Some base classes ready for production

This is the code used in
"Self-Correcting Quantum Memories Beyond the Percolation Threshold"
Matthew B. Hastings, Grant H. Watson, Roger G. Melko
Journal-ref: Phys. Rev. Lett. 112, 070501 (2014)
DOI: 10.1103/PhysRevLett.112.070501

Some of the base classes from this tag will be used in future projects, such as the Surface_Threshold repo