(WIP) Adding stepwise capabilities to simulator

[kbonney]

Summary

This PR contains the current work done towards stepwise simulation. I will populate the summary with more details as the PR gets refined

Tests and documentation

Some tests and documentation for the existing code have been generated.

Acknowledgement

By contributing to this software project, I acknowledge that I have reviewed the software quality assurance guidelines and that my contributions are submitted under the Revised BSD License.