Refactor Simulation class

[anth-volk]

There are a few points where some refactoring would be beneficial. First, a few variables and methods have names that are unclear. Second, there are some fairly deeply nested logic structures, and while they may be required, it'd be great to try to make these clearer, perhaps by breaking out into separate functions/methods, where possible. Third, documentation for newer features is definitely lacking, making it tough to clean up certain issues.