Improve NRM submodel

[artgoldberg]

1. remove reaction_index from self.dependencies[reaction_index] and eliminate the if at line 207
2. discuss how to choose between SSA (the Direct Method) and NRM in a model
3. add logging to the NRM submodel
4. consider this NRM submodel optimization: compute dependencies on species shared with continuous submodels dynamically; no dependency exists if the slope has been 0 since the last reaction was executed. (don't need to look further back, because if the slope was non-0 before the previous reaction, then the propensity would have been calculated then)

[artgoldberg]

Did 1.