付記する学位プログラム名: 京都大学卓越大学院プログラム「先端光・電子デバイス創成学」 / 京都大学 / 新制・課程博士 / 博士(工学) / 甲第25293号 / 工博第5252号 / 京都大学大学院工学研究科電気工学専攻 / (主査)教授 松尾 哲司, 教授 引原 隆士, 教授 土居 伸二 / 学位規則第4条第1項該当 / Doctor of Philosophy (Engineering) / Kyoto University / DFAM

The heart is one the most important organs in the human body and many other live creatures. The electrical activity in the heart controls the heart function, and many heart diseases are linked to the abnormalities in the electrical activity in the heart. Mathematical equations and computer simulation can be used to model the electrical activity in the heart. The heart models are challenging to solve because of the complexity of the models and the huge size of the problems. Several cell models have been proposed to model the electrical activity in a single heart cell. These models must be coupled with a heart model to model the electrical activity in the entire heart. The bidomain model is a popular model to simulate the propagation of electricity in myocardial tissue. It is a continuum-based model consisting of non-linear ordinary differential equations (ODEs) describing the electrical activity at the cellular scale and a system of partial differential equations (PDEs) describing propagation of electricity at the tissue scale. Because of this multi-scale, ODE/PDE structure of the model, splitting methods that treat the ODEs and PDEs in separate steps are natural candidates as numerical methods. First, we need to solve the problem at the cellular scale using ODE solvers. One of the most popular methods to solve the ODEs is known as the Rush-Larsen (RL) method. Its popularity stems from its improved stability over integrators such as the forward Euler (FE) method along with its easy implementation. The RL method partitions the ODEs into two sets: one for the gating variables, which are treated by an exponential integrator, and another for the remaining equations, which are treated by the FE method. The success of the RL method can be understood in terms of its relatively good stability when treating the gating variables. However, this feature would not be expected to be of benefit on cell models for which the stiffness is not captured by the gating equations. We demonstrate that this is indeed the case on a number of stiff cell models. We further propose a new partitioned method based on the combination of a first-order generalization of the RL method with the FE method. This new method leads to simulations of stiff cell models that are often one or two orders of magnitude faster than the original RL method. After solving the ODEs, we need to use bidomain solvers to solve the bidomain model. Two well-known, first-order time-integration methods for solving the bidomain model are the semi-implicit method and the Godunov operator-splitting method. Both methods decouple the numerical procedure at the cellular scale from that at the tissue scale but in slightly different ways. The methods are analyzed in terms of their accuracy, and their relative performance is compared on one-, two-, and three-dimensional test cases. As suggested by the analysis, the test cases show that the Godunov method is significantly faster than the semi-implicit method for the same level of accuracy, specifically, between 5 and 15 times in the cases presented. Second-order bidomain solvers can generally be expected to be more effective than first-order bidomain solvers under normal accuracy requirements. However, the simplest and the most commonly applied second-order method for the PDE step, the Crank-Nicolson (CN) method, may generate unphysical oscillations. We investigate the performance of a two-stage, L-stable singly diagonally implicit Runge-Kutta method for solving the PDEs of the bidomain model and present a stability analysis. Numerical experiments show that the enhanced stability property of this method leads to more physically realistic numerical simulations compared to both the CN and Backward Euler (BE) methods.

