| 1. |
- Hoffman, Johan, 1974-, et al.
(författare)
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Computability and Adaptivity in CFD
- 2018
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Ingår i: Encyclopedia of Computational Mechanics. - : John Wiley & Sons.
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Bokkapitel (refereegranskat)
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| 2. |
- Spühler, Jeannette H., et al.
(författare)
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3D Fluid-Structure Interaction Simulation of Aortic Valves Using a Unified Continuum ALE FEM Model
- 2018
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Ingår i: Frontiers in Physiology. - : Frontiers Media S.A.. - 1664-042X. ; 9
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Tidskriftsartikel (refereegranskat)abstract
- Due to advances in medical imaging, computational fluid dynamics algorithms and high performance computing, computer simulation is developing into an important tool for understanding the relationship between cardiovascular diseases and intraventricular blood flow. The field of cardiac flow simulation is challenging and highly interdisciplinary. We apply a computational framework for automated solutions of partial differential equations using Finite Element Methods where any mathematical description directly can be translated to code. This allows us to develop a cardiac model where specific properties of the heart such as fluid-structure interaction of the aortic valve can be added in a modular way without extensive efforts. In previous work, we simulated the blood flow in the left ventricle of the heart. In this paper, we extend this model by placing prototypes of both a native and a mechanical aortic valve in the outflow region of the left ventricle. Numerical simulation of the blood flow in the vicinity of the valve offers the possibility to improve the treatment of aortic valve diseases as aortic stenosis (narrowing of the valve opening) or regurgitation (leaking) and to optimize the design of prosthetic heart valves in a controlled and specific way. The fluid-structure interaction and contact problem are formulated in a unified continuum model using the conservation laws for mass and momentum and a phase function. The discretization is based on an Arbitrary Lagrangian-Eulerian space-time finite element method with streamline diffusion stabilization, and it is implemented in the open source software Unicorn which shows near optimal scaling up to thousands of cores. Computational results are presented to demonstrate the capability of our framework.
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| 3. |
- Degirmenci, Niyazi Cem, et al.
(författare)
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A Unified Numerical Simulation of Vowel Production That Comprises Phonation and the Emitted Sound
- 2017
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Ingår i: Proceedings of the Annual Conference of the International Speech Communication Association, INTERSPEECH 2017. - : The International Speech Communication Association (ISCA). ; , s. 3492-3496
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Konferensbidrag (refereegranskat)abstract
- A unified approach for the numerical simulation of vowels is presented, which accounts for the self-oscillations of the vocal folds including contact, the generation of acoustic waves and their propagation through the vocal tract, and the sound emission outwards the mouth. A monolithic incompressible fluid-structure interaction model is used to simulate the interaction between the glottal jet and the vocal folds, whereas the contact model is addressed by means of a level set application of the Eikonal equation. The coupling with acoustics is done through an acoustic analogy stemming from a simplification of the acoustic perturbation equations. This coupling is one-way in the sense that there is no feedback from the acoustics to the flow and mechanical fields. All the involved equations are solved together at each time step and in a single computational run, using the finite element method (FEM). As an application, the production of vowel [i] has been addressed. Despite the complexity of all physical phenomena to be simulated simultaneously, which requires resorting to massively parallel computing, the formant locations of vowel [i] have been well recovered.
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| 4. |
- Jansson, Johan, et al.
(författare)
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Adaptive unified continuum FEM modeling of a 3D FSI benchmark problem
- 2017
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Ingår i: International Journal for Numerical Methods in Biomedical Engineering. - : Wiley-Blackwell. - 2040-7939 .- 2040-7947. ; 33:9
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Tidskriftsartikel (refereegranskat)abstract
- In this paper, we address a 3D fluid-structure interaction benchmark problem that represents important characteristics of biomedical modeling. We present a goal-oriented adaptive finite element methodology for incompressible fluid-structure interaction based on a streamline diffusion–type stabilization of the balance equations for mass and momentum for the entire continuum in the domain, which is implemented in the Unicorn/FEniCS software framework. A phase marker function and its corresponding transport equation are introduced to select the constitutive law, where the mesh tracks the discontinuous fluid-structure interface. This results in a unified simulation method for fluids and structures. We present detailed results for the benchmark problem compared with experiments, together with a mesh convergence study.
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| 5. |
- Moragues Ginard, M, et al.
(författare)
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Simulation of floating platforms for marine energy generation
- 2018
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Ingår i: 10th International Conference on Computational Fluid Dynamics, ICCFD 2018. - : International Conference on Computational Fluid Dynamics 2018.
