Add Kennedy simphydro to ELM #3001

pnlfang · 2019-06-17T17:37:26Z

Adding plant hydraulics model of Kennedy et al. (2019).

Kennedy, D., S. Swenson, K. W. Oleson, D. M. Lawrence, R. Fisher, A. C. L. da Costa,
and P. Gentine (2019), Implementing Plant Hydraulics in the Community Land Model,
Version 5, J Adv Model Earth Sy, 11(2), 485-513, doi:10.1029/2018MS001500.

[BFB]

thorntonpe · 2019-06-17T17:41:13Z

@pnlfang has this PR gone through any testing with the test suites? Is it BFB?

rljacob · 2019-06-17T17:48:32Z

Is this a v2 feature? Its needs a pointer to a design document.

https://acme-climate.atlassian.net/wiki/spaces/ED/pages/976946346/W2%2B-%2BPlant%2BHydraulics

pnlfang · 2019-06-17T19:31:56Z

@pnlfang has this PR gone through any testing with the test suites? Is it BFB?
@thorntonpe I'm working on it.

bishtgautam

There are multiple new lines that have been commented. These new lines were probably used for debugging the model and can be deleted now.

components/clm/src/biogeophys/SoilWaterMovementMod.F90

components/clm/src/biogeophys/PhotosynthesisMod.F90

bishtgautam · 2019-06-27T18:04:03Z

components/clm/src/biogeophys/PhotosynthesisMod.F90

+      lai_z_sun     =>    canopystate_inst%laisun_z_patch     ! Input:  [real(r8) (:,:) ]  leaf area index for canopy layer, sunlit or shaded
+      vcmaxcint_sun =>    surfalb_inst%vcmaxcintsun_patch     ! Input:  [real(r8) (:)   ]  leaf to canopy scaling coefficient
+      alphapsn_sun  =>    photosyns_inst%alphapsnsun_patch    ! Input:  [real(r8) (:)   ]  13C fractionation factor for PSN ()
+      !o3coefv_sun   =>    ozone_inst%o3coefvsun_patch         ! Input:  [real(r8) (:)   ]  O3 coefficient used in photosynthesis calculation


Please delete the commented out lines

bishtgautam · 2019-06-27T18:04:44Z

components/clm/src/biogeophys/PhotosynthesisMod.F90

+      ! Photosynthesis and stomatal conductance parameters, from:
+      ! Bonan et al (2011) JGR, 116, doi:10.1029/2010JG001593
+      !==============================================================================!
+! calculate root-soil interface conductance 


Please indent this comment and multiple comments that are below

bishtgautam · 2019-06-27T18:07:14Z

components/clm/src/biogeophys/PhotosynthesisMod.F90

+
+               ! Compare with Ball-Berry model: gs_mol = m * an * hs/cs p + b
+
+               hs = (gb_mol(p)*ceair + gs_m


Please delete the commented out lines

bishtgautam · 2019-06-27T18:07:20Z

components/clm/src/biogeophys/PhotosynthesisMod.F90

+
+               ! Compare with Ball-Berry model: gs_mol = m * an * hs/cs p + b
+
+               hs = (gb_mol(p)*ceair + gs_m


Please delete the commented out lines

bishtgautam · 2019-06-27T18:07:54Z

components/clm/src/biogeophys/PhotosynthesisMod.F90

+
+               ! Compare with Ball-Berry model: gs_mol = m * an * hs/cs p + b
+
+               hs = (gb_mol(p)*ceair + gs_m


Please delete the commented out lines

bishtgautam · 2019-06-27T18:08:02Z

components/clm/src/biogeophys/PhotosynthesisMod.F90

+
+               ! Compare with Ball-Berry model: gs_mol = m * an * hs/cs p + b
+
+               hs = (gb_mol(p)*ceair + gs_m


Please delete the commented out lines

bishtgautam · 2019-06-27T18:08:08Z

components/clm/src/biogeophys/PhotosynthesisMod.F90

+
+               ! Compare with Ball-Berry model: gs_mol = m * an * hs/cs p + b
+
+               hs = (gb_mol(p)*ceair + gs_m


Please delete the commented out lines

jqyin · 2019-07-12T18:08:18Z

@pnlfang just to follow up, is this PR bit-for-bit against the test suites?

pnlfang · 2019-07-15T16:44:47Z

@jqyin yes

rljacob · 2019-08-07T21:40:18Z

@bishtgautam please re-review to see if your requested changes were made.

bishtgautam

Please delete the commented out lines.

bishtgautam · 2019-08-07T22:13:12Z

components/clm/src/biogeophys/PhotosynthesisMod.F90

+!               if (      stomatalcond_mtd == stomatalcond_mtd_bb1987 )then
+                  gsminsun = bbb(p)
+                  gsminsha = bbb(p)
+!               else if ( stomatalcond_mtd == stomatalcond_mtd_medlyn2011 )then


