Strategies for optimization of hexahedral meshes and their comparative study

In this work, we study several strategies based on different objective functions for optimization of hexahedral meshes. We consider two approaches to construct objective functions. The first one is based on the decomposition of a hexahedron into tetrahedra. The second one is derived from the Jacobian matrix of the trilinear mapping between the reference and physical hexahedral element. A detailed description of all proposed strategies is given in the present work. Some computational experiments have been developed to test and compare the untangling capabilities of the considered objective functions. In the experiments, a sample of highly distorted hexahedral elements is optimized with the proposed objective functions, and the rate of success of each function is obtained. The results of these experiments are presented and analyzed.Secretaría de Estado de Universidades e Investigación del Ministerio de Economía y Competitividad del Gobierno de España; Programa de FPU del Ministerio de Educación, Cultura y Deporte; Programa de FPI propio de la ULPGC; Fondos FEDE

A distortion measure to validate and generate curved high-order meshes on CAD surfaces with independence of parameterization

This is the accepted version of the following article: [Gargallo-Peiró, A., Roca, X., Peraire, J., and Sarrate, J. (2016) A distortion measure to validate and generate curved high-order meshes on CAD surfaces with independence of parameterization. Int. J. Numer. Meth. Engng, 106: 1100–1130. doi: 10.1002/nme.5162], which has been published in final form at http://onlinelibrary.wiley.com/doi/10.1002/nme.5162/abstractA framework to validate and generate curved nodal high-order meshes on Computer-Aided Design (CAD) surfaces is presented. The proposed framework is of major interest to generate meshes suitable for thin-shell and 3D finite element analysis with unstructured high-order methods. First, we define a distortion (quality) measure for high-order meshes on parameterized surfaces that we prove to be independent of the surface parameterization. Second, we derive a smoothing and untangling procedure based on the minimization of a regularization of the proposed distortion measure. The minimization is performed in terms of the parametric coordinates of the nodes to enforce that the nodes slide on the surfaces. Moreover, the proposed algorithm repairs invalid curved meshes (untangling), deals with arbitrary polynomial degrees (high-order), and handles with low-quality CAD parameterizations (independence of parameterization). Third, we use the optimization procedure to generate curved nodal high-order surface meshes by means of an a posteriori approach. Given a linear mesh, we increase the polynomial degree of the elements, curve them to match the geometry, and optimize the location of the nodes to ensure mesh validity. Finally, we present several examples to demonstrate the features of the optimization procedure, and to illustrate the surface mesh generation process.Peer ReviewedPostprint (author's final draft

Large-scale Geometric Data Decomposition, Processing and Structured Mesh Generation

Mesh generation is a fundamental and critical problem in geometric data modeling and processing. In most scientific and engineering tasks that involve numerical computations and simulations on 2D/3D regions or on curved geometric objects, discretizing or approximating the geometric data using a polygonal or polyhedral meshes is always the first step of the procedure. The quality of this tessellation often dictates the subsequent computation accuracy, efficiency, and numerical stability. When compared with unstructured meshes, the structured meshes are favored in many scientific/engineering tasks due to their good properties. However, generating high-quality structured mesh remains challenging, especially for complex or large-scale geometric data. In industrial Computer-aided Design/Engineering (CAD/CAE) pipelines, the geometry processing to create a desirable structural mesh of the complex model is the most costly step. This step is semi-manual, and often takes up to several weeks to finish. Several technical challenges remains unsolved in existing structured mesh generation techniques. This dissertation studies the effective generation of structural mesh on large and complex geometric data. We study a general geometric computation paradigm to solve this problem via model partitioning and divide-and-conquer. To apply effective divide-and-conquer, we study two key technical components: the shape decomposition in the divide stage, and the structured meshing in the conquer stage. We test our algorithm on vairous data set, the results demonstrate the efficiency and effectiveness of our framework. The comparisons also show our algorithm outperforms existing partitioning methods in final meshing quality. We also show our pipeline scales up efficiently on HPC environment

Hybrid multigrid methods for high-order discontinuous Galerkin discretizations

The present work develops hybrid multigrid methods for high-order discontinuous Galerkin discretizations of elliptic problems. Fast matrix-free operator evaluation on tensor product elements is used to devise a computationally efficient PDE solver. The multigrid hierarchy exploits all possibilities of geometric, polynomial, and algebraic coarsening, targeting engineering applications on complex geometries. Additionally, a transfer from discontinuous to continuous function spaces is performed within the multigrid hierarchy. This does not only further reduce the problem size of the coarse-grid problem, but also leads to a discretization most suitable for state-of-the-art algebraic multigrid methods applied as coarse-grid solver. The relevant design choices regarding the selection of optimal multigrid coarsening strategies among the various possibilities are discussed with the metric of computational costs as the driving force for algorithmic selections. We find that a transfer to a continuous function space at highest polynomial degree (or on the finest mesh), followed by polynomial and geometric coarsening, shows the best overall performance. The success of this particular multigrid strategy is due to a significant reduction in iteration counts as compared to a transfer from discontinuous to continuous function spaces at lowest polynomial degree (or on the coarsest mesh). The coarsening strategy with transfer to a continuous function space on the finest level leads to a multigrid algorithm that is robust with respect to the penalty parameter of the SIPG method. Detailed numerical investigations are conducted for a series of examples ranging from academic test cases to more complex, practically relevant geometries. Performance comparisons to state-of-the-art methods from the literature demonstrate the versatility and computational efficiency of the proposed multigrid algorithms