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Konferensbidrag (refereegranskat)abstract
- The goal of this work is to study the dynamics of floating platforms that are designed for marine energy generation. This work is done in collaboration with Tecnalia R&I, a company settled in the Basque Country which designs this kind of platforms. To our purpose we present a method for the simulation of two-phase flow with the presence of floating bodies. We consider the variable density incompressible Navier-Stokes equations and discretize them by the finite element method with a variational multiscale stabilization. A level-set type method is adopted to model the interphase between the two fluids. The mixing or smearing in the interphase is prevented with a compression technique. Turbulence is implicitly modeled by the numerical stabilization. The floating device simulation is done by a rigid body motion scheme where a deforming mesh approach is used. The mesh deforms elastically following the movement of the body. Simulation of a decay test on a cube is performed and the results are presented in this paper. All the simulations are done with the open source finite elements parallel software FEniCS-HPC.
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| 6. |
- Nguyen, Van Dang, 1985-, et al.
(författare)
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A fluid-structure interaction model with weak slip velocity boundary conditions on conforming internal interfaces
- 2018
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Konferensbidrag (populärvet., debatt m.m.)abstract
- We develop a PUFEM–Partition of Unity Finite Element Method to impose slip velocity boundary conditions on conforming internal interfaces for a fluid-structure interaction model. The method facilitates a straightforward implementation on the FEniCS/FEniCS-HPC platform. We show two results for 2D model problems with the implementation on FEniCS: (1) optimal convergence rate is shown for a stationary Navier-Stokes flow problem, and (2) the slip velocity conditions give qualitatively the correct result for the Euler flow.
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| 7. |
- Nguyen, Van Dang, 1985-, et al.
(författare)
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A partition of unity finite element method for computational diffusion MRI
- 2018
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Ingår i: Journal of Computational Physics. - : Elsevier. - 0021-9991 .- 1090-2716. ; 375, s. 271-290
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Tidskriftsartikel (refereegranskat)abstract
- The Bloch–Torrey equation describes the evolution of the spin (usually water proton) magnetization under the influence of applied magnetic field gradients and is commonly used in numerical simulations for diffusion MRI and NMR. Microscopic heterogeneity inside the imaging voxel is modeled by interfaces inside the simulation domain, where a discontinuity in the magnetization across the interfaces is produced via a permeability coefficient on the interfaces. To avoid having to simulate on a computational domain that is the size of an entire imaging voxel, which is often much larger than the scale of the microscopic heterogeneity as well as the mean spin diffusion displacement, smaller representative volumes of the imaging medium can be used as the simulation domain. In this case, the exterior boundaries of a representative volume either must be far away from the initial positions of the spins or suitable boundary conditions must be found to allow the movement of spins across these exterior boundaries.Many approaches have been taken to solve the Bloch–Torrey equation but an efficient high-performance computing framework is still missing. In this paper, we present formulations of the interface as well as the exterior boundary conditions that are computationally efficient and suitable for arbitrary order finite elements and parallelization. In particular, the formulations are based on the partition of unity concept which allows for a discontinuous solution across interfaces conforming with the mesh with weak enforcement of real (in the case of interior interfaces) and artificial (in the case of exterior boundaries) permeability conditions as well as an operator splitting for the exterior boundary conditions. The method is straightforward to implement and it is available in FEniCS for moderate-scale simulations and in FEniCS-HPC for large-scale simulations. The order of accuracy of the resulting method is validated in numerical tests and a good scalability is shown for the parallel implementation. We show that the simulated dMRI signals offer good approximations to reference signals in cases where the latter are available and we performed simulations for a realistic model of a neuron to show that the method can be used for complex geometries.
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| 8. |
- Nguyen, Van Dang, 1985-, et al.
(författare)
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Direct Finite Element Simulation of the Turbulent Flow Past a Vertical Axis Wind Turbine
- 2019
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Ingår i: Renewable energy. - : Elsevier. - 0960-1481 .- 1879-0682. ; 135, s. 238-247
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Tidskriftsartikel (refereegranskat)abstract
- There is today a significant interest in harvesting renewable energy, specifically wind energy, in offshore and urban environments. Vertical axis wind turbines get increasing attention since they are able to capture the wind from any direction. They are relatively easy to install and to transport, cheaper to build and maintain, and quite safe for humans and birds. Detailed computer simulations of the fluid dynamics of wind turbines provide an enhanced understanding of the technology and may guide design improvements. In this paper, we simulate the turbulent flow past a vertical axis wind turbine for a range of rotation angles in parked and rotating conditions. We propose the method of Direct Finite Element Simulation in a rotating ALE framework, abbreviated as DFS-ALE. The simulation results are validated against experimental data in the form of force measurements. We find that the simulation results are stable with respect to mesh refinement and that we capture well the general shape of the variation of force measurements over the rotation angles.
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| 9. |
- Nguyen, Van-Dang, 1985-
(författare)
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High-Performance Finite Element Methods : with Application to Simulation of Diffusion MRI and Vertical Axis Wind Turbines
- 2018
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Licentiatavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The finite element methods (FEM) have been developed over decades, and together with the growth of computer engineering, they become more and more important in solving large-scale problems in science and industry. The objective of this thesis is to develop high-performance finite element methods (HP-FEM), with two main applications in mind: computational diffusion magnetic resonance imaging (MRI), and simulation of the turbulent flow past a vertical axis wind turbine (VAWT). In the first application, we develop an efficient high-performance finite element framework HP-PUFEM based on a partition of unity finite element method to solve the Bloch-Torrey equation in heterogeneous domains. The proposed framework overcomes the difficulties that the standard approaches have when imposing the microscopic heterogeneity of the biological tissues. We also propose artificial jump conditions at the external boundaries to approximate the pseudo-periodic boundary conditions which allows for the water exchange at the external boundaries for non-periodic meshes. The framework is of a high level simplicity and efficiency that well facilitates parallelization. It can be straightforwardly implemented in different FEM software packages and it is implemented in FEniCS for moderate-scale simulations and in FEniCS-HPC for the large-scale simulations. The framework is validated against reference solutions, and implementation shows a strong parallel scalability. Since such a high-performance simulation framework is still missing in the field, it can become a powerful tool to uncover diffusion in complex biological tissues. In the second application, we develop an ALE-DFS method which combines advanced techniques developed in recent years to simulate turbulence. We apply a General Galerkin (G2) method which is continuous piecewise linear in both time and space, to solve the Navier-Stokes equations for a rotating turbine in an Arbitrary Lagrangian-Eulerian (ALE) framework. This method is enhanced with dual-based a posterior error control and automated mesh adaptation. Turbulent boundary layers are modeled by a slip boundary condition to avoid a full resolution which is impossible even with the most powerful computers available today. The method is validated against experimental data of parked turbines with good agreements. The thesis presents contributions in the form of both numerical methods for high-performance computing frameworks and efficient, tested software, published open source as part of the FEniCS-HPC platform.
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| 10. |
- Nguyen, Van Dang, 1985-
(författare)
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High Performance Finite Element Methods with Application to Simulation of Vertical Axis Wind Turbines and Diffusion MRI
- 2019
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Finite element methods have been developed over decades, and together with the growth of computer power, they become more and more important in dealing with large-scale simulations in science and industry.The objective of this thesis is to develop high-performance finite element methods, with two concrete applications: computational fluid dynamics (CFD) with simulation of turbulent flow past a vertical axis wind turbine (VAWT), and computational diffusion magnetic resonance imaging (CDMRI). The thesis presents contributions in the form of both new numerical methods for high-performance computing frameworks and efficient, tested software, published open source as part of the FEniCS/FEniCS-HPC platform. More specifically, we have four main contributions through the thesis work.First, we develop a DFS-ALE method which combines the Direct finite element simulation method (DFS) with the Arbitrary Lagrangian-Eulerian method (ALE) to solve the Navier-Stokes equations for a rotating turbine. This method is enhanced with dual-based a posteriori error control and automated mesh adaptation. Turbulent boundary layers are modeled by a slip boundary condition to avoid a full resolution which is impossible even with the most powerful computers available today. The method is validated against experimental data with a good agreement.Second, we propose a partition of unity finite element method to tackle interface problems. In CFD, it allows for imposing slip velocity boundary conditions on conforming internal interfaces for a fluid-structure interaction model. In CDMRI, it helps to overcome the difficulties that the standard approaches have when imposing the microscopic heterogeneity of the biological tissues and allows for efficient solutions of the Bloch-Torrey equation in heterogeneous domains. The method facilitates a straightforward implementation on the FEniCS/ FEniCS-HPC platform. The method is validated against reference solutions, and the implementation shows a strong parallel scalability.Third, we propose a finite element discretization on manifolds in order to efficiently simulate the diffusion MRI signal in domains that have a thin layer or a thin tube geometrical structure. The method helps to significantly reduce the required simulation time, computer memory, and difficulties associated with mesh generation, while maintaining the accuracy. Thus, it opens the possibility to simulate complicated structures at a low cost, for a better understanding of diffusion MRI in the brain.Finally, we propose an efficient portable simulation framework that integrates recent advanced techniques in both mathematics and computer science to enable the users to perform simulations with the Cloud computing technology. The simulation framework consists of Python, IPython and C++ solvers working either on a web browser with Google Colaboratory notebooks or on the Google Cloud Platform with MPI parallelization.
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