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  • 1. Choudhari, M.
    et al.
    Lockard, D. P.
    Jenkins,
    Neuhart,
    Choudhari,
    Cattafesta,
    Murayama,
    Yamamoto,
    Ura,
    Ito,
    Vilela de Abreu, Rodrigo
    KTH, School of Computer Science and Communication (CSC), Computational Science and Technology (CST).
    Hoffman, Johan
    KTH, School of Computer Science and Communication (CSC), Computational Science and Technology (CST).
    Jansson, Johan
    KTH, School of Computer Science and Communication (CSC), Computational Science and Technology (CST).
    Lockard,
    Ueno,
    Knacke,
    Thiele,
    Dahan, Jeremy
    KTH, School of Engineering Sciences (SCI), Aeronautical and Vehicle Engineering.
    Tamaki,
    Imamura,
    Tanaka,
    Amemiya,
    Hirai,
    Ashton,
    West,
    Mendonca,
    Housman,
    Kiris,
    Ribeiro,
    Fares,
    Casalino,
    Terracol,
    Ewert,
    Boenke,
    Simoes,
    Bonatto,
    Souza,
    Medeiros,
    Bodart,
    Larsson,
    Moin,
    Assessment of slat noise predictions for 30P30N high- lift configuration from Banc-III workshop2015In: 21st AIAA/CEAS Aeroacoustics Conference, American Institute of Aeronautics and Astronautics, 2015Conference paper (Refereed)
    Abstract [en]

    This paper presents a summary of the computational predictions and measurement data contributed to Category 7 of the 3rd AIAA Workshop on Benchmark Problems for Airframe Noise Computations (BANC-III), which was held in Atlanta, GA, on June 14-15, 2014. Category 7 represents the first slat-noise configuration to be investigated under the BANC series of workshops, namely, the 30P30N two-dimensional high-lift model (with a slat contour that was slightly modified to enable unsteady pressure measurements) at an angle of attack that is relevant to approach conditions. Originally developed for a CFD challenge workshop to assess computational fluid dynamics techniques for steady high-lift predictions, the 30P30N configurations has provided a valuable opportunity for the airframe noise community to collectively assess and advance the computational and experimental techniques for slat noise. The contributed solutions are compared with each other as well as with the initial measurements that became available just prior to the BANC-III Workshop. Specific features of a number of computational solutions on the finer grids compare reasonably well with the initial measurements from FSU and JAXA facilities and/or with each other. However, no single solution (or a subset of solutions) could be identified as clearly superior to the remaining solutions. Grid sensitivity studies presented by multiple BANC-III participants demonstrated a relatively consistent trend of reduced surface pressure fluctuations, higher levels of turbulent kinetic energy in the flow, and lower levels of both narrow band peaks and the broadband component of unsteady pressure spectra in the nearfield and farfield. The lessons learned from the BANC-III contributions have been used to identify improvements to the problem statement for future Category-7 investigations.

  • 2. Compere, Gaetan
    et al.
    Remacle, Jean-Francois
    Jansson, Johan
    KTH, School of Computer Science and Communication (CSC), Numerical Analysis, NA.
    Hoffman, Johan
    KTH, School of Computer Science and Communication (CSC), Numerical Analysis, NA.
    A mesh adaptation framework for dealing with large deforming meshes2010In: International Journal for Numerical Methods in Engineering, ISSN 0029-5981, E-ISSN 1097-0207, Vol. 82, no 7, p. 843-867Article in journal (Refereed)
    Abstract [en]

    In this paper. we identify and propose solutions for several issues encountered when designing a mesh adaptation package, such as mesh-to-mesh projections and mesh database design, and we describe an algorithm to integrate a mesh adaptation procedure in a physics solver. The open-source MAdLib package is presented as an example of such a mesh adaptation library. A new technique combining global node repositioning and mesh optimization in order to perform arbitrarily large deformations is also proposed. We then present several test cases to evaluate the performances of the proposed techniques and to show their applicability to fluid-structure interaction problems with arbitrarily large deformations. Copyright (C) 2009 John Wiley & Sons, Ltd.

  • 3.
    Degirmenci, Niyazi Cem
    et al.
    KTH, School of Computer Science and Communication (CSC), Computational Science and Technology (CST).
    Jansson, Johan
    KTH, School of Computer Science and Communication (CSC), Computational Science and Technology (CST).
    Hoffman, Johan
    KTH, School of Computer Science and Communication (CSC), Computational Science and Technology (CST).
    Arnela, Marc
    Sánchez-Martín, Patricia
    Guasch, Oriol
    Ternström, Sten
    KTH, School of Computer Science and Communication (CSC), Speech, Music and Hearing, TMH.
    A Unified Numerical Simulation of Vowel Production That Comprises Phonation and the Emitted Sound2017In: Proceedings of the Annual Conference of the International Speech Communication Association, INTERSPEECH 2017, The International Speech Communication Association (ISCA), 2017, p. 3492-3496Conference 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.

  • 4.
    Hoffman, Johan
    et al.
    KTH, School of Computer Science and Communication (CSC), Numerical Analysis, NA.
    Jansson, Johan
    KTH, School of Computer Science and Communication (CSC), Numerical Analysis, NA.
    De Abreu, Rodrigo Vilela
    KTH, School of Computer Science and Communication (CSC), Numerical Analysis, NA.
    Adaptive modeling of turbulent flow with residual based turbulent kinetic energy dissipation2011In: Computer Methods in Applied Mechanics and Engineering, ISSN 0045-7825, E-ISSN 1879-2138, Vol. 200, no 37-40, p. 2758-2767Article in journal (Refereed)
    Abstract [en]

    In this paper we first review our recent work on a new framework for adaptive turbulence simulation: we model turbulence by weak solutions to the Navier-Stokes equations that are wellposed with respect to mean value output in the form of functionals, and we use an adaptive finite element method to compute approximations with a posteriori error control based on the error in the functional output. We then derive a local energy estimate for a particular finite element method, which we connect to related work on dissipative weak Euler solutions with kinetic energy dissipation due to lack of local smoothness of the weak solutions. The ideas are illustrated by numerical results, where we observe a law of finite dissipation with respect to a decreasing mesh size.

  • 5.
    Hoffman, Johan
    et al.
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz).
    Jansson, Johan
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz).
    de Abreu, Rodrigo Vilela
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz).
    Degirmenci, Niyazi Cem
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz).
    Jansson, Niclas
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz).
    Müller, Kaspar
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz).
    Nazarov, Murtazo
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz).
    Spühler, Jeannette Hiromi
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz).
    Unicorn: Parallel adaptive finite element simulation of turbulent flow and fluid-structure interaction for deforming domains and complex geometry2013In: Computers & Fluids, ISSN 0045-7930, E-ISSN 1879-0747, Vol. 80, no SI, p. 310-319Article in journal (Refereed)
    Abstract [en]

    We present a framework for adaptive finite element computation of turbulent flow and fluid structure interaction, with focus on general algorithms that allow for complex geometry and deforming domains. We give basic models and finite element discretization methods, adaptive algorithms and strategies for efficient parallel implementation. To illustrate the capabilities of the computational framework, we show a number of application examples from aerodynamics, aero-acoustics, biomedicine and geophysics. The computational tools are free to download open source as Unicorn, and as a high performance branch of the finite element problem solving environment DOLFIN, both part of the FEniCS project.

