论文标题
无基质的高阶求解器,用于心脏电生理的数值溶液
A matrix-free high-order solver for the numerical solution of cardiac electrophysiology
论文作者
论文摘要
我们提出了一个无基质求解器,用于由单域非线性反应扩散方程以及离子物种的普通微分方程系统组成的心脏电生理模型的数值解。我们的数值近似基于高阶光谱元素方法(SEM),以实现准确的数值离散化,同时使用的自由度要比一阶有限元素少得多。我们将矢量化与总成分结合在一起,从而可以在高性能计算框架中非常有效地使用高阶多项式。我们验证了无基质求解器在各种应用中的有效性,并进行不同的电生理模拟,从简单的心脏组织板到现实的四腔心脏几何形状。我们将SEM与SEM与数值集成(SEM-NI)进行比较,表明它们在准确性和效率方面提供了可比的结果。在这两种情况下,增加本地多项式$ p $的增加都会带来更好的数值结果和较小的计算时间,而不是减少网格尺寸$ h $。我们还实施了无基质的几何多机预处理器,该预处理导致相当数量的线性求解器迭代,相对于基于最新基质的代数多机预处理器。事实上,相对于传统基于矩阵的求解器,此处提出的无基质求解器的速度高达45 $ \ times $。
We propose a matrix-free solver for the numerical solution of the cardiac electrophysiology model consisting of the monodomain nonlinear reaction-diffusion equation coupled with a system of ordinary differential equations for the ionic species. Our numerical approximation is based on the high-order Spectral Element Method (SEM) to achieve accurate numerical discretization while employing a much smaller number of Degrees of Freedom than first-order Finite Elements. We combine vectorization with sum-factorization, thus allowing for a very efficient use of high-order polynomials in a high performance computing framework. We validate the effectiveness of our matrix-free solver in a variety of applications and perform different electrophysiological simulations ranging from a simple slab of cardiac tissue to a realistic four-chamber heart geometry. We compare SEM to SEM with Numerical Integration (SEM-NI), showing that they provide comparable results in terms of accuracy and efficiency. In both cases, increasing the local polynomial degree $p$ leads to better numerical results and smaller computational times than reducing the mesh size $h$. We also implement a matrix-free Geometric Multigrid preconditioner that results in a comparable number of linear solver iterations with respect to a state-of-the-art matrix-based Algebraic Multigrid preconditioner. As a matter of fact, the matrix-free solver proposed here yields up to 45$\times$ speed-up with respect to a conventional matrix-based solver.