Arbitrary function & ODE parser

Use Case

Often for perfusion and metabolic modeling, different systems of differential algebraic equations are included as reaction terms to represent kinetic components of overall metabolism. Often hypotheses about metabolic functionality require the form of these equations to be changed substantially (e.g. the inclusion of fatty acid oxidation in a cardiomyocyte model versus glucose oxidation alone). Therefore, users interested in simulating multiple models for tissue perfusion may require a flexible framework to easily change governing reaction equations.

Problem

Currently, any changes to governing equations require recompiling svFSIplus to integrate. Futhermore, the lack of modularity hinders incorporation of complex reaction terms in more complex advection-diffusion-reaction systems.

Solution

We shall introduce flexible string parser to allow for inclusion of arbitrary algebraic and ordinary differential equations into on-demand c++ functions. Such an approach is attractive for general purpose uses and computational efficiency (as opposed to symbolic solvers which may be large third party packages or too slow for integration in a governing PDE equation).

Alternatives considered

Symbolic approaches may be considered if direct construction of c++ functions cannot easily be accomplished (although this is not desirable).

Additional context

Specifically this will be important for perfusion and metabolic modeling although there are many more general use cases.

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