Analysis and Generation of Quality Polytopal Meshes with Applications to the Virtual Element Method

This thesis explores the concept of the quality of a mesh, the latter being intended as the discretization of a two- or three- dimensional domain. The topic is interdisciplinary in nature, as meshes are massively used in several fields from both the geometry processing and the numerical analysis communities. The goal is to produce a mesh with good geometrical properties and the lowest possible number of elements, able to produce results in a target range of accuracy. In other words, a good quality mesh that is also cheap to handle, overcoming the typical trade-off between quality and computational cost. To reach this goal, we first need to answer the question: ''How, and how much, does the accuracy of a numerical simulation or a scientific computation (e.g., rendering, printing, modeling operations) depend on the particular mesh adopted to model the problem? And which geometrical features of the mesh most influence the result?'' We present a comparative study of the different mesh types, mesh generation techniques, and mesh quality measures currently available in the literature related to both engineering and computer graphics applications. This analysis leads to the precise definition of the notion of quality for a mesh, in the particular context of numerical simulations of partial differential equations with the virtual element method, and the consequent construction of criteria to determine and optimize the quality of a given mesh. Our main contribution consists in a new mesh quality indicator for polytopal meshes, able to predict the performance of the virtual element method over a particular mesh before running the simulation. Strictly related to this, we also define a quality agglomeration algorithm that optimizes the quality of a mesh by wisely agglomerating groups of neighboring elements. The accuracy and the reliability of both tools are thoroughly verified in a series of tests in different scenarios

Stabilized Finite Elements in FUN3D

A Streamlined Upwind Petrov-Galerkin (SUPG) stabilized finite-element discretization has been implemented as a library into the FUN3D unstructured-grid flow solver. Motivation for the selection of this methodology is given, details of the implementation are provided, and the discretization for the interior scheme is verified for linear and quadratic elements by using the method of manufactured solutions. A methodology is also described for capturing shocks, and simulation results are compared to the finite-volume formulation that is currently the primary method employed for routine engineering applications. The finite-element methodology is demonstrated to be more accurate than the finite-volume technology, particularly on tetrahedral meshes where the solutions obtained using the finite-volume scheme can suffer from adverse effects caused by bias in the grid. Although no effort has been made to date to optimize computational efficiency, the finite-element scheme is competitive with the finite-volume scheme in terms of computer time to reach convergence

