I have an implementation of a data structure I have to study for a group project (Fibonacci heaps if you're interested). I'm asked to compare the theoretical results of the operations in amortized time, with the running times of my implementation. Now my question: since amortized times are based on the fact that we look not just at a single operation, but at a series of operations, what can I do with my implementation to receive some experimental results that support (or not) my theoretical analysis?
If you want to compare theory and experiment, you have to perform both analyses under the same assumptions.
Note that this includes what you measure. Since you did not analyse time in theory, there is little sense in measuring running times in the experiments. Use combinatoric measures you can count reliably and independently of the system and its load.