  • 6.
    Hoffman, Johan
    et al.
    KTH, School of Computer Science and Communication (CSC), Numerical Analysis, NA (closed 2012-06-30).
    Jansson, Johan
    KTH, School of Computer Science and Communication (CSC), Numerical Analysis, NA (closed 2012-06-30).
    Degirmenci, Niyazi Cem
    KTH, School of Computer Science and Communication (CSC), Numerical Analysis, NA (closed 2012-06-30).
    Jansson, Niclas
    KTH, School of Computer Science and Communication (CSC), Numerical Analysis, NA (closed 2012-06-30).
    Nazarov, Murtazo
    KTH, School of Computer Science and Communication (CSC), Numerical Analysis, NA (closed 2012-06-30).
    Unicorn: a unified continuum mechanics solver; in automated solution pf differential equations by the finite element method2011In: Automated Solution of Differential Equations by the Finite Element Method, Springer Berlin/Heidelberg, 2011Chapter in book (Refereed)
  • 7.
    Hoffman, Johan
    et al.
    KTH, School of Computer Science and Communication (CSC). Basque Center for Applied Mathematics (BCAM), Bilbao, Spain.
    Jansson, Johan
    KTH, School of Computer Science and Communication (CSC), Computational Science and Technology (CST). Basque Center for Applied Mathematics (BCAM), Bilbao, Spain.
    Degirmenci, Niyazi Cem
    KTH, School of Computer Science and Communication (CSC), Computational Science and Technology (CST).
    Spühler, Jeannette Hiromi
    KTH, School of Computer Science and Communication (CSC), Computational Science and Technology (CST).
    Vilela de Abreu, Rodrigo
    KTH, School of Computer Science and Communication (CSC), Computational Science and Technology (CST).
    Jansson, Niclas
    KTH, School of Computer Science and Communication (CSC), Computational Science and Technology (CST).
    Larcher, Aurélien
    Norwegian University of Science and Technology, Trondheim, Norway.
    FEniCS-HPC: Coupled Multiphysics in Computational Fluid Dynamics2017In: High-Performance Scientific Computing: Jülich Aachen Research Alliance (JARA) High-Performance Computing Symposium / [ed] Edoardo Di Napoli, Marc-André Hermanns, Hristo Iliev, Andreas Lintermann, Alexander Peyser, Springer, 2017, p. 58-69Conference paper (Refereed)
    Abstract [en]

    We present a framework for coupled multiphysics in computational fluid dynamics, targeting massively parallel systems. Our strategy is based on general problem formulations in the form of partial differential equations and the finite element method, which open for automation, and optimization of a set of fundamental algorithms. We describe these algorithms, including finite element matrix assembly, adaptive mesh refinement and mesh smoothing; and multiphysics coupling methodologies such as unified continuum fluid-structure interaction (FSI), and aeroacoustics by coupled acoustic analogies. The framework is implemented as FEniCS open source software components, optimized for massively parallel computing. Examples of applications are presented, including simulation of aeroacoustic noise generated by an airplane landing gear, simulation of the blood flow in the human heart, and simulation of the human voice organ.

  • 8.
    Hoffman, Johan
    et al.
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz).
    Jansson, Johan
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz).
    Jansson, Niclas
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz).
    FEniCS-HPC: Automated predictive high-performance finite element computing with applications in aerodynamics2016In: 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 (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.

  • 9.
    Hoffman, Johan
    et al.
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz). Basque Ctr Appl Math, Spain.
    Jansson, Johan
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz). Basque Ctr Appl Math, Spain.
    Jansson, Niclas
    RIKEN Advanced Institute for Computational Science, Kobe, Japan.
    De Abreu, Rodrigo Vilela
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz).
    Towards a parameter-free method for high Reynolds number turbulent flow simulation based on adaptive finite element approximation2015In: Computer Methods in Applied Mechanics and Engineering, ISSN 0045-7825, E-ISSN 1879-2138, Vol. 288, p. 60-74Article in journal (Refereed)
    Abstract [en]

    We present work towards a parameter-free method for turbulent flow simulation based on adaptive finite element approximation of the Navier-Stokes equations at high Reynolds numbers. In this model, viscous dissipation is assumed to be dominated by turbulent dissipation proportional to the residual of the equations, and skin friction at solid walls is assumed to be negligible compared to inertial effects. The result is a computational model without empirical data, where the only parameter is the local size of the finite element mesh. Under adaptive refinement of the mesh based on a posteriori error estimation, output quantities of interest in the form of functionals of the finite element solution converge to become independent of the mesh resolution, and thus the resulting method has no adjustable parameters. No ad hoc design of the mesh is needed, instead the mesh is optimised based on solution features, in particular no bounder layer mesh is needed. We connect the computational method to the mathematical concept of a dissipative weak solution of the Euler equations, as a model of high Reynolds number turbulent flow, and we highlight a number of benchmark problems for which the method is validated. 

  • 10.
    Hoffman, Johan
    et al.
    KTH, School of Computer Science and Communication (CSC), Numerical Analysis, NA (closed 2012-06-30).
    Jansson, Johan
    KTH, School of Computer Science and Communication (CSC), Numerical Analysis, NA (closed 2012-06-30).
    Jansson, Niclas
    KTH, School of Computer Science and Communication (CSC), Numerical Analysis, NA (closed 2012-06-30).
    Johnsson, Claes
    Vilela de Abreu, Rodrigo
    KTH, School of Computer Science and Communication (CSC), Numerical Analysis, NA (closed 2012-06-30).
    Turbulent flow and fluid-structure interaction; in automated solution of differental equations by the finite element method2011In: Automated Solution of Differential Equations by the Finite Element Method / [ed] Anders Logg Kent-Andre Mardal, Garth Wells, Springer Berlin/Heidelberg, 2011Chapter in book (Refereed)
  • 11.
    Hoffman, Johan
    et al.
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz).
    Jansson, Johan
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz).
    Jansson, Niclas
    KTH, School of Computer Science and Communication (CSC), Computational Science and Technology (CST).
    Vilela de Abreu, Rodrigo
    KTH, School of Computer Science and Communication (CSC), Computational Science and Technology (CST).
    Johnson, Claes
    KTH, School of Computer Science and Communication (CSC), Computational Science and Technology (CST).
    Computability and Adaptivity in CFD2016In: Encyclopedia of Computational Mechanics, John Wiley & Sons, 2016Chapter in book (Refereed)
  • 12.
    Hoffman, Johan
    et al.
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz).
    Jansson, Johan
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz).
    Johnson, Claes
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz).
    New Theory of Flight2015In: Journal of Mathematical Fluid Mechanics, ISSN 1422-6928, E-ISSN 1422-6952, Vol. 18, no 2, p. 219-241Article in journal (Other academic)
    Abstract [en]

