| 1. |
- Ahlberg, Erik, et al.
(author)
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"Vi klimatforskare stödjer Greta och skolungdomarna"
- 2019
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In: Dagens nyheter (DN debatt). - 1101-2447.
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Journal article (pop. science, debate, etc.)abstract
- DN DEBATT 15/3. Sedan industrialiseringens början har vi använt omkring fyra femtedelar av den mängd fossilt kol som får förbrännas för att vi ska klara Parisavtalet. Vi har bara en femtedel kvar och det är bråttom att kraftigt reducera utsläppen. Det har Greta Thunberg och de strejkande ungdomarna förstått. Därför stödjer vi deras krav, skriver 270 klimatforskare.
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| 2. |
- Hoffman, Johan, 1974-, et al.
(author)
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Computability and Adaptivity in CFD
- 2018
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In: Encyclopedia of Computational Mechanics. - : John Wiley & Sons.
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Book chapter (peer-reviewed)
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| 3. |
- Hoffman, Johan, et al.
(author)
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Computation of slat noise sources using adaptive FEM and lighthill's analogy
- 2013
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In: 19th AIAA/CEAS Aeroacoustics Conference.
-
Conference paper (peer-reviewed)abstract
- 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.
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| 4. |
- Hoffman, Johan, et al.
(author)
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FEniCS-HPC : Automated predictive high-performance finite element computing with applications in aerodynamics
- 2016
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In: Proceedings of the 11th International Conference on Parallel Processing and Applied Mathematics, PPAM 2015. - Cham : Springer-Verlag New York. ; , s. 356-365
-
Conference paper (peer-reviewed)abstract
- 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.
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| 5. |
- Hoffman, Johan, et al.
(author)
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FEniCS-HPC: Coupled Multiphysics in Computational Fluid Dynamics
- 2017
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In: High-Performance Scientific Computing. - Cham : Springer. - 9783319538617 - 9783319538624 ; , s. 58-69
-
Conference paper (peer-reviewed)abstract
- 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.
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| 6. |
- Hoffman, Johan, et al.
(author)
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Time-resolved adaptive FEM simulation of the DLR-F11 aircraft model at high Reynolds number
- 2014
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In: 52nd AIAA Aerospace Sciences Meeting - AIAA Science and Technology Forum and Exposition, SciTech 2014. - Reston, Virginia : American Institute of Aeronautics and Astronautics.
-
Conference paper (other academic/artistic)abstract
- We present a time-resolved, adaptive finite element method for aerodynamics, together with the results from the HiLiftPW-2 workshop, where this method is used to compute the flow past a DLR-F11 aircraft model at realistic Reynolds number. The mesh is automatically constructed by the method as part of the computation, and no explicit turbulence model is needed. The effect of unresolved turbulent boundary layers is modeled by a simple parametrization of the wall shear stress in terms of the skin friction. In the extreme 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 that needs tuning. Thus, the simulation methodology by- passes the main challenges posed by high Reynolds number CFD: the design of an optimal computational mesh, turbulence (or subgrid) modeling, and the cost of boundary layer res- olution. The results from HiLiftPW-2 presented in this report show good agreement with experimental data for a range of different angles of attack, while using orders of magnitude fewer degrees of freedom than what is needed in state of the art methods such as RANS.
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| 7. |
- Hoffman, Johan, et al.
(author)
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Towards a parameter-free method for high Reynolds number turbulent flow simulation based on adaptive finite element approximation
- 2015
-
In: Computer Methods in Applied Mechanics and Engineering. - : Elsevier. - 0045-7825 .- 1879-2138. ; 288, s. 60-74
-
Journal article (peer-reviewed)abstract
- 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.
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| 8. |
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| 9. |
- Hoffman, Johan, 1974-, et al.
(author)
-
Turbulent flow and Fluid–structure interaction
- 2012
-
In: Lecture Notes in Computational Science and Engineering. - : Springer Science and Business Media Deutschland GmbH. ; , s. 543-552
-
Book chapter (peer-reviewed)abstract
- 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.
