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At least 19 records

An extension to V ORO ++ for multithreaded computation of Voronoi cells

V ORO ++ is a software library written in C++ for computing the Voronoi tessellation, a technique in computational geometry that is widely used for analyzing systems of particles. V ORO ++ was released in 2009 and is based on computing the Voronoi cell for each particle individually. Here, we take advantage of modern computer hardware, and extend the original serial version to allow for multithreaded computation of Voronoi cells via the OpenMP application programming interface. We test the performance of the code, and demonstrate that it can achieve parallel efficiencies greater than 95% in many cases. Further, the multithreaded extension follows standard OpenMP programming paradigms, allowing it to be incorporated into other programs. We provide an example of this using the VoroTop software library, performing a multithreaded Voronoi cell topology analysis of up to 102.4 million particles.

97 MATHEMATICS AND COMPUTING↗

Meshless discretization of the discrete-ordinates transport equation with integration based on Voronoi cells

The time-dependent, gray, linear radiation transport equation is discretized using the meshless local Petrov-Galerkin method with reproducing kernels. The integration is performed using a Voronoi tessellation, which creates a partition of unity that only depends on the position and extent of the kernels. The resolution of the integration automatically follows the particles and requires no manual adjustment. The discretization includes streamline-upwind Petrov-Galerkin stabilization to prevent oscillations and improve numerical conditioning. The angular quadrature is selectively refineable to increase angular resolution in chosen directions. The time discretization is done using backward Euler. The transport solve for each direction and the solve for the scattering source are both done using Krylov iterative methods. The results indicate first-order convergence in time and second-order convergence in space for linear reproducing kernels.

97 MATHEMATICS AND COMPUTING↗

Voronoi cell analysis: The shapes of particle systems

Many physical systems can be studied as collections of particles embedded in space, often evolving in time. Natural questions arise concerning how to characterize these arrangements—are they ordered or disordered? If they are ordered, how are they ordered and what kinds of defects do they possess? Voronoi tessellations, originally introduced to study problems in pure mathematics, have become a powerful and versatile tool for analyzing countless problems in pure and applied physics. Here we explain the basics of Voronoi tessellations and the shapes that they produce and describe how they can be used to characterize many physical systems.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Constructing a conforming Voronoi mesh for an arbitrarily-shaped enclosed geometric domain

A computing system is described herein, where the computing system includes a processor and memory storing instructions that, when executed by the processor, cause the processor to perform the following acts: 1) receiving a computer-implemented definition of an enclosed geometric domain, wherein the geometric domain is two-dimensional; 2) determining locations of seeds for the enclosed geometric domain; 3) decomposing the enclosed geometric domain into a conforming Voronoi mesh based on the locations of the seeds, wherein the conforming Voronoi mesh comprises Voronoi cells, and further wherein the conforming Voronoi mesh is bounded by the enclosed domain; and 4) performing a numerical simulation to generate simulation results, wherein the numerical simulation is based on at least one Voronoi cell in the Voronoi cells of the conforming Voronoi mesh.

97 MATHEMATICS AND COMPUTING↗

Constructing a conforming voronoi mesh for an arbitrarily-shaped enclosed geometric domain

A computing system is described herein, where the computing system includes a processor and memory storing instructions that, when executed by the processor, cause the processor to perform the following acts: 1) receiving a computer-implemented definition of an enclosed geometric domain, wherein the geometric domain is three-dimensional; 2) determining locations of seeds for the enclosed geometric domain; 3) decomposing the enclosed geometric domain into a conforming Voronoi mesh based on the locations of the seeds, wherein the conforming Voronoi mesh comprises Voronoi cells, and further wherein the conforming Voronoi mesh is bounded by the enclosed domain; and 4) performing a numerical simulation to generate simulation results, wherein the numerical simulation is based on at least one Voronoi cell in the Voronoi cells of the conforming Voronoi mesh.

97 MATHEMATICS AND COMPUTING↗

Position-dependent Voronoi probability distribution functions for matter and halos

Here, we measure the Voronoi density probability distribution function (PDF) for both dark matter and halos in N-body simulations. For the dark matter, Voronoi densities represent the matter density field smoothed on a uniform mass scale, which approximates the Lagrangian density field. For halos, the Voronoi densities contain information about the local environment of each halo. We measure the halo virial masses, the total amount of dark matter within each halo Voronoi cell, and the halo Voronoi cell volumes, and we show how halo abundances depend on these three quantities. We then study the position-dependent Voronoi density PDF, measured within finite subregions of the Universe, using separate universe simulations. We demonstrate that the spatial variation of the position-dependent PDF is due to large-scale density fluctuations, indicating that the position-dependent PDF is a biased tracer of large-scale structure. We measure this bias for the dark matter, and interpret it as the bias of regions of the Lagrangian density field that are selected based on density. For the halos, this bias can be interpreted as a form of assembly bias. We present the mapping from late-time to early-time Voronoi density for each simulation dark matter particle, which is highly stochastic. We compare the median of this stochastic map with spherical collapse calculations and discuss challenges involved in modeling the evolution of the density field on these scales.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Robust Metric-Aligned Quad-Dominant Meshing Using L(sub p) Centroidal Voronoi Tessellation