    We present a new mathematical theory explaining the fluid mechanics of sub-sonic flight, which is fundamentally different from the existing boundary layer-circulation theory by Prandtl-Kutta-Zhukovsky formed 100 year ago. The new the-ory is based on our new resolution of d’Alembert’s paradox showing that slightlyviscous bluff body flow can be viewed as zero-drag/lift potential flow modified by3d rotational slip separation arising from a specific separation instability of po-tential flow, into turbulent flow with nonzero drag/lift. For a wing this separationmechanism maintains the large lift of potential flow generated at the leading edgeat the price of small drag, resulting in a lift to drag quotient of size15

  • 13.
    Hoffman, Johan
    et al.
    KTH, School of Computer Science and Communication (CSC).
    Jansson, Johan
    KTH, School of Computer Science and Communication (CSC).
    Stöckli, Michael
    KTH, School of Computer Science and Communication (CSC).
    Unified Continuum modeling of fluid-structure interaction2011In: Mathematical Models and Methods in Applied Sciences, ISSN 0218-2025, Vol. 21, no 3, p. 491-513Article in journal (Refereed)
    Abstract [en]

    In this paper, we describe an incompressible Unified Continuum(UC) model in Euler (laboratory) coordinates with a moving mesh for tracking the fluid-structure interface as part of the discretization, allowing simple and general formulation and efficient computation. The model consists of conservation equations for mass and momentum, a phase convection equation and a Cauchy stress and phase variable theta as data for defining material properties and constitutive laws. We target realistic 3D turbulent fluid-structure interaction (FSI) applications, where we show simulation results of a flexible flag mounted in the turbulent wake behind a cube as a qualitative test of the method, and quantitative results for 2D benchmarks, leaving adaptive error control for future work. We compute piecewise linear continuous discrete solutions in space and time by a general Galerkin (G2) finite element method (FEM). We introduce and compensate for mesh motion by defining a local arbitrary Euler-Lagrange (ALE) map on each space-time slab as part of the discretization, allowing a sharp phase interface given by theta on cell facets. The Unicorn implementation is published as part of the FEniCS Free Software system for automation of computational mathematical modeling. Simulation results are given for a 2D stationary convergence test, indicating quadratic convergence of the displacement, a simple 2D Poiseuille test for verifying correct treatment of the fluid-structure interface, showing quadratic convergence to the exact drag value, an established 2D dynamic flag benchmark test, showing a good match to published reference solutions and a 3D turbulent flag test as indicated above.

  • 14.
    Hoffman, Johan
    et al.
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz).
    Jansson, Johan
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz).
    Vilela De Abreu, Rodrigo
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz). KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW.
    Computation of slat noise sources using adaptive FEM and lighthill's analogy2013In: 19th AIAA/CEAS Aeroacoustics Conference, 2013Conference paper (Refereed)
    Abstract [en]

    This is a summary of preliminary results from simulations with the 30P30N high-lift device. We used the 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 error estimates for a quantity of interest. The mesh is fully unstructured and the solutions are time-resolved, which are key ingredients for solving challenging industrial applications in the field of aeroacoustics. We present preliminary results containing time-averaged quantities and snapshots of unsteady quantities, all reasonably agreeing with previous computational efforts. One important finding is that the use of adaptively generated meshes seems to be a more effcient way of computing aeroacoustic sources than by using "handmade" meshes.

  • 15.
    Hoffman, Johan
    et al.
    KTH, School of Computer Science and Communication (CSC), Numerical Analysis, NA.
    Jansson, Johan
    KTH, School of Computer Science and Communication (CSC), Numerical Analysis, NA.
    Vilela de Abreu, Rodrigo
    KTH, School of Computer Science and Communication (CSC), Numerical Analysis, NA.
    Degirmenci, Niyazi Cem
    KTH, School of Computer Science and Communication (CSC), Numerical Analysis, NA.
    Jansson, Niclas
    KTH, School of Computer Science and Communication (CSC), Numerical Analysis, NA.
    Müller, Kaspar
    KTH, School of Computer Science and Communication (CSC), Numerical Analysis, NA.
    Nazarov, Murtazo
    KTH, School of Computer Science and Communication (CSC), Numerical Analysis, NA.
    Spühler, Jeannette Hiromi
    Unicorn: Parallel adaptive finite element simulation of turbulent flow and fluid-structure interaction for deforming domains and complex geometry2011Report (Other academic)
    Abstract [en]

    We present a framework for adaptive finite element computation of turbulent flow and fluid-structure interaction, with focus on general algorithms that allow for complex geometry and deforming domains. We give basic models and finite element discretization methods, adaptive algorithms and strategies for e cient parallel implementation. To illustrate the capabilities of the computational framework, we show a number of application examples from aerodynamics, aero-acoustics, biomedicine and geophysics. The computational tools are free to download open source as Unicorn, and as a high performance branch of the finite element problem solving environment DOLFIN, both part of the FEniCS project

  • 16.
    Jansson, Johan
    Chalmers University of Technology.
    Automated Computational Modeling2006Doctoral thesis, monograph (Other academic)
  • 17.
    Jansson, Johan
    et al.
    KTH, School of Computer Science and Communication (CSC), Computational Science and Technology (CST).
    Degirmenci, N. C.
    KTH, School of Computer Science and Communication (CSC).
    Hoffman, Johan
    KTH, School of Computer Science and Communication (CSC), Computational Science and Technology (CST).
    Adaptive unified continuum FEM modeling of a 3D FSI benchmark problem2017In: 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)
    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.

  • 18.
    Jansson, Johan
    et al.
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz). Basque Center for Applied Mathematics (BCAM), Bizkaia Basque-Country, Spain .
    Degirmenci, Niyazi Cem
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz).
    Hoffman, Johan
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz).
    Framework for adaptive fluid-structure interaction with industrial applications2013In: International Journal of Materials Engineering Innovation, ISSN 1757-2754, Vol. 4, no 2, p. 166-186Article in journal (Refereed)
    Abstract [en]

    We present developments in the Unicorn-HPC framework for unified continuum mechanics, enabling adaptive finite element computation of fluid-structure interaction, and an overview of the larger FEniCS-HPC framework for automated solution of partial diffential equations of which Unicorn-HPC is a part. We formulate the basic model and finite element discretisation method and adaptive algorithms. We test the framework on a 2D model problem consisting of a flexible beam in channel flow, and to illustrate the capabilities of the computational framework, we show two application examples from industry and medicine. We simulate a flexible mixer plate in turbulent flow in an exhaust system where the target output is aeroacoustic quantities. The second example is a self-oscillating vocal fold configuration, where the ultimate goal is to predict how the voice is affected by physiological changes from aerodynamics. Here we give the displacement signal of a point on the folds.

