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Nguyen, V. D., Jansson, J., Goude, A. & Hoffman, J. (2019). Direct Finite Element Simulation of the Turbulent Flow Past a Vertical Axis Wind Turbine. Renewable energy, 135, 238-247
Open this publication in new window or tab >>Direct Finite Element Simulation of the Turbulent Flow Past a Vertical Axis Wind Turbine
2019 (English)In: Renewable energy, ISSN 0960-1481, E-ISSN 1879-0682, Vol. 135, p. 238-247Article in journal (Refereed) Published
Abstract [en]

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.

Place, publisher, year, edition, pages
Elsevier, 2019
Keywords
VAWT, Direct FEM simulation, ALE
National Category
Natural Sciences
Research subject
Computer Science; Applied and Computational Mathematics; Vehicle and Maritime Engineering
Identifiers
urn:nbn:se:kth:diva-224801 (URN)10.1016/j.renene.2018.11.098 (DOI)2-s2.0-85058018814 (Scopus ID)
Note

QC 20180326

Available from: 2018-03-26 Created: 2018-03-26 Last updated: 2019-01-09Bibliographically approved
Spühler, J. H., Jansson, J., Jansson, N. & Hoffman, J. (2018). 3D Fluid-Structure Interaction Simulation of Aortic Valves Using a Unified Continuum ALE FEM Model. Frontiers in Physiology, 9, Article ID 363.
Open this publication in new window or tab >>3D Fluid-Structure Interaction Simulation of Aortic Valves Using a Unified Continuum ALE FEM Model
2018 (English)In: Frontiers in Physiology, ISSN 1664-042X, E-ISSN 1664-042X, Vol. 9, article id 363Article in journal (Refereed) Published
Abstract [en]

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.

Place, publisher, year, edition, pages
Frontiers Media S.A., 2018
Keywords
fluid-structure interaction, finite element method, Arbitrary Lagrangian-Eulerian method, parallel algorithm, blood flow, patient specific heart model
National Category
Physiology
Identifiers
urn:nbn:se:kth:diva-226752 (URN)10.3389/fphys.2018.00363 (DOI)000430119500001 ()2-s2.0-85045511659 (Scopus ID)
Funder
Swedish Foundation for Strategic Research Swedish Research Council
Note

QC 20180503

Available from: 2018-05-03 Created: 2018-05-03 Last updated: 2018-05-03Bibliographically approved
Nguyen, V.-D., Jansson, J., Frachon, T., Degirmenci, C. & Hoffman, J. (2018). A fluid-structure interaction model with weak slip velocity boundary conditions on conforming internal interfaces. In: : . Paper presented at ECCM-ECFD 2018.
Open this publication in new window or tab >>A fluid-structure interaction model with weak slip velocity boundary conditions on conforming internal interfaces
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2018 (English)Conference paper, Published paper (Other (popular science, discussion, etc.))
Abstract [en]

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. 

Keywords
fluid-structure interaction, slip boundary conditions, conforming meshes, internal interfaces
National Category
Natural Sciences
Research subject
Applied and Computational Mathematics; Computer Science
Identifiers
urn:nbn:se:kth:diva-225143 (URN)
Conference
ECCM-ECFD 2018
Note

QCR 20180405

Available from: 2018-03-31 Created: 2018-03-31 Last updated: 2018-06-11Bibliographically approved
Nguyen, V. D., Jansson, J., Hoffman, J. & Li, J.-R. (2018). A partition of unity finite element method for computational diffusion MRI. Journal of Computational Physics, 375, 271-290
Open this publication in new window or tab >>A partition of unity finite element method for computational diffusion MRI
2018 (English)In: Journal of Computational Physics, ISSN 0021-9991, E-ISSN 1090-2716, Vol. 375, p. 271-290Article in journal (Refereed) Published
Abstract [en]

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.

Place, publisher, year, edition, pages
Elsevier, 2018
Keywords
Computational diffusion MRI, Bloch–Torrey equation, Partition of unity finite element method, Interface conditions, Weak pseudo-periodic conditions, FEniCS/FEniCS-HPC
National Category
Computational Mathematics
Research subject
Applied and Computational Mathematics; Biological Physics; Computer Science
Identifiers
urn:nbn:se:kth:diva-234286 (URN)10.1016/j.jcp.2018.08.039 (DOI)000450907600014 ()2-s2.0-85054048672 (Scopus ID)
Funder
Swedish Energy Agency, P40435-1
Note