Este é o primeiro trabalho que apresenta simulações tridimensionais completamente adaptativas de um modelo de campo de fase para um fluido incompressível com densidade de massa constante e viscosidade variável, conhecido como Modelo H. Solucionando numericamente as equações desse modelo em malhas refinadas localmente com a técnica AMR, simulamos computacionalmente escoamentos bifásicos tridimensionais. Os modelos de campo de fase oferecem uma aproximação física sistemática para investigar fenômenos que envolvem sistemas multifásicos complexos, tais como fluidos com camadas de mistura, a separação de fases sob forças de cisalhamento e a evolução de micro-estruturas durante processos de solidificação. Como as interfaces são substituídas por delgadas regiões de transição (interfaces difusivas), as simulações de campo de fase requerem muita resolução nessas regiões para capturar corretamente a física do problema em estudo. Porém essa não é uma tarefa fácil de ser executada numericamente. As equações que caracterizam o modelo de campo de fase contêm derivadas de ordem elevada e intrincados termos não lineares, o que exige uma estratégia numérica eficiente capaz de fornecer precisão tanto no tempo quanto no espaço, especialmente em três dimensões. Para obter a resolução exigida no tempo, usamos uma discretização semi-implícita de segunda ordem para solucionar as equações acopladas de Cahn-Hilliard e Navier-Stokes (Modelo H). Para resolver adequadamente as escalas físicas relevantes no espaço, utilizamos malhas refinadas localmente que se adaptam dinamicamente para recobrir as regiões de interesse do escoamento, como por exemplo, as vizinhanças das interfaces do fluido. Demonstramos a eficiência e a robustez de nossa metodologia com simulações que incluem a separação dos componentes de uma mistura bifásica, a deformação de gotas sob cisalhamento e as instabilidades de Kelvin-Helmholtz. / This is the first work that introduces 3D fully adaptive simulations for a phase field model of an incompressible fluid with matched densities and variable viscosity, known as Model H. Solving numerically the equations of this model in meshes locally refined with AMR technique, we simulate computationally tridimensional two-phase flows. Phase field models offer a systematic physical approach to investigate complex multiphase systems phenomena such as fluid mixing layers, phase separation under shear and microstructure evolution during solidification processes. As interfaces are replaced by thin transition regions (diffuse interfaces), phase field simulations need great resolution in these regions to capture correctly the physics of the studied problem. However, this is not an easy task to do numerically. Phase field model equations have high order derivatives and intricate nonlinear terms, which require an efficient numerical strategy that can achieve accuracy both in time and in space, especially in three dimensions. To obtain the required resolution in time, we employ a semi-implicit second order discretization scheme to solve the coupled Cahn-Hilliard/Navier-Stokes equations (Model H). To resolve adequatly the relevant physical scales in space, we use locally refined meshes which adapt dynamically to cover special flow regions, e.g., the vicinity of the fluid interfaces. We demonstrate the efficiency and robustness of our methodology with simulations that include spinodal decomposition, the deformation of drops under shear and Kelvin-Helmholtz instabilities.

Dans cette thèse on a développé des algorithmes semi-implicites procédures partagées et monolithiques pour l'interaction entre un fluide gouverné par le modèle de Navier Stokes et une structure. Dans le premier chapitre, on présente un algorithme semi-implicite procédures partagées pour l'interaction entre un fluide et une structure gouvernée soit par les équations d'élasticité linéaire ou soit par le modèle de Saint-Venant Kirchhoff non linéaire. Dans le second chapitre, on propose un algorithme semi-implicite procédures partagées pour l'interaction entre un fluide et une structure de modèle linéaire et on montre un résultat de stabilité inconditionnelle en temps de l'algorithme. Un problème d'optimisation est résolu dans les deux algorithmes précédents, afin de satisfaire les conditions de continuité des vitesses et d'égalité des contraintes à l'interface. Durant les itérations de BFGS pour résoudre le problème d'optimisation, le maillage fluide reste fixe et la matrice fluide n'est factorisée qu'une seule fois, ce qui réduit l'effort de calcul. Dans le troisième chapitre, un algorithme semi-implicite monolithique pour l'interaction entre un fluide et une structure de modèle linéaire est proposé. L'algorithme utilise un maillage global pour le domaine fluide structure. La condition de continuité des vitesses à l'interface est automatiquement satisfaite et celle de l'égalité des contraintes n'apparaît pas explicitement dans la formulation faible. A chaque pas de temps on résout un système monolithique d'inconnues vitesse et pression définies sur le domaine global. Le temps CPU est réduit quand l'approche monolithique est utilisée à la place des procédures partagées. / Our aim was to develop some partitioned procedures and monolithic semi-implicit algorithms for solving the interaction between a fluid governed by Navier Stokes equations and a structure. In the first chapter, we propose a partitioned procedures semi-implicit algorithm for solving fluid-structure interaction problems, with a structure governed either by linear elasticity equations or by the non-linear Saint-Venant Kirchhoff model. In the second chapter, we present a partitioned procedures semi-implicit algorithm for solving fluid-structure interaction problem with a linear model for the structure and we prove an unconditional stability result of the algorithm. In the above algorithms, an optimization problem must be solved in order to get the continuity of the velocity as well as the continuity of the stress at the interface. During the iterations of BFGS for solving the optimization problem, the fluid mesh does not move and the fluid matrix is only factorized once, which reduces the computational effort. In the fast chapter, we present a monolithic semi-implicit algorithm for solving fluid-structure interaction problem with linear model for the structure. The algorithm uses one global mesh for the fluid-structure domain. The continuity of velocity at the interface is automatically satisfied and the continuity of stress does not appear explicitly in the global weak form due to the action and reaction principle. At each time step, we have to solve a monolithic system of unknowns velocity and pressure defined on the global fluid-structure domain. When the monolithic approach is used the CPU time is reduced compared to a particular partitioned procedures strategy.