  • 19.
    Jansson, Johan
    et al.
    KTH, School of Computer Science and Communication (CSC), Computational Science and Technology (CST).
    Hoffman, Johan
    KTH, School of Computer Science and Communication (CSC), Computational Science and Technology (CST).
    Direct FEM parallel-in-time computation of turbulent flowManuscript (preprint) (Other academic)
  • 20.
    Jansson, Johan
    et al.
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz).
    Hoffman, Johan
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz).
    Degirmenci, Cem
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz).
    Adaptive error control in finite element methods using the error representation as error indicator2013Report (Other academic)
    Abstract [en]

    In this paper we present a new a posteriori adaptive finite elementmethod (FEM) directly using the error representation as a local errorindicator, and representing the primal and dual solutions in the samefinite element space (here piecewise continuous linear functions onthe same mesh). Since this approach gives a global a posteriori errorestimate that is zero (due to the Galerkin orthogonality), the errorrepresentation has historically been thought to contain no informationabout the error. However, we show the opposite, that locally, theorthogonal error representation behaves very similar to thenon-orthogonal error representation using a quadratic approximation ofthe dual. We present evidence of this both in the form of an a prioriestimate for the local error indicator and a detailed computationalinvestigation showing that the two methods exhibit very similarbehavior and performance, and thus confirming the theoreticalprediction. We also present a stabilized version of the method fornon-elliptic partial differential equations (PDE) where the errorrepresentation is no longer orthogonal, and where both the local errorindicator and global error estimate behave similar to the errorrepresentation using a quadratic approximation of the dual.

  • 21.
    Jansson, Johan
    et al.
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz).
    Hoffman, Johan
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz).
    Degirmenci, Cem
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz).
    Spühler, Jeannette
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz).
    Automated adaptive error control in finite element methods using the error representation as error indicator2014Report (Other academic)
    Abstract [en]

    In this paper we present a new adaptive finite element method directly using the a posteriori error representation as a local error  indicator, and representing the primal and dual solutions in the same finite element space (here piecewise continuous linear functions on the same mesh). Since this approach gives a global a posteriori error estimate that is zero (due to Galerkin orthogonality), the error representation has traditionally been thought to contain no information about the error. However, we show the opposite, that locally, the orthogonal error representation behaves very similar to the non-orthogonal error representation using a higher order approximation of the dual,  which is a standard approach to overcome the problem of a zero error estimate. We present evidence of this both in the  form of an a priori estimate for the local error indicator for an elliptic model problem  and a detailed computational investigation showing that the two methods exhibit very similar behavior and performance, and thus confirming the theoretical prediction. We also present computational results using a stabilized version of the method for non-elliptic partial differential equations where the error representation is no longer orthogonal, and where both the local error indicator and global error estimate behave similar to the error representation using a higher order approximation of the dual. The benefits of this adaptive method are generality and simplicity in formulation, sharpness, and efficiency since high order approximation of the dual and computation of additional constructs such as jump terms over interior facets or local problems are avoided.

  • 22.
    Jansson, Johan
    et al.
    KTH, School of Computer Science and Communication (CSC), Numerical Analysis, NA (closed 2012-06-30).
    Hoffman, Johan
    KTH, School of Computer Science and Communication (CSC), Numerical Analysis, NA (closed 2012-06-30).
    Jansson, Niclas
    KTH, School of Computer Science and Communication (CSC), Numerical Analysis, NA (closed 2012-06-30).
    Simulation of 3D unsteady incompressible flow past a NACA 0012 wing section2012Report (Other academic)
    Abstract [en]

    We present computational simulations of three-dimensional unsteady high Reynolds number incompressible flow past a NACA 0012 wing profile, for a range of angles of attack, from low lift through stall. A stabilized finite element method is used, referred to as General Galerkin (G2), with adaptive mesh refinement with respect to the error in target output, such as aerodynamic forces. Computational predictions of aerodynamic forces are validated against experimental data.

  • 23.
    Jansson, Johan
    et al.
    KTH, School of Computer Science and Communication (CSC), Numerical Analysis, NA (closed 2012-06-30).
    Hoffman, Johan
    KTH, School of Computer Science and Communication (CSC), Numerical Analysis, NA (closed 2012-06-30).
    Jansson, Niclas
    KTH, School of Computer Science and Communication (CSC), Numerical Analysis, NA (closed 2012-06-30).
    Simulation of 3d unsteady incompressible flow past a NACA 0012 wing sectionManuscript (preprint) (Other academic)
  • 24.
    Jansson, Johan
    et al.
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz).
    Holmberg, Andreas
    KTH, School of Engineering Sciences (SCI), Aeronautical and Vehicle Engineering, MWL Flow acoustics.
    Vilela De Abreu, Rodrigo
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz).
    Degirmenci, Niyazi Cem
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz).
    Hoffman, Johan
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz).
    Karlsson, Mikael
    Åbom, Mats
    KTH, School of Engineering Sciences (SCI), Aeronautical and Vehicle Engineering, MWL Flow acoustics.
    Adaptive stabilized finite element framework for simulation of vocal fold turbulent fluid-structure interaction2013In: Proceedings of Meetings on Acoustics: Volume 19, 2013, Acoustical Society of America (ASA), 2013, p. 1-9Conference paper (Refereed)
    Abstract [en]

    As a step toward building a more complete model of voice production mechanics, we assess the feasibility of a fluid-structure simulation of the vocal fold mechanics in the Unicorn incompressible Unified Continuum framework. The Unicorn framework consists of conservation equations for mass and momentum, a phase function selecting solid or fluid constitutive laws, a convection equation for the phase function and moving mesh methods for tracking the interface, and discretization through an adaptive stabilized finite element method. The framework has been validated for turbulent flow for both low and high Reynolds numbers and has the following features: implicit turbulence modeling (turbulent dissipation only occurs through numerical stabilization), goal-oriented mesh adaptivity, strong, implicit fluid-structure coupling and good scaling on massively parallel computers. We have applied the framework for turbulent fluid-structure interaction simulation of vocal folds, and present initial results. Acoustic quantities have been extracted from the framework in the setting of an investigation of a configuration approximating an exhaust system with turbulent flow around a flexible triangular steel plate in a circular duct. We present some results of the investigation as well as results of the framework applied to other problems.

  • 25.
    Jansson, Johan
    et al.
    KTH, School of Computer Science and Communication (CSC), Numerical Analysis, NA (closed 2012-06-30).
    Ioakeimidou, Foteini
    KTH, School of Computer Science and Communication (CSC).
    Ericson, Finn
    KTH, School of Computer Science and Communication (CSC).
    Spühler, Jeannette
    KTH, School of Computer Science and Communication (CSC), Numerical Analysis, NA (closed 2012-06-30).
    Hoffman, Johan
    KTH, School of Computer Science and Communication (CSC), Numerical Analysis, NA (closed 2012-06-30).
    Olwal, Alex
    MIT, USA.
    Sallnäs Pysander, Eva-Lotta
    KTH, School of Computer Science and Communication (CSC), Human - Computer Interaction, MDI (closed 20111231).
    Forsslund, Jonas
    KTH, School of Computer Science and Communication (CSC), Human - Computer Interaction, MDI (closed 20111231).
    Gestural 3D Interaction with a Beating Heart: Simulation Visualization and Interaction2011In: Proceedings of SIGRAD 2011: Evaluations of Graphics and Visualization— Efficiency, Usefulness, Accessibility, Usability / [ed] Thomas Larsson, Lars Kjelldahl & Kai-Mikael Jää-Aro, Linköping University Electronic Press, 2011Conference paper (Refereed)
    Abstract [en]

    The KTH School of Computer Science and Communication (CSC) established a strategic platform in Simulation-Visualization-Interaction (SimVisInt) in 2009, focused on the high potential in bringing together CSC core com-petences in simulation technology, visualization and interaction. The main part of the platform takes the form aset of new trans-disciplinary projects across established CSC research groups, within the theme of ComputationalHuman Modeling and Visualization: (i) interactive virtual biomedicine (HEART), (ii) simulation of human mo-tion (MOTION), and (iii) virtual prototyping of human hand prostheses (HAND). In this paper, we present recentresults from the HEART project that focused on gestural and haptic interaction with a heart simulation.

