Complete CCPPization of HB PBL/vertical diffusion solver #410

jimmielin · 2025-08-04T15:21:35Z

Tag name (required for release branches): sima0_08_000
Originator(s): @jimmielin

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

Completes CCPPization of HB PBL scheme.
Completes CCPPization of vertical diffusion solver (no molecular diffusion).
Update FCAM4 testing.

Describe any changes made to build system: N/A

Describe any changes made to the namelist: N/A

List any changes to the defaults for the input datasets (e.g. boundary datasets): N/A

List all files eliminated and why: N/A

List all files added and what they do:

A       cime_config/testdefs/testmods_dirs/cam/outfrq_hb_vdiff_derecho/shell_commands
A       cime_config/testdefs/testmods_dirs/cam/outfrq_hb_vdiff_derecho/user_nl_cam
  - new testmods for vertical diffusion
  
A       cime_config/testdefs/testmods_dirs/cam/outfrq_se_cslam_analy_ic_cam4/shell_commands
A       cime_config/testdefs/testmods_dirs/cam/outfrq_se_cslam_analy_ic_cam4/user_nl_cam
  - new testmods for CAM4 to output all history variables from physics for a baseline

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

M       cime_config/testdefs/testlist_cam.xml
  - new vertical diffusion test
  - update FCAM4 test with new testmods dir

M       cime_config/testdefs/testmods_dirs/cam/outfrq_rk_stratiform_derecho/user_nl_cam
  - include snapshot fix for RK as pbuf_AST now included

M       src/data/registry.xml
  - add registry fields needed for vertical diffusion solver.
  - add registry entry for coords1d ddt.

If there are new failures (compared to the test/existing-test-failures.txt file),
have them OK'd by the gatekeeper, note them here, and add them to the file.
If there are baseline differences, include the test and the reason for the
diff. What is the nature of the change? Roundoff?

derecho/intel/aux_sima:

aux_sima_intel_20250930132119: 6 tests
  SMS_Ln9.ne3pg3_ne3pg3_mg37.FCAM4.derecho_intel.cam-outfrq_se_cslam_analy_ic_cam4 (Overall: DIFF) details:
  - new baseline

derecho/gnu/aux_sima:

aux_sima_gnu_20250930132121: 15 tests
  SMS_Ln2.ne3pg3_ne3pg3_mg37.FPHYStest.derecho_gnu.cam-outfrq_hb_vdiff_derecho (Overall: DIFF) details:
  SMS_Ln9.ne3pg3_ne3pg3_mg37.FCAM4.derecho_gnu.cam-outfrq_se_cslam_analy_ic_cam4 (Overall: DIFF) details:
  - new baselines

  SMS_Ln2.ne3pg3_ne3pg3_mg37.FPHYStest.derecho_gnu.cam-outfrq_rk_stratiform_derecho (Overall: DIFF) details:
  - changed snapshot file due to upstream CAM fix

If this changes climate describe any run(s) done to evaluate the new
climate in enough detail that it(they) could be reproduced:

CAM-SIMA date used for the baseline comparison tests if different than latest:

jimmielin · 2025-09-26T17:07:15Z

Preliminary pre-run of the SIMA regression tests in preparation for CAM tag 64_120 and merging of ESCOMP/atmospheric_physics#270

aux_sima_gnu_20250926091940: 15 tests
  SMS_Ln2.ne3pg3_ne3pg3_mg37.FPHYStest.derecho_gnu.cam-outfrq_hb_vdiff_derecho (Overall: DIFF) details:
  - new baseline

  SMS_Ln2.ne3pg3_ne3pg3_mg37.FPHYStest.derecho_gnu.cam-outfrq_rk_stratiform_derecho (Overall: DIFF) details:
  - new snapshot to maintain b4b-ness

  SMS_Ln9.ne3pg3_ne3pg3_mg37.FCAM4.derecho_gnu.cam-outfrq_se_cslam_analy_ic_cam4 (Overall: DIFF) details:
  - new baseline (changed use_case to _cam4 suffix)

aux_sima_intel_20250926091942: 6 tests
  SMS_Ln9.ne3pg3_ne3pg3_mg37.FCAM4.derecho_intel.cam-outfrq_se_cslam_analy_ic_cam4 (Overall: DIFF) details:
  - new baseline (changed use_case to _cam4 suffix)