Adaptive mesh refinement method for CFD applications

The main objective of this thesis is the development of an adaptive mesh refinement (AMR) algorithm for computational fluid dynamics simulations using hexahedral and tetrahedral meshes. This numerical methodology is applied in the context of large-eddy simulations (LES) of turbulent flows and direct numerical simulations (DNS) of interfacial flows, to bring new numerical research and physical insight. For the fluid dynamics simulations, the governing equations, the spatial discretization on unstructured grids and the numerical schemes for solving Navier-Stokes equations are presented. The equations follow a discretization by conservative finite-volume on collocated meshes. For the turbulent flows formulation, the spatial discretization preserves symmetry properties of the continuous differential operators and the time integration follows a self-adaptive strategy, which has been well tested on unstructured grids. Moreover, LES model consisting of a wall adapting local-eddy-viscosity within a variational multi-scale formulation is used for the applications showed in this thesis. For the two-phase flow formulation, a conservative level-set method is applied for capturing the interface between two fluids and is implemented with a variable density projection scheme to simulate incompressible two-phase flows on unstructured meshes. The AMR algorithm developed in this thesis is based on a quad/octree data structure and keeps a relation of 1:2 between levels of refinement. In the case of tetrahedral meshes, a geometrical criterion is followed to keep the quality metric of the mesh on a reasonable basis. The parallelization strategy consists mainly in the creation of mesh elements in each sub-domain and establishes a unique global identification number, to avoid duplicate elements. Load balance is assured at each AMR iteration to keep the parallel performance of the CFD code. Moreover, a mesh multiplication algorithm (MM) is reported to create large meshes, with different kind of mesh elements, but preserving the topology from a coarser original mesh. This thesis focuses on the study of turbulent flows and two-phase flows using an AMR framework. The cases studied for LES of turbulent flows applications are the flow around one and two separated square cylinders, and the flow around a simplified car model. In this context, a physics-based refinement criterion is developed, consisting of the residual velocity calculated from a multi-scale decomposition of the instantaneous velocity. This criteria ensures grid adaptation following the main vortical structures and giving enough mesh resolution on the zones of interest, i.e., flow separation, turbulent wakes, and vortex shedding. The cases studied for the two-phase flows are the DNS of 2D and 3D gravity-driven bubble, with a particular focus on the wobbling regime. A study of rising bubbles in the wobbling regime and the effect of dimensionless numbers on the dynamic behavior of the bubbles are presented. Moreover, the use of tetrahedral AMR is applied for the numerical simulation of gravity-driven bubbles in complex domains. On this topic, the methodology is validated on bubbles rising in cylindrical channels with different topology, where the study of these cases contributed to having new numerical research and physical insight in the development of a rising bubble with wall effects.El objetivo principal de esta tesis es el desarrollo de un algoritmo adaptativo de refinamiento de malla (AMR) para simulaciones de dinámica de fluidos computacional utilizando mallas hexaédricas y tetraédricas. Esta metodología numérica se aplica en el contexto de simulaciones Large-eddie (LES) de flujos turbulentos y simulaciones numéricas directas (DNS) de flujos interfaciales, para traer nuevas investigaciones numéricas y entendimiento físicas. Para las simulaciones de dinámica de fluidos, se presentan las ecuaciones governantes, la discretización espacial en mallas no estructuradas y los esquemas numéricos para resolver las ecuaciones de Navier-Stokes. Las ecuaciones siguen una discretización conservativa por volumenes finitos en mallas colocadas. Para la formulación de flujos turbulentos, la discretización espacial preserva las propiedades de simetría de los operadores diferenciales continuos y la integración de tiempo sigue una estrategia autoadaptativa, que ha sido bien probada en mallas no estructuradas. Además, para las aplicaciones que se muestran en esta tesis, se utiliza el modelo LES que consiste en una viscosidad local que se adapta a la pared dentro de una formulación multiescala variable. Para la formulación de flujo de dos fases, se aplica un método de conjunto de niveles conservador para capturar la interfaz entre dos fluidos y se implementa con un esquema de proyección de densidad variable para simular flujos de dos fases incompresibles en mallas no estructuradas. El algoritmo AMR desarrollado en esta tesis se basa en una estructura de datos de quad / octree y mantiene una relación de 1: 2 entre los niveles de refinamiento. En el caso de las mallas tetraédricas, se sigue un criterio geométrico para mantener la calidad de la malla en una base razonable. La estrategia de paralelización consiste principalmente en la creación de elementos de malla en cada subdominio y establece un número de identificación global único, para evitar elementos duplicados. El equilibrio de carga está asegurado en cada iteración de AMR para mantener el rendimiento paralelo del código CFD. Además, se ha desarrollado un algoritmo de multiplicación de malla (MM) para crear mallas grandes, con diferentes tipos de elementos de malla, pero preservando la topología de una malla original más pequeña. Esta tesis se centra en el estudio de flujos turbulentos y flujos de dos fases utilizando un marco AMR. Los casos estudiados para aplicaciones de LES de flujos turbulentos son el flujo alrededor de uno y dos cilindros separados de sección cuadrada, y el flujo alrededor de un modelo de automóvil simplificado. En este contexto, se desarrolla un criterio de refinamiento basado en la física, que consiste en la velocidad residual calculada a partir de una descomposición de escala múltiple de la velocidad instantánea. Este criterio garantiza la adaptación de la malla siguiendo las estructuras vorticales principales y proporcionando una resolución de malla suficiente en las zonas de interés, es decir, separación de flujo, estelas turbulentas y desprendimiento de vórtices. Los casos estudiados para los flujos de dos fases son el DNS de la burbuja impulsada por la gravedad en 2D y 3D, con un enfoque particular en el régimen de oscilación. Además, el uso de AMR tetraédrico se aplica para la simulación numérica de burbujas impulsadas por la gravedad en dominios complejos. En este tema, la metodología se valida en burbujas que ascienden en canales cilíndricos con topología diferente, donde el estudio de estos casos contribuyó a tener una nueva investigación numérica y una visión física en el desarrollo de una burbuja con efectos de pared

Virtual reality surgery simulation: A survey on patient specific solution

For surgeons, the precise anatomy structure and its dynamics are important in the surgery interaction, which is critical for generating the immersive experience in VR based surgical training applications. Presently, a normal therapeutic scheme might not be able to be straightforwardly applied to a specific patient, because the diagnostic results are based on averages, which result in a rough solution. Patient Specific Modeling (PSM), using patient-specific medical image data (e.g. CT, MRI, or Ultrasound), could deliver a computational anatomical model. It provides the potential for surgeons to practice the operation procedures for a particular patient, which will improve the accuracy of diagnosis and treatment, thus enhance the prophetic ability of VR simulation framework and raise the patient care. This paper presents a general review based on existing literature of patient specific surgical simulation on data acquisition, medical image segmentation, computational mesh generation, and soft tissue real time simulation