  • 26. Jansson, Johan
    et al.
    Johnson, Claes
    Logg, A.
    Computational modeling of dynamical systems2005In: Mathematical Models and Methods in Applied Sciences, ISSN 0218-2025, Vol. 15, no 3, p. 471-481Article in journal (Refereed)
    Abstract [en]

    In this short note, we discuss the basic approach to computational modeling of dynamical systems. If a dynamical system contains multiple time scales, ranging from very fast to slow, computational solution of the dynamical system can be very costly. By resolving the fast time scales in a short time simulation, a model for the effect of the small time scale variation on large time scales can be determined, making solution possible on a long time interval. This process of computational modeling can be completely automated. Two examples are presented, including a simple model problem oscillating at a time scale of 10(-9) computed over the time interval [0, 100], and a lattice consisting of large and small point masses.

  • 27.
    Jansson, Johan
    et al.
    KTH, School of Computer Science and Communication (CSC), Computational Science and Technology (CST).
    Krishnasamy, Ezhilmathi
    Leoni, Massimiliano
    KTH, School of Electrical Engineering and Computer Science (EECS), Computational Science and Technology (CST).
    Jansson, Niclas
    KTH, School of Electrical Engineering and Computer Science (EECS), Computational Science and Technology (CST).
    Hoffman, Johan
    KTH, School of Computer Science and Communication (CSC), Computational Science and Technology (CST).
    Time-resolved Adaptive Direct FEM Simulation of High-lift Aircraft Configurations: Chapter in "Numerical Simulation of the Aerodynamics of High-Lift Configurations'", SpringerManuscript (preprint) (Other academic)
  • 28.
    Jansson, Johan
    et al.
    KTH, School of Computer Science and Communication (CSC), Numerical Analysis, NA.
    Logg, Anders
    Algorithms and Data Structures for Multi-Adaptive Time-Stepping2008In: ACM Transactions on Mathematical Software, ISSN 0098-3500, E-ISSN 1557-7295, Vol. 35, no 3Article in journal (Refereed)
    Abstract [en]

    Multi-adaptive Galerkin methods are extensions of the standard continuous and discontinuous Galerkin methods for the numerical solution of initial value problems for ordinary or partial differential equations. In particular, the multi-adaptive methods allow individual and adaptive time steps to be used for different components or in different regions of space. We present algorithms for efficient multi-adaptive time-stepping, including the recursive construction of time slabs and adaptive time step selection. We also present data structures for efficient storage and interpolation of the multi-adaptive solution. The efficiency of the proposed algorithms and data structures is demonstrated for a series of benchmark problems.

  • 29.
    Jansson, Johan
    et al.
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz). Basque Center for Applied Mathematics, Spain.
    Nava, V.
    Sanchez, M.
    Aguirre, G.
    De Abreu, Rodrigo Vilela
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz).
    Hoffman, Johan
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz). Basque Center for Applied Mathematics, Spain.
    Villate, J. L.
    Adaptive simulation of unsteady flow past the submerged part of a floating wind turbine platform2015In: MARINE 2015 - Computational Methods in Marine Engineering VI, International Center for Numerical Methods in Engineering (CIMNE), 2015, p. 35-46Conference paper (Refereed)
    Abstract [en]

    Offshore floating platforms for wind turbines represent challenging concepts for designers trying to combine an optimal compromise between cost effectiveness and performance. Modelling of the hydrodynamic behaviour of the structure is still the subject of wide debate in the technical communities. The assessment of the hydrodynamics of the support structure is not an easy task as the floaters consist of an assembly of columns, braces and pontoons, commonly also with heave plates: Each of these components corresponds to a different hydrodynamic model and it further interacts with the other elements. This results in very complex non-linear modeling, which makes it necessary to resort to computational fluid dynamics (CFD) methods for the evaluation of the combined hydrodynamics. In the framework of the collaboration between the Basque Centre for Applied Mathematics (BCAM) and Tecnalia R&I, the interaction of the sea flow with a semisubmersible floating offshore wind platform have been calculated by using the open source solver Unicorn in the FEniCS-HPC framework when subject to a steady inflow. The prototype of the platform consists in a semi-submersible 4-columns column stabilized platform - NAUTILUS Floating Solutions concept-; columns are connected by a rigid ring pontoon provided with heave damping plates at the bottom. The novelty of the approach in FEniCS-HPC hinges upon an implicit formulation for the turbulence, a cheap free slip model of the boundary layer and goal-oriented mesh adaptivity [8, 6, 9, 20, 1]. We find that the results are consistent with experimental results for cylinders at high Reynolds number.

  • 30.
    Jansson, Johan
    et al.
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz). KTH, School of Computer Science and Communication (CSC), Computational Science and Technology (CST). Basque Center for Applied Mathematics, Bilbao, Spain.
    Nguyen, Dang
    KTH, School of Computer Science and Communication (CSC), Computational Science and Technology (CST).
    Margarida, Moragues
    BCAM - Basque Center for Applied Mathematics.
    Castanon, Daniel
    BCAM - Basque Center for Applied Mathematics.
    Saavedra, Laura
    Universidad Politécnica de Madrid.
    Krishnasamy, Ezhilmathi
    BCAM - Basque Center for Applied Mathematics.
    Goude, Anders
    Uppsala University.
    Hoffman, Johan
    KTH, School of Computer Science and Communication (CSC), Computational Science and Technology (CST). Basque Center for Applied Mathematics, Bilbao, Spain.
    Direct finite element simulation of turbulent flow for marine based renewable energyManuscript (preprint) (Other academic)
    Abstract [en]

    In this article we present a computational framework for simulation ofturbulent flow in marine based renewable energy applications. Inparticular, we focus on floating structures and rotatingturbines. This work is an extension to multiphase turbulent flow, ofour existing framework of residual based turbulence modeling forsingle phase turbulent incompressible flow. We illustrate theframework in four examples: a regular wave test where we compareagainst an exact solution, the standard MARIN wave impact benchmarkwith experimental validation data, a vertical axis turbine withcomplex geometry from an existing turbine, and finally a prototypesimulation of decay test in a coupled moving boundary rigid-body andtwo-phase fluid simulation.

