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Yes / A novel Lattice-Boltzmann model to simulate gas mixing in anaerobic digestion is developed and described. For the first time, Euler–Lagrange multiphase, non-Newtonian and turbulence modelling are applied jontly with a novel hybrid boundary condition. The model is validated in a laboratory-scale framework and flow patterns are assessed through Particle Imaging Velocimetry (PIV) and innovative Positron-Emission Particle Tracking (PEPT). The model is shown to reproduce the experimental flow patterns with fidelity in both qualitative and quantitative terms. The model opens up a new approach to computational modelling of the complex multiphase flow in anaerobic digesters and offers specific advantages, such as computational efficiency, over an analogous Euler-Lagrange finite-volume computational fluid dynamics approach. / UK EPSRC Grant (EP/R01485X/1, Computational Methods for Anaerobic Digestion Optimization, “CoMAnDO”). The numerical work was performed in the HPC Cirrus EPSRC Tier-2 National HPC Facility, Edinburgh, UK, under a UK EPSRC Tier-2 Research Allocation Panel (RAP) award.

Yes / We present the OpenLB package, a C++ library providing a flexible framework for lattice Boltzmann simulations. The code is publicly available and published under GNU GPLv2, which allows for adaption and implementation of additional models. The extensibility benefits from a modular code structure achieved e.g. by utilizing template meta-programming. The package covers various methodical approaches and is applicable to a wide range of transport problems (e.g. fluid, particulate and thermal flows). The built-in processing of the STL file format furthermore allows for the simple setup of simulations in complex geometries. The utilization of MPI as well as OpenMP parallelism enables the user to perform those simulations on large-scale computing clusters. It requires a minimal amount of dependencies and includes several benchmark cases and examples. The package presented here aims at providing an open access platform for both, applicants and developers, from academia as well as industry, which facilitates the extension of previous implementations and results to novel fields of application for lattice Boltzmann methods. OpenLB was tested and validated over several code reviews and publications. This paper summarizes the findings and gives a brief introduction to the underlying concepts as well as the design of the parallel data structure.

The cross-sectional geometry of an insect wing has historically been simplified to a rectangular, elliptic, or having a streamlined airfoil shape. Up until this point, no analysis has utilized a morphologically accurate insect wing. As such, there remains significant questions as to whether or not there are aerodynamic benefits to the wing vein structure accompanying the already known structural improvements. The present study uses a bumblebee specimen (Bombus pensylvanicus) acquired by the author, scanned using a skyscan microCT scanner, and post-processed for computational analysis. The resulting geometry captures the naturally occurring vein structures present in the bee wing and is used to better understand aerodynamic effects of biological corrugation. The aerodynamics associated with a morphologically accurate bee wing geometry are explored in two and three dimensions for the first time. Multiple methodologies are validated with experimental results presented in the literature to capture the fluid dynamics in two dimensions including the Lattice-Boltzmann method and unstructured dynamic remeshing using a Navier-Stokes approach. The effects of wing cross-section are compared first with common geometries used in the literature in two dimensions and then between cross-sections extracted at different locations along the wing span. A three-dimensional methodology is validated and used to compare the true bee wing with one using a rectangular cross-section in symmetric hovering. The influence of spanwise cross-section is revisited in three dimensions and compared to the results found in two-dimensions for the same kinematics in forward flight. The final focus of the dissertation is the first simulation of a morphologically accurate wing using kinematics described in the literature. / PHD