Es wurde ein neues Zweifluidmodell entwickelt, um Nichtgleichgewichtseffekte in kritischen und nahkritischen Ein-komponenten-Zweiphasenströmungen von anfänglich unter-kühlten oder siedenden Fluiden durch Rohre und Düsen zu untersuchen. Das vorgeschlagene Sechs-Gleichungsmodell besteht aus den phasenbezogenen Erhaltungsgleichungen für Masse und Impuls, der Bilanzgleichung für die thermische Energie der flüssigen Phase sowie einer zusätzlichen Transport-gleichung für die volumetrische Blasenanzahl. Zur Lösung des Systems aus partiellen Differentialgleichungen wird ein semi-implizites Finite-Differenzen-Zeitschrittverfahren angewendet. Die Schließung des Gleichungssystems wird durch Einbindung thermodynamischer Beziehungen und konstitutiver Gleichungen, die den strömungsformabhängigen Impuls-, Wärme- und Stofftransport beschreiben, erreicht. Für Strömungssysteme mit spontaner Entspannungsverdampfung aus dem rein flüssigen Zustand (Flashing) werden verschiedene Keimbildungsmodelle eingesetzt, die den Anfangszustand der verzögerten Dampfbildung beschreiben. Auf diese Weise werden thermodynamische Nichtgleichgewichtszustände als Folge von Zuständen mit für die Aktivierung von Keimstellen benötigtem Energieüberschuß, eingeschränkt vorhandener Phasengrenzfläche sowie begrenzter Wärmeübertragung zwischen den Phasen betrachtet. Abweichungen vom fluid-dynamischen Gleichgewicht (Phasenschlupf) ergeben sich aufgrund unterschiedlicher Trägheitseigenschaften und verschieden stark ausgeprägter mechanischer Kopplung zwischen den Phasen. Die mit diesem Modell erhaltenen numerischen Ergebnisse stimmen gut mit experimentellen Werten für Zweiphasen-strömungen mit unterschiedlichen Eintrittsbedingungen und Kanalgeometrien überein. / A new two-fluid flow model has been developed in order to examine non-equilibrium effects in critical and near-critical one-component two-phase flows of initially subcooled or saturated fluids through pipes and nozzles. The six-equation model proposed consists of the phasic conservation equations of mass and momentum, the liquid thermal energy, and of an additional transport equation for the bubble number density. To solve for the unknowns of the system of partial differential equations, a semi-implicit finite difference time-marching method is utilized. The closure of the set of equations is accomplished by thermodynamic relationships and additional constitutive equations describing momentum transport, interphase heat, and mass transfer which account for different flow regimes. For fluid flow systems undergoing a sudden change of phase from the pure liquid state (flashing), distinct nucleation models are included to describe the initial state of delayed vapor generation. In this way thermal non-equilibrium states are considered to be the consequence of excessive energy states required to activate nucleation sites, of restricted interfacial area and limited heat transfer between the phases. Deviation from fluid-dynamic equilibrium (phasic slip) results from different inertial properties and from distinct strength of mechanical coupling between the phases. The numerical results obtained with this model agree quite well with experimental data for two-phase flows with various inlet conditions and channel geometries.