  • 31.
    Jansson, Johan
    et al.
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz).
    Spühler, Jeannette
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz).
    Degirmenci, Cem
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz).
    Hoffman, Johan
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz).
    Automated error control in finite element methods withapplications in fluid flow2014Report (Other academic)
    Abstract [en]

    In this paper we present a new adaptive finite element method for thesolution of linear and non-linear partial differential equationsdirectly using the a posteriori error representation as a local errorindicator, with the primal and dual solutions approximated in the samefinite element space, here piecewise continuous linear functions onthe same mesh. Since this approach gives a global a posteriori errorrepresentation that is zero due to Galerkin orthogonality, the errorrepresentation has traditionally been thought to contain noinformation about the error. However, for elliptic andconvection-diffusion model problems we show the opposite, that locallythe orthogonal error representation behaves very similar to thenon-orthogonal error representation using a higher order approximationof the dual.  We have previously proved an a priori estimate of thelocal error indicator for elliptic problems, and in this paper weextend the proof to convection-reaction problems. We also present aversion of the method for non-elliptic and non-linear problems using astabilized finite element method where the a posteriori errorrepresentation is no longer orthogonal. We apply this method to thestationary incompressible Navier-Stokes equation and perform detailednumerical experiments which show that the a posteriori error estimateis within a factor 2 of the error based on a reference value on a finemesh, except in a few data points on very coarse meshes for anon-smooth test case where it is within a factor 3.

  • 32. Jansson, Johan
    et al.
    Vergeest, J. S. M.
    A discrete mechanics model for deformable bodies2002In: Computer-Aided Design, ISSN 0010-4485, E-ISSN 1879-2685, Vol. 34, no 12, p. 913-928Article in journal (Refereed)
    Abstract [en]

    This paper describes the theory and implications of a discrete mechanics model for deformable bodies, incorporating behavior such as motion, collision, deformation, etc. The model is fundamentally based on inter-atomic interaction, and recursively reduces resolution by approximating collections of many high-resolution elements with fewer lower-resolution elements. The model can be viewed as an extended mass-spring model. We begin by examining the domain of conceptual design, and find there is a need for physics based simulation, both for interactive shape modeling and analysis. We then proceed with describing a theoretical base for our model, as well as pragmatic additions. Applications in both interactive physics based shape modeling and analysis are presented. The model is aimed at conceptual mechanical design, rapid prototyping, or similar areas where adherence to physical principles, generality and simplicity are more important than metric correctness.

  • 33. Jansson, Johan
    et al.
    Vergeest, J. S. M.
    Combining deformable- and rigid-body mechanics simulation2003In: The Visual Computer, ISSN 0178-2789, E-ISSN 1432-2315, Vol. 19, no 5, p. 280-290Article in journal (Refereed)
    Abstract [en]

    We present an interface between a deformable-body mechanics model and a rigid-body mechanics model. What is novel with our approach is that the physical representation in both the models is the same, which ensures behavioral correctness and allows great flexibility. We use a mass-spring representation extended with the concept of volume, and thus contact and collision. All physical interaction occurs between the mass elements only; thus there is no need for the explicit handling of interaction between rigid and deformable bodies or between rigid and rigid bodies. This also means that bodies can be partially rigid and partially deformable. It is also possible to change dynamically whether part of a body should be rigid or not. We present a demonstration example and possible applications in conceptual design engineering, geometric modeling, as well as computer animation.

  • 34.
    Jansson, Niclas
    et al.
    KTH, School of Computer Science and Communication (CSC), Numerical Analysis, NA (closed 2012-06-30).
    Hoffman, Johan
    KTH, School of Computer Science and Communication (CSC), Numerical Analysis, NA (closed 2012-06-30).
    Jansson, Johan
    KTH, School of Computer Science and Communication (CSC), Numerical Analysis, NA (closed 2012-06-30).
    Framework For Massively Parallel Adaptive Finite Element Computational Fluid Dynamics On Tetrahedral Meshes2012In: SIAM Journal on Scientific Computing, ISSN 1064-8275, E-ISSN 1095-7197, Vol. 34, no 1, p. C24-C42Article in journal (Refereed)
    Abstract [en]

    In this paper we describe a general adaptive finite element framework for unstructured tetrahedral meshes without hanging nodes suitable for large scale parallel computations. Our framework is designed to scale linearly to several thousands of processors, using fully distributed and efficient algorithms. The key components of our implementation, local mesh refinement and load balancing algorithms, are described in detail. Finally, we present a theoretical and experimental performance study of our framework, used in a large scale computational fluid dynamics computation, and we compare scaling and complexity of different algorithms on different massively parallel architectures.

  • 35.
    Jansson, Niclas
    et al.
    KTH, School of Computer Science and Communication (CSC), Numerical Analysis, NA (closed 2012-06-30).
    Jansson, Johan
    KTH, School of Computer Science and Communication (CSC), Numerical Analysis, NA (closed 2012-06-30).
    Hoffman, Johan
    KTH, School of Computer Science and Communication (CSC), Numerical Analysis, NA (closed 2012-06-30).
    Adaptive finite element computational fluid dynamics for large scale massiverly parallel computing2012In: SIAM Journal on Scientific Computing, ISSN 1064-8275, E-ISSN 1095-7197Article in journal (Refereed)
  • 36. Krishnasamy, E.
    et al.
    Hoffman, Johan
    KTH, School of Computer Science and Communication (CSC), Computational Science and Technology (CST). BCAM - Basque Center for Applied Mathematics, Spain.
    Jansson, Johan
    KTH, School of Computer Science and Communication (CSC), Computational Science and Technology (CST). BCAM - Basque Center for Applied Mathematics, Spain.
    Direct FEM large scale computation of turbulent multiphase flow in urban water systems and marine energy2016In: 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 (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.

  • 37. Lara, Pedro Valero
    et al.
    Pelayo, Fernando L.
    Jansson, Johan
    KTH, School of Computer Science and Communication (CSC), Computational Science and Technology (CST). Basque Center for Applied Mathematics (BCAM), Spain.
    Introduction to the special issue on high performance computing solutions for complex problems2016In: Scalable Computing: Practice and Experience, ISSN 1895-1767, E-ISSN 1895-1767, Vol. 17, no 1, p. III-IIIArticle in journal (Other academic)
  • 38.
    Nguyen, Van Dang
    et al.
    KTH, School of Computer Science and Communication (CSC), Computational Science and Technology (CST).
    Jansson, Johan
    KTH, School of Computer Science and Communication (CSC), Computational Science and Technology (CST).
    Hoffman, Johan
    KTH, School of Engineering Sciences (SCI), Mathematics (Dept.), Numerical Analysis, NA.
    Goude, Anders
    Uppsala University, Uppsala, Sweden.
    Direct Finite Element Simulation of the Turbulent Flow Past a Parked Vertical Axis Wind TurbineManuscript (preprint) (Other academic)
    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 they are 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 parked vertical axis wind turbine for a range of rotation angles. The force on a parked turbine is one of the most important design cases for the survival of the turbine. We use the method of Direct Finite Element Simulation, and the simulation results are validated against experimental data in the form of force measurements. First, simulations are performed for a set of sampled rotation angles, and then a simulation is performed where the turbine is slowly rotated to cover all the rotation angles continuously. We find that the simulation results are stable with respect to mesh refinement and that we capture the general shape of the variation of force measurements over the rotation angles.

