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  • 1. 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.

  • 2.
    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.

    Download full text (pdf)
    fulltext
  • 3. Guasch, O.
    et al.
    Jansson, Johan
    KTH, School of Computer Science and Communication (CSC).
    Modelling voice production with large-scale physics-based numerical simulations2015In: Proceedings and Report - 9th International Workshop on Models and Analysis of Vocal Emissions for Biomedical Applications, MAVEBA 2015, Firenze University Press , 2015, p. 85-88Conference paper (Refereed)
    Abstract [en]

    The human voice organ fits in a small space having a characteristic length of ~cm. Large amounts of complex physical phenomena combine in it so as to produce sounds. Despite of the reduced dimensions of the voice organ, however, a complete numerical simulation of its physics is still out of reach, even when using massively parallel supercomputers. This has led researchers to split the problem of voice generation into parts, independently focusing for instance, on simulating the self-oscillation of the vocal folds to generate the glottal pulse, the propagation of acoustic waves in moving vocal tracts to produce diphthongs, or the diffraction of the glottal jet pressure by the teeth, which results in fricative sounds. In this workshop, a review will be given of the type of equations and difficulties encountered when trying to solve these type of phenomena and show that, under some assumptions, the first unified simulations coupling the mechanics, aerodynamics and acoustics of the vocal folds and vocal tract, may not be as far as one might think. A workflow from 3D biomechanical models, to the generation of vocal fold self-oscillations, flow and acoustic waves to the radiated sound may be feasible in the short term.

  • 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 Electrical Engineering and Computer Science (EECS), Computer Science, Computational Science and Technology (CST).
    Jansson, Johan
    KTH, School of Electrical Engineering and Computer Science (EECS), Computer Science, Computational Science and Technology (CST).
    Degirmenci, Niyasi Cem
    KTH, School of Electrical Engineering and Computer Science (EECS), Computer Science, Computational Science and Technology (CST).
    Jansson, Niclas
    KTH, School of Electrical Engineering and Computer Science (EECS), Computer Science, Computational Science and Technology (CST).
    Nazarov, Murtazo
    KTH, School of Electrical Engineering and Computer Science (EECS), Computer Science, Computational Science and Technology (CST).
    Unicorn: A unified continuum mechanics solver2012In: Lecture Notes in Computational Science and Engineering, Springer Science and Business Media Deutschland GmbH , 2012, p. 339-361Chapter in book (Refereed)
    Abstract [en]

    This chapter provides a description of the technology of Unicorn focusing on simple, efficient and general algorithms and software for the Unified Continuum (UC) concept and the adaptive General Galerkin (G2) discretization as a unified approach to continuum mechanics. We describe how Unicorn fits into the FEniCS framework, how it interfaces to other FEniCS components, what interfaces and functionality Unicorn provides itself and how the implementation is designed. We also present some examples in fluid–structure interaction and adaptivity computed with Unicorn. 

  • 7.
    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.
    Degirmenci, Niyasi 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.
    Nazarov, Murtazo
    KTH, School of Computer Science and Communication (CSC), Numerical Analysis, NA.
    Unicorn: a unified continuum mechanics solver; in automated solution pf differential equations by the finite element method2012In: Automated Solution of Differential Equations by the Finite Element Method / [ed] Anders Logg, Kent-Andre Mardal, Garth Wells, Springer Berlin/Heidelberg, 2012Chapter in book (Refereed)
  • 8.
    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.

  • 9.
    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.

  • 10.
    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. 

