Simple hdf5

adding a simple hdf output
still thinking about:
* what attribute we should add
* creating a new file each calling vs one file for entire simulation

I changed in parcel.py  rhs.diag(rhod, th_d, r_v, t * rhs.dt) ---> rhs.diag(rhod, th_d, r_v, (t+1) * rhs.dt), since for initial output was t=0 and for first time step was also t=0.