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Unicorn: Parallel adaptive finite element simulation of turbulent flow and fluid-structure interaction for deforming domains and complex geometry
KTH, Skolan för datavetenskap och kommunikation (CSC), High Performance Computing and Visualization (HPCViz).ORCID-id: 0000-0003-4256-0463
KTH, Skolan för datavetenskap och kommunikation (CSC), High Performance Computing and Visualization (HPCViz).ORCID-id: 0000-0002-1695-8809
KTH, Skolan för datavetenskap och kommunikation (CSC), High Performance Computing and Visualization (HPCViz).
KTH, Skolan för datavetenskap och kommunikation (CSC), High Performance Computing and Visualization (HPCViz).
Vise andre og tillknytning
2013 (engelsk)Inngår i: Computers & Fluids, ISSN 0045-7930, E-ISSN 1879-0747, Vol. 80, nr SI, s. 310-319Artikkel i tidsskrift (Fagfellevurdert) Published
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.

sted, utgiver, år, opplag, sider
2013. Vol. 80, nr SI, s. 310-319
Emneord [en]
Unicorn, DOLFIN, FEniCS, Parallel adaptive finite element method, Open source software, Turbulent flow, Fluid structure interaction, Complex geometry, Deforming domain
HSV kategori
Identifikatorer
URN: urn:nbn:se:kth:diva-124954DOI: 10.1016/j.compfluid.2012.02.003ISI: 000320427200036Scopus ID: 2-s2.0-84885190916OAI: oai:DiVA.org:kth-124954DiVA, id: diva2:638770
Forskningsfinansiär
EU, European Research CouncilSwedish Foundation for Strategic Research Swedish Research CouncilSwedish Energy Agency
Merknad

QC 20130803

Tilgjengelig fra: 2013-08-02 Laget: 2013-08-02 Sist oppdatert: 2018-05-08bibliografisk kontrollert
Inngår i avhandling
1. High Performance Adaptive Finite Element Methods: With Applications in Aerodynamics
Åpne denne publikasjonen i ny fane eller vindu >>High Performance Adaptive Finite Element Methods: With Applications in Aerodynamics
2013 (engelsk)Doktoravhandling, med artikler (Annet vitenskapelig)
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.

sted, utgiver, år, opplag, sider
Stockholm: KTH Royal Institute of Technology, 2013. s. xii, 50
Serie
TRITA-CSC-A, ISSN 1653-5723 ; 2013:07
HSV kategori
Identifikatorer
urn:nbn:se:kth:diva-125742 (URN)978-91-7501-814-0 (ISBN)
Disputas
2013-09-11, F3, Lindstedtsvägen 26, KTH, Stockholm, 10:15 (engelsk)
Opponent
Veileder
Merknad

QC 20130816

Tilgjengelig fra: 2013-08-16 Laget: 2013-08-13 Sist oppdatert: 2016-02-02bibliografisk kontrollert
2. Patient-Specific Finite Element Modeling of the Blood Flow in the Left Ventricle of a Human Heart
Åpne denne publikasjonen i ny fane eller vindu >>Patient-Specific Finite Element Modeling of the Blood Flow in the Left Ventricle of a Human Heart
2017 (engelsk)Doktoravhandling, med artikler (Annet vitenskapelig)
Abstract [en]

Heart disease is the leading cause of death in the world. Therefore, numerous studies are undertaken to identify indicators which can be applied to discover cardiac dysfunctions at an early age. Among others, the fluid dynamics of the blood flow (hemodymanics) is considered to contain relevant information related to abnormal performance of the heart.This thesis presents a robust framework for numerical simulation of the fluid dynamics of the blood flow in the left ventricle of a human heart and the fluid-structure interaction of the blood and the aortic leaflets.We first describe a patient-specific model for simulating the intraventricular blood flow. The motion of the endocardial wall is extracted from data acquired with medical imaging and we use the incompressible Navier-Stokes equations to model the hemodynamics within the chamber. We set boundary conditions to model the opening and closing of the mitral and aortic valves respectively, and we apply a stabilized Arbitrary Lagrangian-Eulerian (ALE) space-time finite element method to simulate the blood flow. Even though it is difficult to collect in-vivo data for validation, the available data and results from other simulation models indicate that our approach possesses the potential and capability to provide relevant information about the intraventricular blood flow.To further demonstrate the robustness and clinical feasibility of our model, a semi-automatic pathway from 4D cardiac ultrasound imaging to patient-specific simulation of the blood flow in the left ventricle is developed. The outcome is promising and further simulations and analysis of large data sets are planned.In order to enhance our solver by introducing additional features, the fluid solver is extended by embedding different geometrical prototypes of both a native and a mechanical aortic valve in the outflow area of the left ventricle.Both, the contact as well as the fluid-structure interaction, are modeled as a unified continuum problem using conservation laws for mass and momentum. To use this ansatz for simulating the valvular dynamics is unique and has the expedient properties that the whole problem can be described with partial different equations and the same numerical methods for discretization are applicable.All algorithms are implemented in the high performance computing branch of Unicorn, which is part of the open source software framework FEniCS-HPC. The strong advantage of implementing the solvers in an open source software is the accessibility and reproducibility of the results which enhance the prospects of developing a method with clinical relevance.

