Visualization and inspection of the geometry of particle packings

Gegenstand dieser Dissertation ist die Entwicklung von effizienten Verfahren zur Visualisierung und Inspektion der Geometrie von Partikelmischungen. Um das Verhalten der Simulation für die Partikelmischung besser zu verstehen und zu überwachen, sollten nicht nur die Partikel selbst, sondern auch spezielle von den Partikeln gebildete Bereiche, die den Simulationsfortschritt und die räumliche Verteilung von Hotspots anzeigen können, visualisiert werden können. Dies sollte auch bei großen Packungen mit Millionen von Partikeln zumindest mit einer interaktiven Darstellungsgeschwindigkeit möglich sein. . Da die Simulation auf der Grafikkarte (GPU) durchgeführt wird, sollten die Visualisierungstechniken die Daten des GPU-Speichers vollständig nutzen. Um die Qualität von trockenen Partikelmischungen wie Beton zu verbessern, wurde der Korngrößenverteilung große Aufmerksamkeit gewidmet, die die Raumfüllungsrate hauptsächlich beeinflusst und daher zwei der wichtigsten Eigenschaften des Betons bestimmt: die strukturelle Robustheit und die Haltbarkeit. Anhand der Korngrößenverteilung kann die Raumfüllungsrate durch Computersimulationen bestimmt werden, die analytischen Ansätzen in der Praxis wegen der breiten Größenverteilung der Partikel oft überlegen sind. Eine der weit verbreiteten Simulationsmethoden ist das Collective Rearrangement, bei dem die Partikel zunächst an zufälligen Positionen innerhalb eines Behälters platziert werden. Später werden Überlappungen zwischen Partikeln aufgelöst, indem überlappende Partikel voneinander weggedrückt werden. Durch geschickte Anpassung der Behältergröße während der Simulation, kann die Collective Rearrangement-Methode am Ende eine ziemlich dichte Partikelpackung generieren. Es ist jedoch sehr schwierig, den gesamten Simulationsprozess ohne ein interaktives Visualisierungstool zu optimieren oder dort Fehler zu finden. Ausgehend von der etablierten rasterisierungsbasierten Methode zum Darstellen einer großen Menge von Kugeln, bietet diese Dissertation zunächst schnelle und pixelgenaue Methoden zur neuartigen Visualisierung der Überlappungen und Freiräume zwischen kugelförmigen Partikeln innerhalb eines Behälters.. Die auf Rasterisierung basierenden Verfahren funktionieren gut für kleinere Partikelpackungen bis ca. eine Million Kugeln. Bei größeren Packungen entstehen Probleme durch die lineare Laufzeit und den Speicherverbrauch. Zur Lösung dieses Problems werden neue Methoden mit Hilfe von Raytracing zusammen mit zwei neuen Arten von Bounding-Volume-Hierarchien (BVHs) bereitgestellt. Diese können den Raytracing-Prozess deutlich beschleunigen --- die erste kann die vorhandene Datenstruktur für die Simulation wiederverwenden und die zweite ist speichereffizienter. Beide BVHs nutzen die Idee des Loose Octree und sind die ersten ihrer Art, die die Größe von Primitiven für interaktives Raytracing mit häufig aktualisierten Beschleunigungsdatenstrukturen berücksichtigen. Darüber hinaus können die Visualisierungstechniken in dieser Dissertation auch angepasst werden, um Eigenschaften wie das Volumen bestimmter Bereiche zu berechnen. All diese Visualisierungstechniken werden dann auf den Fall nicht-sphärischer Partikel erweitert, bei denen ein nicht-sphärisches Partikel durch ein starres System von Kugeln angenähert wird, um die vorhandene kugelbasierte Simulation wiederverwenden zu können. Dazu wird auch eine neue GPU-basierte Methode zum effizienten Füllen eines nicht-kugelförmigen Partikels mit polydispersen überlappenden Kugeln vorgestellt, so dass ein Partikel mit weniger Kugeln gefüllt werden kann, ohne die Raumfüllungsrate zu beeinträchtigen. Dies erleichtert sowohl die Simulation als auch die Visualisierung. Basierend auf den Arbeiten in dieser Dissertation können ausgefeiltere Algorithmen entwickelt werden, um großskalige nicht-sphärische Partikelmischungen effizienter zu visualisieren. Weiterhin kann in Zukunft Hardware-Raytracing neuerer Grafikkarten anstelle des in dieser Dissertation eingesetzten Software-Raytracing verwendet werden. Die neuen Techniken können auch als Grundlage für die interaktive Visualisierung anderer partikelbasierter Simulationen verwendet werden, bei denen spezielle Bereiche wie Freiräume oder Überlappungen zwischen Partikeln relevant sind.The aim of this dissertation is to find efficient techniques for visualizing and inspecting the geometry of particle packings. Simulations of such packings are used e.g. in material sciences to predict properties of granular materials. To better understand and supervise the behavior of these simulations, not only the particles themselves but also special areas formed by the particles that can show the progress of the simulation and spatial distribution of hot spots, should be visualized. This should be possible with a frame rate that allows interaction even for large scale packings with millions of particles. Moreover, given the simulation is conducted in the GPU, the visualization techniques should take full use of the data in the GPU memory. To improve the performance of granular materials like concrete, considerable attention has been paid to the particle size distribution, which is the main determinant for the space filling rate and therefore affects two of the most important properties of the concrete: the structural robustness and the durability. Given the particle size distribution, the space filling rate can be determined by computer simulations, which are often superior to analytical approaches due to irregularities of particles and the wide range of size distribution in practice. One of the widely adopted simulation methods is the collective rearrangement, for which particles are first placed at random positions inside a container, later overlaps between particles will be resolved by letting overlapped particles push away from each other to fill empty space in the container. By cleverly adjusting the size of the container according to the process of the simulation, the collective rearrangement method could get a pretty dense particle packing in the end. However, it is very hard to fine-tune or debug the whole simulation process without an interactive visualization tool. Starting from the well-established rasterization-based method to render spheres, this dissertation first provides new fast and pixel-accurate methods to visualize the overlaps and free spaces between spherical particles inside a container. The rasterization-based techniques perform well for small scale particle packings but deteriorate for large scale packings due to the large memory requirements that are hard to be approximated correctly in advance. To address this problem, new methods based on ray tracing are provided along with two new kinds of bounding volume hierarchies (BVHs) to accelerate the ray tracing process --- the first one can reuse the existing data structure for simulation and the second one is more memory efficient. Both BVHs utilize the idea of loose octree and are the first of their kind to consider the size of primitives for interactive ray tracing with frequently updated acceleration structures. Moreover, the visualization techniques provided in this dissertation can also be adjusted to calculate properties such as volumes of the specific areas. All these visualization techniques are then extended to non-spherical particles, where a non-spherical particle is approximated by a rigid system of spheres to reuse the existing simulation. To this end a new GPU-based method is presented to fill a non-spherical particle with polydisperse possibly overlapping spheres efficiently, so that a particle can be filled with fewer spheres without sacrificing the space filling rate. This eases both simulation and visualization. Based on approaches presented in this dissertation, more sophisticated algorithms can be developed to visualize large scale non-spherical particle mixtures more efficiently. Besides, one can try to exploit the hardware ray tracing of more recent graphic cards instead of maintaining the software ray tracing as in this dissertation. The new techniques can also become the basis for interactively visualizing other particle-based simulations, where special areas such as free space or overlaps between particles are of interest

