A number of small code refactors.

- Remove meaningless variable name 'value'
- Add method to SpeciesParam to specify a default value to avoid checking for NaNs over and over
- Add IntelliJ files, random.state, results and bin to gitignore
- Fix typos in documentation
- Add error message to ReactionFactor to improve debugging
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