Malgré l'efficacité informatique et la faible dissipation numérique de la méthode de Boltzmann sur réseau (LBM) classique reposant sur un algorithme de propagation-collision, cette méthode est limitée aux maillages cartésiens uniformes. L'adaptation de l'étape de discrétisation à différentes échelles de la mécanique des fluides est généralement réalisée par des schémas LBM à échelles multiples, dans lesquels le domaine de calcul est décomposé en plusieurs sous-domaines uniformes avec différentes résolutions spatiales et temporelles. Pour des raisons de connectivité, le facteur de résolution des sous-domaines adjacents doit être un multiple de deux, introduisant un changement abrupt des échelles spatio-temporelles aux interfaces. Cette spécificité peut déclencher des instabilités numériques et produire des sources de bruit parasite rendant l'exploitation de simulations à finalités aéroacoustiques impossible. Dans la présente thèse, nous avons d'abord élucidé le sujet du raffinement de maillage dans la LBM classique en soulignant les défis et les sources potentielles d'erreur. Par la suite, une méthode de Boltzmann sur réseau hybride (HLBM) est proposée, combinant l'algorithme de propagation-collision avec un algorithme de flux au sens eulérien obtenu à partir d'une discrétisation en volumes finis des équations de Boltzmann à vitesse discrète. La HLBM combine à la fois les avantages de la LBM classique et une flexibilité géométrique accrue. La HLBM permet d'utiliser des maillages cartésiens non-uniformes. La validation de la méthode hybride sur des cas tests 2D à finalité aéroacoustique montre qu'une telle approche constitue une alternative viable aux schémas Boltzmann sur réseau à échelles multiples, permettant de réaliser des raffinements locaux en H. Enfin, un couplage original, basé sur l'algorithme de propagation-collision et une formulation isotherme des équations de Navier-Stokes en volumes finis, est proposé. Une telle tentative présente l'avantage de réduire le nombre d'équations du solveur volumes finis tout en augmentant la stabilité numérique de celui-ci, en raison d'une condition CFL plus favorable. Les deux solveurs sont couplés dans l'espace des moments, où la solution macroscopique du solveur Navier-Stokes est injectée dans l'algorithme de propagation-collision à l'aide de la collision des moments centrés. La faisabilité d'un tel couplage est démontrée sur des cas tests 2D, et les résultas obtenus sont comparés avec la HLBM. / Despite the inherent efficiency and low dissipative behaviour of the standard lattice Boltzmann method (LBM) relying on a two step stream and collide algorithm, a major drawback of this approach is the restriction to uniform Cartesian grids. The adaptation of the discretization step to varying fluid dynamic scales is usually achieved by multi-scale lattice Boltzmann schemes, in which the computational domain is decomposed into multiple uniform subdomains with different spatial resolutions. For the sake of connectivity, the resolution factor of adjacent subdomains has to be a multiple of two, introducing an abrupt change of the space-time discretization step at the interface that is prone to trigger instabilites and generate spurious noise sources that contaminate the expected physical pressure signal. In the present PhD thesis, we first elucidate the subject of mesh refinement in the standard lattice Boltzmann method and point out challenges and potential sources of error. Subsequently, we propose a novel hybrid lattice Boltzmann method (HLBM) that combines the stream and collide algorithm with an Eulerian flux-balance algorithm that is obtained from a finite-volume discretization of the discrete velocity Boltzmann equations. The interest of a hybrid lattice Boltzmann method is the pairing of efficiency and low numerical dissipation with an increase in geometrical flexibility. The HLBM allows for non-uniform grids. In the scope of 2D periodic test cases, it is shown that such an approach constitutes a valuable alternative to multi-scale lattice Boltzmann schemes by allowing local mesh refinement of type H. The HLBM properly resolves aerodynamics and aeroacoustics in the interface regions. A further part of the presented work examines the coupling of the stream and collide algorithm with a finite-volume formulation of the isothermal Navier-Stokes equations. Such an attempt bears the advantages that the number of equations of the finite-volume solver is reduced. In addition, the stability is increased due to a more favorable CFL condition. A major difference to the pairing of two kinetic schemes is the coupling in moment space. Here, a novel technique is presented to inject the macroscopic solution of the Navier-Stokes solver into the stream and collide algorithm using a central moment collision. First results on 2D tests cases show that such an algorithm is stable and feasible. Numerical results are compared with those of the previous HLBM.

<div>As high performance computing systems are advancing from petascale to exascale, scientific workflows to integrate simulation and visualization/analysis are a key factor to influence scientific campaigns. As one of the campaigns to study fluid behaviors, computational fluid dynamics (CFD) simulations have progressed rapidly in the past several decades, and revolutionized our lives in many fields. Lattice Boltzmann method (LBM) is an evolving CFD approach to significantly reducing the complexity of the conventional CFD methods, and can simulate complex fluid flow phenomena with cheaper computational cost. This research focuses on accelerating the workflow of LBM simulation and data analysis.</div><div><br></div><div>I start my research on how to effectively integrate each component of a workflow at extreme scales. Firstly, we design an in-situ workflow benchmark that integrates seven state-of-the-art in-situ workflow systems with three synthetic applications, two real-world CFD applications, and corresponding data analysis. Then detailed performance analysis using visualized tracing shows that even the fastest existing workflow system still has 42% overhead. Then, I develop a novel minimized end-to-end workflow system, Zipper, which combines the fine-grain task parallelism of full asynchrony and pipelining. Meanwhile, I design a novel concurrent data transfer optimization method, which employs a multi-threaded work-stealing algorithm to transfer data using both channels of network and parallel file system. It significantly reduces the data transfer time by up to 32%, especially when the simulation application is stalled. Then investigation on the speedup using OmniPath network tools shows that the network congestion has been alleviated by up to 80%. At last, the scalability of the Zipper system has been verified by a performance model and various largescale workflow experiments on two HPC systems using up to 13,056 cores. Zipper is the fastest workflow system and outperforms the second-fastest by up to 2.2 times.</div><div><br></div><div>After minimizing the end-to-end time of the LBM workflow, I began to accelerate the memory-bound LBM algorithms. We first design novel parallel 2D memory-aware LBM algorithms. Then I extend to design 3D memory-aware LBM that combine features of single-copy distribution, single sweep, swap algorithm, prism traversal, and merging multiple temporal time steps. Strong scalability experiments on three HPC systems show that 2D and 3D memory-aware LBM algorithms outperform the existing fastest LBM by up to 4 times and 1.9 times, respectively. The speedup reasons are illustrated by theoretical algorithm analysis. Experimental roofline charts on modern CPU architectures show that memory-aware LBM algorithms can improve the arithmetic intensity (AI) of the fastest existing LBM by up to 4.6 times.</div>

