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

Due to advances in medical imaging, computational fluid dynamics algorithms and high performance computing, computer simulation is developing into an important tool for understanding the relationship between cardiovascular diseases and intraventricular blood flow. The field of cardiac flow simulation is challenging and highly interdisciplinary. We apply a computational framework for automated solutions of partial differential equations using Finite Element Methods where any mathematical description directly can be translated to code. This allows us to develop a cardiac model where specific properties of the heart such as fluid-structure interaction of the aortic valve can be added in a modular way without extensive efforts. In previous work, we simulated the blood flow in the left ventricle of the heart. In this paper, we extend this model by placing prototypes of both a native and a mechanical aortic valve in the outflow region of the left ventricle. Numerical simulation of the blood flow in the vicinity of the valve offers the possibility to improve the treatment of aortic valve diseases as aortic stenosis (narrowing of the valve opening) or regurgitation (leaking) and to optimize the design of prosthetic heart valves in a controlled and specific way. The fluid-structure interaction and contact problem are formulated in a unified continuum model using the conservation laws for mass and momentum and a phase function. The discretization is based on an Arbitrary Lagrangian-Eulerian space-time finite element method with streamline diffusion stabilization, and it is implemented in the open source software Unicorn which shows near optimal scaling up to thousands of cores. Computational results are presented to demonstrate the capability of our framework.

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

QC 20180503

Available from: 2018-05-03 Created: 2018-05-03 Last updated: 2018-05-03Bibliographically approved
Jansson, N., Bale, R., Onishi, K. & Tsubokura, M. (2018). CUBE: A scalable framework for large-scale industrial simulations. The international journal of high performance computing applications
Open this publication in new window or tab >>CUBE: A scalable framework for large-scale industrial simulations
2018 (English)In: The international journal of high performance computing applications, ISSN 1094-3420, E-ISSN 1741-2846Article in journal (Refereed) Published
Place, publisher, year, edition, pages
Sage Publications, 2018
National Category
Fluid Mechanics and Acoustics Computational Mathematics
Identifiers
urn:nbn:se:kth:diva-236495 (URN)10.1177/1094342018816377 (DOI)
Note

QCR 20181030

Available from: 2018-10-18 Created: 2018-10-18 Last updated: 2018-12-13Bibliographically approved
Vilela de Abreu, R., Jansson, N. & Hoffman, J. (2016). Computation of aeroacoustic sources for a Gulfstream G550 nose landing gear model using adaptive FEM. Computers & Fluids, 124, 136-146
Open this publication in new window or tab >>Computation of aeroacoustic sources for a Gulfstream G550 nose landing gear model using adaptive FEM
2016 (English)In: Computers & Fluids, ISSN 0045-7930, E-ISSN 1879-0747, Vol. 124, p. 136-146Article in journal (Refereed) Published
Abstract [en]

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

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

Updated from Manuscript to Article.

QC 20160128

Available from: 2016-01-28 Created: 2016-01-26 Last updated: 2018-01-10Bibliographically approved
Hoffman, J., Jansson, J. & Jansson, N. (2016). FEniCS-HPC: Automated predictive high-performance finite element computing with applications in aerodynamics. In: Proceedings of the 11th International Conference on Parallel Processing and Applied Mathematics, PPAM 2015: . Paper presented at 11th International Conference on Parallel Processing and Applied Mathematics (pp. 356-365). Springer-Verlag New York, 9573
Open this publication in new window or tab >>FEniCS-HPC: Automated predictive high-performance finite element computing with applications in aerodynamics
2016 (English)In: Proceedings of the 11th International Conference on Parallel Processing and Applied Mathematics, PPAM 2015, Springer-Verlag New York, 2016, Vol. 9573, p. 356-365Conference paper, Published paper (Refereed)
Abstract [en]

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

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

QC 20151215

Available from: 2015-06-29 Created: 2015-06-29 Last updated: 2018-01-11Bibliographically approved
Spühler, J. H., Jansson, J., Jansson, N. & Hoffman, J. (2015). A finite element framework for high performance computer simulation of blood flow in the left ventricle of the human heart. KTH Royal Institute of Technology
Open this publication in new window or tab >>A finite element framework for high performance computer simulation of blood flow in the left ventricle of the human heart
2015 (English)Report (Other academic)
Abstract [en]