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| 10. |
- Hoffman, Johan, et al.
(author)
-
Unicorn : Parallel adaptive finite element simulation of turbulent flow and fluid-structure interaction for deforming domains and complex geometry
- 2011
-
Reports (other academic/artistic)abstract
- 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
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| 11. |
- Hoffman, Johan, et al.
(author)
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Unicorn : Parallel adaptive finite element simulation of turbulent flow and fluid-structure interaction for deforming domains and complex geometry
- 2013
-
In: Computers & Fluids. - : Elsevier BV. - 0045-7930 .- 1879-0747. ; 80:SI, s. 310-319
-
Journal article (peer-reviewed)abstract
- 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.
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| 12. |
- Hoffman, Johan, 1974-, et al.
(author)
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Unicorn : A unified continuum mechanics solver
- 2012
-
In: Lecture Notes in Computational Science and Engineering. - : Springer Science and Business Media Deutschland GmbH. ; , s. 339-361
-
Book chapter (peer-reviewed)abstract
- 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.
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| 13. |
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| 14. |
- Jansson, Anton, 1983, et al.
(author)
-
Humaniora i välfärdssamhället : En inledning
- 2023
-
In: Humaniora i välfärdssamhället : Kunskapshistorier om efterkrigstiden - Kunskapshistorier om efterkrigstiden. - Göteborg : Makadam. - 2002-2131. - 9789170614019 - 9789170619014 ; 49, s. 9-29
-
Book chapter (peer-reviewed)
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| 15. |
- Jansson, Johan, 1978-, et al.
(author)
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Simulation of 3D unsteady incompressible flow past a NACA 0012 wing section
- 2012
-
Reports (other academic/artistic)abstract
- 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.
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| 16. |
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| 17. |
- Jansson, Johan, 1978-, et al.
(author)
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Time-resolved Adaptive Direct FEM Simulation of High-lift Aircraft Configurations : Chapter in "Numerical Simulation of the Aerodynamics of High-Lift Configurations'", Springer
- 2018
-
In: Numerical Simulation of the Aerodynamics of High-Lift Configurations. - Cham : Springer. - 9783319621364 - 9783319621357 ; , s. 67-92
-
Book chapter (peer-reviewed)abstract
- 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.
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| 18. |
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| 19. |
- Jansson, Niclas, et al.
(author)
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Framework For Massively Parallel Adaptive Finite Element Computational Fluid Dynamics On Tetrahedral Meshes
- 2012
-
In: SIAM Journal on Scientific Computing. - : Society for Industrial & Applied Mathematics (SIAM). - 1064-8275 .- 1095-7197. ; 34:1, s. C24-C42
-
Journal article (peer-reviewed)abstract
- 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.
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| 20. |
- Jansson, Niclas, 1983-
(author)
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High Performance Adaptive Finite Element Methods : With Applications in Aerodynamics
- 2013
-
Doctoral thesis (other academic/artistic)abstract
- The massive computational cost for resolving all scales in a turbulent flow makes a direct numerical simulation of the underlying Navier-Stokes equations impossible in most engineering applications. Recent advances in adaptive finite element methods offer a new powerful tool in Computational Fluid Dynamics (CFD). The computational cost for simulating turbulent flow can be minimized by adaptively resolution of the mesh, based on a posteriori error estimation. Such adaptive methods have previously been implemented for efficient serial computations, but the extension to an efficient parallel solver is a challenging task. This work concerns the development of an adaptive finite element method that enables efficient computation of time resolved approximations of turbulent flow for complex geometries with a posteriori error control. We present efficient data structures and data decomposition methods for distributed unstructured tetrahedral meshes. Our work also concerns an efficient parallelization of local mesh refinement methods such as recursive longest edge bisection, and the development of an a priori predictive dynamic load balancing method, based on a weighted dual graph. We also address the challenges of emerging supercomputer architectures with the development of new hybrid parallel programming models, combining traditional message passing with lightweight one-sided communication. Our implementation has proven to be both general and efficient, scaling up to more than twelve thousands cores.
