Adaptive mesh refinement method. Part 2: Application to tsunamis propagation

Numerical simulations of multi dimensional large scale fluid-flows such as tsunamis, are still nowadays a challenging and a difficult problem. To this purpose, a parallel finite volume scheme on adaptive unstructured meshes for multi dimensional Saint-Venant system is presented. The adaptive mesh refinement method is based on a block-based decomposition (called BB-AMR) which allows quick meshing and easy parallelization. The main difficulty addressed here concerns the selection of the mesh refinement threshold which is certainly the most important parameter in the AMR method. Usually, the threshold is calibrated according to the test problem to balance the accuracy of the solution and the computational cost. To avoid " hand calibration " , we apply an automatic threshold method based on the decreasing rearrangement function of the mesh refinement criterion. This method is applied and validated successfully to the one and two dimensional non homogeneous Saint-Venant system through several tsunamis propagation test cases

From genomics to metagenomics: benchmark of variation graphs

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Simulation de la propagation et du déferlement d’une vague et de l’inondation d’unrèclif 2D: évaluation comparative des codes numérique pour la modélisation des tsunamis

In the framework of the French research project TANDEM dedicated to tsunami modelling, a series of benchmarks has been set up, addressing the various stages of a tsunami event: generation, propagation, run-up and inundation. We present here the results of five codes, involving both depth-averaged Boussinesq and fully 3D Navier-Stokes equations, aimed at being applicable to tsunami modelling. The codes are evaluated on a flow involving propagation, run-up, overtopping and reflection of the waves on two-dimensional reefs, and compared with the experimental data produced from a set of laboratory experiments carried out at the O.H. Hinsdale Wave Research Laboratory, Oregon State University (OSU, see Roeber et al., 2010 and Roeber and Chung, 2012).Dans le cadre du projet de recherche français TANDEM dédié à la modélisation de tsunamis, une série de tests a été mise enplace concernant les différentes étapes d'un tsunami : la génération, la propagation et l'inondation. Les résultats obtenus par cinq codessont présentés ici. Chacun d'eux utilise les équations de Boussinesq moyennées sur la profondeur et les équations de Naver-Stokes entrois dimensions adaptées à la modélisation de tsunamis. Ces codes sont évalués sur un écoulement impliquant la propagation, lasubmersion, et la réflexion des vagues sur un récif en deux dimensions. Une comparaison est effectuée à partir de données expérimentalesprovenant du laboratoire d'Hinsdale (O.H Hinsdale Wave Research Laboratory, Oregon State University, OSU, voir Roeber et al.,2010 etRoeber et Chung, 2012)

Tsunami modeling : propagation and impact

Cette thèse traite de la modélisation des tsunamis, des grandes échelles de propagation aux impacts sur des structures côtières. Un inventaire des phénomènes physiques associés est établi et des modèles adéquats sont présentés. Une étude numérique avec le modèle de Saint-Venant est effectuée avec le développement d’une méthode de raffinement de maillage à seuil automatique. La simplicité et les performances de l’approche sont démontrées. Pour améliorer la précision des prévisions, un système original approchant le modèle Serre-Green-Nahgdi est investigué. Une méthode pour prendre en compte la dissipation d’énergie au déferlement est proposée. Ce modèle permet d’envisager la modélisation fine de la propagation et de l’arrivée à la côte des tsunamis dispersifs et non linéaires en des temps de calcul acceptables. Les différents types d’impact sur des structures sont modélisés grâce à un modèle diphasique compressible permettant de considérer les écoulements à phases séparées et les milieux aérés. Pour envisager une résolution à tous les régimes, des schémas Tous Mach sont investigués. Un schéma Tous Mach à variation totale limitée est proposé. Grâce à cette approche, des impacts incompressibles et compressibles sont investigués avec le même modèle. Les impacts d’écoulements aérés induisent des pressions moins élevées mais sur des temps plus longs que leurs homologues en phases pures. Bien que le schéma Tous Mach proposé soit moins sujet aux oscillations numériques que les préconditionnements classiques de la littérature, des oscillations non physiques à bas nombre de Mach sont mises en évidence sur certains cas tests. Pour finir, une méthode de couplage entre modèles de propagation et d’impact est proposée, afin de pouvoir simuler un tsunami finement avec des modèles appropriés à chacune de ces phases.This thesis deals with tsunami modeling, from the large propagation scales to impacts on coastal structures. An inventory of the associated physical phenomena is given and some adequate models are presented. A numerical study is carried out with the Saint-Venant model with the development of an automatic refinement adaptive mesh method. The resolution efficiency and simplicity is justified. To increase the accuracy forecasts, an original system which approximates the Serre-Green-Naghdi model is investigated. A breaking wave method associated with this model is proposed. This dissipative model allows thinking about accurate dispersive non linear tsunamis simulations up to the coast. Several wave impacts on structures are investigated with a general two-phase model allowing separate phases as well as aerated impact studies. The all Mach regime numerical difficulties are investigated. A new all Mach scheme with limited total variation bound is proposed. Thanks to this approach, incompressible and compressible impacts are investigated with the same model. Aerated impacts are shown to give smaller impact pressure but on longer time than pure fluid impacts. In spite that the all Mach scheme proposed reduces the numerical oscillations of classical literature preconditioning, some unphysical oscillations are highlighted on some test cases. At the end, a coupling method is proposed in order to accurately model the propagation and the impact of a tsunami with appropriated models for each phases

