def write_settings in io.py has the random seed and the size of the simulation as hardcoded.

These should not be hardcoded. They should be options that a person can set in the Project class ("kmc_model" object) and the numbers should be pulled from there. The random seed might need to be converted into a PRNG object, which means it might need to be converted into something like 30 digits even if it is one digit.