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| 21. |
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| 22. |
- Spühler, Jeannette H., et al.
(author)
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3D Fluid-Structure Interaction Simulation of Aortic Valves Using a Unified Continuum ALE FEM Model
- 2018
-
In: Frontiers in Physiology. - : Frontiers Media S.A.. - 1664-042X. ; 9
-
Journal article (peer-reviewed)abstract
- Due to advances in medical imaging, computational fluid dynamics algorithms and high performance computing, computer simulation is developing into an important tool for understanding the relationship between cardiovascular diseases and intraventricular blood flow. The field of cardiac flow simulation is challenging and highly interdisciplinary. We apply a computational framework for automated solutions of partial differential equations using Finite Element Methods where any mathematical description directly can be translated to code. This allows us to develop a cardiac model where specific properties of the heart such as fluid-structure interaction of the aortic valve can be added in a modular way without extensive efforts. In previous work, we simulated the blood flow in the left ventricle of the heart. In this paper, we extend this model by placing prototypes of both a native and a mechanical aortic valve in the outflow region of the left ventricle. Numerical simulation of the blood flow in the vicinity of the valve offers the possibility to improve the treatment of aortic valve diseases as aortic stenosis (narrowing of the valve opening) or regurgitation (leaking) and to optimize the design of prosthetic heart valves in a controlled and specific way. The fluid-structure interaction and contact problem are formulated in a unified continuum model using the conservation laws for mass and momentum and a phase function. The discretization is based on an Arbitrary Lagrangian-Eulerian space-time finite element method with streamline diffusion stabilization, and it is implemented in the open source software Unicorn which shows near optimal scaling up to thousands of cores. Computational results are presented to demonstrate the capability of our framework.
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| 23. |
- Spühler, Jeannette Hiromi, 1981-, et al.
(author)
-
A finite element framework for high performance computer simulation of blood flow in the left ventricle of the human heart
- 2015
-
Reports (other academic/artistic)abstract
- 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.
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| 24. |
- Spühler, Jeannette Hiromi, 1981-, et al.
(author)
-
A High Performance Computing Framework for Finite Element Simulation of Blood Flow in the Left Ventricle of the Human Heart
- 2020
-
In: Lecture Notes in Computational Science and Engineering. - Cham : Springer. ; , s. 155-164
-
Conference paper (peer-reviewed)abstract
- We present a high performance computing framework for finite element simulation of blood flow in the left ventricle of the human heart. The mathematical model is described together with the discretization method and the parallel implementation in Unicorn which is part of the open source software framework FEniCS-HPC. We show results based on patient-specific data that 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 other 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.
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| 25. |
- Attauabi, Mohamed, et al.