@jimmielin

…usion solver (#270) Companion PRs: ESCOMP/CAM#1361 and ESCOMP/CAM-SIMA#410 Originator(s): @jimmielin Description (include issue title and the keyword ['closes', 'fixes', 'resolves'] and issue number): * Partial cleanup and refactoring of HB PBL scheme for CCPPization. * Completes #239. Moves HB (`hb_diff.F90`) both `compute_hb_diff` and `compute_hb_free_atm_diff` to atmospheric_physics `holtslag_boville.F90`. * Interstitials necessary for inputs into HB in `holtslag_boville_interstitials.F90`. * (is there an issue for diffusion solver?) Moves vertical diffusion solver (`compute_vdiff`) without molecular diffusion (i.e., not WACCM-X) into CCPPized schemes in `diffusion_solver.F90`. * Creates stub (zeroed outputs) interstitial schemes for Turbulent Mountain Stress (TMS) and Beljaars orographic surface drag and other code for WACCM (e.g., UBC; use of composition-dependent rair) in `diffusion_stubs.F90` -- schemes in this file will eventually be moved to their corresponding schemes, e.g., tms, beljaars, ubc, ... when they are fully CCPPized. List all namelist files that were added or changed: ``` A schemes/holtslag_boville/holtslag_boville_diff_options_namelist.xml A schemes/vertical_diffusion/vertical_diffusion_options_namelist.xml - separate "namelist" scheme for HB. - separate "namelist" scheme for diffusion solver. ``` List all files eliminated and why: N/A List all files added and what they do: ``` A to_be_ccppized/coords_1d.meta - metadata file for coords1d DDT. A to_be_ccppized/vdiff_lu_solver.F90 - LU solver for diffusion_solver.F90, moved from CAM A schemes/holtslag_boville/holtslag_boville_diff.F90 A schemes/holtslag_boville/holtslag_boville_diff.meta A schemes/holtslag_boville/holtslag_boville_diff_options.F90 A schemes/holtslag_boville/holtslag_boville_diff_options.meta - CCPPized Holtslag-Boville boundary layer scheme (originally hb_diff.F90) A schemes/holtslag_boville/holtslag_boville_diff_interstitials.F90 A schemes/holtslag_boville/holtslag_boville_diff_interstitials.meta - CCPPized interstitial schemes supporting inputs into HB. A schemes/vertical_diffusion/diffusion_solver.F90 A schemes/vertical_diffusion/diffusion_solver.meta A schemes/vertical_diffusion/vertical_diffusion_options.F90 A schemes/vertical_diffusion/vertical_diffusion_options.meta - CCPPized vertical diffusion solver without support for molecular diffusion (originally diffusion_solver.F90 in CAM) A schemes/vertical_diffusion/diffusion_stubs.F90 A schemes/vertical_diffusion/diffusion_stubs.meta - CCPPized stub for UBC (upper boundary conditions) - CCPPized stub for TMS (Turbulent Mountain Stress) surface orographic drag. - CCPPized stub for Beljaars surface orographic drag. - CCPPized stub for WACCM to use composition-dependent rair in vertical diffusion. A schemes/vertical_diffusion/vertical_diffusion_sponge_layer.F90 A schemes/vertical_diffusion/vertical_diffusion_sponge_layer.meta - CCPPized interstitial for sponge layer kvm (originally in vertical_diffusion_tend) A test/test_suites/suite_vdiff_holtslag_boville.xml - draft SDF for vertical diffusion using HB PBL scheme. ``` List all existing files that have been modified, and describe the changes: (Helpful git command: `git diff --name-status development...<your_branch_name>`) ``` M to_be_ccppized/coords_1d.F90 - make coords1d lowercase to workaround upstream framework limitation ``` List all automated tests that failed, as well as an explanation for why they weren't fixed: - CAM-SIMA will not build without removing `to_be_ccppized/nlte_fomichev.F90` due to dependency on CAM-only module `chem_surfvals` Is this an answer-changing PR? If so, is it a new physics package, algorithm change, tuning change, etc? B4B with CAM - new physics package If yes to the above question, describe how this code was validated with the new/modified features: * CAM regression tests: bit-for-bit unchanged as of cam6_4_107; compared against Derecho Intel only, Izumi tests will be ran before merging. * CAM-SIMA regression tests using new tests defined in ESCOMP/CAM-SIMA#410 bit-for-bit unchanged, except for Derecho GNU physics tests: - new baselines in hb_vdiff derecho gnu test (new test) - updated baselines in rk_stratiform test due to change in snapshots necessary due to CAM pbuf field change. and updated baselines in CAM4 tests due to adding HB PBL and vertical diffusion solver. --------- Co-authored-by: Jesse Nusbaumer <[email protected]>

