Automated adjoints of coupled PDE-ODE systems
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Publication:5230591
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)
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.
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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
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