Complete CCPPization of CAM5 UW PBL scheme (diag_TKE)

[jimmielin]

Tag name (The PR title should also include the tag name):
Originator(s): @jimmielin

Companion PR in CAM - ESCOMP/CAM#1445

Description (include issue title and the keyword ['closes', 'fixes', 'resolves'] and issue number):

• Fix qmin for chemistry/aerosol species read in from snapshot are incorrectly initialized in initialize_constituents #332 (incorrect qmin for initialize_constituents from snapshot)
• Completes Convert UW PBL (diag_TKE) scheme #330 - CCPPizes UW PBL scheme (diag_TKE)
• CCPPize UW interstitial to adjust diffusivity above PBL
• Rearranging of interstitials for vertical diffusion, to accommodate for using either HB or UW PBL: new interstitial for handling Coords1D and potential temperature; new interstitial for computing kinematic water vapor flux and Obklen.
• New stub to only zero out Beljaars, not TMS - used for CAM5 snapshot tests (TMS on, Beljaars off)

List all namelist files that were added or changed:

A       schemes/bretherton_park/bretherton_park_diff_namelist.xml
A       schemes/bretherton_park/eddy_diffusivity_adjustment_above_pbl_namelist.xml
  - for UW PBL

List all files eliminated and why: N/A

List all files added and what they do:

A       schemes/bretherton_park/bretherton_park_diff.F90
A       schemes/bretherton_park/bretherton_park_diff_namelist.xml
  - initial CCPPized subroutines for UW PBL

A       schemes/bretherton_park/eddy_diff.F90
  - moved from CAM (main driver module for UW PBL)

A       schemes/bretherton_park/eddy_diffusivity_adjustment_above_pbl.F90
A       schemes/bretherton_park/eddy_diffusivity_adjustment_above_pbl.meta
A       schemes/bretherton_park/eddy_diffusivity_adjustment_above_pbl_namelist.xml
  - mini-scheme used by the end of UW PBL

A       schemes/vertical_diffusion/vertical_diffusion_interstitials.F90
A       schemes/vertical_diffusion/vertical_diffusion_interstitials.meta
  - new interstitial for common vertical diffusion schemes
  - new interstitial for computing kinematic fluxes and Obukhov length

A       test/test_suites/suite_vdiff_bretherton_park.xml
  - SDF file

A       schemes/sima_diagnostics/bretherton_park_diff_diagnostics.F90
A       schemes/sima_diagnostics/bretherton_park_diff_diagnostics.meta
  - diagnostics for UW PBL

List all existing files that have been modified, and describe the changes:
(Helpful git command: git diff --name-status development...<your_branch_name>)

M       schemes/holtslag_boville/holtslag_boville_diff.F90
M       schemes/holtslag_boville/holtslag_boville_diff.meta
M       schemes/holtslag_boville/holtslag_boville_diff_interstitials.F90
M       schemes/holtslag_boville/holtslag_boville_diff_interstitials.meta
  - rearrange interstitials

M       schemes/sima_diagnostics/diffusion_solver_diagnostics.F90
  - comment update to clarify which surface stress is used here

M       schemes/vertical_diffusion/diffusion_solver.F90
M       schemes/vertical_diffusion/diffusion_solver.meta
  - init phase: changes for dropmixnuc (ndrop vertical mixing)-handled species to skip diffusion solver for tracers

M       schemes/vertical_diffusion/diffusion_stubs.F90
M       schemes/vertical_diffusion/diffusion_stubs.meta
  - new stub to only zero out Beljaars, not TMS
  - new stub for handling surface fluxes for dropmixnuc (ndrop vertical mixing)-handled species

M       suites/suite_cam4.xml
M       test/test_suites/suite_vdiff_holtslag_boville.xml
  - rearrange interstitials

M       test/test_schemes/initialize_constituents.F90
  - fix for #332 qmin incorrect for chemistry and aerosols species when initialized from snapshot

M       schemes/sima_diagnostics/diffusion_solver_diagnostics.F90
M       schemes/sima_diagnostics/diffusion_solver_diagnostics.meta
  - standard name update for clarity

List all automated tests that failed, as well as an explanation for why they weren't fixed:

Is this an answer-changing PR? If so, is it a new physics package, algorithm change, tuning change, etc?

If yes to the above question, describe how this code was validated with the new/modified features: