Merge branch 'woodCN_fixes'

Allow for resorbtion in transition from live to dead wood N

This PR allows for resorbtion in transition from live to dead wood N,
which also moves to NPOOL for free.

Resolves #443

cime_config/testdefs/ExpectedTestFails.xml

@@ -37,6 +37,13 @@
     </phase>
   </test>
 
+  <test name="ERS_Ln9.ne0ARCTICne30x4_ne0ARCTICne30x4_mt12.IHistClm50SpGs.cheyenne_intel.clm-clm50cam6LndTuningMode_1979Start">
+    <phase name="COMPARE_base_rest">
+      <status>FAIL</status>
+      <issue>#1117</issue>
+    </phase>
+  </test>
+
   <!-- fates test suite failures -->
 
   <test name="ERS_Ld60.f45_f45_mg37.I2000Clm45Fates.hobart_nag.clm-Fates">

doc/ChangeLog

@@ -1,4 +1,125 @@
 ===============================================================
+Tag name:  ctsm1.0.dev109
+Originator(s):  negins (Negin Sobhani,UCAR/TSS,303-497-1224)
+Date: Thu Aug 20 11:40:07 MDT 2020
+One-line Summary: Allow for resorbtion in transition from live to dead wood N
+
+Purpose of changes
+------------------
+
+This PR allows for resorbtion in transition from live to dead wood N, which also move
+to NPOOL for free.
+
+Bugs fixed or introduced
+------------------------
+
+Issues fixed (include CTSM Issue #): Issue #443
+
+
+Significant changes to scientifically-supported configurations
+--------------------------------------------------------------
+
+Does this tag change answers significantly for any of the following physics configurations?
+(Details of any changes will be given in the "Answer changes" section below.)
+
+[x] clm5_0
+
+[x] ctsm5_0-nwp
+
+[ ] clm4_5
+
+Notes of particular relevance for users
+---------------------------------------
+
+Caveats for users (e.g., need to interpolate initial conditions): None
+
+Changes to CTSM's user interface (e.g., new/renamed XML or namelist
+variables): None
+
+Changes made to namelist defaults (e.g., changed parameter values): None
+
+Changes to the datasets (e.g., parameter, surface or initial files): None
+
+Substantial timing or memory changes: [For timing changes, can check PFS test(s) in the test suite]
+
+Notes of particular relevance for developers: None
+---------------------------------------------
+NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide
+
+Caveats for developers (e.g., code that is duplicated that requires double maintenance):
+
+Changes to tests or testing: None
+
+Code reviewed by: Erik Kluzek
+
+
+CTSM testing:
+
+ [PASS means all tests PASS and OK means tests PASS other than expected fails.]
+
+  build-namelist tests:
+
+    cheyenne - not run
+
+  tools-tests (test/tools):
+
+    cheyenne - not run
+
+  PTCLM testing (tools/shared/PTCLM/test):
+
+    cheyenne - not run
+
+  python testing (see instructions in python/README.md; document testing done):
+
+    (any machine) - not run
+
+  regular tests (aux_clm):
+
+    cheyenne ---- PASS
+    izumi ------- PASS
+
+If the tag used for baseline comparisons was NOT the previous tag, note that here:
+
+
+Answer changes
+--------------
+
+Changes answers relative to baseline: YES
+
+
+  If a tag changes answers relative to baseline comparison the
+  following should be filled in (otherwise remove this section):
+
+  Summarize any changes to answers, i.e.,
+    - what code configurations: Clm50 with Bgc or Cn
+    - what platforms/compilers: all
+    - nature of change (roundoff; larger than roundoff/same climate; new
+	climate): larger than roundoff/same climate
+
+   If bitwise differences were observed, how did you show they were no worse
+   than roundoff?
+
+   If this tag changes climate describe the run(s) done to evaluate the new
+   climate (put details of the simulations in the experiment database)
+
+   Will Wieder thought the changes were small enough that we didn't need to do
+   a long simulation. Erik Kluzek thinks the changes were verified with single
+   point simulations. 
+
+
+   URL for LMWG diagnostics output used to validate new climate:
+
+
+Detailed list of changes
+------------------------
+
+List any externals directories updated (cime, rtm, mosart, cism, fates, etc.):
+
+Pull Requests that document the changes (include PR ids):
+(https://github.com/ESCOMP/ctsm/pull)
+
+===============================================================
+===============================================================
 Tag name:  ctsm1.0.dev108
 Originator(s):  erik (Erik Kluzek,UCAR/TSS,303-497-1326)
 Date: Wed Aug 19 17:23:47 MDT 2020

doc/ChangeSum

@@ -1,5 +1,6 @@
 Tag                   Who      Date  Summary
 ============================================================================================================================
+  ctsm1.0.dev109   negins 08/20/2020 Allow for resorbtion in transition from live to dead wood N
   ctsm1.0.dev108     erik 08/19/2020  Update default PE layouts for new SE/FV3 grids
   ctsm1.0.dev107     erik 08/10/2020 Answer changes needed for CESM2.2.0
   ctsm1.0.dev106     erik 08/06/2020 Bit-for-bit updates for the CESM2.2.0 release

