An Adaptable Simulation Framework Based on a Linearized Octree

Roller, Sabine; Bernsdorf, J.; Klimach, Harald; Hasert, Manuel; Harlacher, Daniel F.; Cakircali, Metin; Zimny, Simon; Masilamani, Kannan; Didinger, Laura; Zudrop, Jens

doi:10.1007/978-3-642-22244-3_7

Cited by 24 publications

(15 citation statements)

References 5 publications

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“…The models were discretized with cubical cells of δ x = 32 μm side using the mesh generator Seeder —a part of the end‐to‐end parallel simulation framework adaptable poly engineering simulator (APES) . The resulting number of cells for each model are as follows: Control: 863 531 743 Patient1: 709 482 055 Patient2: 772 152 392 …”

Section: Methodsmentioning

confidence: 99%

“…The models were discretized with cubical cells of x = 32 m side using the mesh generator Seeder 32 -a part of the end-to-end parallel simulation framework adaptable poly engineering simulator (APES). 33,34 The resulting number of cells for each model are as follows: The employed spatial resolution resulted in approximately 86 fluid cells along the diameter of the narrowest conduit among all the geometries, namely the CVJ of Patient2. This ensured the stability and accuracy of the bulk flow 17 and minimized the effects of boundary conditions.…”

Section: Computational Detailsmentioning

confidence: 99%

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Direct numerical simulation of transitional hydrodynamics of the cerebrospinal fluid in Chiari I malformation: The role of cranio‐vertebral junction

Jain

Ringstad

Eide

et al. 2017

Numer Methods Biomed Eng

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Obstruction to the cerebrospinal fluid (CSF) outflow caused by the herniation of cerebellar tonsils as a result of Chiari malformation type I leads to altered CSF hydrodynamics. This contribution explores the minutest characteristics of the CSF hydrodynamics in cervical subarachnoid space (SAS) of a healthy subject and 2 Chiari patients by performing highly resolved direct numerical simulation. The lattice Boltzmann method is used for the simulations because of its scalability on modern supercomputers that allow us to simulate up to approximately 10 cells while resolving the Kolmogorov microscales. The results depict that whereas the complex CSF flow remains largely laminar in the SAS of a healthy subject, constriction of the cranio-vertebral junction in Chiari I patients causes manifold fluctuations in the hydrodynamics of the CSF. These fluctuations resemble a flow that is in a transitional regime rather than laminar or fully developed turbulence. The fluctuations confine near the cranio-vertebral junction and are triggered due to the tonsillar herniation, which perturbs the flow as a result of altered anatomy of the SAS.

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Section: Methodsmentioning

confidence: 99%

Section: Computational Detailsmentioning

confidence: 99%

Direct numerical simulation of transitional hydrodynamics of the cerebrospinal fluid in Chiari I malformation: The role of cranio‐vertebral junction

Jain

Ringstad

Eide

et al. 2017

Numer Methods Biomed Eng

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“…The employed simulation tool-chain is contained in the end-to-end parallel framework APES (adaptable poly engineering simulator) [17,24]. 2 Meshes are created using the mesh generator Seeder [9] and computations are carried out using the LBM solver Musubi [10].…”

Section: The Simulation Frameworkmentioning

confidence: 99%

Efficacy of the FDA nozzle benchmark and the lattice Boltzmann method for the analysis of biomedical flows in transitional regime

Jain¹

2020

Med Biol Eng Comput

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Flows through medical devices as well as in anatomical vessels despite being at moderate Reynolds number may exhibit transitional or even turbulent character. In order to validate numerical methods and codes used for biomedical flow computations, the US Food and Drug Administration (FDA) established an experimental benchmark, which was a pipe with gradual contraction and sudden expansion representing a nozzle. The experimental results for various Reynolds numbers ranging from 500 to 6500 were publicly released. Previous and recent computational investigations of flow in the FDA nozzle found limitations in various CFD approaches and some even questioned the adequacy of the benchmark itself. This communication reports the results of a lattice Boltzmann method (LBM)-based direct numerical simulation (DNS) approach applied to the FDA nozzle benchmark for transitional cases of Reynolds numbers 2000 and 3500. The goal is to evaluate if a simple off the shelf LBM would predict the experimental results without the use of complex models or synthetic turbulence at the inflow. LBM computations with various spatial and temporal resolutions are performed-in the extremities of 45 million to 2.88 billion lattice cells-executed respectively on 32 CPU cores of a desktop to more than 300, 000 cores of a modern supercomputer to explore and characterize miniscule flow details and quantify Kolmogorov scales. The LBM simulations transition to turbulence at a Reynolds number 2000 like the FDA's experiments and acceptable agreement in jet breakdown locations, average velocity, shear stress, and pressure is found for both the Reynolds numbers.

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“…The total number of cells with highest resolution of 8 µm was nearly one billion for Model B and 400 million for Model A due to the respective difference in the volumes of the two. The Lattice Boltzmann flow solver Musubi 17 was used for simulations which is a part of the end-to-end parallel simulation tool chain -Adaptable Poly Engineering Simulator, APES 43 The simulations were performed on the SuperMUC 1 petascale system, which is a tier-0 PRACE 2 supercomputer installed at the Leibniz Supercomputing Center, Munich. The SuperMUC is one of the main federal compute resources in Germany and it is ranked among the top 20 supercomputers of the world 3 .…”

Section: High Performance Computationsmentioning

confidence: 99%

Transitional flow in intracranial aneurysms – A space and time refinement study below the Kolmogorov scales using Lattice Boltzmann Method

2016

Self Cite

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Most Computational Fluid Dynamics (CFD) studies of hemodynamics in intracranial aneurysms are based on the assumption of laminar flow due to a relatively low (below 500) parent artery Reynolds number. A few studies have recently demonstrated the occurrence of transitional flow in aneurysms, but these studies employed special finite element schemes tailored to capture transitional nature of flow. In this study we investigate the occurrence of transition using a standard Lattice Boltzmann method (LBM). The LBM is used because of its computational efficiency, which in the present study allowed us to perform simulations at a higher resolution than has been done in the context of aneurysms before. The high space-time resolutions of 8 µm and 0.11 µs resulted in nearly 1 × 10 9 cells and 9 × 10 6 time steps per second and allowed us to quantify the turbulent kinetic energy at resolutions below the Kolmogorov scales. We perform an in-depth space and time refinement study on 2 aneurysms; one was previously reported laminar, while the other was reported transitional. Furthermore, we investigate the critical Reynolds number at which the flow transitions in aneurysms under time constant inflow conditions.

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An Adaptable Simulation Framework Based on a Linearized Octree

Cited by 24 publications

References 5 publications

Direct numerical simulation of transitional hydrodynamics of the cerebrospinal fluid in Chiari I malformation: The role of cranio‐vertebral junction

Direct numerical simulation of transitional hydrodynamics of the cerebrospinal fluid in Chiari I malformation: The role of cranio‐vertebral junction

Efficacy of the FDA nozzle benchmark and the lattice Boltzmann method for the analysis of biomedical flows in transitional regime

Transitional flow in intracranial aneurysms – A space and time refinement study below the Kolmogorov scales using Lattice Boltzmann Method

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