(author)
-
Influence of Genetics, Immunity and the Microbiome on the Prognosis of Inflammatory Bowel Disease (IBD Prognosis Study) : the protocol for a Copenhagen IBD Inception Cohort Study
- 2022
-
In: BMJ Open. - : BMJ Publishing Group Ltd. - 2044-6055. ; 12:6, s. e055779-e055779
-
Journal article (peer-reviewed)abstract
- Introduction: Inflammatory bowel diseases (IBD), encompassing Crohn's disease and ulcerative colitis, are chronic, inflammatory diseases of the gastrointestinal tract. We have initiated a Danish population-based inception cohort study aiming to investigate the underlying mechanisms for the heterogeneous course of IBD, including need for, and response to, treatment.Methods and analysis: IBD Prognosis Study is a prospective, population-based inception cohort study of unselected, newly diagnosed adult, adolescent and paediatric patients with IBD within the uptake area of Hvidovre University Hospital and Herlev University Hospital, Denmark, which covers approximately 1 050 000 inhabitants (~20% of the Danish population). The diagnosis of IBD will be according to the Porto diagnostic criteria in paediatric and adolescent patients or the Copenhagen diagnostic criteria in adult patients. All patients will be followed prospectively with regular clinical examinations including ileocolonoscopies, MRI of the small intestine, validated patient-reported measures and objective examinations with intestinal ultrasound. In addition, intestinal biopsies from ileocolonoscopies, stool, rectal swabs, saliva samples, swabs of the oral cavity and blood samples will be collected systematically for the analysis of biomarkers, microbiome and genetic profiles. Environmental factors and quality of life will be assessed using questionnaires and, when available, automatic registration of purchase data. The occurrence and course of extraintestinal manifestations will be evaluated by rheumatologists, dermatologists and dentists, and assessed by MR cholangiopancreatography, MR of the spine and sacroiliac joints, ultrasonography of peripheral joints and entheses, clinical oral examination, as well as panoramic radiograph of the jaws. Fibroscans and dual-energy X-ray absorptiometry scans will be performed to monitor occurrence and course of chronic liver diseases, osteopenia and osteoporosis.Ethics and dissemination: This study has been approved by Ethics Committee of the Capital Region of Denmark (approval number: H-20065831). Study results will be disseminated through publication in international scientific journals and presentation at (inter)national conferences.
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| 26. |
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| 27. |
- Clemente, Francesco, et al.
(author)
-
Touch and Hearing Mediate Osseoperception
- 2017
-
In: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 7
-
Journal article (peer-reviewed)abstract
- Osseoperception is the sensation arising from the mechanical stimulation of a bone-anchored prosthesis. Here we show that not only touch, but also hearing is involved in this phenomenon. Using mechanical vibrations ranging from 0.1 to 6 kHz, we performed four psychophysical measures (perception threshold, sensation discrimination, frequency discrimination and reaction time) on 12 upper and lower limb amputees and found that subjects: consistently reported perceiving a sound when the stimulus was delivered at frequencies equal to or above 400 Hz; were able to discriminate frequency differences between stimuli delivered at high stimulation frequencies (similar to 1500 Hz); improved their reaction time for bimodal stimuli (i.e. when both vibration and sound were perceived). Our results demonstrate that osseoperception is a multisensory perception, which can explain the improved environment perception of bone-anchored prosthesis users. This phenomenon might be exploited in novel prosthetic devices to enhance their control, thus ultimately improving the amputees' quality of life.
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| 28. |
- Compere, Gaetan, et al.
(author)
-
A mesh adaptation framework for dealing with large deforming meshes
- 2010
-
In: International Journal for Numerical Methods in Engineering. - : Wiley. - 0029-5981 .- 1097-0207. ; 82:7, s. 843-867
-
Journal article (peer-reviewed)abstract
- 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.
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| 29. |
- Degirmenci, Niyazi Cem, et al.
(author)
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A Unified Numerical Simulation of Vowel Production That Comprises Phonation and the Emitted Sound
- 2017
-
In: Proceedings of the Annual Conference of the International Speech Communication Association, INTERSPEECH 2017. - : The International Speech Communication Association (ISCA). ; , s. 3492-3496
-
Conference paper (peer-reviewed)abstract
- A unified approach for the numerical simulation of vowels is presented, which accounts for the self-oscillations of the vocal folds including contact, the generation of acoustic waves and their propagation through the vocal tract, and the sound emission outwards the mouth. A monolithic incompressible fluid-structure interaction model is used to simulate the interaction between the glottal jet and the vocal folds, whereas the contact model is addressed by means of a level set application of the Eikonal equation. The coupling with acoustics is done through an acoustic analogy stemming from a simplification of the acoustic perturbation equations. This coupling is one-way in the sense that there is no feedback from the acoustics to the flow and mechanical fields. All the involved equations are solved together at each time step and in a single computational run, using the finite element method (FEM). As an application, the production of vowel [i] has been addressed. Despite the complexity of all physical phenomena to be simulated simultaneously, which requires resorting to massively parallel computing, the formant locations of vowel [i] have been well recovered.
