172 research outputs found
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
Identification of weakly coupled multiphysics problems. Application to the inverse problem of electrocardiography
This work addresses the inverse problem of electrocardiography from a new
perspective, by combining electrical and mechanical measurements. Our strategy
relies on the defini-tion of a model of the electromechanical contraction which
is registered on ECG data but also on measured mechanical displacements of the
heart tissue typically extracted from medical images. In this respect, we
establish in this work the convergence of a sequential estimator which combines
for such coupled problems various state of the art sequential data assimilation
methods in a unified consistent and efficient framework. Indeed we ag-gregate a
Luenberger observer for the mechanical state and a Reduced Order Unscented
Kalman Filter applied on the parameters to be identified and a POD projection
of the electrical state. Then using synthetic data we show the benefits of our
approach for the estimation of the electrical state of the ventricles along the
heart beat compared with more classical strategies which only consider an
electrophysiological model with ECG measurements. Our numerical results
actually show that the mechanical measurements improve the identifiability of
the electrical problem allowing to reconstruct the electrical state of the
coupled system more precisely. Therefore, this work is intended to be a first
proof of concept, with theoretical justifications and numerical investigations,
of the ad-vantage of using available multi-modal observations for the
estimation and identification of an electromechanical model of the heart
A multiresolution space-time adaptive scheme for the bidomain model in electrocardiology
This work deals with the numerical solution of the monodomain and bidomain
models of electrical activity of myocardial tissue. The bidomain model is a
system consisting of a possibly degenerate parabolic PDE coupled with an
elliptic PDE for the transmembrane and extracellular potentials, respectively.
This system of two scalar PDEs is supplemented by a time-dependent ODE modeling
the evolution of the so-called gating variable. In the simpler sub-case of the
monodomain model, the elliptic PDE reduces to an algebraic equation. Two simple
models for the membrane and ionic currents are considered, the
Mitchell-Schaeffer model and the simpler FitzHugh-Nagumo model. Since typical
solutions of the bidomain and monodomain models exhibit wavefronts with steep
gradients, we propose a finite volume scheme enriched by a fully adaptive
multiresolution method, whose basic purpose is to concentrate computational
effort on zones of strong variation of the solution. Time adaptivity is
achieved by two alternative devices, namely locally varying time stepping and a
Runge-Kutta-Fehlberg-type adaptive time integration. A series of numerical
examples demonstrates thatthese methods are efficient and sufficiently accurate
to simulate the electrical activity in myocardial tissue with affordable
effort. In addition, an optimalthreshold for discarding non-significant
information in the multiresolution representation of the solution is derived,
and the numerical efficiency and accuracy of the method is measured in terms of
CPU time speed-up, memory compression, and errors in different norms.Comment: 25 pages, 41 figure
A parallel solver for reaction-diffusion systems in computational electrocardiology
In this work, a parallel three-dimensional solver for numerical
simulations in computational electrocardiology is introduced and studied. The
solver is based on the anisotropic Bidomain %(AB) cardiac model, consisting of
a system of two degenerate parabolic reaction-diffusion equations describing
the intra and extracellular potentials of the myocardial tissue. This model
includes intramural fiber rotation and anisotropic conductivity coefficients
that can be fully orthotropic or axially symmetric around the fiber direction.
%In case of equal anisotropy ratio, this system reduces to The solver also
includes the simpler anisotropic Monodomain model, consisting of only one
reaction-diffusion equation. These cardiac models are coupled with a membrane
model for the ionic currents, consisting of a system of ordinary differential
equations that can vary from the simple FitzHugh-Nagumo (FHN) model to the more
complex phase-I Luo-Rudy model (LR1). The solver employs structured
isoparametric finite elements in space and a semi-implicit adaptive
method in time. Parallelization and portability are based on the PETSc parallel
library. Large-scale computations with up to unknowns have been run
on parallel computers, simulating excitation and repolarization phenomena in
three-dimensional domains
BPX preconditioners for the Bidomain model of electrocardiology
The aim of this work is to develop a BPX preconditioner for the Bidomain model of electrocardiology. This model describes the bioelectrical activity of the cardiac tissue and consists of a system of a non-linear parabolic reaction\u2013diffusion partial differential equation (PDE) and an elliptic linear PDE, modeling at macroscopic level the evolution of the transmembrane and extracellular electric potentials of the anisotropic cardiac tissue. The evolution equation is coupled through the non-linear reaction term with a stiff system of ordinary differential equations, the so-called membrane model, describing the ionic currents through the cellular membrane. The discretization of the coupled system by finite elements in space and semi-implicit finite differences in time yields at each time step the solution of an ill-conditioned linear system. The goal of the present study is to construct, analyze and numerically test a BPX preconditioner for the linear system arising from the discretization of the Bidomain model. Optimal convergence rate estimates are established and verified by two- and three-dimensional numerical tests on both structured and unstructured meshes. Moreover, in a full heartbeat simulation on a three-dimensional wedge of ventricular tissue, the BPX preconditioner is about 35% faster in terms of CPU times than ILU(0) and an Algebraic Multigrid preconditioner
Highly parallel multi-physics simulation of muscular activation and EMG
Simulation of skeletal muscle activation can help to interpret electromyographic measurements and infer the behavior of the muscle ïŹbers. Existing models consider simpliïŹed geometries or a low number of muscle ïŹbers to reduce the computation time. We demonstrate how to simulate a ïŹnely-resolved model of biceps brachii with a typical number of 270.000 ïŹbers. We have used domain decomposition to run simulations on 27.000 cores of the supercomputer HazelHen at HLRS in Stuttgart, Germany. We present details on opendihu, our software framework. Its conïŹgurability, eïŹcient data structures and modular software architecture target usability, performance and extensibility for future models. We present good parallel weak scaling of the simulations
Parallel Newton-Krylov-BDDC and FETI-DP deluxe solvers for implicit time discretizations of the cardiac Bidomain equations
Two novel parallel Newton-Krylov Balancing Domain Decomposition by
Constraints (BDDC) and Dual-Primal Finite Element Tearing and Interconnecting
(FETI-DP) solvers are here constructed, analyzed and tested numerically for
implicit time discretizations of the three-dimensional Bidomain system of
equations.
This model represents the most advanced mathematical description of the
cardiac bioelectrical activity and it consists of a degenerate system of two
non-linear reaction-diffusion partial differential equations (PDEs), coupled
with a stiff system of ordinary differential equations (ODEs).
A finite element discretization in space and a segregated implicit
discretization in time, based on decoupling the PDEs from the ODEs, yields at
each time step the solution of a non-linear algebraic system.
The Jacobian linear system at each Newton iteration is solved by a Krylov
method, accelerated by BDDC or FETI-DP preconditioners, both augmented with the
recently introduced {\em deluxe} scaling of the dual variables.
A polylogarithmic convergence rate bound is proven for the resulting parallel
Bidomain solvers.
Extensive numerical experiments on linux clusters up to two thousands
processors confirm the theoretical estimates, showing that the proposed
parallel solvers are scalable and quasi-optimal
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