Partially addresses #519.

Current situation

1. Coupling of electrophysiology and mechanics through active stress had been removed in Object oriented refactoring of ionic models and plotting calcium #540, pending this refactoring;
2. only one active stress model was implemented, was tightly coupled to specific ionic models, and was not accessible through the user-exposed parameters.

Release Notes

Many of the implementation choices here are modeled after the implementation of IonicModel in #540. Here, I took some further steps towards encapsulation which might be ported to IonicModel as well, although maybe in a separate PR. I'll add some comments to the code about this.

1. The PR introduces the following hierarchy of classes for active stress models, with the idea that new active stress model can be added easily by deriving new classes from ActiveStress or ActiveStressODE.

---
config:
    class:
      hideEmptyMembersBox: true
---
classDiagram
  ActiveStress <|-- ActiveStressODE
  ActiveStressODE <|-- NashPanfilov
  ActiveStress <|-- UniformSteadyActiveStress
  dmnType *-- ActiveStress
  ActiveStressFactory .. ActiveStress : instantiates
  Factory~BaseClass~ <|.. ActiveStressFactory : BaseClass=ActiveStress

2. A new abstract Factory class is introduced, by templating the IonicModelFactory; aliases are provided for both Factory<IonicModel> and Factory<ActiveStress>.

3. The ActiveStress class and derived classes manage their own XML parameters through the abstract class ActiveStressParameters and the methods get_parameters, read_parameters, distribute_parameters, so that the addition of model parameters can be localized to the source files where the model is defined.

4. A (shared) pointer to ActiveStress is stored in dmnType, to allow different active stress models in different domains.

5. Time stepping of ActiveStress instances is managed by Integrator::predictor. After advancing one time step, the active tension along the three principal directions is stored in the vector CepMod::cem.Ya_{f,s,n}, whose entries are then passed on to the constitutive law routines.

6. The XML section for a struct domain now can optionally contain the following tag:

   <ActiveStress>
     <Model>Model name (e.g. NashPanfilov, UniformSteady, ...)</Model>
   
     <Directional_distribution>
       <!-- optional, and same as currently implemented for Fiber_reinforcement_stress -->
     </Directional_distribution>
   
     <UniformSteady>
       <Value>123</Value>
     <UniformSteady>
   
     <!-- other sections for every implemented model, if needed -->
   </ActiveStress>

   If present, the tag enables active stress through the ActiveStress class. If the active stress model is calcium-based, and no electrophysiology equation is present, the calcium will be kept to zero.

Documentation

New additions are documented via Doxygen comments. Documentation for ActiveStress and ActiveStressODE also includes a brief list of steps needed to implement a new model.

Testing

Existing automatic tests pass with the new implementation, although they do not cover the newly added features.

I have tested this on a basic electromechanics example based on cases/cep/slab_domains. I attach below a preview of the simulation.

I plan to turn this into an integration test (running one timestep is reasonably fast).

TODO before marking as ready

• add integration test for coupled electromechanics

Code of Conduct & Contributing Guidelines

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