    Download full text (pdf)
    kth-ctl-4031
  • 11.
    Hoffman, Johan
    et al.
    KTH, School of Electrical Engineering and Computer Science (EECS), Computer Science, Computational Science and Technology (CST).
    Jansson, Johan
    KTH, School of Electrical Engineering and Computer Science (EECS), Computer Science, Computational Science and Technology (CST).
    Jansson, Niclas
    KTH, School of Electrical Engineering and Computer Science (EECS), Computer Science, Computational Science and Technology (CST).
    Johnson, Claes
    KTH, School of Computer Science and Communication (CSC).
    Vilela de Abreu, Rodrigo
    KTH, School of Computer Science and Communication (CSC).
    Turbulent flow and Fluid–structure interaction2012In: Lecture Notes in Computational Science and Engineering, Springer Science and Business Media Deutschland GmbH , 2012, p. 543-552Chapter in book (Refereed)
    Abstract [en]

    The FEniCS Project aims towards the goals of generality, efficiency, and simplicity, concerning mathematical methodology, implementation and application, and the Unicorn project is an implementation aimed at FSI and high Re turbulent flow guided by these principles. Unicorn is based on the DOLFIN/FFC/FIAT suite and the linear algebra package PETSc. We here present some key elements of Unicorn, and a set of computational results from applications. The details of the Unicorn implementation are described in Chapter 18. 

  • 12.
    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.
    Jansson, Niclas
    KTH, School of Computer Science and Communication (CSC), Numerical Analysis, NA.
    Johnsson, Claes
    Vilela de Abreu, Rodrigo
    KTH, School of Computer Science and Communication (CSC), Numerical Analysis, NA.
    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)
  • 13.
    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), Centres, Centre for High Performance Computing, PDC.
    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.

  • 14.
    Hoffman, Johan
    et al.
    KTH, School of Computer Science and Communication (CSC), Computational Science and Technology (CST). Basque Center for Applied Mathematics, Bilbao, Spain.
    Jansson, Johan
    KTH, School of Computer Science and Communication (CSC), Computational Science and Technology (CST). Basque Center for Applied Mathematics, Bilbao, Spain.
    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 CFD2018In: Encyclopedia of Computational Mechanics / [ed] Erwin Stein, René de Borst, Thomas J. R. Hughes, John Wiley & Sons, 2018Chapter in book (Refereed)
  • 15.
    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 Flight2016In: Journal of Mathematical Fluid Mechanics, ISSN 1422-6928, E-ISSN 1422-6952, Vol. 18, no 2, p. 219-241Article in journal (Refereed)
    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

  • 16.
    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.

  • 17.
    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

    Download full text (pdf)
    fulltext
  • 18. Janson, C. -E
    et al.
    Shiri, A.
    Jansson, Johan
    KTH, School of Electrical Engineering and Computer Science (EECS), Computer Science, Computational Science and Technology (CST).
    Moragues, M.
    Castanon, D.
    Saavedra, L.
    Degirmenci, C.
    Leoni, M.
    Nonlinear computations of heave motions for a generic wave energy converter2018In: Technology and Science for the Ships of the Future - Proceedings of NAV 2018: 19th International Conference on Ship and Maritime Research, Associazione Italiana di Tecnica Navale , 2018, no 221499, p. 283-290Conference paper (Refereed)
    Abstract [en]

    A bench-marking activity of numerical methods for analysis of Wave Energy Converters (WEC) was proposed under the Ocean Energy Systems (OES) International Energy Agency (IEA) Task 10 in 2015. The purpose of the benchmark is to do a code-2-code comparison of the predicted motions and power take out for a WEC. A heaving sphere was used as a first simple test case. The participants simulated heave decay and regular and irregular wave cases. The numerical methods ranged from linear methods to viscous methods solving the Navier-Stokes equations (CFD). An overview of the results from the first phase of the benchmark was reported in [1]. The present paper focus on the simulations of the sphere using one fully nonlinear time-domain BEM one transient RANS method and one transient Direct FE method with no turbulence model. The theory of the three methods as well as the modeling of the sphere are described. Heave decay and heave motions for steep regular waves were selected as test cases in order to study and compare the capability to handle nonlinear effects. Computational efficiency and applicability of the three methods are also discussed. 

  • 19.
    Jansson, Johan
    Chalmers University of Technology.
    Automated Computational Modeling2006Doctoral thesis, monograph (Other academic)
    Download full text (pdf)
    automated_computational_modeling.pdf
  • 20.
    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.

