That's the thing. Fitness is an unknown that can only be evaluated through competition/survival. There is a function that compares organism size (the number of cells) and bigger organisms win collisions. But just because being bigger has an advantage, doesn't mean that size is the only determining factor. Organisms can move/reproduce in such a way that they end up colliding with their direct relatives, so like parents killing children. That is obviously not good for collective survival. On the other hand smaller organisms may be more organized, so the damage they inflict adds to self-inflicted damage by the bigger organisms, so the smaller ones end up winning.
Can you explain how you are evaluating fitness? Your readme says that it's based on collective success rather than individual. How do you score that?