Modélisation des tsunamis : propagation et impact

This thesis deals with tsunami modeling, from the large propagation scales to impacts on coastal structures. An inventory of the associated physical phenomena is given and some adequate models are presented. A numerical study is carried out with the Saint-Venant model with the development of an automatic refinement adaptive mesh method. The resolution efficiency and simplicity is justified. To increase the accuracy forecasts, an original system which approximates the Serre-Green-Naghdi model is investigated. A breaking wave method associated with this model is proposed. This dissipative model allows thinking about accurate dispersive non linear tsunamis simulations up to the coast. Several wave impacts on structures are investigated with a general two-phase model allowing separate phases as well as aerated impact studies. The all Mach regime numerical difficulties are investigated. A new all Mach scheme with limited total variation bound is proposed. Thanks to this approach, incompressible and compressible impacts are investigated with the same model. Aerated impacts are shown to give smaller impact pressure but on longer time than pure fluid impacts. In spite that the all Mach scheme proposed reduces the numerical oscillations of classical literature preconditioning, some unphysical oscillations are highlighted on some test cases. At the end, a coupling method is proposed in order to accurately model the propagation and the impact of a tsunami with appropriated models for each phases.Cette thèse traite de la modélisation des tsunamis, des grandes échelles de propagation aux impacts sur des structures côtières. Un inventaire des phénomènes physiques associés est établi et des modèles adéquats sont présentés. Une étude numérique avec le modèle de Saint-Venant est effectuée avec le développement d’une méthode de raffinement de maillage à seuil automatique. La simplicité et les performances de l’approche sont démontrées. Pour améliorer la précision des prévisions, un système original approchant le modèle Serre-Green-Nahgdi est investigué. Une méthode pour prendre en compte la dissipation d’énergie au déferlement est proposée. Ce modèle permet d’envisager la modélisation fine de la propagation et de l’arrivée à la côte des tsunamis dispersifs et non linéaires en des temps de calcul acceptables. Les différents types d’impact sur des structures sont modélisés grâce à un modèle diphasique compressible permettant de considérer les écoulements à phases séparées et les milieux aérés. Pour envisager une résolution à tous les régimes, des schémas Tous Mach sont investigués. Un schéma Tous Mach à variation totale limitée est proposé. Grâce à cette approche, des impacts incompressibles et compressibles sont investigués avec le même modèle. Les impacts d’écoulements aérés induisent des pressions moins élevées mais sur des temps plus longs que leurs homologues en phases pures. Bien que le schéma Tous Mach proposé soit moins sujet aux oscillations numériques que les préconditionnements classiques de la littérature, des oscillations non physiques à bas nombre de Mach sont mises en évidence sur certains cas tests. Pour finir, une méthode de couplage entre modèles de propagation et d’impact est proposée, afin de pouvoir simuler un tsunami finement avec des modèles appropriés à chacune de ces phases

Adaptive mesh refinement method. Part 1: Automatic thresholding based on a distribution function

The accurate numerical simulation of large scale flows, together with the detailed modeling of flooding or drying of small-scale regions, is a difficult and a challenging problem. Adaptive mesh method allows, in principle, to solve accurately those scales. However in practice, on one hand, the lack of a priori or efficient a posteriori error estimates, especially for multidimensional hyperbolic problems, make the analysis harder. On the other hand, once a mesh refinement criterion is chosen, the difficult problem is to determine the mesh refinement threshold parameter which is certainly the most important part of the adaptive process. The smaller this parameter is, the higher the number of cells refined is at the expense of the computational cost. In this work, we numerically investigate different refinement criteria and we present a general procedure to determine automatically a mesh refinement threshold for any given mesh refinement criterion. To this end the decreasing rearrangement (distribution) function of the mesh refinement criterion is introduced to catch relevant scales. The efficiency of the automatic thresholding method is illustrated through the one dimensional Saint-Venant system. Multidimensional and real life applications such as Tsunamis propagations are dealt in the second part