  • 21.
    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.

  • 22.
    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)
  • 23.
    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.

    Download full text (pdf)
    representation-adaptivity.pdf
  • 24.
    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.

  • 25.
    Jansson, Johan
    et al.
    KTH, School of Computer Science and Communication (CSC), Numerical Analysis, NA.
    Hoffman, Johan
    KTH, School of Computer Science and Communication (CSC), Numerical Analysis, NA.
    Jansson, Niclas
    KTH, School of Computer Science and Communication (CSC), Numerical Analysis, NA.
    Simulation of 3d unsteady incompressible flow past a NACA 0012 wing sectionManuscript (preprint) (Other academic)
  • 26.
    Jansson, Johan
    et al.
    KTH, School of Computer Science and Communication (CSC), Numerical Analysis, NA.
    Hoffman, Johan
    KTH, School of Computer Science and Communication (CSC), Numerical Analysis, NA.
    Jansson, Niclas
    KTH, School of Computer Science and Communication (CSC), Numerical Analysis, NA.
    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.

    Download full text (pdf)
    fulltext
  • 27.
    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.

  • 28.
    Jansson, Johan
    et al.
    KTH, School of Computer Science and Communication (CSC), Numerical Analysis, NA.
    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.
    Hoffman, Johan
    KTH, School of Computer Science and Communication (CSC), Numerical Analysis, NA.
    Olwal, Alex
    MIT, USA.
    Sallnäs Pysander, Eva-Lotta
    KTH, School of Computer Science and Communication (CSC), Human - Computer Interaction, MDI.
    Forsslund, Jonas
    KTH, School of Computer Science and Communication (CSC), Human - Computer Interaction, MDI.
    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.

  • 29. 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.

  • 30.
    Jansson, Johan
    et al.
    KTH, School of Electrical Engineering and Computer Science (EECS), Computer Science, Computational Science and Technology (CST).
    Johnson, Claes
    KTH, School of Electrical Engineering and Computer Science (EECS).
    Scott, R.
    Predictive Euler CFD-Resolution of NASA Vision 20302022In: AIAA AVIATION 2022 Forum, American Institute of Aeronautics and Astronautics (AIAA) , 2022Conference paper (Refereed)
    Abstract [en]

    We show that computing turbulent solutions to Euler’s equations with a slip boundary condition offers a Theory of Everything ToE for slightly viscous incompressible fluid flow as a parameter-free model, covering a vast area of applications in vehicle aero/hydrodynamics including airplanes, ships and cars. This work resolves the Grand Challenges of fluid dynamics described in NASA Vision 2030. The foundation of the methodology is an extremely efficient Direct FEM Simulation (DFS) method. We describe a breakthrough in efficiency, allowing extrenely small numerical dissipation by choosing very small stabilization coefficients, while allowing very large time step size. This work is developed as part of the Digital Math framework [2]-as the foundation of modern science based on constructive digital mathematical computation. We show that Euler CFD by the scientific method in Digital Math predicts drag, lift and pressure distribution in close correspondence with observations for real problems with complex geometry and so can serve to deliver complete realistic aero/hydro-data for simulators without input from model experiments in wind tunnel and towing tank or full-scale experiments, as a new revolutionary capability. 

  • 31.
    Jansson, Johan
    et al.
    KTH, School of Computer Science and Communication (CSC), Computational Science and Technology (CST).
    Krishnasamy, Ezhilmathi
    Leoni, Massimiliano
    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).
    Time-resolved Adaptive Direct FEM Simulation of High-lift Aircraft Configurations: Chapter in "Numerical Simulation of the Aerodynamics of High-Lift Configurations'", Springer2018In: Numerical Simulation of the Aerodynamics of High-Lift Configurations / [ed] Omar Darío López Mejia andJaime A. Escobar Gomez, Springer, 2018, p. 67-92Chapter in book (Refereed)
    Abstract [en]