Dynamic triangulations for efficient 3D simulation of granular materials

Granular materials are omnipresent in many fields ranging from civil engineering to food, mining and pharmaceutical industries. Often considered a fourth state of matter, they exhibit specific phenomena such as segregation, arching effects, pattern formation, etc. Due to its potential capability of realistically rendering these behaviors, the Distinct Element Method (DEM) is a very enticing simulation technique. Indeed it makes it possible to analyze and observe phenomena that are barely if at all accessible experimentally. DEM works by tracking every particle in the system individually, maintaining for each a trajectory influenced by external factors such as gravitation or contacts with boundary objects and by the interactions with other grains. The mathematical problem of identifying pairs of grains that interact and locating precisely where the contact occurs is highly dependent on the shape of the grains. We focus in this thesis on 3D spherical grains and use dynamic weighted Delaunay triangulations to track the collisions. The triangulation is built on the centers of the grains and evolves to follow their motion. We prove that all potentially colliding pairs of spheres are adjacent in the triangulation. As there are 6n to 8n edges for n spheres in most practical cases, the complexity of the collision detection becomes linear instead of quadratic in the number of particles, with a small overhead in maintaining the triangulation with efficient local operations. For the physical problem of realistically rendering the collision in a numerical contact model suitable for computer simulation, we have used widely accepted theories such as the viscoelastic model of Cundall, but have also tested some recent, more sophisticated developments in the field. The collision detection and contact models have been implemented in a modular DEM simulation code with advanced features in data structures storing the triangulation, in numerical robustness of the geometric computations, and in parallel processing on shared memory computers. Optimal packing of powders is important in many industrial processes, yet no theoretical result exists when dealing with grains of different sizes. We have performed simulations of such cases and could compare our results with experimental data. Preliminary results have been obtained regarding the relation between the size and proportion of grains and the density of the packing. Other simulations have also been performed, such as the granular flow through an hourglass. As no efficient simulation method is currently known for non-spherical 3D grains, we propose an intermediate approach of gluing spheres together into arbitrary shaped clusters and show some examples based on this approach

New Geometric Data Structures for Collision Detection

We present new geometric data structures for collision detection and more, including: Inner Sphere Trees - the first data structure to compute the peneration volume efficiently. Protosphere - an new algorithm to compute space filling sphere packings for arbitrary objects. Kinetic AABBs - a bounding volume hierarchy that is optimal in the number of updates when the objects deform. Kinetic Separation-List - an algorithm that is able to perform continuous collision detection for complex deformable objects in real-time. Moreover, we present applications of these new approaches to hand animation, real-time collision avoidance in dynamic environments for robots and haptic rendering, including a user study that exploits the influence of the degrees of freedom in complex haptic interactions. Last but not least, we present a new benchmarking suite for both, peformance and quality benchmarks, and a theoretic analysis of the running-time of bounding volume-based collision detection algorithms

Automatic calculation and evaluation of flow in complex geometries using finite volume and lattice boltzmann methods