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| 30. |
- Degirmenci, Niyazi Cem, 1982-
(author)
-
Adaptive Finite Element Methods for Fluid Structure Interaction Problems with Applications to Human Phonation
- 2018
-
Doctoral thesis (other academic/artistic)abstract
- This work presents a unified framework for numerical solution of Fluid Structure Interaction (FSI) and acoustics problems with focus on human phonation. The Finite Element Method is employed for numerical investigation of partial differential equations that model conservation of momentum and mass. Since the resulting system of equations is very large, an efficient open source high performance implementation is constructed and provided. In order to gain accuracy for the numerical solutions, an adaptive mesh refinement strategy is employed which reduces the computational cost in comparison to a uniform refinement. Adaptive refinement of the mesh relies on computable error indicators which appear as a combination of a computable residual and the solution of a so-called dual problem acting as weights on computed residuals. The first main achievement of this thesis is to apply this strategy to numerical simulations of a benchmark problem for FSI. This FSI model is further extended for contact handling and applied to a realistic vocal folds geometry where the glottic wave formation was captured in the numerical simulations. This is the second achievement in the presented work. The FSI model is further coupled to an acoustics model through an acoustic analogy, for vocal folds with flow induced oscillations for a domain constructed to create the vowel /i/. The comparisons of the obtained pressure signal at specified points with respect to results from literature for the same vowel is reported, which is the final main result presented.
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| 31. |
- Flyborg, Johan
(author)
-
The use of the intelligent powered toothbrush in health technology
- 2022
-
Licentiate thesis (other academic/artistic)abstract
- BackgroundApplied health technology is a research field that ties together several disciplines to improve and preserve the health and quality of life of individuals and society. Helping especially elderly to meet the above goals is an important and necessary task and assistive technology and collection of health data are part of this work.AimsPaper I aims to investigate whether the use of a powered toothbrush could maintain oral health in a group of individuals with MCI and if changes in oral health affect various aspects of quality of life. Paper II and III aims to examine the capacity of a powered toothbrush as a carrier and mediator of health-related data.MethodsFor papers I and II, the participants were recruited from the Swedish site of the multicenter project Support Monitoring And Reminder Technology for Mild Dementia and for paper III from the Department of Health at Blekinge Institute of Technology. In all three papers, a powered toothbrush has been used as a tool, sensor carrier and transmitter of data. For Quality-of-life assessment two instruments are used, The QoL-AD and OHIP 14.ResultsBy introducing an intelligent powered toothbrush in the group of older individuals with mild cognitive impairment we have showed that they, regardless of cognitive level,improved their scores for plaque index, bleeding index and deepened periodontal pockets ≥ 4mm, over 12 months. The quality-of-life instrument related to oral health improved in parallel with the improvement in oral health. Furthermore, it is possible to use the intelligent powered toothbrush both as a carrier for healt related sensors and to transfer user data via Bluetooth technology to a single-core processor that stores or forwards the data via Wifi to an external computer for processing, analysis and storage. A fesibility study regarding temperature sensor for measuring body temperature during toothbrushing have been evaluated and found to be comparable to traditional oral temperature measurement. ConclusionsAn intelligent powered toothbrush is a well-functioning tool for maintaining oral health in older people with mild cognitive impairment as well as for collecting and transferring brush and health data to external units for storage and analysis.
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| 32. |
- Hoffman, Johan, et al.
(author)
-
A General Galerkin Finite Element Method for the Compressible Euler Equations
- 2008
-
In: SIAM Journal on Scientific Computing. - 1064-8275 .- 1095-7197.
-
Journal article (peer-reviewed)abstract
- In this paper we present a General Galerkin (G2) method for the compressible Euler equations, including turbulent ow. The G2 method presented in this paper is a nite element method with linear approximation in space and time, with componentwise stabilization in the form of streamline diusion and shock-capturing modi cations. The method conserves mass, momentum and energy, and we prove an a posteriori version of the 2nd Law of thermodynamics for the method. We illustrate the method for a laminar shock tube problem for which there exists an exact analytical solution, and also for a turbulent flow problem
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| 33. |
- Hoffman, Johan, et al.