Please delete the commented out lines.

rljacob · 2019-08-08T16:12:59Z

@jqyin please start merging this.

rljacob · 2019-08-08T18:20:35Z

Nevermind, still needs a code review document approval from @kvcalvin

thorntonpe

@pnlfang I'm sorry for the slow action on this review. I have two questions/suggestions: If there is a new namelist variable that triggers this capability, could you add that as documentation in the design document? And have you considered adding a new test to the land developer's test suite to protect this new capability against unintended harm by subsequent PRs? I think with so much new mechanism within the model it would be wise to have both a multi-day smoke test and an exact restart test.

pnlfang · 2019-08-27T15:36:50Z

@thorntonpe I added a new namelist variable "use_hydrstress" to trigger this capability. This capability also requires an updated clm_params parameter file, which needs to be parameterized for application. I'll add this in the design document. I have a global test case that could potentially be added to the land developer's test suit.

rljacob · 2019-10-17T18:42:47Z

Reassigning to balance load.

rljacob · 2019-10-24T00:35:28Z

@thorntonpe can you please finish the review for this?

rljacob · 2019-10-24T18:02:49Z

@bishtgautam looks like this can finally be merged.

bishtgautam · 2019-10-24T22:44:01Z

Today I re-merged #3107, so I will merge this PR tomorrow.

Adding plant hydraulics model of Kennedy et al. (2019). Kennedy, D., S. Swenson, K. W. Oleson, D. M. Lawrence, R. Fisher, A. C. L. da Costa, and P. Gentine (2019), Implementing Plant Hydraulics in the Community Land Model, Version 5, J Adv Model Earth Sy, 11(2), 485-513, doi:10.1029/2018MS001500. [BFB]

rljacob added the Land label Jun 17, 2019

rljacob assigned jqyin Jun 17, 2019

rljacob changed the title ~~Pnlfang elm simphydro~~ Add Kennedy simphydro to ELM Jun 17, 2019

bishtgautam added this to the v2.0alpha milestone Jun 17, 2019

pnlfang closed this Jun 17, 2019

pnlfang reopened this Jun 17, 2019

yfang-repo added 5 commits June 17, 2019 17:33

Add simple phs scheme from Kennedy et al.

839ac63

Add simple phs scheme from Kennedy et al.

534d515

Add name for Kenney PHS model

2d19f52

Resolve conflicts.

064457b

Resolving conflicts after rebase

fcd0c3d

pnlfang force-pushed the pnlfang_elm_simphydro branch from c041942 to fcd0c3d Compare June 19, 2019 18:33

jqyin requested review from thorntonpe and bishtgautam June 27, 2019 14:08

bishtgautam requested changes Jun 27, 2019

View reviewed changes

yfang-repo added 5 commits June 28, 2019 10:28

Clean up the code

8f8ad26

Correct error

a54ad57

Add variables for restart with PHS option

675243c

Add variables for restart with PHS option

491acb4

Change data type

83435ac

jqyin added the BFB PR leaves answers BFB label Jul 15, 2019

bishtgautam requested changes Aug 7, 2019

View reviewed changes

bishtgautam self-requested a review August 7, 2019 22:21

bishtgautam approved these changes Aug 7, 2019

View reviewed changes

rljacob modified the milestones: v2.0alpha, v2.0BGC Aug 22, 2019

thorntonpe reviewed Aug 26, 2019

View reviewed changes

rljacob modified the milestones: v2.0alpha, v2.0alphaBGC Aug 30, 2019

rljacob assigned bishtgautam and unassigned jqyin Oct 17, 2019

thorntonpe approved these changes Oct 24, 2019

View reviewed changes

bishtgautam merged commit 83435ac into master Oct 28, 2019

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Add Kennedy simphydro to ELM #3001

Add Kennedy simphydro to ELM #3001

pnlfang commented Jun 17, 2019 •

edited by bishtgautam

thorntonpe commented Jun 17, 2019 •

edited by pnlfang

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jqyin commented Jul 12, 2019

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pnlfang commented Aug 27, 2019 •

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rljacob commented Oct 17, 2019

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rljacob commented Oct 24, 2019

bishtgautam commented Oct 24, 2019


		! Compare with Ball-Berry model: gs_mol = m * an * hs/cs p + b

		hs = (gb_mol(p)*ceair + gs_m

Add Kennedy simphydro to ELM #3001

Add Kennedy simphydro to ELM #3001

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pnlfang commented Jun 17, 2019 • edited by bishtgautam

thorntonpe commented Jun 17, 2019 • edited by pnlfang

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pnlfang commented Aug 27, 2019 • edited

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pnlfang commented Jun 17, 2019 •

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