Phase 1 of UW PBL (diag_TKE) CCPPization: move to atmos_phys; rearrange interstitials for vertical_diffusion/HB

[jimmielin]

Originator(s): @jimmielin

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)
• Phase 1 of UW PBL (Convert UW PBL (diag_TKE) scheme #330): moving to atmos_phys
• Phase 1 of UW PBL (Convert UW PBL (diag_TKE) scheme #330): 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

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

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?
All B4B
Part of new physics package (UW PBL for CAM5)

If yes to the above question, describe how this code was validated with the new/modified features:
CAM regression tests ALL PASS
CAM-SIMA regression tests ALL PASS