A Visualization System for Hexahedral Mesh Quality Study

In this paper, we introduce a new 3D hex mesh visual analysis system that emphasizes poor-quality areas with an aggregated glyph, highlights overlapping elements, and provides detailed boundary error inspection in three forms. By supporting multi-level analysis through multiple views, our system effectively evaluates various mesh models and compares the performance of mesh generation and optimization algorithms for hexahedral meshes.Comment: Accepted by IEEE VIS 2023 Short Papers and will be published on IEEE Xplore. Paper contains 4 pages, and 1 reference page. Supplemental includes 4 page

Loopy Cuts: Surface-Field Aware Block Decomposition for Hex-Meshing.

We present a new fully automatic block-decomposition hexahedral meshing algorithm capable of producing high quality meshes that strictly preserve feature curve networks on the input surface and align with an input surface cross-field. We produce all-hex meshes on the vast majority of inputs, and introduce localized non-hex elements only when the surface feature network necessitates those. The input to our framework is a closed surface with a collection of geometric or user-demarcated feature curves and a feature-aligned surface cross-field. Its output is a compact set of blocks whose edges interpolate these features and are loosely aligned with this cross-field. We obtain this block decomposition by cutting the input model using a collection of simple cutting surfaces bounded by closed surface loops. The set of cutting loops spans the input feature curves, ensuring feature preservation, and is obtained using a field-space sampling process. The computed loops are uniformly distributed across the surface, cross orthogonally, and are loosely aligned with the cross-field directions, inducing the desired block decomposition. We validate our method by applying it to a large range of complex inputs and comparing our results to those produced by state-of-the-art alternatives. Contrary to prior approaches, our framework consistently produces high-quality field aligned meshes while strictly preserving geometric or user-specified surface features

High-quality conforming hexahedral meshes of patient-specific abdominal aortic aneurysms including their intraluminal thrombi

In order to perform finite element (FE) analyses of patient-specific abdominal aortic aneurysms, geometries derived from medical images must be meshed with suitable elements. We propose a semi-automatic method for generating conforming hexahedral meshes directly from contours segmented from medical images. Magnetic resonance images are generated using a protocol developed to give the abdominal aorta high contrast against the surrounding soft tissue. These data allow us to distinguish between the different structures of interest. We build novel quadrilateral meshes for each surface of the sectioned geometry and generate conforming hexahedral meshes by combining the quadrilateral meshes. The three-layered morphology of both the arterial wall and thrombus is incorporated using parameters determined from experiments. We demonstrate the quality of our patient-specific meshes using the element Scaled Jacobian. The method efficiently generates high-quality elements suitable for FE analysis, even in the bifurcation region of the aorta into the iliac arteries. For example, hexahedral meshes of up to 125,000 elements are generated in less than 130 s, with 94.8 % of elements well suited for FE analysis. We provide novel input for simulations by independently meshing both the arterial wall and intraluminal thrombus of the aneurysm, and their respective layered morphologies

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

Parallel paving: An algorithm for generating distributed, adaptive, all-quadrilateral meshes on parallel computers

Paving is an automated mesh generation algorithm which produces all-quadrilateral elements. It can additionally generate these elements in varying sizes such that the resulting mesh adapts to a function distribution, such as an error function. While powerful, conventional paving is a very serial algorithm in its operation. Parallel paving is the extension of serial paving into parallel environments to perform the same meshing functions as conventional paving only on distributed, discretized models. This extension allows large, adaptive, parallel finite element simulations to take advantage of paving`s meshing capabilities for h-remap remeshing. A significantly modified version of the CUBIT mesh generation code has been developed to host the parallel paving algorithm and demonstrate its capabilities on both two dimensional and three dimensional surface geometries and compare the resulting parallel produced meshes to conventionally paved meshes for mesh quality and algorithm performance. Sandia`s {open_quotes}tiling{close_quotes} dynamic load balancing code has also been extended to work with the paving algorithm to retain parallel efficiency as subdomains undergo iterative mesh refinement