QC 20180906

Available from: 2018-09-06 Created: 2018-09-06 Last updated: 2018-12-11Bibliographically approved
Degirmenci, N. C., Jansson, J., Hoffman, J., Arnela, M., Sánchez-Martín, P., Guasch, O. & Ternström, S. (2017). A Unified Numerical Simulation of Vowel Production That Comprises Phonation and the Emitted Sound. In: Proceedings of the Annual Conference of the International Speech Communication Association, INTERSPEECH 2017: . Paper presented at 18th Annual Conference of the International Speech Communication Association, INTERSPEECH 2017, Stockholm, Sweden, 20 August 2017 through 24 August 2017 (pp. 3492-3496). The International Speech Communication Association (ISCA)
Open this publication in new window or tab >>A Unified Numerical Simulation of Vowel Production That Comprises Phonation and the Emitted Sound
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2017 (English)In: Proceedings of the Annual Conference of the International Speech Communication Association, INTERSPEECH 2017, The International Speech Communication Association (ISCA), 2017, p. 3492-3496Conference paper, Published paper (Refereed)
Abstract [en]

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.

Place, publisher, year, edition, pages
The International Speech Communication Association (ISCA), 2017
Series
Proceedings of the Annual Conference of the International Speech Communication Association, INTERSPEECH, ISSN 2308-457X ; 2017
Keywords
Numerical voice production, phonation, vocal tract acoustics, fluid-structure interaction, finite element method
National Category
Fluid Mechanics and Acoustics
Research subject
Applied and Computational Mathematics
Identifiers
urn:nbn:se:kth:diva-219554 (URN)10.21437/Interspeech.2017-1239 (DOI)2-s2.0-85039159138 (Scopus ID)
Conference
18th Annual Conference of the International Speech Communication Association, INTERSPEECH 2017, Stockholm, Sweden, 20 August 2017 through 24 August 2017
Projects
Eunison
Funder
EU, FP7, Seventh Framework Programme, 308874
Note

QC 20171211

Available from: 2017-12-07 Created: 2017-12-07 Last updated: 2018-05-08Bibliographically approved
Jansson, J., Degirmenci, N. C. & Hoffman, J. (2017). Adaptive unified continuum FEM modeling of a 3D FSI benchmark problem. International Journal for Numerical Methods in Biomedical Engineering, 33(9), Article ID e2851.
Open this publication in new window or tab >>Adaptive unified continuum FEM modeling of a 3D FSI benchmark problem
2017 (English)In: International Journal for Numerical Methods in Biomedical Engineering, ISSN 2040-7939, E-ISSN 2040-7947, Vol. 33, no 9, article id e2851Article in journal (Refereed) Published
Abstract [en]

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.

Place, publisher, year, edition, pages
Wiley-Blackwell, 2017
Keywords
adaptive finite element method, benchmark problem, fluid-structure interaction, Benchmarking, Computer programming, Diffusion in liquids, Finite element method, Mesh generation, Transport properties, Adaptive finite element, Adaptive finite element methods, Bench-mark problems, Bio-medical models, Fluid-structure interfaces, Incompressible fluid-structure interaction, Software frameworks, Streamline diffusion, Fluid structure interaction
National Category
Computer and Information Sciences
Identifiers
urn:nbn:se:kth:diva-216185 (URN)10.1002/cnm.2851 (DOI)000409217800004 ()2-s2.0-85017639985 (Scopus ID)
Note

QC 20171124

Available from: 2017-11-24 Created: 2017-11-24 Last updated: 2018-05-08Bibliographically approved
Larsson, D., Spühler, J. H., Petersson, S., Nordenfur, T., Colarieti-Tosti, M., Hoffman, J., . . . Larsson, M. (2017). Patient-Specific Left Ventricular Flow Simulations From Transthoracic Echocardiography: Robustness Evaluation and Validation Against Ultrasound Doppler and Magnetic Resonance Imaging. IEEE Transactions on Medical Imaging, 36(11), 2261-2275
Open this publication in new window or tab >>Patient-Specific Left Ventricular Flow Simulations From Transthoracic Echocardiography: Robustness Evaluation and Validation Against Ultrasound Doppler and Magnetic Resonance Imaging
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2017 (English)In: IEEE Transactions on Medical Imaging, ISSN 0278-0062, E-ISSN 1558-254X, Vol. 36, no 11, p. 2261-2275Article in journal (Refereed) Published
Abstract [en]