    We present an adaptive finite element method for time-resolved simulation of aerodynamics without any turbulence-model parameters, which is applied to a benchmark problem from the HiLiftPW-3workshop to compute the flowpast a JAXA Standard Model (JSM) aircraft model at realistic Reynolds numbers. The mesh is automatically constructed by the method as part of an adaptive algorithm based on a posteriori error estimation using adjoint techniques. No explicit turbulence model is used, and the effect of unresolved turbulent boundary layers is modeled by a simple parametrization of the wall shear stress in terms of a skin friction. In the case of very high Reynolds numbers, we approximate the small skin friction by zero skin friction, corresponding to a free-slip boundary condition, which results in a computational model without any model parameter to be tuned, and without the need for costly boundary-layer resolution. We introduce a numerical tripping-noise term to act as a seed for growth of perturbations; the results support that this triggers the correct physical separation at stall and has no significant pre-stall effect. We show that the methodology quantitavely and qualitatively captures the main features of the JSM experiment-aerodynamic forces and the stall mechanism-with a much coarser mesh resolution and lower computational cost than the state-of-the-art methods in the field, with convergence under mesh refinement by the adaptive method. Thus, the simulation methodology appears to be a possible answer to the challenge of reliably predicting turbulent-separated flows for a complete air vehicle.

  • 32.
    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.

  • 33.
    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.

  • 34.
    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.

  • 35.
    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.

  • 36. 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.

  • 37. 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.

  • 38.
    Jansson, Niclas
    et al.
    KTH, School of Computer Science and Communication (CSC), Numerical Analysis, NA.
    Hoffman, Johan
    KTH, School of Computer Science and Communication (CSC), Numerical Analysis, NA.
    Jansson, Johan
    KTH, School of Computer Science and Communication (CSC), Numerical Analysis, NA.
    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.

    Download full text (pdf)
    fulltext
  • 39.
    Jansson, Niclas
    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.
    Hoffman, Johan
    KTH, School of Computer Science and Communication (CSC), Numerical Analysis, NA.
    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)
  • 40. 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.

  • 41. 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)
  • 42. Moragues Ginard, M
    et al.
    Degirmenci, Niyasi Cem
    KTH, School of Computer Science and Communication (CSC), Computational Science and Technology (CST).
    Castañón Quiroz, D
    Leoni, Massimiliano
    KTH, School of Electrical Engineering and Computer Science (EECS), Computer Science, Computational Science and Technology (CST).
    Jansson, Johan
    KTH, School of Electrical Engineering and Computer Science (EECS), Computer Science, Computational Science and Technology (CST).
    Nava, V
    Krishnasamy, Ezhilmathi
    KTH.
    Hoffman, Johan
    KTH, School of Engineering Sciences (SCI), Mathematics (Dept.), Numerical Analysis, NA.
    Simulation of floating platforms for marine energy generation2018In: 10th International Conference on Computational Fluid Dynamics, ICCFD 2018, International Conference on Computational Fluid Dynamics 2018 , 2018Conference paper (Refereed)
    Abstract [en]

    The goal of this work is to study the dynamics of floating platforms that are designed for marine energy generation. This work is done in collaboration with Tecnalia R&I, a company settled in the Basque Country which designs this kind of platforms. To our purpose we present a method for the simulation of two-phase flow with the presence of floating bodies. We consider the variable density incompressible Navier-Stokes equations and discretize them by the finite element method with a variational multiscale stabilization. A level-set type method is adopted to model the interphase between the two fluids. The mixing or smearing in the interphase is prevented with a compression technique. Turbulence is implicitly modeled by the numerical stabilization. The floating device simulation is done by a rigid body motion scheme where a deforming mesh approach is used. The mesh deforms elastically following the movement of the body. Simulation of a decay test on a cube is performed and the results are presented in this paper. All the simulations are done with the open source finite elements parallel software FEniCS-HPC. 