Trotz großen Fortschritts kann die numerische Strömungsmechanik (englisch Computational Fluid Dynamics, CFD) nicht als Blackbox-Verfahren verwendet werden, da Schritte wie die Gittergenerierung oder die Wahl numerischer Parameter vertiefte Kenntnisse der Theorie von CFD erfordert. Eine Verbesserung von CFD in Richtung einer Blackbox-Lösung würde nicht nur die Anwendungsbarriere verringern, weil weniger spezielles Wissen notwendig ist, sondern auch wissenschaftliche Erkenntnisse ermöglichen. Beispielsweise können viel mehr Datenpunkte erzeugt werden, die für die Entwicklung genauer Modelle für manche Fragestellungen notwendig sind. Diese Arbeit veranschaulicht die Vorteile einer automatisierten Berechnung anhand dreier beispielhafter Anwendungen: • Die genaue Vorhersage des Druckverlusts einer Kugelschüttung ist von großer Bedeutung in der Verfahrenstechnik. Für Schüttungen, bei denen die Kugeln relativ groß verglichen mit den Abmessungen des Behälters sind, spielt zudem der Wandeffekt eine wichtige Rolle. Viele Korrelationen, die üblicherweise auf experimentellen Messungen basieren, wurden in der Literatur vorgestellt, zeigen aber Abweichungen von ca. 20 % voneinander. Die Kombination von simulierter Generierung von Kugelschüttung und CFD wird hier verwendet, um den Druckverlust einer großen Anzahl von Kugelpackungen mit unterschiedlichen Kugeldurchmessern und für unterschiedliche Abmessungen des Behälters zu berechnen. Es wird gezeigt, dass der Druckverlust eine nicht-monotone Funktion für kleine Verhältnisse von Kugeldurchmesser zu hydraulischem Durchmesser des Reaktors ist, was die Abweichungen in den experimentellen Ergebnissen erklären kann. • Die Fischer-Tropsch-Synthese ist wieder von wachsendem Interesse, da sie die Herstellung von CO2 neutralen Treibstoffen erlaubt. Transportporen können genutzt werden, um den Stofftransport im benötigten Katalysator zu beschleunigen und somit auch die Ausbeute zu erhöhen. Ein eindimensionales Modell aus der Literatur wird in dieser Arbeit auf drei Dimensionen erweitert. Die Berechnung wird automatisiert wodurch die Katalysatorschichten algorithmisch optimiert werden können. Die Ergebnisse zeigen, dass für Transportporen mit einem Durchmesser größer als 50 µm eine drei-dimensionale Betrachtung nötig ist. Größere Transportporen mit einem Durchmesser von bis zu 250 µm können ebenfalls verwendet werden, um die Ausbeute pro Zeit und Fläche zu erhöhen, erfordern aber dickere Katalysatorschichten und eine größere Transportporenporosität um die Nachteile der größeren Poren zu kompensieren. • Nasenscheidewandverkrümmungen sind sehr verbreitet in der Bevölkerung, aber es ist unklar, warum einige Betroffene Beschwerden entwickeln während andere hingegen keine Einschränkungen haben. Bisherige Arbeiten setzten den Schwerpunkt auf die Analyse einiger ausgewählter Fälle, was aufgrund der hohen natürlichen Variationen der Nasenscheidewand zu keinen klaren Ergebnissen führte. In dieser Arbeit wird ein vollautomatischer Ansatz zur Berechnung integraler Beiwerte wie Druckverlust und der Strömungsverteilung zwischen den beiden Atemwegen ausgehend von Computertomographie-Aufnahmen vorgestellt. Zusätzlich wird eine Methode zur Verringerung des Rechenaufwandes durch das Entfernen der Nasennebenhöhlen in den CT-Bildern basierend auf maschinellem Lernen vorgeschlagen. Für diesen Anwendungsfall kann die automatische Berechnung und Auswertung verwendet werden, um eine ganze Datenbank von CT-Aufnahmen in strömungsmechanische Kennziffern umzuwandeln, die für eine statistische Analyse verwendet werden können. Weiterhin könnte sie die Anwendung von CFD in der klinischen Praxis ermöglichen. Das Lattice-Boltzmann Verfahren (LBM) ist eine alternative Methode zu „klassischen“, Finite-Volumen basierten Lösern der Navier-Stokes-Gleichungen. Da es eine einfache Generierung von Gittern erlaubt, wird hier eine neue LBM-Implementierung verwendet um die Strömung durch die Kugelschüttung und Nasenhöhle zu berechnen. Die Implementierung bietet gute Portabilität zu unterschiedlichen Systemen und zu unterschiedlicher Hardware wie Grafikkarten (GPUs), die aufgrund ihrer Kosteneffektivität die Anwendbarkeit von CFD erhöhen. Sie kann außerdem Gitterverfeinerung verwenden und es wird ein Algorithmus zur Gittergenerierung, der auch für Grafikkarten geeignet ist, vorgestellt. Um den Flaschenhals langsamer Datenspeicher zu umgehen und die Auswertung zu vereinfachen, wird eine GPU basierte in-situ Verarbeitung implementiert. Der