Este é o primeiro trabalho que apresenta simulações tridimensionais completamente adaptativas de um modelo de campo de fase para um fluido incompressível com densidade de massa constante e viscosidade variável, conhecido como Modelo H. Solucionando numericamente as equações desse modelo em malhas refinadas localmente com a técnica AMR, simulamos computacionalmente escoamentos bifásicos tridimensionais. Os modelos de campo de fase oferecem uma aproximação física sistemática para investigar fenômenos que envolvem sistemas multifásicos complexos, tais como fluidos com camadas de mistura, a separação de fases sob forças de cisalhamento e a evolução de micro-estruturas durante processos de solidificação. Como as interfaces são substituídas por delgadas regiões de transição (interfaces difusivas), as simulações de campo de fase requerem muita resolução nessas regiões para capturar corretamente a física do problema em estudo. Porém essa não é uma tarefa fácil de ser executada numericamente. As equações que caracterizam o modelo de campo de fase contêm derivadas de ordem elevada e intrincados termos não lineares, o que exige uma estratégia numérica eficiente capaz de fornecer precisão tanto no tempo quanto no espaço, especialmente em três dimensões. Para obter a resolução exigida no tempo, usamos uma discretização semi-implícita de segunda ordem para solucionar as equações acopladas de Cahn-Hilliard e Navier-Stokes (Modelo H). Para resolver adequadamente as escalas físicas relevantes no espaço, utilizamos malhas refinadas localmente que se adaptam dinamicamente para recobrir as regiões de interesse do escoamento, como por exemplo, as vizinhanças das interfaces do fluido. Demonstramos a eficiência e a robustez de nossa metodologia com simulações que incluem a separação dos componentes de uma mistura bifásica, a deformação de gotas sob cisalhamento e as instabilidades de Kelvin-Helmholtz. / This is the first work that introduces 3D fully adaptive simulations for a phase field model of an incompressible fluid with matched densities and variable viscosity, known as Model H. Solving numerically the equations of this model in meshes locally refined with AMR technique, we simulate computationally tridimensional two-phase flows. Phase field models offer a systematic physical approach to investigate complex multiphase systems phenomena such as fluid mixing layers, phase separation under shear and microstructure evolution during solidification processes. As interfaces are replaced by thin transition regions (diffuse interfaces), phase field simulations need great resolution in these regions to capture correctly the physics of the studied problem. However, this is not an easy task to do numerically. Phase field model equations have high order derivatives and intricate nonlinear terms, which require an efficient numerical strategy that can achieve accuracy both in time and in space, especially in three dimensions. To obtain the required resolution in time, we employ a semi-implicit second order discretization scheme to solve the coupled Cahn-Hilliard/Navier-Stokes equations (Model H). To resolve adequatly the relevant physical scales in space, we use locally refined meshes which adapt dynamically to cover special flow regions, e.g., the vicinity of the fluid interfaces. We demonstrate the efficiency and robustness of our methodology with simulations that include spinodal decomposition, the deformation of drops under shear and Kelvin-Helmholtz instabilities.

Cette thèse est consacrée à l'étude de quelques problèmes mathématiques issus du micromagnétisme. Le but est d'analyser le comportement des modèles en fonction de différents paramètres physiques, dont les fines variations sont parfois difficilement mesurables. Nous adoptons des approches numériques, asymptotiques ou d'homogénéisation. Les modèles considérés reposent sur l'utilisation de l'équation de Landau-Lifshitz-Gilbert (LLG) décrivant l'évolution du champ d'aimantation dans un matériau ferromagnétique. Nous rappelons d'abord quelques notions importantes en ferromagnétisme. Ensuite, nous menons une étude numérique d'un modèle de la dynamique d'aimantation avec effets d'inertie. Nous proposons un schéma aux différences finies semi-implicite qui respecte de façon intrinsèque les propriétés du modèle continu. Des simulations numériques sont réalisées pour cerner l'effet du paramètre d'inertie. Ces simulations montrent aussi la performance du schéma et confirment l'ordre de convergence obtenu théoriquement. Nous étudions ensuite un modèle de la dynamique de l'aimantation avec amortissement non local. La sensibilité de la dynamique d'aimantation au paramètre d'amortissement est étudiée en donnant le problème limite pour de