Mesh generation for voxel -based objects

A new physically-based approach to unstructured mesh generation via Monte-Carlo simulation is proposed. Geometrical objects to be meshed are represented by systems of interacting particles with a given interaction potential. A new way of distributing nodes in complex domains is proposed based on a concept of dynamic equilibrium ensemble, which represents a liquid state of matter. The algorithm is simple, numerically stable and produces uniform node distributions in domains of complex geometries and different dimensions. Well-shaped triangles or tetrahedra can be created by connecting a set of uniformly-spaced nodes. The proposed method has many advantages and potential applications.;The new method is applied to the problem of meshing of voxel-based objects. By customizing system potential energy function to reflect surface features, particles can be distributed into desired locations, such as sharp corners and edges. Feature-preserved surface mesh can then be constructed by connecting the node set.;A heuristic algorithm using an advancing front approach is proposed to generate triangulated surface meshes on voxel-based objects. The resultant surface meshes do not inherit the anisotropy of the underlying hexagonal grid. However, the important surface features, such as edges and corners may not be preserved in the mesh.;To overcome this problem, surface features such as edges, corners need to be detected. A new approach of edge capturing is proposed and demonstrated. The approach is based on a Laplace solver with incomplete Jacobi iterations, and as such is very simple and efficient. This edge capturing approach combined with the mesh generation methods above forms a simple and robust technique of unstructured mesh generation on voxel-based objects.;A graphical user interface (GUI) capable of complex geometric design and remote simulation control was implemented. The GUI was used in simulations of large fuel-cell stacks. It enables one to setup, run and monitor simulations remotely through secure shell (SSH2) connections. A voxel-based 3D geometrical modeling module is built along with the GUI. The flexibility of voxel-based geometry representation enables one to use this technique for both geometric design and visualization of volume data

