One machine, one minute, three billion tetrahedra

This paper presents a new scalable parallelization scheme to generate the 3D Delaunay triangulation of a given set of points. Our first contribution is an efficient serial implementation of the incremental Delaunay insertion algorithm. A simple dedicated data structure, an efficient sorting of the points and the optimization of the insertion algorithm have permitted to accelerate reference implementations by a factor three. Our second contribution is a multi-threaded version of the Delaunay kernel that is able to concurrently insert vertices. Moore curve coordinates are used to partition the point set, avoiding heavy synchronization overheads. Conflicts are managed by modifying the partitions with a simple rescaling of the space-filling curve. The performances of our implementation have been measured on three different processors, an Intel core-i7, an Intel Xeon Phi and an AMD EPYC, on which we have been able to compute 3 billion tetrahedra in 53 seconds. This corresponds to a generation rate of over 55 million tetrahedra per second. We finally show how this very efficient parallel Delaunay triangulation can be integrated in a Delaunay refinement mesh generator which takes as input the triangulated surface boundary of the volume to mesh

Improved Incremental Randomized Delaunay Triangulation

We propose a new data structure to compute the Delaunay triangulation of a set of points in the plane. It combines good worst case complexity, fast behavior on real data, and small memory occupation. The location structure is organized into several levels. The lowest level just consists of the triangulation, then each level contains the triangulation of a small sample of the levels below. Point location is done by marching in a triangulation to determine the nearest neighbor of the query at that level, then the march restarts from that neighbor at the level below. Using a small sample (3%) allows a small memory occupation; the march and the use of the nearest neighbor to change levels quickly locate the query.Comment: 19 pages, 7 figures Proc. 14th Annu. ACM Sympos. Comput. Geom., 106--115, 199

Self-Improving Algorithms

We investigate ways in which an algorithm can improve its expected performance by fine-tuning itself automatically with respect to an unknown input distribution D. We assume here that D is of product type. More precisely, suppose that we need to process a sequence I_1, I_2, ... of inputs I = (x_1, x_2, ..., x_n) of some fixed length n, where each x_i is drawn independently from some arbitrary, unknown distribution D_i. The goal is to design an algorithm for these inputs so that eventually the expected running time will be optimal for the input distribution D = D_1 * D_2 * ... * D_n. We give such self-improving algorithms for two problems: (i) sorting a sequence of numbers and (ii) computing the Delaunay triangulation of a planar point set. Both algorithms achieve optimal expected limiting complexity. The algorithms begin with a training phase during which they collect information about the input distribution, followed by a stationary regime in which the algorithms settle to their optimized incarnations.Comment: 26 pages, 8 figures, preliminary versions appeared at SODA 2006 and SoCG 2008. Thorough revision to improve the presentation of the pape

Computation of protein geometry and its applications: Packing and function prediction

This chapter discusses geometric models of biomolecules and geometric constructs, including the union of ball model, the weigthed Voronoi diagram, the weighted Delaunay triangulation, and the alpha shapes. These geometric constructs enable fast and analytical computaton of shapes of biomoleculres (including features such as voids and pockets) and metric properties (such as area and volume). The algorithms of Delaunay triangulation, computation of voids and pockets, as well volume/area computation are also described. In addition, applications in packing analysis of protein structures and protein function prediction are also discussed.Comment: 32 pages, 9 figure

Dense point sets have sparse Delaunay triangulations

The spread of a finite set of points is the ratio between the longest and shortest pairwise distances. We prove that the Delaunay triangulation of any set of n points in R^3 with spread D has complexity O(D^3). This bound is tight in the worst case for all D = O(sqrt{n}). In particular, the Delaunay triangulation of any dense point set has linear complexity. We also generalize this upper bound to regular triangulations of k-ply systems of balls, unions of several dense point sets, and uniform samples of smooth surfaces. On the other hand, for any n and D=O(n), we construct a regular triangulation of complexity Omega(nD) whose n vertices have spread D.Comment: 31 pages, 11 figures. Full version of SODA 2002 paper. Also available at http://www.cs.uiuc.edu/~jeffe/pubs/screw.htm

Aspects of Unstructured Grids and Finite-Volume Solvers for the Euler and Navier-Stokes Equations

One of the major achievements in engineering science has been the development of computer algorithms for solving nonlinear differential equations such as the Navier-Stokes equations. In the past, limited computer resources have motivated the development of efficient numerical schemes in computational fluid dynamics (CFD) utilizing structured meshes. The use of structured meshes greatly simplifies the implementation of CFD algorithms on conventional computers. Unstructured grids on the other hand offer an alternative to modeling complex geometries. Unstructured meshes have irregular connectivity and usually contain combinations of triangles, quadrilaterals, tetrahedra, and hexahedra. The generation and use of unstructured grids poses new challenges in CFD. The purpose of this note is to present recent developments in the unstructured grid generation and flow solution technology

Betti number signatures of homogeneous Poisson point processes

The Betti numbers are fundamental topological quantities that describe the k-dimensional connectivity of an object: B_0 is the number of connected components and B_k effectively counts the number of k-dimensional holes. Although they are appealing natural descriptors of shape, the higher-order Betti numbers are more difficult to compute than other measures and so have not previously been studied per se in the context of stochastic geometry or statistical physics. As a mathematically tractable model, we consider the expected Betti numbers per unit volume of Poisson-centred spheres with radius alpha. We present results from simulations and derive analytic expressions for the low intensity, small radius limits of Betti numbers in one, two, and three dimensions. The algorithms and analysis depend on alpha-shapes, a construction from computational geometry that deserves to be more widely known in the physics community.Comment: Submitted to PRE. 11 pages, 10 figure

Generalizing the Convex Hull of a Sample: The R Package alphahull

This paper presents the R package alphahull which implements the ñ-convex hull and the ñ-shape of a finite set of points in the plane. These geometric structures provide an informative overview of the shape and properties of the point set. Unlike the convex hull, the ñ-convex hull and the ñ-shape are able to reconstruct non-convex sets. This flexibility make them specially useful in set estimation. Since the implementation is based on the intimate relation of theses constructs with Delaunay triangulations, the R package alphahull also includes functions to compute Voronoi and Delaunay tesselations. The usefulness of the package is illustrated with two small simulation studies on boundary length estimation.