  • 39.
    Nguyen, Van Dang
    et al.
    KTH, School of Computer Science and Communication (CSC), Computational Science and Technology (CST).
    Jansson, Johan
    KTH, School of Computer Science and Communication (CSC), Computational Science and Technology (CST).
    Hoffman, Johan
    KTH, School of Computer Science and Communication (CSC), Computational Science and Technology (CST).
    Li, Jing-Rebecca
    A partition of unity finite element method for computational diffusion MRIManuscript (preprint) (Other academic)
    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 efforts have been made to solve the equation but there is still missing an efficient high performance computing framework. In this work, 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 use extended finite elements with weak enforcement of real (in the case of interior interfaces) and artificial (in the case of exterior boundaries) permeability conditions as well as operator splitting for the exterior boundary conditions. The method appears to be straightforward to implement and it is implemented in the FEniCS for moderate-scale simulations and in the FEniCS-HPC for the large-scale simulations. The accuracy of the resulting method is validated numerically 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. Finally, we do simulations on a complex neuron to study how the signals decay under the effect of the permeable membrane and to show that the method can be used to simulate for complex geometries that we have not done before.

    Highlights:

    • The discontinuity in the magnetization across the interior interfaces of the medium is weakly imposed, allowing generalization to arbitrary order finite elements.
    • Spin exchange across the external boundaries is implemented by weakly imposing an artificial, high permeability, condition, allowing generalization to non-matching meshes.
    • Thus, optimal convergence with respect to the space discretization is achieved.
    • The second-order Crank-Nicolson method is chosen for the time discretization to reduce oscillations at high gradient strengths and allows for larger time-step sizes.
    • The method is of a high level of simplicity and suitable for parallelization.
    • An efficient open-source code is implemented in the FEniCS and FEniCS-HPC platforms.
  • 40.
    Nguyen, Van Dang
    et al.
    KTH, School of Computer Science and Communication (CSC), Computational Science and Technology (CST).
    Jansson, Johan
    KTH, School of Computer Science and Communication (CSC), Computational Science and Technology (CST).
    Leoni, Massimiliano
    Janssen, Barbel
    KTH, School of Computer Science and Communication (CSC), Computational Science and Technology (CST).
    Goude, Anders
    Hoffman, Johan
    KTH, School of Computer Science and Communication (CSC), Computational Science and Technology (CST).
    Modelling of rotating vertical axis turbines using a multiphase finite element method2017In: MARINE 2017: Computational Methods in Marine Engineering VII15 - 17 May 2017, Nantes, France, 2017, p. 950-960Conference paper (Other academic)
  • 41.
    Nguyen, Van-Dang
    et al.
    KTH, School of Computer Science and Communication (CSC), Computational Science and Technology (CST).
    Jansson, Johan
    KTH, School of Electrical Engineering and Computer Science (EECS), Computational Science and Technology (CST).
    Frachon, Thomas
    Degirmenci, Cem
    Hoffman, Johan
    KTH, School of Engineering Sciences (SCI), Mathematics (Dept.), Numerical Analysis, NA.
    A fluid-structure interaction model with weak slip velocity boundary conditions on conforming internal interfaces2018Conference 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. 

  • 42.
    Spühler, Jeannette H.
    et al.
    KTH, School of Computer Science and Communication (CSC), Computational Science and Technology (CST).
    Jansson, Johan
    KTH, School of Computer Science and Communication (CSC), Computational Science and Technology (CST).
    Jansson, Niclas
    KTH, School of Computer Science and Communication (CSC), Computational Science and Technology (CST).
    Hoffman, Johan
    KTH, School of Computer Science and Communication (CSC), Computational Science and Technology (CST).
    3D Fluid-Structure Interaction Simulation of Aortic Valves Using a Unified Continuum ALE FEM Model2018In: Frontiers in Physiology, ISSN 1664-042X, E-ISSN 1664-042X, Vol. 9, article id 363Article in journal (Refereed)
    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.

  • 43.
    Spühler, Jeannette Hiromi
    et al.
    KTH, School of Computer Science and Communication (CSC), Computational Science and Technology (CST).
    Degirmenci, Niyazi Cem
    KTH, School of Computer Science and Communication (CSC), Computational Science and Technology (CST).
    Jansson, Johan
    KTH, School of Computer Science and Communication (CSC), Computational Science and Technology (CST).
    Hoffman, Johan
    KTH, School of Computer Science and Communication (CSC), Computational Science and Technology (CST).
    A 3D full-friction contact model for fluid-structure interaction problemsManuscript (preprint) (Other academic)
  • 44.
    Spühler, Jeannette Hiromi
    et al.
    KTH, School of Computer Science and Communication (CSC), Computational Science and Technology (CST).
    Jansson, Johan
    KTH, School of Computer Science and Communication (CSC), Computational Science and Technology (CST).
    Jansson, Niclas
    KTH, School of Computer Science and Communication (CSC), Computational Science and Technology (CST).
    Hoffman, Johan
    KTH, School of Computer Science and Communication (CSC), Computational Science and Technology (CST).
    3D Fluid-Structure Interaction Simulation of Aortic Valves Using a Unified Continuum ALE-FEM ModelManuscript (preprint) (Other academic)
  • 45.
    Spühler, Jeannette Hiromi
    et al.
    KTH, School of Computer Science and Communication (CSC), Computational Science and Technology (CST).
    Jansson, Johan
    KTH, School of Computer Science and Communication (CSC), Computational Science and Technology (CST). BCAM - Basque Center for Applied Mathematics, Spain.
    Jansson, Niclas
    KTH, School of Computer Science and Communication (CSC), Computational Science and Technology (CST).
    Hoffman, Johan
    KTH, School of Computer Science and Communication (CSC), Computational Science and Technology (CST). BCAM - Basque Center for Applied Mathematics, Spain.
    A finite element framework for high performance computer simulation of blood flow in the left ventricle of the human heart2015Report (Other academic)
    Abstract [en]

    Progress in medical imaging, computational fluid dynamics and high performance computing (HPC) enables computer simulations to emerge as a significant tool to enhance our understanding of the relationship between cardiac diseases and hemodynamics. The field of cardiac modelling is diverse, covering different aspects on microscopic and macroscopic level. In our research, we develop a cardiac model which is embedded in a computational environment where specific properties of the heart such as fluid-structure interaction of the aortic valve can be modeled, or numerical and computational algorithms as parallel computing or adaptivity can be added in a modular way without extensive efforts. In this paper, we present a patient-specific Arbitrary Lagrangian-Eulerian (ALE) finite element framework for simulating the blood flow in the left ventricle of a human heart using HPC, which forms the core of our cardiac model. The mathematical model is described together with the discretization method, mesh smoothing algorithms, and the parallel implementation in Unicorn which is part of the open source software framework FEniCS-HPC. The parallel performance is demonstrated, a convergence study is conducted and intraventricular flow patterns are visualized. The results capture essential features observed with other computational models and imaging techniques, and thus indicate that our framework possesses the potential to provide relevant clinical information for diagnosis and medical treatment. Several studies have been conducted to simulate the three dimensional blood flow in the left ventricle of the human heart with prescribed wall movement. Our contribution to the field of cardiac research lies in establishing an open source framework modular both in modelling and numerical algorithms.