We introduce a meshing algorithm that can be used to both generate and adapt meshes for bounded domains in an anisotropic manner. This is particularly beneficial when anisotropic flow features like shock waves or contact discontinuities are present in the computational domain. The algorithm presented in this paper is based upon meshing under the imposed Riemannian metric tensor, which controls the orientation and size of the mesh elements. In this way there is no need for user intervention to recognize these features. We demonstrate that the method indeed aligns the elements with the underlying metric and produces right-angled simplices that can be recombined into quadrilateral elements. The aim is to eventually incorporate this meshing strategy in the monolithic high-order spectral element solver that is currently being developed at NASA Ames. This paper has two main contributions: First, we demonstrate that we can generate quad-dominant metric-aligned meshes for bounded domains using a generalized form of L(sub p)-Centroidal Voronoi Tessellation (L(sub p)-CVT). Unlike previous works, we do not rely on a background mesh and discretize the bounded domain in a hierarchical way by first discretizing the boundaries and then the volume using the underlying metric. Second, we present an alternative for clipping the Voronoi cells on the boundary, which is common practice in CVT-based meshing algorithms, by reconstructing the Voronoi cells using the defined metric field. In this way we avoid the geometrical complexity of the clipping procedure and we show that we evaluate the energy and its gradient correctly. We show that the reconstruction of the computational domain is consistent with the Lloyds’ algorithm that is used to compute the L(sub p)-CVT.

Centroidal↗

The Area Localized Coupled Model for Analytical Mean Flow Prediction in Arbitrary Wind Farm Geometries

This work introduces the area localized coupled (ALC) model, which extends the applicability of approaches that couple classical wake superposition models and atmospheric boundary layer models to wind farms with arbitrary layouts. Coupling wake and top–down boundary layer models is particularly challenging since the latter requires averaging over planform areas associated with turbine-specific regions of the flow that need to be specified. The ALC model uses Voronoi tessellation to define this local area around each turbine. A top–down description of a developing internal boundary layer is then applied over Voronoi cells upstream of each turbine to estimate the local mean velocity profile. Coupling between the velocity at hub-height based on this localized top–down model and a wake model is achieved by enforcing a minimum least-square-error in mean velocity in each cell. The wake model in the present implementation takes into account variations in wind farm inflow velocity and represents the wake profile behind each turbine as a super-Gaussian function that smoothly transitions between a top-hat shape in the region immediately following the turbine to a Gaussian profile downstream. Detailed comparisons to large-eddy simulation (LES) data from two different wind farms demonstrate the efficacy of the model in accurately predicting both wind farm power output and local turbine hub-height velocity for different wind farm geometries. These validations using data generated from two different LES codes demonstrate the model's versatility with respect to capturing results from different simulation setups and wind farm configurations.

49 EE - Wind and Water Power Program - Wind (EE-4W↗

An invertible seven-dimensional Dirichlet cell characterization of lattices

Characterization of crystallographic lattices is an important tool in structure solution, crystallographic database searches and clustering of diffraction images in serial crystallography. Characterization of lattices by Niggli-reduced cells (based on the three shortest non-coplanar lattice vectors) or by Delaunay-reduced cells (based on four non-coplanar vectors summing to zero and all meeting at obtuse or right angles) is commonly performed. The Niggli cell derives from Minkowski reduction. The Delaunay cell derives from Selling reduction. All are related to the Wigner–Seitz (or Dirichlet, or Voronoi) cell of the lattice, which consists of the points at least as close to a chosen lattice point as they are to any other lattice point. The three non-coplanar lattice vectors chosen are here called the Niggli-reduced cell edges. Starting from a Niggli-reduced cell, the Dirichlet cell is characterized by the planes determined by 13 lattice half-edges: the midpoints of the three Niggli cell edges, the six Niggli cell face-diagonals and the four body-diagonals, but seven of the lengths are sufficient: three edge lengths, the three shorter of each pair of face-diagonal lengths, and the shortest body-diagonal length. These seven are sufficient to recover the Niggli-reduced cell.