petites et de grandes valeurs du paramètre. Enfin, nous étudions l'homogénéisation de l'équation LLG dans deux types de matériau, à savoir les composites présentant un fort contraste des propriétés magnétiques et les matériaux périodiquement perforés avec énergie d'anisotropie de surface. Des modèles homogénéisés sont d'abord obtenus formellement puis une dérivation rigoureuse est établie en se basant principalement sur les concepts de la convergence à double échelle et de la convergence à double échelle en surface. Pour traiter les non-linéarités, nous introduisons une nouvelle méthode basée sur le couplage d'un opérateur de dilatation calibré sur les contrastes d'échelle et d'un outil de réduction de dimension, par construction de grilles emboitées adaptées à la géométrie du domaine microscopique. / This thesis is devoted to the study of some mathematical problems arising in micromagnetism. The models considered here are based on the Landau-Lifshitz-Gilbert equation (LLG) describing the evolution of the magnetization field in a ferromagnetic material. Our aim is the analysis of the behavior of the models regarding the slight variations of some physical parameters. We first recall some important notions about ferromagnetism. Then, we carry out a numerical study of a model of magnetization dynamics with inertial effects. We propose a semi-implicit finite difference scheme which intrinsically respects the properties of the continuous model. Numerical simulations are provided for emphasizing the effect of the inertia parameter. These simulations also show the performance of the scheme and confirm the order of convergence obtained theoretically. We then study a model of magnetization dynamics with a non-local damping. The sensitivity of the magnetization dynamics to the damping coefficient is studied by giving the limiting problem for small and large values of the parameter. Finally, we study the homogenization of the LLG equation in two types of structures, namely a composite material with strongly contrasted magnetic properties, and a periodically perforated material with surface anisotropy energy. The homogenized models are first obtained formally. The rigorous derivation is then performed using mainly the concepts of two-scale convergence, two-scale convergence on surfaces together with a new homogenization procedure for handling with the nonlinear terms. More precisely, an appropriate dilation operator is applied in a embedded cells network, the network being constrained by the microscopic geometry.

L'amélioration du code Emedge3D (code de bord électromagnétique) est abordée sous plusieurs axes. Premier axe, des innovations sur les méthodes numériques ont été mises en oeuvre. L'avantage des méthodes de type semi-implicite est décrit, leur stabilité inconditionnelle permet l'augmentation du pas de temps, et donc la diminution du nombre d'itérations temporelles requises pour une simulation. Les avantages de la montée en ordre en espace et en temps sont détaillés. Deuxième axe, des réponses sont proposées pour la parallélisation du code. Le cadre de cette étude est proche du problème général d'advection-diffusion non linéaire. Les parties coûteuses ont tout d'abord été optimisées séquentiellement puis fait l'objet d'une parallélisation OpenMP. Pour la partie du code la plus sensible aux contraintes de bande passante mémoire, une solution parallèle MPI sur machine à mémoire distribuée est décrite et analysée. Une bonne extensibilité est observée jusque 384 cœurs. Cette thèse s'inscrit dans le projet interdisciplinaire ANR E2T2 (CEA/IRFM, Université Aix-Marseille/PIIM, Université Strasbourg/Icube). / The main goal of this work is to significantly reduce the computational cost of the scientific application Emedge3D, simulating the edge of tokamaks. Improvements to this code are made on two axes. First, innovations on numerical methods have been implemented. The advantage of semi-implicit time schemes are described. Their inconditional stability allows to consider larger timestep values, and hence to lower the number of temporal iteration required for a simulation. The benefits of a high order (time and space) are also presented. Second, solutions to the parallelization of the code are proposed. This study addresses the more general non linear advection-diffusion problem. The hot spots of the application have been sequentially optimized and parallelized with OpenMP. Then, a hybrid MPI OpenMP parallel algorithm for the memory bound part of the code is described and analyzed. Good scalings are observed up to 384 cores. This Ph. D. thesis is part of the interdisciplinary project ANR E2T2 (CEA/IRFM, University of Aix-Marseille/PIIM, University of Strasbourg/ICube).