Adaptive Mesh Refinement Method Applied to Shallow Water Model: A Mass Conservative Projection

International audienc

Validation of CFD models for tsunami simulation. TANDEM Projec

International audienc

Identifying the range of sub-inhibitory concentrations of antibiotics triggering bacterial functions of relevant interest

International audienceBeyond their selective role, some antibiotics continue to exert an effect below their minimum inhibitory concentration level, where they can act as signaling molecules to modulate various bacterial activities: biofilm formation, exopolymers production, virulence, quorum sensing, cell mobility, and even the dissemination of specific antibiotic resistance genes. This clearly asks the question of the possible effects antibiotics can have once diluted after the disposal of reclaimed wastewater into the aquatic environment or during its reuse. Lately we developed a biosensor approach to identify antibiotics interfering with gene regulation. This approach lies on the use of bacteria genetically modified to express a bioluminescence once the promoter of a relevant function is induced by a modulating antibiotic. Rather than testing arbitrary chosen concentrations, the biosensor is exposed to diffusion gradients of antibiotics in agar plate (as for antibiograms) while luminescence profiles are recorded by CCD camera. With such approach we could detect several antibiotics able to trigger the activation of promoters controlling the mobility functions of "integrative and conjugative elements" (ICEs) such as Tn916 and SXT. An automated image analysis algorithm combined with a modelling of the diffusion process in the agar has been developed to convert the luminescence profile into a concentration profile information, enabling to estimate the level of induction and the range of sub-MIC concentration at which an antibiotic remain effective. The biosensor strains are first spread onto the agar of a square Petri dish before receiving one to sixteen antibiotics loaded disks deposited in an equispaced manner. The agar plate is incubated at 30°C allowing the antibiotics to diffuse and luminescence and transmitted light images are regularly acquired over time. An automated image processing system has been developed to detect the induction and inhibition zones around each antibiotic loaded disk. For the present experiment two antibiotics were used: ciprofloxacin (CIP) (broad spectrum) and nalidixic acid (NAL) (limited spectrum). Both inhibit the DNA gyrase while CIP inhibits also topoisomerase IV. Commercially available discs (BioRad) were used (30 µg for NAL and 5 µg for CIP). Additional discs were prepared by loading cellulose discs with antibiotic solutions. The MIC values were determined in separate experiments in liquid phase for each antibiotic. The diffusion of antibiotics in agar is modelled through a finite element computational model based on Fick's second law of diffusion. The simulations are performed using a Computational Fluid Dynamics software (Fluent by ANSYS). The mesh contains ≈ 80,000 cells. It is assumed that the antibiotics deposited in the thin top agar layer exhibit higher diffusivities in this layer than in the bulk solid agar. Bulk agar Top agar The key parameters are the antibiotic diffusivity in the top agar and the diffusivity ratio between the top and the bulk agar. Here D top /D bulk = 1000. Effect of clone and concentration with NAL Effect of Petri dish with NAL and CIP (same clone) Effect of concentration on CIP (same clone) MIC (CIP) = 0.015 µg/mL = 4.5310-5 mole/m 3 MIC (NAL) = 3 µg/mL = 1.2910-2 mole/m 3 D = 1. 10-14 m 2 /s D = 1. 10-11 m 2 /s %of total time D = 1. 10-14 m 2 /s D = 1. 10-13 m 2 /s D = 1. 10-12 m 2 /s D = 1. 10-11 m 2 /s D = 1. 10-10 m 2 /s Range of D for CIP (5 µg) D = 1. 10-10 m 2 /s D = 1. 10-11 m 2 /s D = 1. 10-11 m 2 /s Order of magnitude of D for NAL (30 µg) Simulated MIC paths The effect of experimental parameters such as clone and antibiotic type and concentration has been tested. An improvement of the spatial resolution would be useful for antibiotics such as NAL with a high MIC. First simulation results show that it is possible to estimate the diffusivity of an antibiotic in gelose media. A refinement of the simulation mesh is however necessary, especially for high-MIC antibiotics, to estimate properly sub-inhibitory concentrations. Such refinement is currently tested