Anwendungsfall der Fischer-Tropsch-Synthese zeigt dennoch, dass „klassische“, Finite-Volumen basierte Löser wie OpenFOAM eine ebenso valide Wahl für automatische Berechnungen sind, wenn strukturierte Gitter verwendet werden. Außerdem ist es für einige Anwendungen einfacher, die Fragestellung mittels partieller Differenzialgleichungen zu modellieren, die mittels Finite-Volumen-Verfahren direkt gelöst werden können.Despite significant progress, computational fluid dynamics (CFD) can still not be used as a “black box approach” as meshing often requires manual intervention and the choosing of numerical parameters deep knowledge of the methods behind CFD. Improving CFD towards such a black box solution not only reduces the barrier of application as less specialized knowledge is required, but also allows for scientific insight. For example, much more data can be generated that is needed to develop accurate models for some problems. This thesis illustrates these benefits with three exemplary applications: • The accurate prediction of the pressure drop of a sphere packed bed is of great importance in engineering. For geometries where the spheres are relatively large compared to the confinement, the wall effect plays another important role. Many correlations have been presented, usually based on experimental measurements that differ in a range of approx. 20 %. Here, the combination of simulated packing generation and CFD is used to evaluate the pressure drop for a very large number of packings with different sphere diameters and different geometries of the confining walls. It is shown that for small ratios of sphere diameter to hydraulic diameter of the reactor the pressure drop is a non-monotonic function which can explain the differences in experimental findings. • The Fischer-Tropsch synthesis is again of increasing interest as it allows the production of carbon-neutral fuel. Transport pores can be added to the catalyst needed for the reaction to enhance transport and consequently the yield. A three-dimensional extension of a one-dimensional model from literature for transport and reaction is presented here. The automation of the calculation is used to enable the algorithmic optimization of the catalyst layers. The results show that for transport pores larger than 50 µm the problem must be treated as three-dimensional. Larger transport pores up to a diameter of 250 µm can also be used to achieve a gain in area-time yield, but thicker catalyst layers and a higher transport pore porosity are needed to overcome the drawbacks of larger pores. • Nasal septum deviation is very common in general population but it is unclear why it causes symptoms for certain patients while others report no discomfort. Previous studies focused on the analysis of few selected cases which did not lead to clear results as the human nose shows high natural variations in geometry. Here, a fully automatic approach for calculating critical parameters like the pressure drop and the flow distribution between the two airways from computed tomography (CT) scans is presented. Furthermore, a method to reduce the computational time by removing paranasal sinuses from the scan incorporating machine learning algorithms is proposed. For this case, fully automatic processing can be used to convert a whole database of CT scans to fluid dynamic parameters that can be used for statistical analysis. Furthermore, it could allow the introduction of CFD analysis to clinical practice. The lattice Boltzmann method (LBM) is an alternative method to “classical” finite-volume based solvers of the Navier-Stokes equations. Since it offers easy generation of grids, a novel LBM implementation is used here to calculate the flow through the sphere packings and the nasal cavity. The implementation features good portability to various systems and hardware like GPUs which due to their cost-effectiveness broaden the applicability of CFD. It can utilize grid refinement and a meshing algorithm suitable for GPUs is presented. To overcome slow IO and to simplify automatic evaluation, GPU assisted co-processing is implemented. Nevertheless, the application case of Fischer-Tropsch synthesis shows that “classical”, finite volume based solvers like OpenFOAM are also valid choice for automatic processing if structured meshes can be used. Furthermore, for some applications, it is easier to model the problem using partial differential equations which can be directly solved using FVM

