Numpy cleaning and moving output

I changes slightly importing from numpy.

I moved function outside another functions. What about having a separate file for common physics equations?
 
I moved output relate stuff to the new file (IMO it was too much related to output in file rhs_l...). I didn't finish chem part - need help.

I add some simple test - comparing the output with reference one. 

dt * np.arange(0, nt+1, outfreq) ?