(author)
-
Adaptive modeling of turbulent flow with residual based turbulent kinetic energy dissipation
- 2011
-
In: Computer Methods in Applied Mechanics and Engineering. - : Elsevier BV. - 0045-7825 .- 1879-2138. ; 200:37-40, s. 2758-2767
-
Journal article (peer-reviewed)abstract
- 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.
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| 34. |
- Hoffman, Johan, et al.
(author)
-
New Theory of Flight
- 2016
-
In: Journal of Mathematical Fluid Mechanics. - : Springer. - 1422-6928 .- 1422-6952. ; 18:2, s. 219-241
-
Journal article (peer-reviewed)abstract
- 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
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| 35. |
- Hoffman, Johan, et al.
(author)
-
Unified Continuum modeling of fluid-structure interaction
- 2011
-
In: Mathematical Models and Methods in Applied Sciences. - : World Scientific. - 0218-2025. ; 21:3, s. 491-513
-
Journal article (peer-reviewed)abstract
- 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.
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| 36. |
- Isaksson-Daun, Johan, et al.
(author)
-
Using Portable Virtual Reality to Assess Mobility of Blind and Low-Vision Individuals With the Audomni Sensory Supplementation Feedback
- 2024
-
In: IEEE Access. - 2169-3536. ; 12
-
Journal article (peer-reviewed)abstract
- Numerous electronic travel aids (ETAs) to increase the mobility of blind or low-vision (BLV) individuals have been proposed. However, the lack of established and well-motivated methods, and of recruiting enough BLV test participants, keeps a successful aid illusory. To combat this, a new aid-agnostic questionnaire focused on mobility, the Desire of Use Questionnaire for Mobility of BLV individuals (DoUQ-MoB) and a new portable, large-scale-exploration virtual reality (VR) system, the Parrot-VR, were employed to evaluate the ETA Audomni. Through VR and Audomni, 19 heterogenous BLV participants traversed large-scale urban environments. Their experiences were probed through the DoUQ-MoB, and their movement analyzed. Numerous results are presented, a highlight being that most participants, 76 %, responded that it was very or extremely likely that they would want to use Audomni along with their current aid. Further, Parrot-VR assists in recruiting a satisfying number of diverse BLV participants; and DoUQ-MoB allows to systematically probe their opinions of an aid, and how it relates to others aids, in a considerable quantity of mobility aid aspects. This work illuminates some shortcomings of Audomni, but also shows a majority of BLV participants actually wanting to use a proposed ETA — a result rarely seen so distinctly in the field, and which encourages the continuing efforts of the project. The results are supported by a novel test procedure, which might serve as future inspiration to the field.
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| 37. |
- Isaksson, Johan, et al.
(author)
-
Audomni : Super-Scale Sensory Supplementation to Increase the Mobility of Blind and Low-Vision Individuals - A Pilot Study
- 2020
-
In: IEEE Transactions on Neural Systems and Rehabilitation Engineering. - 1534-4320. ; 28:5, s. 1187-1197
-
Journal article (peer-reviewed)abstract
- Objective: Blindness and low vision have severe effects on individuals' quality of life and socioeconomic cost; a main contributor of which is a prevalent and acutely decreased mobility level. To alleviate this, numerous technological solutions have been proposed in the last 70 years; however, none has become widespread. Method: In this paper, we introduce the vision-to-audio, super-scale sensory substitution/supplementation device Audomni; we address the field-encompassing issues of ill-motivated and overabundant test methodologies and metrics; and we utilize our proposed Desire of Use model to evaluate proposed pilot user tests, their results, and Audomni itself. Results: Audomni holds a spatial resolution of 80 x 60 pixels at 1.2° angular resolution and close to real-time temporal resolution, outdoor-viable technology, and several novel differentiation methods. The tests indicated that Audomni has a low learning curve, and several key mobility subtasks were accomplished; however, the tests would benefit from higher real-life motivation and data collection affordability. Conclusion: Audomni shows promise to be a viable mobility device - with some addressable issues. Employing Desire of Use to design future tests should provide both high real-life motivation and relevance to them. Significance: As far as we know, Audomni features the greatest information conveyance rate in the field, yet seems to offer comprehensible and fairly intuitive sonification; this work is also the first to utilize Desire of Use as a tool to evaluate user tests, a device, and to lay out an overarching project aim.