Modeling Residence Time Distribution of Chromatographic Perfusion Resin for Large Biopharmaceutical Molecules: A Computational Fluid Dynamic Study

The need for production processes of large biotherapeutic particles, such as virus-based particles and extracellular vesicles, has risen due to increased demand in the development of vaccinations, gene therapies, and cancer treatments. Liquid chromatography plays a significant role in the purification process and is routinely used with therapeutic protein production. However, performance with larger macromolecules is often inconsistent, and parameter estimation for process development can be extremely time- and resource-intensive. This thesis aimed to utilize advances in computational fluid dynamic (CFD) modeling to generate a first-principle model of the chromatographic process while minimizing model parameter estimation\u27s physical resource demand. Specifically, I utilized explicit geometric rendering to develop a CFD steady-state model to simulate fluid flow through and around a perfusive porous resin in a pseudo packed bed flow-cell to predicted fluid velocities and shear stress. I generated different explicit geometries, and compared the velocity profiles of steady-state simulations against reported literature values of commercially available resin\u27s intraparticle convective flow. I then developed a two-part transient CFD discrete phase model to model a tracer protein\u27s capture and release from a resin. Particle age distribution functions were calculated to characterize the macromixing in the model and compared them with existing single parameter models. These models exhibited similar distribution profiles and provided additional information about the shear forces acting on the particles. These preliminary studies revealed that shear is relatively low shear at process operating conditions, and the low yield of large biotherapeutic particles in chromatography is likely not due to shear forces