The combination of medical imaging with computational fluid dynamics (CFD) has enabled the study of 3D blood flow on a patient-specificlevel. However, with models based on gated high-resolution data, the study of transient flows, and any model implementation into routine cardiac care, is challenging. The present paper presents a novel pathway for patient-specific CFD modelling of the left ventricle (LV), using 4D transthoracic echocardiography (TTE) as input modality. To evaluate the clinical usability, two sub-studies were performed. First, a robustness evaluation was performed where repeated models with alternating input variables were generated for 6 subjects and changes in simulated output quantified. Second, a validation study was carried out where the pathway accuracy was evaluated against pulsed-wave Doppler (100 subjects), and 2D through-plane phase-contrast magnetic resonance imaging measurements over 7 intraventricular planes (6 subjects). The robustness evaluation indicated a model deviation of <12%, with highest regional and temporal deviations at apical segments and at peak systole, respectively. The validation study showed an error of < 11% (velocities < 10 cm/s) for all subjects, with no significant regional or temporal differences observed. With the patient-specific pathway shown to provide robust output with high accuracy, and with the pathway dependent only on 4DTTE, the method has a high potential to be used within future clinical studies on 3D intraventricular flowpatterns. To this, future model developments in the form of e.g. anatomically accurate LV valves may further enhance the clinical value of the simulations.

Place, publisher, year, edition, pages
Institute of Electrical and Electronics Engineers (IEEE), 2017
National Category
Medical Image Processing
Research subject
Medical Technology
Identifiers
urn:nbn:se:kth:diva-215187 (URN)10.1109/TMI.2017.2718218 (DOI)000414134200007 ()
Funder
Swedish Research Council, 2015-04237Swedish Foundation for Strategic Research , AM13-0049
Note

QC 20171006

Available from: 2017-10-04 Created: 2017-10-04 Last updated: 2017-12-12Bibliographically approved
Vilela de Abreu, R., Jansson, N. & Hoffman, J. (2016). Computation of aeroacoustic sources for a Gulfstream G550 nose landing gear model using adaptive FEM. Computers & Fluids, 124, 136-146
Open this publication in new window or tab >>Computation of aeroacoustic sources for a Gulfstream G550 nose landing gear model using adaptive FEM
2016 (English)In: Computers & Fluids, ISSN 0045-7930, E-ISSN 1879-0747, Vol. 124, p. 136-146Article in journal (Refereed) Published
Abstract [en]

This work presents a direct comparison of unsteady, turbulent flow simulations with measurements performed using a Gulfstream G550 nose landing gear model. The experimental campaign, which was carried out by researchers from the NASA Langley Research Center, provided a series of detailed, well documented wind-tunnel measurements for comparison and validation of computational fluid dynamics (CFD) and computational aeroacoustics (CAA) methodologies. Several computational efforts were collected and presented at the Benchmark for Airframe Noise Computation workshops, BANC-I and II. For our simulations, we used a General Galerkin finite element method (G2), where no explicit subgrid model is used, and where the computational mesh is adaptively refined with respect to a posteriori estimates of the error in a quantity of interest, here the source term in Lighthill's equation. The mesh is fully unstructured and the solution is time-resolved, which are key ingredients for solving problems of industrial relevance in the field of aeroacoustics. Moreover, we choose to model the boundary layers on the landing gear geometry with a free-slip condition for the velocity, which we previously observed to produce good results for external flows at high Reynolds numbers, and which considerably reduces the amount of cells required in the mesh. The comparisons presented here are an attempt to quantify the accuracy of our models, methods and assumptions; to that end, several results containing both time-averaged and unsteady flow quantities, always side by side with corresponding experimental values, are reported. The main finding is that we are able to simulate a complex, unsteady flow problem using a parameter-free methodology developed for high Reynolds numbers, external aerodynamics and aeroacoustics applications.

Place, publisher, year, edition, pages
Elsevier, 2016
Keywords
Landing gear noise, Computational fluid dynamics, Computational aeroacoustics, Adaptive finite element methods, Turbulence, CAA, CFD, FEM
National Category
Computer Sciences
Identifiers
urn:nbn:se:kth:diva-180964 (URN)10.1016/j.compfluid.2015.10.017 (DOI)000367282700011 ()2-s2.0-84946867009 (Scopus ID)
Note

Updated from Manuscript to Article.

