Abstract
Palabos-npFEM is a computational framework for the simulation of blood flow with fully resolved constituents. The software resolves the trajectories and deformed state of blood cells, such as red blood cells and platelets, and the complex interaction between them. The tool combines the lattice Boltzmann solver Palabos for the simulation of blood plasma (fluid phase), a finite element method (FEM) solver for the resolution of blood cells (solid phase), and an immersed boundary method (IBM) for the coupling of the two phases. Palabos-npFEM provides, on top of a CPU-only version, the option to simulate the deformable bodies on GPUs, thus the code is tailored for the fastest supercomputers. The software is integrated in the Palabos core library, and is available on the Git repository https://gitlab.com/unigespc/palabos. It offers the possibility to simulate various setups, e.g. several geometries and blood parameters, and due to its modular design, it allows external solvers to readily replace the provided ones.
Highlights
Palabos-nodal projective finite elements method (npFEM) is a highly versatile computational tool for the simulation of cellular blood flow, focusing on high performance computing (HPC) without compromising accuracy or complexity.Blood plays a vital role in living organisms, transporting oxygen, nutrients, waste products, and various kinds of cells, to tissues and organs
Our blood vessels are characterised by a variety of scales, i.e. the diameter of arteries/ veins ranges from few millimetres to few centimetres, the diameter of arterioles/venules ranges from few micrometres to few hundred micrometres, and the capillaries are about the size of a red blood cells (RBCs) diameter
IMPLEMENTATION AND ARCHITECTURE Palabos-npFEM is build on top of two independent solvers, i.e. fluid and solid solvers, and couples them through the Fluid-Solid Interaction (FSI) module
Summary
Palabos-npFEM is a highly versatile computational tool for the simulation of cellular blood flow (at the micrometre scale), focusing on high performance computing (HPC) without compromising accuracy or complexity.Blood plays a vital role in living organisms, transporting oxygen, nutrients, waste products, and various kinds of cells, to tissues and organs. Palabos-npFEM solves equations (1) & (2) in a modular way, and performs the Fluid-Solid Interaction (FSI) through the Immersed Boundary Method (IBM). The IBM [14, 13], for the coupling of the solid & fluid phases, is implemented in the Palabos library.
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