stepon.F:

• Used prognostics, which is eliminated in 3.5.07, and now use dyn_comp.
• dynpkg, which is eliminated in 3.5.07, replaced now by dyn_run.
• d_p_coupling
  • geopotential
• physpkg
• p_d_coupling

physpkg.F:
calls physics initialization routines

• phys_init
  • gw_inti
  • verticaL_diffusion_init

• phys_run1
  • tphysbc

• phys_run2
  • tphysac: which calls major and minor diffusion routines.
    • vertical_diffusion: uses routines in diffusion_solver, which calls compute_molec_diff. Have to figure out how to modify eddy_diff.
    • mspd_intr

chemistry.F90: change the ubc.
physics_types.F90: calls physics_update, geopotential.