Real-time simulation of surgery by Proper Generalized Decomposition techniques

La simulación quirúrgica por ordenador en tiempo real se ha convertido en una alternativa muy atractiva a los simuladores quirúrgicos tradicionales. Entre otras ventajas, los simuladores por ordenador consiguen ahorros importantes de tiempo y de costes de mantenimiento, y permiten que los estudiantes practiquen sus habilidades quirúrgicas en un entorno seguro tantas veces como sea necesario. Sin embargo, a pesar de las capacidades de los ordenadores actuales, la cirugía computacional sigue siendo un campo de investigación exigente. Uno de sus mayores retos es la alta velocidad a la que se tienen que resolver complejos problemas de mecánica de medios continuos para que los interfaces hápticos puedan proporcionar un sentido del tacto realista (en general, se necesitan velocidades de respuesta de 500-1000 Hz).Esta tesis presenta algunos métodos numéricos novedosos para la simulación interactiva de dos procedimientos quirúrgicos habituales: el corte y el rasgado (o desgarro) de tejidos blandos. El marco común de los métodos presentados es el uso de la Descomposición Propia Generalizada (PGD en inglés) para la generación de vademécums computacionales, esto es, metasoluciones generales de problemas paramétricos de altas dimensiones que se pueden evaluar a velocidades de respuesta compatibles con entornos hápticos.En el caso del corte, los vademécums computacionales se utilizan de forma conjunta con técnicas basadas en XFEM, mientras que la carga de cálculo se distribuye entre una etapa off-line (previa a la ejecución interactiva) y otra on-line (en tiempo de ejecución). Durante la fase off-line, para el órgano en cuestión se precalculan tanto un vademécum computacional para cualquier posición de una carga, como los desplazamientos producidos por un conjunto de cortes. Así, durante la etapa on-line, los resultados precalculados se combinan de la forma más adecuada para obtener en tiempo real la respuesta a las acciones dirigidas por el usuario. En cuanto al rasgado, a partir de una ecuación paramétrica basada en mecánica del daño continuo, se obtiene un vademécum computacional. La complejidad del modelo se reduce mediante técnicas de Descomposición Ortogonal Propia (POD en inglés), y el vademécum se incorpora a una formulación incremental explícita que se puede interpretar como una especie de integrador temporal.A modo de ejemplo, el método para el corte se aplica a la simulación de un procedimiento quirúrgico refractivo de la córnea conocido como queratotomía radial, mientras que el método para el rasgado se centra en la simulación de la colecistectomía laparoscópica (la extirpación de la vesícula biliar mediante laparoscopia). En ambos casos, los métodos implementados ofrecen excelentes resultados en términos de velocidades de respuesta y producen simulaciones muy realistas desde los puntos de vista visual y háptico.The real-time computer-based simulation of surgery has proven to be an appealing alternative to traditional surgical simulators. Amongst other advantages, computer-based simulators provide considerable savings on time and maintenance costs, and allow trainees to practice their surgical skills in a safe environment as often as necessary. However, in spite of the current computer capabilities, computational surgery continues to be a challenging field of research. One of its major issues is the high speed at which complex problems in continuum mechanics have to be solved so that haptic interfaces can render a realistic sense of touch (generally, feedback rates of 500–1 000 Hz are required). This thesis introduces some novel numerical methods for the interactive simulation of two usual surgical procedures: cutting and tearing of soft tissues. The common framework of the presented methods is the use of the Proper Generalised Decomposition (PGD) for the generation of computational vademecums, i. e. general meta-solutions of parametric high-dimensional problems that can be evaluated at feedback rates compatible with haptic environments. In the case of cutting, computational vademecums are used jointly with XFEM-based techniques, and the computing workload is distributed into an off-line and an on-line stage. During the off-line stage, both a computational vademecum for any position of a load and the displacements produced by a set of cuts are pre-computed for the organ under consideration. Thus, during the on-line stage, the pre-computed results are properly combined together to obtain in real-time the response to the actions driven by the user. Concerning tearing, a computational vademecum is obtained from a parametric equation based on continuum damage mechanics. The complexity of the model is reduced by Proper Orthogonal Decomposition (POD) techniques, and the vademecum is incorporated into an explicit incremental formulation that can be viewed as a sort of time integrator. By way of example, the cutting method is applied to the simulation of a corneal refractive surgical procedure known as radial keratotomy, whereas the tearing method focuses on the simulation of laparoscopic cholecystectomy (i. e. the removal of the gallbladder). In both cases, the implemented methods offer excellent performances in terms of feedback rates, and produce.<br /

Parallel contact detection algorithm for transient solid dynamics simulations using PRONTO3D

An efficient, scalable, parallel algorithm for treating material surface contacts in solid mechanics finite element programs has been implemented in a modular way for MIMD parallel computers. The serial contact detection algorithm that was developed previously for the transient dynamics finite element code PRONTO3D has been extended for use in parallel computation by devising a dynamic (adaptive) processor load balancing scheme

Connectivity Control for Quad-Dominant Meshes

abstract: Quad-dominant (QD) meshes, i.e., three-dimensional, 2-manifold polygonal meshes comprising mostly four-sided faces (i.e., quads), are a popular choice for many applications such as polygonal shape modeling, computer animation, base meshes for spline and subdivision surface, simulation, and architectural design. This thesis investigates the topic of connectivity control, i.e., exploring different choices of mesh connectivity to represent the same 3D shape or surface. One key concept of QD mesh connectivity is the distinction between regular and irregular elements: a vertex with valence 4 is regular; otherwise, it is irregular. In a similar sense, a face with four sides is regular; otherwise, it is irregular. For QD meshes, the placement of irregular elements is especially important since it largely determines the achievable geometric quality of the final mesh. Traditionally, the research on QD meshes focuses on the automatic generation of pure quadrilateral or QD meshes from a given surface. Explicit control of the placement of irregular elements can only be achieved indirectly. To fill this gap, in this thesis, we make the following contributions. First, we formulate the theoretical background about the fundamental combinatorial properties of irregular elements in QD meshes. Second, we develop algorithms for the explicit control of irregular elements and the exhaustive enumeration of QD mesh connectivities. Finally, we demonstrate the importance of connectivity control for QD meshes in a wide range of applications.Dissertation/ThesisDoctoral Dissertation Computer Science 201