The development of numerical methods for the incompressible Navier-Stokes equations received much attention in the past 50 years. Finite element methods emerged given their robustness and reliability. In our work, we choose the P2-P1 finite element for space approximation which gives 2nd-order accuracy for velocity and 1st-order accuracy for pressure. Our research focuses on the development of several high-order semi-implicit time-stepping methods to compute unsteady flows. The methods investigated include backward difference formulae (SBDF) and defect correction strategy (DC). Using the defect correction strategy, we investigate two variants, the first one being based on high-order artificial compressibility and bootstrapping strategy proposed by Guermond and Minev (GM) and the other being a combination of GM methods with sequential regularization method (GM-SRM). Both GM and GM-SRM methods avoid solving saddle point problems as for SBDF and DC methods. This approach reduces the complexity of the linear systems at the expense that many smaller linear systems need to be solved. Next, we proposed several numerical improvements in terms of better approximations of the nonlinear advection term and high-order initialization for all methods. To further minimize the complexity of the resulting linear systems, we developed several new variants of grad-div splitting algorithms besides the one studied by Guermond and Minev. Splitting algorithm allows us to handle larger flow problems. We showed that our new methods are capable of reproducing flow characteristics (e.g., lift and drag parameters and Strouhal numbers) published in the literature for 2D lid-driven cavity and 2D flow around the cylinder. SBDF methods with grad-div stabilization terms are found to be very stable, accurate and efficient when computing flows with high Reynolds numbers. Lastly, we showcased the robustness of our methods to carry 3D computations.

Es wurde ein neues Zweifluidmodell entwickelt, um Nichtgleichgewichtseffekte in kritischen und nahkritischen Ein-komponenten-Zweiphasenströmungen von anfänglich unter-kühlten oder siedenden Fluiden durch Rohre und Düsen zu untersuchen. Das vorgeschlagene Sechs-Gleichungsmodell besteht aus den phasenbezogenen Erhaltungsgleichungen für Masse und Impuls, der Bilanzgleichung für die thermische Energie der flüssigen Phase sowie einer zusätzlichen Transport-gleichung für die volumetrische Blasenanzahl. Zur Lösung des Systems aus partiellen Differentialgleichungen wird ein semi-implizites Finite-Differenzen-Zeitschrittverfahren angewendet. Die Schließung des Gleichungssystems wird durch Einbindung thermodynamischer Beziehungen und konstitutiver Gleichungen, die den strömungsformabhängigen Impuls-, Wärme- und Stofftransport beschreiben, erreicht. Für Strömungssysteme mit spontaner Entspannungsverdampfung aus dem rein flüssigen Zustand (Flashing) werden verschiedene Keimbildungsmodelle eingesetzt, die den Anfangszustand der verzögerten Dampfbildung beschreiben. Auf diese Weise werden thermodynamische Nichtgleichgewichtszustände als Folge von Zuständen mit für die Aktivierung von Keimstellen benötigtem Energieüberschuß, eingeschränkt vorhandener Phasengrenzfläche sowie begrenzter Wärmeübertragung zwischen den Phasen betrachtet. Abweichungen vom fluid-dynamischen Gleichgewicht (Phasenschlupf) ergeben sich aufgrund unterschiedlicher Trägheitseigenschaften und verschieden stark ausgeprägter mechanischer Kopplung zwischen den Phasen. Die mit diesem Modell erhaltenen numerischen Ergebnisse stimmen gut mit experimentellen Werten für Zweiphasen-strömungen mit unterschiedlichen Eintrittsbedingungen und Kanalgeometrien überein. / A new two-fluid flow model has been developed in order to examine non-equilibrium effects in critical and near-critical one-component two-phase flows of initially subcooled or saturated fluids through pipes and nozzles. The six-equation model proposed consists of the phasic conservation equations of mass and momentum, the liquid thermal energy, and of an additional transport equation for the bubble number density. To solve for the unknowns of the system of partial differential equations, a semi-implicit finite difference time-marching method is utilized. The closure of the set of equations is accomplished by thermodynamic relationships and additional constitutive equations describing momentum transport, interphase heat, and mass transfer which account for different flow regimes. For fluid flow systems undergoing a sudden change of phase from the pure liquid state (flashing), distinct nucleation models are included to describe the initial state of delayed vapor generation. In this way thermal non-equilibrium states are considered to be the consequence of excessive energy states required to activate nucleation sites, of restricted interfacial area and limited heat transfer between the phases. Deviation from fluid-dynamic equilibrium (phasic slip) results from different inertial properties and from distinct strength of mechanical coupling between the phases. The numerical results obtained with this model agree quite well with experimental data for two-phase flows with various inlet conditions and channel geometries.