Isolate electrolyte model calculations into subfunction(s)

The calculation of the dxvec, dxd1, dxd2 length vectors, the porosvec and poros_edges vectors should all be moved to separate functions (within a geometry module).

The ("optional" -- if it's not a single-volume simulation) application of the c/phi boundary conditions should be placed within the main DeclareEquations function.

Then, the actual calculation of the RHS for the species and charge conservation equations should be its own function as well which should be called from plot_data.py (so it should take parameters as input and not refer to self.ndD).

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