Review if updating `model.h5` file independent parameters like `bond_stiffness` and `critical_stretch` should have its own method

[bb515]

The current solution to updating a model parameter (when no update the model.h5 file is required after said update) is to simply run a simulation with that new parameter as a key word argument. Is this the best solution though? Wouldn't it be less confusing to explicitly update the model parameters before a simulation is done.
Disadvantages:

• Adds 1 line of code to the example files.

Advantages:

• Cleaner under-the-hood code at _simulate_initiate
• More interpretable and clear code at the example file level
• Flatter code
• simulate should be conceptually separated from model, in that simulate is applying boundary conditions to a preexisting model and watching what happens. Suggested change goes towards that ideal.

Advantages seem to outweigh disadvantages, so I'll impliment this.