src/biogeochem/CNNStateUpdate1Mod.F90

@@ -88,6 +88,7 @@ end subroutine NStateUpdateDynPatch
   !-----------------------------------------------------------------------
   subroutine NStateUpdate1(num_soilc, filter_soilc, num_soilp, filter_soilp, &
        cnveg_nitrogenflux_inst, cnveg_nitrogenstate_inst, soilbiogeochem_nitrogenflux_inst) 
+     use CNSharedParamsMod               , only : use_fun
     !
     ! !DESCRIPTION:
     ! On the radiation time step, update all the prognostic nitrogen state
@@ -98,7 +99,7 @@ subroutine NStateUpdate1(num_soilc, filter_soilc, num_soilp, filter_soilp, &
     integer                                 , intent(in)    :: filter_soilc(:) ! filter for soil columns
     integer                                 , intent(in)    :: num_soilp       ! number of soil patches in filter
     integer                                 , intent(in)    :: filter_soilp(:) ! filter for soil patches
-    type(cnveg_nitrogenflux_type)           , intent(in)    :: cnveg_nitrogenflux_inst
+    type(cnveg_nitrogenflux_type)           , intent(inout) :: cnveg_nitrogenflux_inst
     type(cnveg_nitrogenstate_type)          , intent(inout) :: cnveg_nitrogenstate_inst
     type(soilbiogeochem_nitrogenflux_type)  , intent(inout) :: soilbiogeochem_nitrogenflux_inst
     !
@@ -189,6 +190,13 @@ subroutine NStateUpdate1(num_soilc, filter_soilc, num_soilp, filter_soilp, &
             ns_veg%deadcrootn_patch(p)   = ns_veg%deadcrootn_patch(p) + nf_veg%livecrootn_to_deadcrootn_patch(p)*dt
             ns_veg%livecrootn_patch(p)   = ns_veg%livecrootn_patch(p) - nf_veg%livecrootn_to_retransn_patch(p)*dt
             ns_veg%retransn_patch(p)     = ns_veg%retransn_patch(p)   + nf_veg%livecrootn_to_retransn_patch(p)*dt
+            ! WW change logic so livestem_retrans goes to npool (via free_retrans flux)
+            ! this should likely be done more cleanly if it works, i.e. not update fluxes w/ states
+            ! additional considerations for crop?
+            if (use_fun ) then
+               nf_veg%free_retransn_to_npool_patch(p) = nf_veg%free_retransn_to_npool_patch(p) + nf_veg%livestemn_to_retransn_patch(p)
+               nf_veg%free_retransn_to_npool_patch(p) = nf_veg%free_retransn_to_npool_patch(p) + nf_veg%livecrootn_to_retransn_patch(p)
+            end if
          end if
          if (ivt(p) >= npcropmin) then ! Beth adds retrans from froot
             ns_veg%frootn_patch(p)       = ns_veg%frootn_patch(p)     - nf_veg%frootn_to_retransn_patch(p)*dt

src/biogeochem/CNPhenologyMod.F90

@@ -2751,11 +2751,12 @@ subroutine CNLivewoodTurnover (num_soilp, filter_soilp, &
             if (CNratio_floating .eqv. .true.) then    
                if (livestemc(p) == 0.0_r8) then    
                    ntovr = 0.0_r8    
+                   livestemn_to_deadstemn(p) = 0.0_r8 
                 else    
                    ntovr = ctovr * (livestemn(p) / livestemc(p))   
+                   livestemn_to_deadstemn(p) = ctovr / deadwdcn(ivt(p)) 
                 end if   
 
-                livestemn_to_deadstemn(p) = 0.5_r8 * ntovr   ! assuming 50% goes to deadstemn 
             end if    
 
             livestemn_to_retransn(p)  = ntovr - livestemn_to_deadstemn(p)
@@ -2770,19 +2771,15 @@ subroutine CNLivewoodTurnover (num_soilp, filter_soilp, &
             if (CNratio_floating .eqv. .true.) then    
               if (livecrootc(p) == 0.0_r8) then    
                   ntovr = 0.0_r8    
+                  livecrootn_to_deadcrootn(p) = 0.0_r8 
                else    
                   ntovr = ctovr * (livecrootn(p) / livecrootc(p))   
+                   livecrootn_to_deadcrootn(p) = ctovr / deadwdcn(ivt(p)) 
                end if   
 
-               livecrootn_to_deadcrootn(p) = 0.5_r8 * ntovr   ! assuming 50% goes to deadstemn 
             end if    
 
             livecrootn_to_retransn(p)  = ntovr - livecrootn_to_deadcrootn(p)
-            if(use_fun)then
-               !TURNED OFF FLUXES TO CORRECT N ACCUMULATION ISSUE. RF. Oct 2015. 
-               livecrootn_to_retransn(p) = 0.0_r8
-               livestemn_to_retransn(p)  = 0.0_r8
-            endif
 
          end if