  • 43.
    Nguyen, Van Dang
    et al.
    KTH, School of Electrical Engineering and Computer Science (EECS), Computer Science, Computational Science and Technology (CST).
    Jansson, Johan
    KTH, School of Electrical Engineering and Computer Science (EECS), Computer Science, Computational Science and Technology (CST).
    Frachon, Thomas
    KTH, School of Engineering Sciences (SCI), Mathematics (Dept.), Numerical Analysis, NA.
    Degirmenci, Cem
    Hoffman, Johan
    KTH, School of Electrical Engineering and Computer Science (EECS), Computer Science, Computational Science and Technology (CST).
    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. 

  • 44.
    Nguyen, Van Dang
    et al.
    KTH, School of Electrical Engineering and Computer Science (EECS), Computer Science, Computational Science and Technology (CST).
    Jansson, Johan
    KTH, School of Electrical Engineering and Computer Science (EECS), Computer Science, Computational Science and Technology (CST).
    Goude, Anders
    Uppsala University, Uppsala, Sweden.
    Hoffman, Johan
    KTH, School of Electrical Engineering and Computer Science (EECS), Computer Science, Computational Science and Technology (CST).
    Direct Finite Element Simulation of the Turbulent Flow Past a Vertical Axis Wind Turbine2019In: Renewable energy, ISSN 0960-1481, E-ISSN 1879-0682, Vol. 135, p. 238-247Article in journal (Refereed)
    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.

  • 45.
    Nguyen, Van Dang
    et al.
    KTH, School of Electrical Engineering and Computer Science (EECS), Computer Science, Computational Science and Technology (CST).
    Jansson, Johan
    KTH, School of Electrical Engineering and Computer Science (EECS), Computer Science, Computational Science and Technology (CST).
    Goude, Anders
    Hoffman, Johan
    KTH, School of Electrical Engineering and Computer Science (EECS), Computer Science, Computational Science and Technology (CST).
    Technical Report -- Comparison of Direct Finite Element Simulation with Actuator Line Models and Vortex Models for Simulation of Turbulent Flow Past a Vertical Axis wind Turbine2019Report (Other (popular science, discussion, etc.))
    Abstract [en]

    We compare three different methodologies for simulation of turbulent flow past a vertical axis wind turbine: (i) full resolution of the turbine blades in a Direct Finite Element Simulation (DFS), (ii) implicit representation of the turbine blades in a 3D Actuator Line Method (ALM), and (iii) implicit representation of the turbine blades as sources in a Vortex Model (VM). The integrated normal force on one blade is computed for a range of azimuthal angles, and is compared to experimental data for the different tip speed ratios, 2.55, 3.44 and 4.09.

  • 46.
    Nguyen, Van Dang
    et al.
    KTH, School of Electrical Engineering and Computer Science (EECS), Computer Science, Computational Science and Technology (CST).
    Jansson, Johan
    KTH, School of Electrical Engineering and Computer Science (EECS), Computer Science, Computational Science and Technology (CST).
    Hoffman, Johan
    KTH, School of Electrical Engineering and Computer Science (EECS), Computer Science, Computational Science and Technology (CST).
    Li, Jing-Rebecca
    INRIA Saclay-Equipe DEFI, CMAP, Ecole Polytechnique Route de Saclay, 91128, Palaiseau Cedex, France.
    A partition of unity finite element method for computational diffusion MRI2018In: Journal of Computational Physics, ISSN 0021-9991, E-ISSN 1090-2716, Vol. 375, p. 271-290Article in journal (Refereed)
    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.