Chemistry↗

Evolution of the age-included nearest pair distribution in disperse multiphase flows

The age of the nearest particle pair is introduced as the difference between the current time and the most recent time when the nearest particle pair was formed. The evolution equation for the age-included nearest pair distribution function is derived. With the assumption of random destruction of the nearest particle pairs, the evolution equation predicts the exponential probability distribution of the ages of the nearest particle pairs. Particle-resolved numerical simulations with moving particles are performed to verify this prediction. The equation is then used to derive the evolution equation for the particle–fluid–particle (PFP) stress, which is known to be related to hyperbolicity of the two-fluid equations. It is found that the relaxation time of the age probability distribution is also the relaxation time for the PFP stress. Guided by the closure terms in the PFP stress evolution equation, we study kinematics of the nearest particle pairs in the particle-resolved simulations for flows caused by sedimentation of the particles with initially isotropic and homogeneous particle distributions. At the steady states, the particle Reynolds numbers are around 20. Anisotropy and inhomogeneity of particle distributions are seen to develop in these flows. The mean distances to the nearest particles and evolution of the distribution of the Voronoi cell volumes are studied. We also found the PFP stress is closely related to the changes in these inter-particle scale quantities.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Distributed approximate minimal Steiner trees with millions of seed vertices on billion-edge graphs

In this report, we present a parallel 2-approximation Steiner minimal tree algorithm and its MPI-based distributed implementation. In place of expensive distance computations between all pairs of seed vertices, the solution we employ exploits a cheaper Voronoi cell computation. Our design leverages asynchronous processing and message prioritization to accelerate convergence of distance computations, and harnesses vertex and edge centric processing to offer fast time-to-solution. We demonstrate scalability and performance using real-world graphs with up to 128 billion edges and 512 compute nodes, and show the ability to find Steiner trees with up to one million seed vertices. Using 12 data instances, we present comparison with the state-of-the-art exact solver, SCIP-Jack, and two sequential 2-approximate algorithms. We empirically show that, on average, the total distance of the Steiner tree identified by our solution is 1.1290 times greater than the Steiner minimal tree – well within the theoretical approximation bound of 2.

97 MATHEMATICS AND COMPUTING↗

Peridynamic Model for Microballistic Perforation of Multilayer Graphene

The peridynamic theory of solid mechanics is applied to the continuum modeling of the impact of small, high-velocity silica spheres on multilayer graphene targets. The model treats the laminate as a brittle elastic membrane. The material model includes separate failure criteria for the initial rupture of the membrane and for propagating cracks. Material variability is incorporated by assigning random variations in elastic properties within Voronoi cells. Here, the computational model is shown to reproduce the primary aspects of the response observed in experiments, including the growth of a family of radial cracks from the point of impact.

42 ENGINEERING↗

High-Fidelity CFD Simulation of Mixed Convection and Forced Convection in a Pebble Bed Test Reactor Core

The Hermes low-power [35-MW(thermal)] reactor will be built and operated by Kairos Power LLC (KP) to demonstrate its fluoride salt-cooled high-temperature reactor (FHR) technology. In the KP FHR, the reactor core is composed of randomly packed pebbles with TRISO fuel particles inside with FLiBe flow upward through the core acting as a coolant. Previous numerical and experimental studies have been limited to either a small-size bed or to a lack of detailed measurements for heat transfer. Here, to address the lack of high-fidelity heat transfer data in a real-size FHR core, in this study, we simulated a pebble bed core with 34 374 pebbles randomly packed, similar to the Hermes reactor's size. The core radius was 14 times that of the pebble diameter, while the core height was 45 times. In this work, we were particularly interested in a mixed convection regime, where buoyancy is important. Therefore, we performed several large-eddy simulations at different Reynolds numbers (160 to 1000) with gravitational force included. The spectral element computational fluid dynamics code NekRS with graphics processing unit acceleration was used for this study. The low-Mach number approximation was applied to address property changes in the FLiBe and to account for buoyancy. A pure hexahedral mesh with 60 million elements was generated by the Voronoi cell method. At the polynomial order of 5, the total degrees of freedom was 7.5 billion. The developed case in this work is the first of its kind in terms of size and complexity. The local numerical data across the domain were obtained and compared with empirical correlations. After examining the data, we found the following conclusions. For pressure drop, the Reger correlation predicted less than a 5% error. On the other hand, for heat transfer, the Wakao correlation outperformed the others. Based on our findings, we recommend the use of the Wakao correlation for the Nusselt number calculation, and for pressure drop, the KTA (Kerntechnischer Ausschuss) correclation, among the available experimental correlations. In conclusion, the Reger direct numerical simulation-driven correlation for pressure drops should also be considered, given its best agreement with our calculations.

