Merge pull request #52 from fophillips/minor-refactors

A number of small code refactors
Add species diffusivity.

Add 'diffusivity' param to species, use species grids from agent
container when constructing diffusivity grid.
Refactor if statements
Add diffusivity to output
Move reset of species grid to 0 to fitSpeciesMassOnGrid
Fix, pass simulator to species fit
TODO FIX remove call to calculateComputationDomainGrids before agentgrid is defined
Prevent rock from moving