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

Place, publisher, year, edition, pages
KTH Royal Institute of Technology, 2015. p. 17
Series
CTL Technical Report ; 34
Keywords
Finite element method, Arbitrary Lagrangian-Eulerian method, parallel algorithm, blood flow, left ventricle, patient-specific heart model
National Category
Computational Mathematics
Identifiers
urn:nbn:se:kth:diva-181110 (URN)
Funder
EU, European Research Council, 202984Swedish Research CouncilSwedish Foundation for Strategic Research
Note

QC 20160212

Available from: 2016-01-29 Created: 2016-01-29 Last updated: 2017-10-06Bibliographically approved
Hoffman, J., Jansson, J., Jansson, N. & De Abreu, R. V. (2015). Towards a parameter-free method for high Reynolds number turbulent flow simulation based on adaptive finite element approximation. Computer Methods in Applied Mechanics and Engineering, 288, 60-74
Open this publication in new window or tab >>Towards a parameter-free method for high Reynolds number turbulent flow simulation based on adaptive finite element approximation
2015 (English)In: Computer Methods in Applied Mechanics and Engineering, ISSN 0045-7825, E-ISSN 1879-2138, Vol. 288, p. 60-74Article in journal (Refereed) Published
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. 

Place, publisher, year, edition, pages
Elsevier, 2015
Keywords
finite element method, adaptive mesh refinement, turbulent
National Category
Computational Mathematics
Research subject
Applied and Computational Mathematics
Identifiers
urn:nbn:se:kth:diva-143878 (URN)10.1016/j.cma.2014.12.004 (DOI)000352081900005 ()2-s2.0-84920828659 (Scopus ID)
External cooperation:
Funder
Swedish Foundation for Strategic Research EU, European Research Council, 202984Swedish Research Council, 90032202
Note

QC 20140708

Available from: 2014-04-01 Created: 2014-04-01 Last updated: 2017-12-05Bibliographically approved
Vilela de Abreu, R., Jansson, N. & Hoffman, J. (2014). Adaptive Computation of Aeroacoustic Sources for a Rudimentary Landing Gear. International Journal for Numerical Methods in Fluids, 74(6), 406-421
Open this publication in new window or tab >>Adaptive Computation of Aeroacoustic Sources for a Rudimentary Landing Gear
2014 (English)In: International Journal for Numerical Methods in Fluids, ISSN 0271-2091, E-ISSN 1097-0363, Vol. 74, no 6, p. 406-421Article in journal (Refereed) Published
Abstract [en]

We present our simulation results for the benchmark problem of the flow past a rudimentary landing gear using a General Galerkin FEM, also referred to as adaptive DNS/LES. In General Galerkin, no explicit subgrid model is used; instead, the computational mesh is adaptively refined with respect to an a posteriori error estimate of a quantity of interest in the computation, in this case, the drag force on the rudimentary landing gear. Turbulent boundary layers are modeled using a simple wall-layer model with the shear stress at walls proportional to the skin friction, which here is assumed to be small and, therefore, can be approximated by zero skin friction. We compare our results with experimental data and other state of the art computations, where we find good agreement in sound pressure levels, surface velocities, and flow separation. We also compare with detailed surface pressure experimental data where we find largely good agreement, apart from some local differences for which we discuss possible explanations.

Keywords
aeroacoustics, aerodynamics, finite element, incompressible flow, LES, large Eddy simulations;turbulent flow
National Category
Computational Mathematics
Identifiers
urn:nbn:se:kth:diva-125722 (URN)10.1002/fld.3856 (DOI)000329509500002 ()2-s2.0-84891832461 (Scopus ID)
Funder
Swedish Foundation for Strategic Research EU, European Research CouncilSwedish Research CouncilSwedish Energy Agency
Note

QC 20140131

Available from: 2013-08-13 Created: 2013-08-13 Last updated: 2017-12-06Bibliographically approved
Hoffman, J., Jansson, J., Jansson, N. & Vilela De Abrea, R. (2014). Time-resolved adaptive FEM simulation of the DLR-F11 aircraft model at high Reynolds number. In: 52nd AIAA Aerospace Sciences Meeting - AIAA Science and Technology Forum and Exposition, SciTech 2014: . Paper presented at 52nd AIAA Aerospace Sciences Meeting - AIAA Science and Technology Forum and Exposition, SciTech 2014; National Harbor, MD; United States; 13 January 2014 through 17 January 2014.
Open this publication in new window or tab >>Time-resolved adaptive FEM simulation of the DLR-F11 aircraft model at high Reynolds number
2014 (English)In: 52nd AIAA Aerospace Sciences Meeting - AIAA Science and Technology Forum and Exposition, SciTech 2014, 2014Conference paper, Published paper (Other academic)
Abstract [en]

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. 