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| 38. |
- Isaksson, Johan, et al.
(author)
-
Desire of Use : A Hierarchical Decomposition of Activities and its Application on Mobility of by Blind and Low-Vision Individuals
- 2020
-
In: IEEE Transactions on Neural Systems and Rehabilitation Engineering. - 1534-4320. ; 28:5, s. 1146-1156
-
Journal article (peer-reviewed)abstract
- Objective: Blind and low-vision individuals often have severely reduced mobility, affecting their quality of life and associated socioeconomic cost. Despite numerous efforts and great technological progress, the only used primary mobility aids are still white canes and seeing-eye dogs. Furthermore, there is a permeating tendency in the field to ignore knowledge of both mobility and the target group, as well as constantly design new metrics and tests that makes comparisons between solutions markedly more difficult. Method: The Desire of Use model is introduced in an effort to promote a more holistic approach; it should be generalizable for any activity by any user, but is here applied on mobility of blind and low-vision individuals by a proposal and integration of parameters. Results: An embodiment of the model is presented and with it we show why popular mobility metrics of today are insufficient to guide design; what tasks and metrics that should provide better understanding; as well as which fundamental properties determine them and are critical to discuss. Conclusion: Desire of Use has been introduced as a tool and a theoretical framework, and a realization has been proposed. Significance: Desire of Use offers both a structured perspective of pertinent design challenges facing a given solution, as well as a platform from which to compare test results and properties of existing solutions; in for example the field of electronic travel aids it should prove valuable for designing and evaluating new tests and devices.
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| 39. |
- Jansson, Johan, 1978-, et al.
(author)
-
Adaptive error control in finite element methods using the error representation as error indicator
- 2013
-
Reports (other academic/artistic)abstract
- 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.
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| 40. |
- Jansson, Johan, et al.
(author)
-
Adaptive simulation of unsteady flow past the submerged part of a floating wind turbine platform
- 2015
-
In: MARINE 2015 - Computational Methods in Marine Engineering VI. - : International Center for Numerical Methods in Engineering (CIMNE). - 9788494392863 ; , s. 35-46
-
Conference paper (peer-reviewed)abstract
- 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.
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| 41. |
- Jansson, Johan, et al.
(author)
-
Adaptive stabilized finite element framework for simulation of vocal fold turbulent fluid-structure interaction
- 2013
-
In: Proceedings of Meetings on Acoustics. - : Acoustical Society of America (ASA). ; , s. 1-9
-
Conference paper (peer-reviewed)abstract
- 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.
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| 42. |
- Jansson, Johan, et al.
(author)
-
Adaptive unified continuum FEM modeling of a 3D FSI benchmark problem
- 2017
-
In: International Journal for Numerical Methods in Biomedical Engineering. - : Wiley-Blackwell. - 2040-7939 .- 2040-7947. ; 33:9
-
Journal article (peer-reviewed)abstract
- In this paper, we address a 3D fluid-structure interaction benchmark problem that represents important characteristics of biomedical modeling. We present a goal-oriented adaptive finite element methodology for incompressible fluid-structure interaction based on a streamline diffusion–type stabilization of the balance equations for mass and momentum for the entire continuum in the domain, which is implemented in the Unicorn/FEniCS software framework. A phase marker function and its corresponding transport equation are introduced to select the constitutive law, where the mesh tracks the discontinuous fluid-structure interface. This results in a unified simulation method for fluids and structures. We present detailed results for the benchmark problem compared with experiments, together with a mesh convergence study.
