Complete CCPPization of CAM5 UW PBL scheme (diag_TKE) by jimmielin · Pull Request #370 · ESCOMP/atmospheric_physics

jimmielin · 2026-03-09T16:10:12Z

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

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

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       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:

…itial

…and ndrop vertical mixing stub

…e standard name (need CAM update) -- refactor for CAM4/5 cross-compat

nusbaume

Thank you so much for helping bring in our first (!) CAM5 physics scheme @jimmielin! I realize I have what look like a ton of comments, but hopefully the vast majority of them are easy to resolve. Of course if you have any questions, comments, or concerns with any of my suggestions then just let me know. Thanks again!

nusbaume · 2026-04-13T16:37:26Z

+    use ccpp_constituent_prop_mod, only: ccpp_constituent_prop_ptr_t
+
+    ! dependency to get constituent index
+    use ccpp_const_utils,          only: ccpp_const_get_idx


Can we use the CCPP-framework equivalent for this?

Suggested change

use ccpp_const_utils, only: ccpp_const_get_idx

use ccpp_scheme_utils, only: ccpp_const_get_idx=>ccpp_constituent_index

This way we can eventually get rid of the helper scheme we currently have in atmospheric_physics.

Thanks for the suggestion! I think this doesn't have an equivalent stub in CAM yet - https://github.com/ESCOMP/CAM/blob/cam_development/src/utils/cam_ccpp/ccpp_scheme_utils.F90 is a no-op stub right now. I am happy to write the stub but that adds yet another tangential fix to the stub which will be a nightmare to my house of cards.

I added a CAM issue to write the stub: ESCOMP/CAM#1541

The atmos_phys issue is existing: #215 - I can volunteer at the end of CAM5 to sweep through all of these once the stub is in, if that is OK?

Thanks for the response @jimmielin! I'm leaving this comment open so that we remember, but otherwise will consider it resolved for the purposes of this PR.

Co-authored-by: Jesse Nusbaumer <nusbaume@ucar.edu>

nusbaume

Thanks for responding to all my comments @jimmielin! I just had a few final questions/suggestions.

nusbaume · 2026-04-23T16:56:55Z

+    use ccpp_constituent_prop_mod, only: ccpp_constituent_prop_ptr_t
+
+    ! dependency to get constituent index
+    use ccpp_const_utils,          only: ccpp_const_get_idx


Thanks for the response @jimmielin! I'm leaving this comment open so that we remember, but otherwise will consider it resolved for the purposes of this PR.

nusbaume · 2026-04-23T20:43:43Z

+# these are for the diffusion solver to compute implicit surface stress.
+# for UW PBL, this is taux = wsx; tauy = wsy
+# currently handled by hb_prepare_vertical_diffusion_inputs run phase.
+#[ taux ]


Thanks for the explanation! Maybe we can get a scientist's input on this whenever we open the "future work" PR. For now I'll leave it open so we can find this again, but will consider it "resolved" for this particular PR.

nusbaume · 2026-04-23T21:38:44Z

+    type(ccpp_constituent_prop_ptr_t), &
+                        intent(in)  :: const_props(:)          ! CCPP constituent properties pointer


I'm going to leave this comment open so that we can remember to remove the const_props input once we do the constituent subroutine update, but will consider this "resolved" for this particular PR. Thanks!

…ospheric_physics into hplin/diag_tke_rebase_main

nusbaume

Thanks again for all of this work @jimmielin! I had one last comment-fix that was missed from earlier, but otherwise everything looks great to me. Thanks again!

peverwhee

Apologies for the delay on this! A few (mostly aesthetic) requests.

jimmielin · 2026-05-12T22:13:35Z

Thanks @nusbaume and @peverwhee for your reviews and comments!