  • 46. Valero-Lara, P.
    et al.
    Jansson, J.
    KTH, School of Computer Science and Communication (CSC).
    Heterogeneous CPU+GPU approaches for mesh refinement over Lattice-Boltzmann simulations2016In: Concurrency and Computation, ISSN 1532-0626, E-ISSN 1532-0634Article in journal (Refereed)
    Abstract [en]

    The use of mesh refinement in CFD is an efficient and widely used methodology to minimize the computational cost by solving those regions of high geometrical complexity with a finer grid. In this work, the author focuses on studying two methods, one based on Multi-Domain and one based on Irregular meshing, to deal with mesh refinement over LBM simulations. The numerical formulation is presented in detail. It is proposed two approaches, homogeneous GPU and heterogeneous CPU+GPU, on each of the refinement methods. Obviously, the use of the two architectures, CPU and GPU, to compute the same problem involves more important challenges with respect to the homogeneous counterpart. These challenges and the strategies to deal with them are described in detail into the present work. We pay a particular attention to the differences among both methodologies/implementations in terms of programmability, memory management, and performance. The size of the refined sub-domain has important consequences over both methodologies; however, the influence on Multi-Domain approach is much higher. For instance, when dealing with a big refined sub-domain, the Multi-Domain approach achieves an important fall in performance with respect to other cases, where the size of the refined sub-domain is smaller. Otherwise, using the Irregular approach, there is no such a dramatic fall in performance when increasing the size of the refined sub-domain. © 2016 John Wiley & Sons, Ltd.

  • 47. Valero-Lara, P.
    et al.
    Jansson, Johan
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz).
    A Non-uniform Staggered Cartesian Grid approach for Lattice-Boltzmann method2015In: Procedia Computer Science, Elsevier, 2015, no 1, p. 296-305Conference paper (Refereed)
    Abstract [en]

    We propose a numerical approach based on the Lattice-Boltzmann method (LBM) for dealing with mesh refinement of Non-uniform Staggered Cartesian Grid. We explain, in detail, the strategy for mapping LBM over such geometries. The main benefit of this approach, compared to others, consists of solving all fluid units only once per time-step, and also reducing considerably the complexity of the communication and memory management between different refined levels. Also, it exhibits a better matching for parallel processors. To validate our method, we analyze several standard test scenarios, reaching satisfactory results with respect to other stateof-the-art methods. The performance evaluation proves that our approach not only exhibits a simpler and efficient scheme for dealing with mesh refinement, but also fast resolution, even in those scenarios where our approach needs to use a higher number of fluid units.

  • 48. Valero-Lara, P.
    et al.
    Jansson, Johan
    KTH, School of Computer Science and Communication (CSC), Computational Science and Technology (CST).
    LBM-HPC - An open-source tool for fluid simulations. Case study: Unified parallel C (UPC-PGAS)2015In: Proceedings - IEEE International Conference on Cluster Computing, ICCC, Institute of Electrical and Electronics Engineers (IEEE), 2015, p. 318-321Conference paper (Refereed)
    Abstract [en]

    The main motivation of this work is the evaluation of the Unified Parallel C (UPC) model, for Boltzmann-fluid simulations. UPC is one of the current models in the so-called Partitioned Global Address Space paradigm. This paradigm attempts to increase the simplicity of codes and achieve a better efficiency and scalability. Two different UPC-based implementations, explicit and implicit, are presented and evaluated. We compare the fundamental features of our UPC implementations with other parallel programming model, MPI-OpenMP. In particular each of the major steps of any LBM code, i.e., Boundary Conditions, Communication, and LBM solver, are analyzed.

  • 49. Valero-Lara, P.
    et al.
    Jansson, Johan
    KTH, School of Computer Science and Communication (CSC), Computational Science and Technology (CST). Basque Center for Applied Mathematics (BCAM).
    Multi-domain grid refinement for lattice-Boltzmann simulations on heterogeneous platforms2015In: Proceedings - IEEE 18th International Conference on Computational Science and Engineering, CSE 2015, IEEE Computer Society, 2015, p. 1-8Conference paper (Refereed)
    Abstract [en]

    The main contribution of the present work consists of several parallel approaches for grid refinement based on a multi-domain decomposition for lattice-Boltzmann simulations. The proposed method for discretizing the fluid incorporates different regular Cartesian grids with no homogeneous spatial domains, which are in need to be communicated each other. Three different parallel approaches are proposed, homogeneous Multicore, homogeneous GPU, and heterogeneous Multicore-GPU. Although, the homogeneous implementations exhibit satisfactory results, the heterogeneous approach achieves up to 30% extra efficiency, in terms of Millions of Fluid Lattice Updates per Second (MFLUPS), by overlapping some of the steps on both architectures, Multicore and GPU. © 2015 IEEE.

  • 50. Valero-Lara, P.
    et al.
    Krishnasamy, E.
    Jansson, Johan
    KTH, School of Computer Science and Communication (CSC), Computational Science and Technology (CST). Basque Center for Applied Mathematics (BCAM), Spain.
    Towards HPC-embedded. Case study: Kalray and message-passing on NoC2017In: Scalable Computing: Practice and Experience, ISSN 1895-1767, E-ISSN 1895-1767, Vol. 18, no 2, p. 151-160Article in journal (Refereed)
    Abstract [en]

    Today one of the most important challenges in HPC is the development of computers with a low power consumption. In this context, recently, new embedded many-core systems have emerged. One of them is Kalray. Unlike other many-core architectures, Kalray is not a co-processor (self-hosted). One interesting feature of the Kalray architecture is the Network on Chip (NoC) connection. Habitually, the communication in many-core architectures is carried out via shared memory. However, in Kalray, the communication among processing elements can also be via Message-Passing on the NoC. One of the main motivations of this work is to present the main constraints to deal with the Kalray architecture. In particular, we focused on memory management and communication. We assess the use of NoC and shared memory on Kalray. Unlike shared memory, the implementation of Message-Passing on NoC is not transparent from programmer point of view. The synchronization among processing elements and NoC is other of the challenges to deal with in the Karlay processor. Although the synchronization using Message-Passing is more complex and consuming time than using shared memory, we obtain an overall speedup close to 6 when using Message-Passing on NoC with respect to the use of shared memory. Additionally, we have measured the power consumption of both approaches. Despite of being faster, the use of NoC presents a higher power consumption with respect to the approach that exploits shared memory. This additional consumption in Watts is about a 50%. However, the reduction in time by using NoC has an important impact on the overall power consumption as well.

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