sted, utgiver, år, opplag, sider
Stockholm: KTH Royal Institute of Technology, 2017. s. 51
Serie
TRITA-CSC-A, ISSN 1653-5723 ; 2017:21
Emneord
Finite element method, Arbitrary Lagrangian-Eulerian method, Fluid-Structure interaction, Contact model, parallel algorithm, blood flow, left ventricle, aortic valves, patient-specific heart model
HSV kategori
Identifikatorer
urn:nbn:se:kth:diva-215277 (URN)978-91-7729-566-2 (ISBN)
Disputas
2017-10-27, Fantum, F-huset, plan 5, KTH Campus, Lindstedtsvägen 24, Stockholm, 10:00 (engelsk)
Opponent
Veileder
Forskningsfinansiär
Swedish Foundation for Strategic Research Swedish Research CouncilEU, European Research Council, 202984
Merknad

QC 20171006

Tilgjengelig fra: 2017-10-06 Laget: 2017-10-05 Sist oppdatert: 2017-10-09bibliografisk kontrollert
3. Adaptive Finite Element Methods for Fluid Structure Interaction Problems with Applications to Human Phonation
Åpne denne publikasjonen i ny fane eller vindu >>Adaptive Finite Element Methods for Fluid Structure Interaction Problems with Applications to Human Phonation
2018 (engelsk)Doktoravhandling, med artikler (Annet vitenskapelig)
Abstract [en]

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.

Abstract [sv]

Detta arbete presenterar en enhetlig ram för numerisk lösning av fluid-strukturinteraktion (FSI) och akustikproblem med fokus på det mänskligatalet. En finita elementmetod används för numerisk lösning av de partiella differentialekvationer som beskriver konserveringslagar för moment och massa.Eftersom det resulterande systemet av ekvationer är mycket stort, konstruerasen öppen källkod med hög prestanda. För att få hög noggrannhet i de numeriska lösningarna används en adaptiv nätförfiningsstrategi vilken minskar beräkningskostnaden jämfört med en uniform förfining.Adaptiv förfining av nätet bygger på beräknade felindikatorer som bygger på en kombination av en beräkningsbar residual och lösningen av ett såkallat dualt problem. Den första huvudresultatet av denna avhandling är attutveckla en och validera denna strategi för en FSI-modell i ett benchmarkproblem.Denna FSI-modell utvidgas vidare för att hantera kontaktmekanik, ochanvänds sedan för en realistisk modell av stämbandsstrukturerna där denglottiska vågformationen fångas i de numeriska simuleringarna. Detta är detandra huvudresultatet i det presenterade arbetet.FSI-modellen kopplas också till en akustikmodell genom en akustisk analogi,för modell konstruerad för att skapa vokalen / i /. Den erhållna trycksignaleni ett antal punkter jämförs med resultat från litteraturen, vilket är det slutligahuvudresultatet som presenteras.

sted, utgiver, år, opplag, sider
Stockholm, Sweden: KTH Royal Institute of Technology, 2018. s. 48
Serie
TRITA-EECS-AVL ; 2018:38
Emneord
Fluid Structure Interaction, Finite Element Method, Contact Modeling, Acoustic Coupling, High Performance Computing
HSV kategori
Forskningsprogram
Tillämpad matematik och beräkningsmatematik
Identifikatorer
urn:nbn:se:kth:diva-227252 (URN)978-91-7729-764-2 (ISBN)
Disputas
2018-05-23, F3, Sing-Sing, floor 2, KTH Kungliga Tekniska högskolan, Lindstedtsvägen 26, Stockholm, Stockholm, 10:30 (engelsk)
Opponent
Veileder
Forskningsfinansiär
EU, FP7, Seventh Framework Programme, 308874Swedish Foundation for Strategic Research Swedish Research CouncilEU, European Research Council
Merknad

QC 20180509

Tilgjengelig fra: 2018-05-09 Laget: 2018-05-08 Sist oppdatert: 2018-05-09bibliografisk kontrollert

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