refactor Simulation class

[valentinsulzer]

Refactor Simulation class to run the whole process (create model, set parameters, discretise, solve, visualise). Needs to take optional inputs for the parameter class, parameter file, mesh/discretisation, solver, and set defaults if these are None. Can later add capability to save solution, load a saved solution, etc.

class Simulation(object):
   def __init__(
        self,
        model,
        parameter_values=None,
        discretisation=None,
        solver=None,
        name="unnamed",
    ):
        # Defaults
        if parameter_values is None:
           # default parameter_values
        if discretisation is None:
           # default discretisation
        if solver is None:
            # default solver

        self.model = model
        self.parameter_values = parameter_values
        self.discretisation = discretisation
        self.solver = solver
        self.name = name

    def set_parameters(self):
        self.parameter_values.process(self.model)

    def discretise(self):
        y0 = self.discretisation.process(self.model)
        return y0

    def solve(self, y0):
        self.solver.solve(self.model, y0)

    def run(self):
        self.set_parameters()
        y0 = self.discretise()
        self.solve(y0)

    def load(self):

    def save(self):

    def plot(self):

[valentinsulzer]

re-opening following discussions in meetings

[valentinsulzer]

Now in #688