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| 43. |
- Jansson, Johan, 1978-, et al.
(author)
-
Automated adaptive error control in finite element methods using the error representation as error indicator
- 2014
-
Reports (other academic/artistic)abstract
- 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.
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| 44. |
- Jansson, Johan, 1978-, et al.
(author)
-
Automated error control in finite element methods withapplications in fluid flow
- 2014
-
Reports (other academic/artistic)abstract
- 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.
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| 45. |
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| 46. |
- Jansson, Johan, 1978-, et al.
(author)
-
Direct finite element simulation of turbulent flow for marine based renewable energy
-
Other publication (other academic/artistic)abstract
- 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.
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| 47. |
- Jansson, Johan, et al.
(author)
-
Framework for adaptive fluid-structure interaction with industrial applications
- 2013
-
In: International Journal of Materials Engineering Innovation. - 1757-2754. ; 4:2, s. 166-186
-
Journal article (peer-reviewed)abstract
- 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.
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| 48. |
- Jansson, Johan, 1978-, et al.
(author)
-
Gestural 3D Interaction with a Beating Heart : Simulation Visualization and Interaction
- 2011
-
In: Proceedings of SIGRAD 2011. - : Linköping University Electronic Press. - 9789173930086
-
Conference paper (peer-reviewed)abstract
- 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.
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| 49. |
- Jansson, Jan-Håkan, et al.
(author)
-
Snus (Swedish smokeless tobacco) use and risk of stroke: pooled analyses of incidence and survival
- 2014
-
In: Journal of Internal Medicine. - : Wiley. - 1365-2796 .- 0954-6820. ; 276:1, s. 87-95
-
Journal article (peer-reviewed)abstract
- Background. Snus is a moist smokeless tobacco product with high nicotine content. Its use has a short-term effect on the cardiovascular system, but the relationship between snus use and stroke is unclear. Objective. The aim of this study was to assess the associations between use of snus and incidence of and survival after stroke, both overall and according to subtypes. Methods. Pooled analyses of eight Swedish prospective cohort studies were conducted, including 130 485 men who never smoked. We estimated hazard ratios (HRs) with 95% confidence intervals (CIs) of incidence and death after diagnosis using Cox proportional hazard regression models and case fatality and survival using logistic regression and Kaplan-Meier methods, respectively. Results. No associations were observed between the use of snus and the risk of overall stroke (HR 1.04, 95% CI 0.92-1.17) or of any of the stroke subtypes. The odds ratio (OR) of 28-day case fatality was 1.42 (95% CI 0.99-2.04) amongst users of snus who had experienced a stroke, and the HR of death during the follow-up period was 1.32 (95% CI 1.08-1.61). Conclusion. Use of snus was not associated with the risk of stroke. Hence, nicotine is unlikely to contribute importantly to the pathophysiology of stroke. However, case fatality was increased in snus users, compared with nonusers, but further studies are needed to determine any possible causal mechanisms.
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| 50. |
- Jansson, Robert, et al.
(author)
-
Reduction of fire spalling of concrete with small doses of polypropylene fibers
-
Other publication (other academic/artistic)abstract
- The addition of polypropylene fibers has been shown to reduce the fire spalling propensity of concrete. This has been proven in many fire tests; but, very few large scale tests exist showing the function of polypropylene fibers at low dosages. In this study results on polypropylene fibers included in w/c 0.40 mixes typical used in tunnel construction that is spalling sensitive without fibers shows that an amount of only 0.6 kg/m3 (1.01 lb/yd3) has a significant effect on the spalling propensity and that even lower amounts reduce the spalling although they do not eliminate it entirely. During one of the fire tests on large slabs loaded in compression, unloaded cubes of the same mixes were also included in the furnace. None of the small specimens spalled whereas some of the corresponding large slabs spalled beyond the layer of reinforcement. This showed that the cube test method is not conservative.
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