An exact general remeshing scheme applied to physically conservative voxelization

We present an exact general remeshing scheme to compute analytic integrals of polynomial functions over the intersections between convex polyhedral cells of old and new meshes. In physics applications this allows one to ensure global mass, momentum, and energy conservation while applying higher-order polynomial interpolation. We elaborate on applications of our algorithm arising in the analysis of cosmological N-body data, computer graphics, and continuum mechanics problems. We focus on the particular case of remeshing tetrahedral cells onto a Cartesian grid such that the volume integral of the polynomial density function given on the input mesh is guaranteed to equal the corresponding integral over the output mesh. We refer to this as "physically conservative voxelization". At the core of our method is an algorithm for intersecting two convex polyhedra by successively clipping one against the faces of the other. This algorithm is an implementation of the ideas presented abstractly by Sugihara (1994), who suggests using the planar graph representations of convex polyhedra to ensure topological consistency of the output. This makes our implementation robust to geometric degeneracy in the input. We employ a simplicial decomposition to calculate moment integrals up to quadratic order over the resulting intersection domain. We also address practical issues arising in a software implementation, including numerical stability in geometric calculations, management of cancellation errors, and extension to two dimensions. In a comparison to recent work, we show substantial performance gains. We provide a C implementation intended to be a fast, accurate, and robust tool for geometric calculations on polyhedral mesh elements.Comment: Code implementation available at https://github.com/devonmpowell/r3

On estimating the interface normal and curvature in PLIC-VOF approach for 3D arbitrary meshes

Volume of fluid (VOF) method with its Piecewise Linear Interface Calculation (PLIC) reconstruction algorithm is one of the most popular approaches in numerical simulation of interfacial flows with a wide range of applications in different areas. In an effort to evaluate the similarity of the PLIC-generated planes in comparison with the exact interface, a point-cloud, based on the polygon centers of PLIC planes is extracted, which later is used to form a triangular grid that represents the estimated interface. The main objective of this article is to evaluate the interface geometrical properties based on the extracted triangular grid of the interface. The methods presented in this article, characterized by a higher spatially convergence ratio, are compared with the commonly used methods. The proposed methods are tested for two 3-dimensional general test cases, where an evident improvement is seen in calculation accuracy and spatial convergence of the errors of interface normal vector and curvature.This work has been financially supported by MCIN/AEI/10.13039/ 501100011033 Spain, project PID2020-115837RBI00. E. Schillaci acknowledges the financial support of the Programa Torres Quevedo (PTQ2018-010060).Peer ReviewedPostprint (author's final draft

An adaptive Cartesian embedded boundary approach for fluid simulations of two- and three-dimensional low temperature plasma filaments in complex geometries

We review a scalable two- and three-dimensional computer code for low-temperature plasma simulations in multi-material complex geometries. Our approach is based on embedded boundary (EB) finite volume discretizations of the minimal fluid-plasma model on adaptive Cartesian grids, extended to also account for charging of insulating surfaces. We discuss the spatial and temporal discretization methods, and show that the resulting overall method is second order convergent, monotone, and conservative (for smooth solutions). Weak scalability with parallel efficiencies over 70\% are demonstrated up to 8192 cores and more than one billion cells. We then demonstrate the use of adaptive mesh refinement in multiple two- and three-dimensional simulation examples at modest cores counts. The examples include two-dimensional simulations of surface streamers along insulators with surface roughness; fully three-dimensional simulations of filaments in experimentally realizable pin-plane geometries, and three-dimensional simulations of positive plasma discharges in multi-material complex geometries. The largest computational example uses up to $800$ million mesh cells with billions of unknowns on $4096$ computing cores. Our use of computer-aided design (CAD) and constructive solid geometry (CSG) combined with capabilities for parallel computing offers possibilities for performing three-dimensional transient plasma-fluid simulations, also in multi-material complex geometries at moderate pressures and comparatively large scale.Comment: 40 pages, 21 figure

