Move circ_mod_cont -related parts of input and output to circ_mod_cont

I want to experiment with a different type of circ_mod. Swapping out the circ_mod will make the input and output fail. We should think about how we can move the content specific to the species in the circ_mod to the circ_mod while leaving the geometry-related input/output parsing/constructing in the input/output modules respectively.