This should be ready for merging once a CAM tag is assigned. I did a test run of Nag tests:

GNU all passed
Nag all passed except the known failure subcolumn test

When Derecho is back I can do a test run there as well to ensure atmos_phys is all good then it'll just have to wait for its turn in the CAM tagging queue.

jimmielin added 15 commits March 9, 2026 11:58

Initial push of UW PBL

86dd6e9

Update interfaces to run phase

a972d91

Refactor HB: move kinematic fluxes and obklen to common vdiff interst…

a3a6794

…itial

Draft metadata

a544023

Remove unused metadata that was removed

8e83bb0

Keep removing moved metadata

3e6fb40

Keep removing moved metadata (2)

1f935fc

Initial fixes for b4b in SIMA -- up to constituent diffusion

633b8a6

Fix for ESCOMP#332

06fdad4

Handle dropmixnuc; batch of fixes for constituent vertical diffusion …

8de2a05

…and ndrop vertical mixing stub

Change cflx from coupler to from interstitial

92c64a8

Do not mutate const_array; mutate q1 in vdiff ndropmixed alternate

0a75ad2

Sketch out UW PBL diagnostics; REARRANGE HB tautotx/tautoty and chang…

ca7f025

…e standard name (need CAM update) -- refactor for CAM4/5 cross-compat

Fix turbtype_real dimension to pverp

7896907

Remove extraneous comments (as they are documented in the actual scheme)

c47066c

jimmielin self-assigned this Mar 9, 2026

jimmielin added the enhancement New feature or request label Mar 9, 2026

jimmielin added this to CAM Development Mar 9, 2026

jimmielin mentioned this pull request Mar 9, 2026

Complete CCPPization of CAM5 UW (diag_TKE) PBL scheme; cleanup to vertical_diffusion_tend ESCOMP/CAM#1445

Open

Fix qrl unit - should be adj by pressure thickness

f7ca8e7

jimmielin requested a review from nusbaume March 11, 2026 16:36

jimmielin mentioned this pull request Mar 17, 2026

Science/Cleanup: Verify handling of surface stresses for PBL scheme vs. diffusion solver #309

Open

nusbaume requested changes Apr 21, 2026

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Merge branch 'main' into hplin/diag_tke_rebase_main

ea0f256

jimmielin and others added 2 commits April 21, 2026 17:11

Address review comments.

7b38644

Update schemes/bretherton_park/bretherton_park_diff.meta

466253f

Co-authored-by: Jesse Nusbaumer <nusbaume@ucar.edu>

jimmielin requested a review from nusbaume April 21, 2026 21:12

nusbaume requested changes Apr 23, 2026

View reviewed changes

jimmielin added 3 commits April 23, 2026 22:06

Fix qrl output unit

f70b041

Address review comments

04d7c80

Merge branch 'hplin/diag_tke_rebase_main' of github.com:jimmielin/atm…

a82989a

…ospheric_physics into hplin/diag_tke_rebase_main

jimmielin requested a review from nusbaume April 24, 2026 18:36

nusbaume approved these changes Apr 24, 2026

View reviewed changes

Comment thread schemes/bretherton_park/eddy_diffusivity_adjustment_above_pbl_namelist.xml Outdated

nusbaume requested a review from peverwhee April 24, 2026 21:32

jimmielin and others added 2 commits April 24, 2026 18:02

Fix namelist comment

7742067

Merge branch 'main' into hplin/diag_tke_rebase_main

401c2ba

peverwhee requested changes May 11, 2026

View reviewed changes

jimmielin mentioned this pull request May 12, 2026

Change coords1d ddt metadata units to Pa #391

Open

Address second reviewer comments

a73195d

jimmielin requested a review from peverwhee May 12, 2026 03:31

peverwhee approved these changes May 12, 2026

View reviewed changes

	use ccpp_const_utils, only: ccpp_const_get_idx
	use ccpp_scheme_utils, only: ccpp_const_get_idx=>ccpp_constituent_index

		type(ccpp_constituent_prop_ptr_t), &
		intent(in) :: const_props(:) ! CCPP constituent properties pointer

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jimmielin commented Mar 9, 2026 •

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