QC 20160128

Available from: 2016-01-28 Created: 2016-01-26 Last updated: 2018-01-10Bibliographically approved
Krishnasamy, E., Hoffman, J. & Jansson, J. (2016). Direct FEM large scale computation of turbulent multiphase flow in urban water systems and marine energy. In: ECCOMAS Congress 2016 - Proceedings of the 7th European Congress on Computational Methods in Applied Sciences and Engineering: . Paper presented at 7th European Congress on Computational Methods in Applied Sciences and Engineering, ECCOMAS Congress 2016, 5 June 2016 through 10 June 2016 (pp. 1339-1351). National Technical University of Athens
Open this publication in new window or tab >>Direct FEM large scale computation of turbulent multiphase flow in urban water systems and marine energy
2016 (English)In: ECCOMAS Congress 2016 - Proceedings of the 7th European Congress on Computational Methods in Applied Sciences and Engineering, National Technical University of Athens , 2016, p. 1339-1351Conference paper, Published paper (Refereed)
Abstract [en]

High-Reynolds number turbulent incompressible multiphase flow represents a large class of engineering problems of key relevance to society. Here we describe our work on modeling two such problems: 1. The Consorcio de Aguas Bilbao Bizkaia is constructing a new storm tank system with an automatic cleaning system, based on periodically pushing tank water out in a tunnel 2. In the framework of the collaboration between BCAM - Basque Center for Applied Mathematics and Tecnalia R & I, the interaction of the sea flow with a semi submersible floating offshore wind platform is computationally investigated. We study the MARIA' benchmark modeling breaking waves over objects in marine environments. Both of these problems are modeled in the the Direct FEM/General Galerkin methodology for turbulent incompressible variable-densitv flow 1,2 in the FEniCS software framework.

Place, publisher, year, edition, pages
National Technical University of Athens, 2016
Keywords
Adaptive, FEM, Marine engineering, Turbulence, Computer programming, Finite element method, Multiphase flow, Reynolds number, Tanks (containers), Automatic cleaning systems, Engineering problems, High Reynolds number, Large scale computation, Software frameworks, Turbulent multiphase flows, Urban water systems, Computational methods
National Category
Computer Systems
Identifiers
urn:nbn:se:kth:diva-201987 (URN)2-s2.0-84995426921 (Scopus ID)9786188284401 (ISBN)
Conference
7th European Congress on Computational Methods in Applied Sciences and Engineering, ECCOMAS Congress 2016, 5 June 2016 through 10 June 2016
Note

QC 20170303

Available from: 2017-03-03 Created: 2017-03-03 Last updated: 2017-03-03Bibliographically approved
Hoffman, J., Jansson, J. & Jansson, N. (2016). FEniCS-HPC: Automated predictive high-performance finite element computing with applications in aerodynamics. In: Proceedings of the 11th International Conference on Parallel Processing and Applied Mathematics, PPAM 2015: . Paper presented at 11th International Conference on Parallel Processing and Applied Mathematics (pp. 356-365). Springer-Verlag New York, 9573
Open this publication in new window or tab >>FEniCS-HPC: Automated predictive high-performance finite element computing with applications in aerodynamics
2016 (English)In: Proceedings of the 11th International Conference on Parallel Processing and Applied Mathematics, PPAM 2015, Springer-Verlag New York, 2016, Vol. 9573, p. 356-365Conference paper, Published paper (Refereed)
Abstract [en]

Developing multiphysics nite element methods (FEM) andscalable HPC implementations can be very challenging in terms of soft-ware complexity and performance, even more so with the addition ofgoal-oriented adaptive mesh renement. To manage the complexity we inthis work presentgeneraladaptive stabilized methods withautomatedimplementation in the FEniCS-HPCautomatedopen source softwareframework. This allows taking the weak form of a partial dierentialequation (PDE) as input in near-mathematical notation and automati-cally generating the low-level implementation source code and auxiliaryequations and quantities necessary for the adaptivity. We demonstratenew optimal strong scaling results for the whole adaptive frameworkapplied to turbulent ow on massively parallel architectures down to25000 vertices per core with ca. 5000 cores with the MPI-based PETScbackend and for assembly down to 500 vertices per core with ca. 20000cores with the PGAS-based JANPACK backend. As a demonstration ofthe high impact of the combination of the scalability together with theadaptive methodology allowing prediction of gross quantities in turbulent ow we present an application in aerodynamics of a full DLR-F11 aircraftin connection with the HiLift-PW2 benchmarking workshop with goodmatch to experiments.

Place, publisher, year, edition, pages
Springer-Verlag New York, 2016
Series
Lecture Notes in Computer Science, ISSN 0302-9743
National Category
Computational Mathematics Computer Sciences
Identifiers
urn:nbn:se:kth:diva-170369 (URN)10.1007/978-3-319-32149-3_34 (DOI)000400134500034 ()2-s2.0-84968610610 (Scopus ID)
Conference
11th International Conference on Parallel Processing and Applied Mathematics
Note

QC 20151215

Available from: 2015-06-29 Created: 2015-06-29 Last updated: 2018-01-11Bibliographically approved
Organisations
Identifiers
ORCID iD: ORCID iD iconorcid.org/0000-0003-4256-0463

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