in practice. We subject the resulting grids to visual and quantitative comparisons and conclude that all the methods considered produce high-quality uniform grids and that the CVT-based grids are at least as good as any of the others.     

Delaunay Triangulation of Manifolds

We present an algorithm for producing Delaunay triangulations of manifolds. The algorithm can accommodate abstract manifolds that are not presented as submanifolds of Euclidean space. Given a set of sample points and an atlas on a compact manifold, a manifold Delaunay complex is produced for a perturbed point set provided the transition functions are bi-Lipschitz with a constant close to 1, and the original sample points meet a local density requirement; no smoothness assumptions are required. If the transition functions are smooth, the output is a triangulation of the manifold. The output complex is naturally endowed with a piecewise-flat metric which, when the original manifold is Riemannian, is a close approximation of the original Riemannian metric. In this case the output complex is also a Delaunay triangulation of its vertices with respect to this piecewise-flat metric.     

Aspects of the Facet-Edge Data Structure for the Construction of Voronoi Cells

The construction of Voronoi diagrams has two main aspects: The construction algorithm and the data structure. For the construction of planar Voronoi diagrams e.g. the well known plane sweep algorithm can be applied. Another efficient method is the incremental construction of the Delaunay triangulation by using the quad-edge data structure. Within this data structure the Delaunay triangulation is treated as a planar graph. Incremental construction implies that manipulations of the triangulation are allowed. Its Voronoi diagram is obtained simply by accessing the triangulation's dual graph. We extend this method to tree dimensions, by implementing a 3D Delaunay triangulation on the facet-edge data structure. (© 2010 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim)     

Off-centers: A new type of Steiner points for computing size-optimal quality-guaranteed Delaunay triangulations

We introduce a new type of Steiner points, called off-centers, as an alternative to circumcenters, to improve the quality of Delaunay triangulations in two dimensions. We propose a new Delaunay refinement algorithm based on iterative insertion of off-centers. We show that this new algorithm has the same quality and size optimality guarantees of the best known refinement algorithms. In practice, however, the new algorithm inserts fewer Steiner points, runs faster, and generates smaller triangulations than the best previous algorithms. Performance improvements are significant especially when user-specified minimum angle is large, e.g., when the smallest angle in the output triangulation is 30°, the number of Steiner points is reduced by about 40%, while the mesh size is down by about 30%. As a result of its shown benefits, the algorithm described here has already replaced the well-known circumcenter insertion algorithm of Ruppert and has been the default quality triangulation method in the popular meshing software Triangle.¹     

Guaranteed-quality parallel Delaunay refinement for restricted polyhedral domains

We describe a distributed memory parallel Delaunay refinement algorithm for simple polyhedral domains whose constituent bounding edges and surfaces are separated by angles between 90° to 270° inclusive. With these constraints, our algorithm can generate meshes containing tetrahedra with circumradius to shortest edge ratio less than 2, and can tolerate more than 80% of the communication latency caused by unpredictable and variable remote gather operations.

Our experiments show that the algorithm is efficient in practice, even for certain domains whose boundaries do not conform to the theoretical limits imposed by the algorithm. The algorithm we describe is the first step in the development of much more sophisticated guaranteed-quality parallel mesh generation algorithms.     

A Delaunay Refinement Algorithm for Quality 2-Dimensional Mesh Generation

We present a simple new algorithm for triangulating polygons and planar straightline graphs, It provides "shape" and "size" guarantees:

• All triangles have a bounded aspect ratio.

• The number of triangles is within a constant factor of optimal.

Such "quality" triangulations are desirable as meshes for the finite element method, in which the running time generally increases with the number of triangles, and where the convergence and stability may be hurt by very skinny triangles. The technique we use-successive refinement of a Delaunay triangulation-extends a mesh generation technique of Chew by allowing triangles of varying sizes. Compared with previous quadtree-based algorithms for quality mesh generation, the Delaunay refinement approach is much simpler and generally produces meshes with fewer triangles. We also discuss an implementation of the algorithm and evaluate its performance on a variety of inputs.     

A Linear Bound on the Complexity of the Delaunay Triangulation of Points on Polyhedral Surfaces

Delaunay triangulations and Voronoi diagrams have found numerous applications in surface modeling, surface mesh generation, deformable surface modeling and surface reconstruction. Many algorithms in these applications begin by constructing the three-dimensional Delaunay triangulation of a finite set of points scattered over a surface. Their running-time therefore depends on the complexity of the Delaunay triangulation of such point sets. Although the complexity of the Delaunay triangulation of points in R³ may be quadratic in the worst case, we show in this paper that it is only linear when the points are distributed on a fixed set of well-sampled facets of R³ (e.g. the planar polygons in a polyhedron). Our bound is deterministic and the constants are explicitly given.     

Delaunay refinement algorithms for triangular mesh generation

Delaunay refinement is a technique for generating unstructured meshes of triangles for use in interpolation, the finite element method, and the finite volume method. In theory and practice, meshes produced by Delaunay refinement satisfy guaranteed bounds on angles, edge lengths, the number of triangles, and the grading of triangles from small to large sizes. This article presents an intuitive framework for analyzing Delaunay refinement algorithms that unifies the pioneering mesh generation algorithms of L. Paul Chew and Jim Ruppert, improves the algorithms in several minor ways, and most importantly, helps to solve the difficult problem of meshing nonmanifold domains with small angles.

