Documentation: Initialization of domain

[amoodie]

A documentation section on initialization of the domain, similar to hydrodynamics and morphodynamics documentation, is needed.

The user guide covers how to actually specify model parameters in YAML and command line, but there is a need for some narrative description about what these parameters do to the model domain.

Should be able to do something clever with a

matrix specification --> preprocessor --> plots of the domains

workflow in the docs to cover this.