A new isosurface extraction method on arbitrary grids

The development of interface-capturing methods (such as level-set, phase-field or volume of fluid (VOF) methods) for arbitrary 3D grids has further highlighted the need for more accurate and efficient interface reconstruction procedures. In this work, we propose a new method for the extraction of isosurfaces on arbitrary polyhedra that can be used with advantage for this purpose. The isosurface is extracted from volume fractions by a general polygon tracing procedure, which is valid for convex or non-convex geometries, even with non-planar faces. The proposed method, which can be considered as an extension of the marching cubes technique, produces consistent results even for ambiguous situations in polyhedra of arbitrary shape. To show the reproducibility of the results presented in this work, we provide the open source library isoap, which has been developed to implement the proposed method and includes test programs to demonstrate the successful extraction of isosurfaces on several grids with polyhedral cells of different types. We present results obtained not only for isosurface extraction from discrete volume fractions resulting from a volume of fluid method, but also from data sets obtained from implicit mathematical functions and signed distances to scanned surfaces. The improvement provided by the proposed method for the extraction of isosurfaces in arbitrary grids will also be very useful in other fields, such as CFD visualization or medical imaging.The authors gratefully acknowledge the support of the Spanish Ministerio de Ciencia, Innovación y Universidades - Agencia Estatal de Investigación and FEDER through projects DPI2017-87826-C2-1-P and DPI2017-87826-C2-2-P

Unstructured un-split geometrical Volume-of-Fluid methods -- A review

Geometrical Volume-of-Fluid (VoF) methods mainly support structured meshes, and only a small number of contributions in the scientific literature report results with unstructured meshes and three spatial dimensions. Unstructured meshes are traditionally used for handling geometrically complex solution domains that are prevalent when simulating problems of industrial relevance. However, three-dimensional geometrical operations are significantly more complex than their two-dimensional counterparts, which is confirmed by the ratio of publications with three-dimensional results on unstructured meshes to publications with two-dimensional results or support for structured meshes. Additionally, unstructured meshes present challenges in serial and parallel computational efficiency, accuracy, implementation complexity, and robustness. Ongoing research is still very active, focusing on different issues: interface positioning in general polyhedra, estimation of interface normal vectors, advection accuracy, and parallel and serial computational efficiency. This survey tries to give a complete and critical overview of classical, as well as contemporary geometrical VOF methods with concise explanations of the underlying ideas and sub-algorithms, focusing primarily on unstructured meshes and three dimensional calculations. Reviewed methods are listed in historical order and compared in terms of accuracy and computational efficiency

SKIRT: the design of a suite of input models for Monte Carlo radiative transfer simulations

The Monte Carlo method is the most popular technique to perform radiative transfer simulations in a general 3D geometry. The algorithms behind and acceleration techniques for Monte Carlo radiative transfer are discussed extensively in the literature, and many different Monte Carlo codes are publicly available. On the contrary, the design of a suite of components that can be used for the distribution of sources and sinks in radiative transfer codes has received very little attention. The availability of such models, with different degrees of complexity, has many benefits. For example, they can serve as toy models to test new physical ingredients, or as parameterised models for inverse radiative transfer fitting. For 3D Monte Carlo codes, this requires algorithms to efficiently generate random positions from 3D density distributions. We describe the design of a flexible suite of components for the Monte Carlo radiative transfer code SKIRT. The design is based on a combination of basic building blocks (which can be either analytical toy models or numerical models defined on grids or a set of particles) and the extensive use of decorators that combine and alter these building blocks to more complex structures. For a number of decorators, e.g. those that add spiral structure or clumpiness, we provide a detailed description of the algorithms that can be used to generate random positions. Advantages of this decorator-based design include code transparency, the avoidance of code duplication, and an increase in code maintainability. Moreover, since decorators can be chained without problems, very complex models can easily be constructed out of simple building blocks. Finally, based on a number of test simulations, we demonstrate that our design using customised random position generators is superior to a simpler design based on a generic black-box random position generator.Comment: 15 pages, 4 figures, accepted for publication in Astronomy and Computin