Although small angles inherent in the input geometry cannot be removed, one would like to triangulate a domain without creating any new small angles. Unfortunately, this problem is not always soluble. A compromise is necessary. A Delaunay refinement algorithm is presented that can create a mesh in which most angles are 30° or greater and no angle is smaller than arcsin[( , where φ60°is the smallest angle separating two segments of the input domain. New angles smaller than 30° appear only near input angles smaller than 60°. In practice, the algorithm's performance is better than these bounds suggest.

Another new result is that Ruppert's analysis technique can be used to reanalyze one of Chew's algorithms. Chew proved that his algorithm produces no angle smaller than 30° (barring small input angles), but without any guarantees on grading or number of triangles. He conjectures that his algorithm offers such guarantees. His conjecture is conditionally confirmed here: if the angle bound is relaxed to less than 26.5°, Chew's algorithm produces meshes (of domains without small input angles) that are nicely graded and size-optimal.     

Boundary conforming Delaunay mesh generation

A boundary conforming Delaunay mesh is a partitioning of a polyhedral domain into Delaunay simplices such that all boundary simplices satisfy the generalized Gabriel property. It’s dual is a Voronoi partition of the same domain which is preferable for Voronoi-box based finite volume schemes. For arbitrary 2D polygonal regions, such meshes can be generated in optimal time and size. For arbitrary 3D polyhedral domains, however, this problem remains a challenge. The main contribution of this paper is to show that boundary conforming Delaunay meshes for 3D polyhedral domains can be generated efficiently when the smallest input angle of the domain is bounded by arccos 1/3 ≈ 70.53°. In addition, well-shaped tetrahedra and an appropriate mesh size can be obtained. Our new results are achieved by reanalyzing a classical Delaunay refinement algorithm. Note that our theoretical guarantee on the input angle (70.53°) is still too strong for many practical situations. We further discuss variants of the algorithm to relax the input angle restriction and to improve the mesh quality.     

Perturbations for Delaunay and weighted Delaunay 3D triangulations

The Delaunay triangulation and the weighted Delaunay triangulation are not uniquely defined when the input set is degenerate. We present a new symbolic perturbation that allows to always define these triangulations in a unique way, as soon as the points are not all coplanar. No flat tetrahedron exists in the defined triangulation. The perturbation scheme is easy to code. It is implemented in cgal, and guarantees that both vertex insertion and vertex removal are fully robust.     

Approximation for Minimum Triangulations of Simplicial Convex 3-Polytopes

A minimum triangulation of a convex 3-polytope is a triangulation that contains the minimum number of tetrahedra over all its possible triangulations. Since finding minimum triangulations of convex 3-polytopes was recently shown to be NP-hard, it becomes significant to find algorithms that give good approximation. In this paper we give a new triangulation algorithm with an improved approximation ratio 2 - Ω(1/\sqrt n ) , where n is the number of vertices of the polytope. We further show that this is the best possible for algorithms that only consider the combinatorial structure of the polytopes. Received August 5, 2000, and in revised form March 29, 2001, and May 3, 2001. Online publication October 12, 2001.     

Optimality of the Delaunay triangulation in ℝ d

In this paper we present new optimality results for the Delaunay triangulation of a set of points in ℝ ^d . These new results are true in all dimensionsd. In particular, we define a power function for a triangulation and show that the Delaunay triangulation minimizes the power function over all triangulations of a point set. We use this result to show that (a) the maximum min-containment radius (the radius of the smallest sphere containing the simplex) of the Delaunay triangulation of a point set in ℝ ^d is less than or equal to the maximum min-containment radius of any other triangulation of the point set, (b) the union of circumballs of triangles incident on an interior point in the Delaunay triangulation of a point set lies inside the union of the circumballs of triangles incident on the same point in any other triangulation of the point set, and (c) the weighted sum of squares of the edge lengths is the smallest for Delaunay triangulation, where the weight is the sum of volumes of the triangles incident on the edge. In addition we show that if a triangulation consists of only self-centered triangles (a simplex whose circumcenter falls inside the simplex), then it is the Delaunay triangulation.     

How to generate local refinements of unstructured tetrahedral meshes satisfying a regularity ball condition

A simple algorithm that generates local refinements of tetrahedral meshes is proposed. Refinements are made by tetrahedra, which are subdivided into eight, four, three, or two smaller tetrahedra. We prove that a regularity ball condition is satisfied for the refined mesh. This guarantees that tetrahedra do not become flat when the mesh size tends to zero. © 1997 John Wiley & Sons, Inc.     

A framework for advancing front techniques of finite element mesh generation

Advancing front techniques are a family of methods for finite element mesh generation that are particularly effective in dealing with complicated boundary geometries. In the first part of this paper, conditions are presented which ensure that any planar aft algorithm that meets these conditions terminates in a finite number of steps with a valid triangulation of the input domain. These conditions are described by specifying a framework of subtasks that can accommodate many aft methods and by prescribing the minimal requirements on each subtask that ensure correctness of an algorithm that conforms to the framework.An important efficiency factor in implementing an aft is the data structure used to represent the unmeshed regions during the execution of the algorithm. In the second part of the paper, we discuss the use of the constrained Delaunay triangulation as an efficient abstract data structure for the unmeshed regions. We indicate how the correctness conditions of the first part of the paper can be met using this representation. In this case, we also discuss the additional requirements on the framework which ensure that the generated mesh is a constrained Delaunay triangulation for the original boundary.The first author has been supported by CERFACS, Toulouse, France. Support was provided to the second author by the Natural Sciences and Engineering Research Council of Canada, and by the Information Technology Research Centre of Ontario.