@jimmielin

…for atmos_phys (#310) Tag name (The PR title should also include the tag name): atmos_phys0_18_000 Originator(s): @jimmielin @nusbaume List all `development` PR numbers included in this PR and the title of each: - Add Github action to use git-fleximod for externals checking #306 by @nusbaume - Complete CCPPization of Holtslag-Boville PBL scheme and vertical diffusion solver #270 by @jimmielin List all automated tests that failed, as well as an explanation for why they weren't fixed: All B4B in CAM verified via Izumi/Nag Izumi/GNU (previously via Derecho/Intel) B4B in SIMA with HB testcase see ESCOMP/CAM-SIMA#410

nusbaume

Thanks @jimmielin! I just had one request, but it doesn't require a re-review.

nusbaume · 2025-09-30T15:23:30Z

src/data/registry.xml

+      <long_name>should free atmosphere HB vertical diffusion apply non-water-vapor upward fluxes from coupler?</long_name>
+      <!-- should be false for CAM7 and true for CAM6; ignored elsewhere -->
+      <initial_value>.false.</initial_value>
+      <!--<initial_value phys_suite="cam6">.true.</initial_value>-->


I would either uncomment or delete this line.

Thanks, removed!

peverwhee

two small questions!

src/data/registry.xml

peverwhee

thanks @jimmielin !

jimmielin added 5 commits June 25, 2025 16:32

Add draft registry -- with coords1d

9472580

Merge branch 'development' into hplin/hb_diff

83d58e1

Draft tests; update RK snapshot

af62eed

Merge branch 'development' into hplin/hb_diff

6f8c144

Fix registry duplicates from merge

fb3d3ad

jimmielin self-assigned this Aug 4, 2025

jimmielin added this to CAM Development Aug 4, 2025

jimmielin added 2 commits August 15, 2025 00:23

Merge branch 'development' into hplin/hb_diff

e1f2fa3

Update testing namelists.

2fd28e2

jimmielin marked this pull request as ready for review August 15, 2025 05:24

jimmielin mentioned this pull request Aug 15, 2025

Complete CCPPization of Holtslag-Boville PBL scheme and vertical diffusion solver ESCOMP/atmospheric_physics#270

Merged

jimmielin added 5 commits August 26, 2025 10:28

Update registry with Beljaars stress stubs; free_atm clubbtop

fe4730d

Update qpert standard name.

e19a673

Change to apply_nonwv_cflx for free atm hb diff interstitial.

39bbd60

Merge branch 'development' into hplin/hb_diff

2f42e45

Add HB diagnostics to FCAM4 test

1be726c

jimmielin mentioned this pull request Sep 26, 2025

atmos_phys0_18_000: Complete CCPPization of HB scheme; fleximod test for atmos_phys ESCOMP/atmospheric_physics#310

Merged

jimmielin requested a review from nusbaume September 29, 2025 15:31

nusbaume approved these changes Sep 30, 2025

View reviewed changes

jimmielin requested a review from peverwhee September 30, 2025 16:55

peverwhee reviewed Sep 30, 2025

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jimmielin added 2 commits September 30, 2025 13:36

Merge branch 'development' into hplin/hb_diff

cc45df2

Address review comments

5ee114d

jimmielin requested a review from peverwhee September 30, 2025 17:39

peverwhee approved these changes Sep 30, 2025

View reviewed changes

Update atmos_phys to atmos_phys0_18_000

f3b7cbe

jimmielin merged commit 6337cc0 into ESCOMP:development Sep 30, 2025
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github-project-automation bot moved this to Tag in CAM Development Sep 30, 2025

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Complete CCPPization of HB PBL/vertical diffusion solver #410

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jimmielin commented Aug 4, 2025 •

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Complete CCPPization of HB PBL/vertical diffusion solver #410

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