Fixing the problem that km_opt=5 breaks km_opt=2 and cleaning codes

[zhangxsms]

TYPE: bug fix

KEYWORDS: SMS-3DTKE, package

SOURCE: Xu Zhang (Shanghai Typhoon Institute)

DESCRIPTION OF CHANGES:

1. Redefined the variable l_scale using a new name l_diss, which does not conflict with
   variables used in km_opt=2.
2. Packaged seven variables used in the km_opt=5.
3. Deleted most diagnostic variables such as u_h_tend, v_h_tend, w_h_tend that are
   seldom used by most users, and cleaned up the related codes. Only seven state variables used
   in km_opt=5 are left.

LIST OF MODIFIED FILES:
Registry/Registry.EM_COMMON
Registry/Registry.NMM
dyn_em/module_diffusion_em.F
dyn_em/module_first_rk_step_part2.F
dyn_em/solve_em.F
share/module_check_a_mundo.F

TESTS CONDUCTED:

• em_fire test with km_opt=2.
• em_les tests with km_opt=2 and km_opt=5.
• em_tropical_cyclone with km_opt=2, km_opt=5, and some PBL schemes.

[davegill]

Generic comment to reviewers @weiwangncar @dudhia @smileMchen @kkeene44
Even though this is a bug fix, this is a bug-fix that correctly belongs on the develop branch. This fixes a problem that is only on the develop branch right now.

[davegill]

@zhangxsms @dudhia @weiwangncar
With km_opt=5, I am trying an idealized case which has sf_sfclay_surface = 0, 0, 0,
I am getting this error:

--- ERROR: SMS-3DTKE scheme works with sf_sfclay_physics = 1,5,91
  --- ERROR: Fix km_opt or sf_sfclay_physics in namelist.input.

Is it mandatory that a surface layer scheme be used with km_opt=5? If not, the test in check_a_mundo needs to be corrected.

[zhangxsms]

@zhangxsms @dudhia @weiwangncar
With km_opt=5, I am trying an idealized case which has sf_sfclay_surface = 0, 0, 0,
I am getting this error:

--- ERROR: SMS-3DTKE scheme works with sf_sfclay_physics = 1,5,91
  --- ERROR: Fix km_opt or sf_sfclay_physics in namelist.input.

Is it mandatory that a surface layer scheme be used with km_opt=5? If not, the test in check_a_mundo needs to be corrected.

It is not mandatory, km_opt=5 can be used without surface layer (sf_sfclay_physics = 0).

[davegill]

@zhangxsms
The last commit should address the ability to run with NO surface layer scheme.

[davegill]

@weiwangncar @dudhia @llpcarson @kkeene44
Folks,
I need Wei or Jimy to approve as this is physics related, and I need Laurie to approve as I added a line in the NMM registry (for a check_a_mundo mod).

Kelly is there because she has superpowers and can approve anything at all, but let's do this by the book.