Lattice Boltzmann method (LBM) has been developed as a powerful numerical approach to simulate the complex fluid flow and heat transfer phenomena during the past two decades. As a mesoscale method based on the kinetic theory, LBM has several advantages compared with traditional numerical methods such as physical representation of microscopic interactions, dealing with complex geometries and highly parallel nature. Lattice Boltzmann method has been applied to solve various fluid behaviors and heat transfer process like conjugate heat transfer, magnetic and electric field, diffusion and mixing process, chemical reactions, multiphase flow, phase change process, non-isothermal flow in porous medium, microfluidics, fluid-structure interactions in biological system and so on. In addition, as a non-body-conformal grid method, the immersed boundary method (IBM) could be applied to handle the complex or moving geometries in the domain. The immersed boundary method could be coupled with lattice Boltzmann method to study the heat transfer and fluid flow problems. Heat transfer and fluid flow are solved on Euler nodes by LBM while the complex solid geometries are captured by Lagrangian nodes using immersed boundary method. Parallel computing has been a popular topic for many decades to accelerate the computational speed in engineering and scientific fields. Today, almost all the laptop and desktop have central processing units (CPUs) with multiple cores which could be used for parallel computing. However, the cost of CPUs with hundreds of cores is still high which limits its capability of high performance computing on personal computer. Graphic processing units (GPU) is originally used for the computer video cards have been emerged as the most powerful high-performance workstation in recent years. Unlike the CPUs, the cost of GPU with thousands of cores is cheap. For example, the GPU (GeForce GTX TITAN) which is used in the current work has 2688 cores and the price is only 1,000 US dollars. The release of NVIDIA's CUDA architecture which includes both hardware and programming environment in 2007 makes GPU computing attractive. Due to its highly parallel nature, lattice Boltzmann method is successfully ported into GPU with a performance benefit during the recent years. In the current work, LBM CUDA code is developed for different fluid flow and heat transfer problems. In this dissertation, lattice Boltzmann method and immersed boundary method are used to study natural convection in an enclosure with an array of conduting obstacles, double-diffusive convection in a vertical cavity with Soret and Dufour effects, PCM melting process in a latent heat thermal energy storage system with internal fins, mixed convection in a lid-driven cavity with a sinusoidal cylinder, and AC electrothermal pumping in microfluidic systems on a CUDA computational platform. It is demonstrated that LBM is an efficient method to simulate complex heat transfer problems using GPU on CUDA.

This thesis focuses on two problems lying within the field of soft condensed matter: the viscous fingering or Saffman-Taylor instability and nematic liquid crystals in confinement. Whenever a low viscosity fluid displaces a high viscosity fluid in a porous medium, for example water pushing oil out of oil reservoirs, the interface between the two fluids is rendered unstable. Viscous fingers develop, grow and compete until a single finger spans all the way from inlet to outlet. Here, using a free energy lattice Boltzmann algorithm, we examine the Saffman-Taylor instability for two different wetting situations: (a) when neither of the two fluids wet the walls of the channel and (b) when the displacing fluids completely wets the walls. We demonstrate that curvature effects in the third dimension, which arise because of the wetting boundary conditions, can lead to a novel suppression of the instability. Recent experiments in microchannels using colloid-polymer mixtures support our findings. In the second part of the thesis we examine nematic liquid crystals confined in wedge-structured geometries. In these systems the final stable configuration of the liquid crystal system is controlled by the complex interplay between confinement, elasticity and surface anchoring. Varying the wedge opening angle this competition leads to a splay to bend transition mediated by a defect in the bulk of the wedge. Using a hybrid lattice Boltzmann algorithm we study the splay-bend transition and compare to recent experiments on {em fd} virus particles in microchannels. Our numerical results, in quantitative agreement with the experiments, enable us to predict the position of the defect as a function of opening angle, and elucidate its role in the change of director structure. This has relevance to novel energy saving, liquid crystal devices which rely on defect motion and pinning to create bistable director configurations.

Title: Non-newtonian fluid flow simulation using lattice Boltzmann method Author: Bc. Pavel Kuriščák Department: Mathematical Institute, Charles University Supervisor: RNDr. Ing. Jaroslav Hron Ph.D. Supervisor's e-mail address: Jaroslav.Hron@mff.cuni.cz Abstract: The aim of this thesis is to find and estabilish a modification to the Lattice Boltzmann Method, allowing it to simulate non-newtonian behaviour of fluids. In the theoretical part of thesis, there is introduced a derivation, based on the work of [22], that is capable of arriving to macroscopical Navier-Stokes equa- tions completely a priori from the Boltzmann equation, utilizing the Hermite basis expansion. This derivation is afterwards applied to the method suggested by [11], that uses the changed equilibrium distribution to fine-tune the local fluid viscosity according to the non-newtonian model. In the last part of thesis, this method is implemented in the form of lattice kinetic scheme and tested on three sample problems. Keywords: Lattice Boltzmann Method, non-newtonian fluids, Hermite expansion, lattice kinetic scheme