Automated adjoints of coupled PDE-ODE systems

DOI10.1137/17M1144532zbMATH Open1420.65077arXiv1708.07648OpenAlexW2963843244WikidataQ127742812 ScholiaQ127742812MaRDI QIDQ5230591FDOQ5230591

Authors: J. E. Hake, S. W. Funke, Marie E. Rognes, P. E. Farrell 

Publication date: 28 August 2019

Published in: SIAM Journal on Scientific Computing (Search for Journal in Brave)

Abstract: Mathematical models that couple partial differential equations (PDEs) and spatially distributed ordinary differential equations (ODEs) arise in biology, medicine, chemistry and many other fields. In this paper we discuss an extension to the FEniCS finite element software for expressing and efficiently solving such coupled systems. Given an ODE described using an augmentation of the Unified Form Language (UFL) and a discretisation described by an arbitrary Butcher tableau, efficient code is automatically generated for the parallel solution of the ODE. The high-level description of the solution algorithm also facilitates the automatic derivation of the adjoint and tangent linearization of coupled PDE-ODE solvers. We demonstrate the capabilities of the approach on examples from cardiac electrophysiology and mitochondrial swelling.

Full work available at URL: https://arxiv.org/abs/1708.07648

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zbMATH Keywords

finite element methodsFEniCSadjointscode generationcoupled PDE-ODEdolfin-adjoint

Mathematics Subject Classification ID

PDEs in connection with biology, chemistry and other natural sciences (35Q92) Multistep, Runge-Kutta and extrapolation methods for ordinary differential equations (65L06) Numerical methods for inverse problems for initial value and initial-boundary value problems involving PDEs (65M32) Finite element, Rayleigh-Ritz and Galerkin methods for initial value and initial-boundary value problems involving PDEs (65M60)

Cites Work

• DOLFIN: automated finite element computing
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• \texttt{Feel++}: a computational framework for Galerkin methods and advanced numerical methods
• Algorithm 799: revolve
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• FATODE: A Library for Forward, Adjoint, and Tangent Linear Integration of ODEs
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Cited In (12)

• Hybrid FEM-NN models: combining artificial neural networks with the finite element method
• \texttt{PETSc TSAdjoint}: a discrete adjoint ODE solver for first-order and second-order sensitivity analysis
• Coupling vs decoupling approaches for PDE/ODE systems modeling intercellular signaling
• Automated derivation of the adjoint of high-level transient finite element programs
• Rapid development and adjoining of transient finite element models
• Automatic pre- and postconditions for partial differential equations
• An automatic adjoint theorem and its applications
• A 3D Haar wavelet method for a coupled degenerate system of parabolic equations with nonlinear source coupled with non-linear ODEs
• Adaptive finite element solution of multiscale PDE-ODE systems
• Automated Transformations for PDE Systems with Application to Multigrid Solvers
• Automated adjoints of coupled PDE-ODE systems
• Long time behavior of a parabolic \(p\)-Laplacian equation coupled to a compartmental ODE system with an induction threshold phenomenon

Uses Software

• Chaste
• revolve
• SUNDIALS
• DOLFIN
• FEniCS
• CVODES
• Feel++
• FATODE
• UFL
• FFC
• Firedrake

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