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
- tphysac: which calls major and minor diffusion routines.
chemistry.F90: change the ubc.
physics_types.F90: calls physics_update, geopotential.