Combine model_creation into the Model Refiner class

[PinkShnack]

Problem

After talking with @michaelhennessyjr (or rather, after trying to show Mike how the model creation works), I have decided to put as much of the model creation into the Model Refiner class.

This will make creation and refinement of models easier. And it will make folding the necessary 2D material model creation workflow into Atomap.

What would need to be done:

• Break up model creation functions and place them into the model refiner.
  • Make sure to add a note linking the old and new functions to each other.
  • Add a workflow example(s) to the documentation and make a jupyter notebook.
• Add all the scaling factors as a dict attribute in the Model Refiner.
• Update the model file outputs to the latest. (probably using ASE and Atomap sublattice).
• Use the latest version of Atomap for assignment of elements and z_height (dict format, rather than current one in Atomap dev 0.1.2 version). Should be its own issue.