Design of decorative 3D models: from geodesic ornaments to tangible assemblies

L'obiettivo di questa tesi è sviluppare strumenti utili per creare opere d'arte decorative digitali in 3D. Uno dei processi decorativi più comunemente usati prevede la creazione di pattern decorativi, al fine di abbellire gli oggetti. Questi pattern possono essere dipinti sull'oggetto di base o realizzati con l'applicazione di piccoli elementi decorativi. Tuttavia, la loro realizzazione nei media digitali non è banale. Da un lato, gli utenti esperti possono eseguire manualmente la pittura delle texture o scolpire ogni decorazione, ma questo processo può richiedere ore per produrre un singolo pezzo e deve essere ripetuto da zero per ogni modello da decorare. D'altra parte, gli approcci automatici allo stato dell'arte si basano sull'approssimazione di questi processi con texturing basato su esempi o texturing procedurale, o con sistemi di riproiezione 3D. Tuttavia, questi approcci possono introdurre importanti limiti nei modelli utilizzabili e nella qualità dei risultati. Il nostro lavoro sfrutta invece i recenti progressi e miglioramenti delle prestazioni nel campo dell'elaborazione geometrica per creare modelli decorativi direttamente sulle superfici. Presentiamo una pipeline per i pattern 2D e una per quelli 3D, e dimostriamo come ognuna di esse possa ricreare una vasta gamma di risultati con minime modifiche dei parametri. Inoltre, studiamo la possibilità di creare modelli decorativi tangibili. I pattern 3D generati possono essere stampati in 3D e applicati a oggetti realmente esistenti precedentemente scansionati. Discutiamo anche la creazione di modelli con mattoncini da costruzione, e la possibilità di mescolare mattoncini standard e mattoncini custom stampati in 3D. Ciò consente una rappresentazione precisa indipendentemente da quanto la voxelizzazione sia approssimativa. I principali contributi di questa tesi sono l'implementazione di due diverse pipeline decorative, un approccio euristico alla costruzione con mattoncini e un dataset per testare quest'ultimo.The aim of this thesis is to develop effective tools to create digital decorative 3D artworks. Real-world art often involves the use of decorative patterns to enrich objects. These patterns can be painted on the base or might be realized with the application of small decorative elements. However, their creation in digital media is not trivial. On the one hand, users can manually perform texture paint or sculpt each decoration, in a process that can take hours to produce a single piece and needs to be repeated from the ground up for every model that needs to be decorated. On the other hand, automatic approaches in state of the art rely on approximating these processes with procedural or by-example texturing or with 3D reprojection. However, these approaches can introduce significant limitations in the models that can be used and in the quality of the results. Instead, our work exploits the recent advances and performance improvements in the geometry processing field to create decorative patterns directly on surfaces. We present a pipeline for 2D and one for 3D patterns and demonstrate how each of them can recreate a variety of results with minimal tweaking of the parameters. Furthermore, we investigate the possibility of creating decorative tangible models. The 3D patterns we generate can be 3D printed and applied to previously scanned real-world objects. We also discuss the creation of models with standard building bricks and the possibility of mixing standard and custom 3D-printed bricks. This allows for a precise representation regardless of the coarseness of the voxelization. The main contributions of this thesis are the implementation of two different decorative pipelines, a heuristic approach to brick construction, and a dataset to test the latter

Doctor of Philosophy

dissertationOne of the fundamental building blocks of many computational sciences is the construction and use of a discretized, geometric representation of a problem domain, often referred to as a mesh. Such a discretization enables an otherwise complex domain to be represented simply, and computation to be performed over that domain with a finite number of basis elements. As mesh generation techniques have become more sophisticated over the years, focus has largely shifted to quality mesh generation techniques that guarantee or empirically generate numerically well-behaved elements. In this dissertation, the two complementary meshing subproblems of vertex placement and element creation are analyzed, both separately and together. First, a dynamic particle system achieves adaptivity over domains by inferring feature size through a new information passing algorithm. Second, a new tetrahedral algorithm is constructed that carefully combines lattice-based stenciling and mesh warping to produce guaranteed quality meshes on multimaterial volumetric domains. Finally, the ideas of lattice cleaving and dynamic particle systems are merged into a unified framework for producing guaranteed quality, unstructured and adaptive meshing of multimaterial volumetric domains