National Category
Computational Mathematics
Identifiers
urn:nbn:se:kth:diva-139947 (URN)2-s2.0-84938348951 (Scopus ID)978-162410256-1 (ISBN)
Conference
52nd AIAA Aerospace Sciences Meeting - AIAA Science and Technology Forum and Exposition, SciTech 2014; National Harbor, MD; United States; 13 January 2014 through 17 January 2014
Note

QC 20140708

Available from: 2014-01-15 Created: 2014-01-15 Last updated: 2016-03-07Bibliographically approved
Jansson, N. (2013). High Performance Adaptive Finite Element Methods: With Applications in Aerodynamics. (Doctoral dissertation). Stockholm: KTH Royal Institute of Technology
Open this publication in new window or tab >>High Performance Adaptive Finite Element Methods: With Applications in Aerodynamics
2013 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

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.

Abstract [sv]

Den höga beräkningskostnaden för att lösa upp alla turbulenta skalor för ett realistiskt problem gör en direkt numerisk simulering av Navier-Stokes ekvationer omöjlig. De senaste framstegen inom adaptiva finita element metoder ger ett nytt kraftfullt verktyg inom Computational Fluid Dynamics (CFD). Beräkningskostnaden för en simulering av turbulent flöde kan minimeras genom att beräkningsnätet adaptivt förfinas baserat på en a posteriori feluppskattning. Dessa adaptiva metoder har tidigare implementerats för seriella beräkningar, medan en effektiv parallellisering av metoden inte är trivial. I denna avhandling presenterar vi vår utveckling av en adaptiv finita element lösare, anpassad för att effektivt beräkna tidsupplösta approximationer i komplicerade geometrier med a posteriori felkontroll. Effektiva datastrukturer och metoder för ostrukturerade beräkningsnät av tetrahedrar presenteras. Avhandlingen behandlar även effektiv parallellisering av lokala nätförfiningsmetoder, exempelvis recursive longest edge bisection. Även lastbalanseringsproblematiken behandlas, där problemet lösts genom utvecklandet av en prediktiv dynamisk lastbalanseringsmetod, baserad på en viktad dualgraf av beräkningsnätet. Slutligen avhandlas även problematiken med att effektivt utnyttja nytillkomna superdatorarkitekturer, genom utvecklandet av en hybrid parallelliserings modell som kombinerar traditionell meddelande baserad parallellisering med envägskommunikation. Detta har resulterat i en generell samt effektiv implementation med god skalning upp till fler än tolv tusen processorkärnor.

Place, publisher, year, edition, pages
Stockholm: KTH Royal Institute of Technology, 2013. p. xii, 50
Series
TRITA-CSC-A, ISSN 1653-5723 ; 2013:07
National Category
Computational Mathematics
Identifiers
urn:nbn:se:kth:diva-125742 (URN)978-91-7501-814-0 (ISBN)
Public defence
2013-09-11, F3, Lindstedtsvägen 26, KTH, Stockholm, 10:15 (English)
Opponent
Supervisors
Note

QC 20130816

Available from: 2013-08-16 Created: 2013-08-13 Last updated: 2016-02-02Bibliographically approved
Jansson, N. & Hoffman, J. (2013). Improving Parallel Performance of FEniCS Finite Element Computations by Hybrid MPI/PGAS.
Open this publication in new window or tab >>Improving Parallel Performance of FEniCS Finite Element Computations by Hybrid MPI/PGAS
2013 (English)Report (Other academic)
Abstract [en]

We present our work on developing a hybrid parallel programming model for a general finite element solver. The main focus of our work is to demonstrate that legacy codes with high latency, two-sided communication in the form of message passing can be improved using lightweight one-sided communication. We introduce a new hybrid MPI/PGAS implementation of the open source general finite element framework FEniCS, replacing the linear algebra backend (PETSc) with a new library written in UPC. A detailed description of the linear algebra backend implementation and the hybrid interface to FEniCS is given. We also present a detailed analysis of the performance of this hybrid solver on the Cray XE6 Lindgren at PDC/KTH including a comparison with the MPI only implementation, where we find that the hybrid implementation results in significant improvements in performance of the solver.

Publisher
p. 9
Series
CTL Technical Report ; 29
National Category
Computer Sciences Computational Mathematics
Identifiers
urn:nbn:se:kth:diva-121346 (URN)
Note

QC 20130429

Available from: 2013-04-29 Created: 2013-04-29 Last updated: 2018-01-11Bibliographically approved
Organisations
Identifiers
ORCID iD: ORCID iD iconorcid.org/0000-0002-5020-1631

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