Create more flexible run loop

In testbench mode, we need to read input data every time step (#61) and possibly verify tendencies from physics (#24). However, when running a normal run, we only read in initial data.

In addition, we need a more flexible way to decide what physics suite(s) to run. At the least, physics and chemistry suite names should be read in via namelist variables.

Create a somewhat flexible, interim run sequence to handle these situations.