Subscribe to the gold package and get unlimited access to Shamra Academy
Register a new userPerformance of preconditioned iterative linear solvers for cardiovascular simulations in rigid and deformable vessels
67
0
0.0
(
0
)
Ask ChatGPT about the research
No Arabic abstract
Computing the solution of linear systems of equations is invariably the most time consuming task in the numerical solutions of PDEs in many fields of computational science. In this study, we focus on the numerical simulation of cardiovascular hemodynamics with rigid and deformable walls, discretized in space and time through the variational multi-scale finite element method. We focus on three approaches: the problem agnostic generalized minimum residual (GMRES) and stabilized bi-conjugate gradient (BICGS) methods, and a recently proposed, problem specific, bi-partitioned (BIPN) method. We also perform a comparative analysis of several preconditioners, including diagonal, block-diagonal, incomplete factorization, multi-grid, and resistance based methods. Solver performance and matrix characteristics (diagonal dominance, symmetry, sparsity, bandwidth and spectral properties) are first examined for an idealized cylindrical geometry with physiologic boundary conditions and then successively tested on several patient-specific anatomies representative of realistic cardiovascular simulation problems. Incomplete factorization pre-conditioners provide the best performance and results in terms of both strong and weak scalability. The BIPN method was found to outperform other methods in patient-specific models with rigid walls. In models with deformable walls, BIPN was outperformed by BICG with diagonal and Incomplete LU preconditioners.
rate research
Read More
Numerical simulations of cardiovascular mass transport pose significant challenges due to the wide range of Peclet numbers and backflow at Neumann boundaries. In this paper we present and discuss several numerical tools to address these challenges in the context of a stabilized finite element computational framework. To overcome numerical instabilities when backflow occurs at Neumann boundaries, we propose an approach based on the prescription of the total flux. In addition, we introduce a consistent flux outflow boundary condition and demonstrate its superior performance over the traditional zero diffusive flux boundary condition. Lastly, we discuss discontinuity capturing (DC) stabilization techniques to address the well-known oscillatory behavior of the solution near the concentration front in advection-dominated flows.We present numerical examples in both idealized and patient-specific geometries to demonstrate the efficacy of the proposed procedures. The three contributions dis-cussed in this paper enable to successfully address commonly found challenges when simulating mass transport processes in cardiovascular flows.
Deformable elastic bodies in viscous and viscoelastic media constitute a large portion of synthetic and biological complex fluids. We present a parallelized 3D-simulation methodology which fully resolves the momentum balance in the solid and fluid domains. An immersed boundary algorithm is exploited known as the immersed finite element method (IFEM) which accurately determines the internal forces in the solid domain. The scheme utilized has the advantages of requiring no costly re-meshing, handling finite Reynolds number, as well as incorporating non-linear viscoelasticity in the fluid domain. Our algorithm is designed for computationally efficient simulation of multi-particle suspensions with mixed structure types. The internal force calculation in the solid domain in the IFEM is coupled with a finite volume based incompressible fluid solver, both of which are massively parallelized for distributed memory architectures. We performed extensive case studies to ensure the fidelity of our algorithm. Namely, a series of single particle simulations for capsules, red blood cells, and elastic solid deformable particles were conducted in viscous and viscoelastic media. All of our results are in excellent quantitative agreement with the corresponding reported data in the literature which are based on different simulation platforms. Furthermore, we assess the accuracy of multi-particle simulation of blood suspensions (red blood cells in plasma) with and without platelets. Finally, we present the results of a novel simulation of multiple solid deformable objects in a viscoelastic medium.
This paper presents a Graphics Processing Units (GPUs) acceleration method of an iterative scheme for gas-kinetic model equations. Unlike the previous GPU parallelization of explicit kinetic schemes, this work features a fast converging iterative scheme. The memory reduction techniques in this method enable full three-dimensional (3D) solution of kinetic model equations in contemporary GPUs usually with a limited memory capacity that otherwise would need terabytes of memory. The GPU algorithm is validated against the DSMC simulation of the 3D lid-driven cavity flow and the supersonic rarefied gas flow past a cube with grids size up to 0.7 trillion points in the phase space. The performance of the GPU algorithm is assessed by comparing with the corresponding parallel CPU program using Message Passing Interface (MPI). The profiling on several models of GPUs shows that the algorithm has a medium to high level of utilization of the GPUs computing and memory resources. A $190times$ speedup can be achieved on the Tesla K40 GPUs against a single core of Intel Xeon-E5-2680v3 CPU for the 3D lid-driven cavity flow.
Dispersion of low-density rigid particles with complex geometries is ubiquitous in both natural and industrial environments. We show that while explicit methods for coupling the incompressible Navier-Stokes equations and Newtons equations of motion are often sufficient to solve for the motion of cylindrical particles with low density ratios, for more complex particles - such as a body with a protrusion - they become unstable. We present an implicit formulation of the coupling between rigid body dynamics and fluid dynamics within the framework of the immersed boundary projection method. Similarly to previous work on this method, the resulting matrix equation in the present approach is solved using a block-LU decomposition. Each step of the block-LU decomposition is modified to incorporate the rigid body dynamics. We show that our method achieves second-order accuracy in space and first-order in time (third-order for practical settings), only with a small additional computational cost to the original method. Our implicit coupling yields stable solution for density ratios as low as $10^{-4}$. We also consider the influence of fictitious fluid located inside the rigid bodies on the accuracy and stability of our method.
With a noticeable increase in research centered on modeling micro fluid interfaces in the framework of mesoscopic methods, we conduct an exhaustive study of discrete unified gas-kinetics scheme (DUGKS) in handling complicated interface deformations. High-order isotropic finite-difference schemes are first utilized in DUGKS to improve its capability in tracking interfaces. The performance of third-stage third-order DUGKS where source term is incorporated has also been assessed for the first time and a series of numerical tests have been conducted to investigate their capability. The comparative analysis have revealed the reason why the performance of lattice Boltzmann method is superior to that of discrete velocity method and DUGKS in general condition from an informed perspective. The mechanism behind the performance distinction between the central scheme and upwind scheme utilized in meso-flux construction in DUGKS have also been clarified. Numerical results have shown that the employment of high-order schemes in DUGKS does have an effect on the reduction of numerical dissipation, but the overall accuracy of this method is limited by the precision of prediction of source terms on mesh interface. The capability of third-stage third-order DUGKS is severely inhibited by its intrinsic limitation of the ratio of time step to particle collision time. Among the various kinds of DUGKS employed with different reconstruction methods, the most promising scheme is the one with third-order isotropic reconstruction and upwind-based meso-flux evaluation, which is able to ensure an unique balance between efficiency and accuracy.
Log in to be able to interact and post comments
comments
Fetching comments
Sign in to be able to follow your search criteria