Mixed Convection↗

Computational Model for Microballistic Perforation of Multilayer Graphene

The peridynamic theory of solid mechanics is applied to the continuum modeling of the impact of small, high-velocity silica spheres on multilayer graphene targets. The model treats the laminate as a brittle elastic membrane. The material model includes separate failure criteria for the initial rupture of the membrane and for propagating cracks. Material variability is incorporated by assigning random variations in elastic properties within Voronoi cells. The computational model is shown to reproduce the primary aspects of the response observed in experiments, including the growth of a family of radial cracks from the point of impact.

36 MATERIALS SCIENCE↗

Multi-Sensor Optimal Motion Planning for Radiological Contamination Surveys by Using Prediction-Difference Maps

Distributed and networked mobile sensor platforms using unmanned aerial and/or ground vehicles to survey areas of interest offer a safer and more efficient method for radiological contamination mapping; however, most applications rely on uniformly sweeping of the area in a raster-type motion without utilizing the information available in a dynamic sense. We have developed a fully autonomous optimal motion planning procedure for networks with two or more mobile sensors. The procedure utilizes well-established concepts of Gaussian processes in combination with control laws based on centroidal Voronoi tessellations to achieve optimal next-iteration sensor movements. A new method of informing optimal motion planning is proposed, whereby the absolute difference between the prior and current full-map prediction, referred to as the prediction-difference map, is used as the spatial density function within each Voronoi cell, providing immediate and iterative feedback for dynamic use of available information. The Gaussian process regression model used to estimate the contamination in unvisited locations also provides prediction uncertainties, and can be used as a quantitative metric to assess the confidence in the calculated contamination map; these estimates and prediction uncertainties are unavailable for standard uniform survey routines as they can only produce maps in the vicinity of observed locations. We present through simulation the achievable performance gains from using this new method by directly comparing to a uniform survey method. Results show that using the prediction-difference maps to inform motion planning procedures offers a faster rate of producing an accurate and convergent map relative to a uniform survey route.

47 OTHER INSTRUMENTATION↗

Characterizing structural features of two-dimensional particle systems through Voronoi topology

This paper introduces a new approach toward characterizing local structural features of two-dimensional particle systems. The approach can accurately identify and characterize defects in high-temperature crystals, distinguish a wide range of nominally disordered systems, and robustly describe complex structures such as grain boundaries. This paper also introduces two-dimensional functionality into the open-source software program VoroTop which automates this analysis. This software package is built on a recently-introduced multithreaded version of V ORO ++, enabling the analysis of systems with billions of particles on high-performance computer architectures.

36 MATERIALS SCIENCE↗

Self-Organizing-Map Program for Analyzing Multivariate Data

SOM_VIS is a computer program for analysis and display of multidimensional sets of Earth-image data typified by the data acquired by the Multi-angle Imaging Spectro-Radiometer [MISR (a spaceborne instrument)]. In SOM_VIS, an enhanced self-organizing-map (SOM) algorithm is first used to project a multidimensional set of data into a nonuniform three-dimensional lattice structure. The lattice structure is mapped to a color space to obtain a color map for an image. The Voronoi cell-refinement algorithm is used to map the SOM lattice structure to various levels of color resolution. The final result is a false-color image in which similar colors represent similar characteristics across all its data dimensions. SOM_VIS provides a control panel for selection of a subset of suitably preprocessed MISR radiance data, and a control panel for choosing parameters to run SOM training. SOM_VIS also includes a component for displaying the false-color SOM image, a color map for the trained SOM lattice, a plot showing an original input vector in 36 dimensions of a selected pixel from the SOM image, the SOM vector that represents the input vector, and the Euclidean distance between the two vectors.

Li, P. Peggy↗

LAVA Voronoi Mesher for Wall-Modeled Large-Eddy Simulations

The unstructured Voronoi mesher currently being developed within the Launch, Ascent, and Vehicle Aerodynamics (LAVA) software framework at NASA Ames Research Center is described in detail. The discussions include, but are not limited to, the strategies used in the seeding and smoothing phases to ensure a high-quality mesh for Wall-Modeled Large-Eddy Simulations (WMLES), the methods behind the cell clipping algorithm responsible for conforming the mesh to a complex geometry, and the approach to create a global mesh from the distinct Voronoi cells. Applications and benefits of the Voronoi meshing approach are also presented. The automated meshing paradigm introduced was able to significantly reduce the time necessary to create a high-quality mesh around a complex geometry when compared against the current LAVA curvilinear overset meshing standard. For example, the task of generating a single mesh around the high-lift common research model requires the full dedication of a mesh generation expert for a period between one and two months. A family of meshes with different refinement levels up to six hundred million cells can be generated by a single engineer in a day or two. This technology has the potential for decreasing the turnaround time for conducting WMLES around complex geometries, as well as facilitating comprehensive mesh refinement studies.

Victor C B Sousa↗