The LifeV library: engineering mathematics beyond the proof of concept

LifeV is a library for the finite element (FE) solution of partial differential equations in one, two, and three dimensions. It is written in C++ and designed to run on diverse parallel architectures, including cloud and high performance computing facilities. In spite of its academic research nature, meaning a library for the development and testing of new methods, one distinguishing feature of LifeV is its use on real world problems and it is intended to provide a tool for many engineering applications. It has been actually used in computational hemodynamics, including cardiac mechanics and fluid-structure interaction problems, in porous media, ice sheets dynamics for both forward and inverse problems. In this paper we give a short overview of the features of LifeV and its coding paradigms on simple problems. The main focus is on the parallel environment which is mainly driven by domain decomposition methods and based on external libraries such as MPI, the Trilinos project, HDF5 and ParMetis. Dedicated to the memory of Fausto Saleri.Comment: Review of the LifeV Finite Element librar

Comparisons between reduced order models and full 3D models for fluid-structure interaction problems in haemodynamics

When modelling the cardiovascular system, the effect of the vessel wall on the blood flow has great relevance. Arterial vessels are complex living tissues and three-dimensional specific models have been proposed to represent their behaviour. The numerical simulation of the 3D-3D Fluid-Structure Interaction (FSI) coupled problem has high computational costs in terms of required time and memory storage. Even if many possible solutions have been explored to speed up the resolution of such problem, we are far from having a 3D-3D FSI model that can be solved quickly. In 3D-3D FSI models two of the main sources of complexity are represented by the domain motion and the coupling between the fluid and the structural part. Nevertheless, in many cases, we are interested in the blood flow dynamics in compliant vessels, whereas the displacement of the domain is small and the structure dynamics is less relevant. In these situations, techniques to reduce the complexity of the problem can be used. One consists in using transpiration conditions for the fluid model as surrogate for the wall displacement, thus allowing problem's solution on a fixed domain. Another strategy consists in modelling the arterial wall as a thin membrane under specific assumptions (Figueroa et al., 2006, Nobile and Vergara, 2008) instead of using a more realistic (but more computationally intensive) 3D elastodynamic model. Using this strategy the dynamics of the vessel motion is embedded in the equation for the blood flow. Combining the transpiration conditions with the membrane model assumption, we obtain an attractive formulation, in fact, instead of solving two different models on two moving physical domains, we solve only a Navier-Stokes system in a fixed fluid domain where the structure model is integrated as a generalized Robin condition. In this paper, we present a general formulation in the boundary conditions which is independent of the time discretization scheme choice and on the stress-strain constitutive relation adopted for the vessel wall structure. Our aim is, first, to write a formulation of a reduced order model with zero order transpiration conditions for a generic time discretization scheme, then to compare a 3D-3D PSI model and a reduced FSI one in two realistic patient-specific cases: a femoropopliteal bypass and an aorta. In particular, we are interested in comparing the wall shear stresses, in fact this quantity can be used as a risk factor for some pathologies such as atherosclerosis or thrombogenesis. More in general we want to assess the accuracy and the computational convenience to use simpler formulations based on reduced order models. In particular, we show that, in the case of small displacements, using a 3D-3D PSI linear elastic model or the correspondent reduced order one yields many similar results. (c) 2013 Elsevier B.V. All rights reserved

Coupling schemes for the FSI forward prediction challenge: comparative study and validation

International audienceThis paper presents a numerical study in which several partitioned solution procedures for incompressible fluid-structure interaction are compared and validated against the results of an experimental FSI benchmark. The numerical methods discussed cover the three main families of coupling schemes: strongly coupled, semi-implicit and loosely coupled. Very good agreement is observed between the numerical and experimental results. The comparisons confirm that strong coupling can be efficiently avoided, via semi-implicit and loosely coupled schemes, without compromising stability and accuracy.Cet article présente une étude numérique dans laquelle plusieurs algorithmes partitionnés pour l'interaction fluide structure sont comparés et validés avec des résultats expérimentaux. Les méthodes numériques discutées couvrent les trois familles principales de schémasde couplage: fortement couplés, semi implicites et faiblement couplés. Un très bon accord est obtenu entre les résultats numériques et expérimentaux. Les comparaisons confirment que le couplage fort peut être contourné efficacement, par l'intermédiaire de schémas semi implicites et faiblement couplés, sans compromettre la stabilité et la précision

Modelling cell movement and chemotaxis pseudopod based feedback

A computational framework is presented for the simulation of eukaryotic cell migration and chemotaxis. An empirical pattern formation model, based on a system of non-linear reaction-diffusion equations, is approximated on an evolving cell boundary using an Arbitrary Lagrangian Eulerian surface finite element method (ALE-SFEM). The solution state is used to drive a mechanical model of the protrusive and retractive forces exerted on the cell boundary. Movement of the cell is achieved using a level set method. Results are presented for cell migration with and without chemotaxis. The simulated behaviour is compared with experimental results of migrating Dictyostelium discoideum cells

Well-posedness and Robust Preconditioners for the Discretized Fluid-Structure Interaction Systems

In this paper we develop a family of preconditioners for the linear algebraic systems arising from the arbitrary Lagrangian-Eulerian discretization of some fluid-structure interaction models. After the time discretization, we formulate the fluid-structure interaction equations as saddle point problems and prove the uniform well-posedness. Then we discretize the space dimension by finite element methods and prove their uniform well-posedness by two different approaches under appropriate assumptions. The uniform well-posedness makes it possible to design robust preconditioners for the discretized fluid-structure interaction systems. Numerical examples are presented to show the robustness and efficiency of these preconditioners.Comment: 1. Added two preconditioners into the analysis and implementation 2. Rerun all the numerical tests 3. changed title, abstract and corrected lots of typos and inconsistencies 4. added reference