  • 47.
    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.
  • 48.
    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. 950-959Conference paper (Other academic)
    Download full text (pdf)
    fulltext
  • 49.
    Nguyen, Van Dang
    et al.
    KTH, School of Electrical Engineering and Computer Science (EECS), Computer Science, Computational Science and Technology (CST).
    Jansson, Johan
    KTH, School of Electrical Engineering and Computer Science (EECS), Computer Science, Computational Science and Technology (CST).
    Tran, Hoang Trong An
    CMAP, Polytechnique, France.
    Hoffman, Johan
    KTH, School of Electrical Engineering and Computer Science (EECS), Computer Science, Computational Science and Technology (CST).
    Li, Jing-Rebecca
    CMAP, Ecole Polytechnique, France.
    Diffusion MRI simulation in thin-layer and thin-tube media using a discretization on manifolds2019In: Journal of magnetic resonance, ISSN 1090-7807, E-ISSN 1096-0856, Vol. 299, p. 176-187Article in journal (Refereed)
    Abstract [en]

    The Bloch-Torrey partial differential equation can be used to describe the evolution of the transverse magnetization of the imaged sample under the influence of diffusion-encoding magnetic field gradients inside the MRI scanner. The integral of the magnetization inside a voxel gives the simulated diffusion MRI signal. This paper proposes a finite element discretization on manifolds in order to efficiently simulate the diffusion MRI signal in domains that have a thin layer or a thin tube geometrical structure. The variable thickness of the three-dimensional domains is included in the weak formulation established on the manifolds. We conducted a numerical study of the proposed approach by simulating the diffusion MRI signals from the extracellular space (a thin layer medium) and from neurons (a thin tube medium), comparing the results with the reference signals obtained using a standard three-dimensional finite element discretization. We show good agreements between the simulated signals using our proposed method and the reference signals for a wide range of diffusion MRI parameters. The approximation becomes better as the diffusion time increases. The method helps to significantly reduce the required simulation time, computational memory, and difficulties associated with mesh generation, thus opening the possibilities to simulating complicated structures at low cost for a better understanding of diffusion MRI in the brain.

  • 50.
    Nguyen, Van Dang
    et al.
    KTH, School of Electrical Engineering and Computer Science (EECS), Computer Science, Computational Science and Technology (CST).
    Leoni, Massimiliano
    KTH, School of Electrical Engineering and Computer Science (EECS), Computer Science, Computational Science and Technology (CST).
    Dancheva, Tamara
    KTH, School of Electrical Engineering and Computer Science (EECS), Computer Science, Computational Science and Technology (CST).
    Jansson, Johan
    KTH, School of Electrical Engineering and Computer Science (EECS), Computer Science, Computational Science and Technology (CST).
    Hoffman, Johan
    KTH, School of Electrical Engineering and Computer Science (EECS), Computer Science, Computational Science and Technology (CST).
    Wassermann, Demian
    Li, Jing-Rebecca
    Portable simulation framework for diffusion MRI2019In: Journal of magnetic resonance, ISSN 1090-7807, E-ISSN 1096-0856, Vol. 309, article id 106611Article in journal (Refereed)
    Abstract [en]

    The numerical simulation of the diffusion MRI signal arising from complex tissue micro-structures is helpful for understanding and interpreting imaging data as well as for designing and optimizing MRI sequences. The discretization of the Bloch-Torrey equation by finite elements is a more recently developed approach for this purpose, in contrast to random walk simulations, which has a longer history. While finite elements discretization is more difficult to implement than random walk simulations, the approach benefits from a long history of theoretical and numerical developments by the mathematical and engineering communities. In particular, software packages for the automated solutions of partial differential equations using finite elements discretization, such as FEniCS, are undergoing active support and development. However, because diffusion MRI simulation is a relatively new application area, there is still a gap between the simulation needs of the MRI community and the available tools provided by finite elements software packages. In this paper, we address two potential difficulties in using FEniCS for diffusion MRI simulation. First, we simplified software installation by the use of FEniCS containers that are completely portable across multiple platforms. Second, we provide a portable simulation framework based on Python and whose code is open source. This simulation framework can be seamlessly integrated with cloud computing resources such as Google Colaboratory notebooks working on a web browser or with Google Cloud Platform with MPI parallelization. We show examples illustrating the accuracy, the computational times, and parallel computing capabilities. The framework contributes to reproducible science and open-source software in computational diffusion MRI with the hope that it will help to speed up method developments and stimulate research collaborations.

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