Merge branch 'bbye/lnd/cropmodel-bugfixes' into next (PR #966)

Fixes bugs introduced into crop model
Contains:
	* Harvest of phosphorus
        * Add grain phosphorus to allometry
	* Remove retranslocation during harvest
	* Fixes allocation when peak lai is reached
        * Remove unnecessary print statements

This commit fixes various bugs that are in the crop model from
the phosphorus code, dynamic nutrients, and some misc others.
First, harvest of the phosphorus is added including a 1-yr
product pool. Also, the grain phosphorus demand is included
in the calculation of phosphorus allometry. Retranslocation
terms are removed from the offset litterfall since crops are
annual and completely harvested. Finally, the allocation when
crops reach peak lai is modified to prevent unrealistic
biomass partitioning in roots and stems.

[Non-BFB] - Non Bit-For-Bit

Conflicts:
	cime/scripts-acme/update_acme_tests.py
	components/clm/bld/namelist_files/namelist_defaults_clm4_5.xml
	components/clm/src/biogeochem/CNPhenologyMod.F90

cime/scripts-acme/update_acme_tests.py

@@ -42,6 +42,7 @@
                              ("ERS.f19_f19.I1850CLM45CN",
                               "ERS.f09_g16.I1850CLM45CN",
                               "SMS.hcru_hcru.I1850CRUCLM45CN",
+                              ("SMS_Ly3.1x1_smallvilleIA.ICLM45BGCCROP", "force_netcdf_pio"),
                               "ERS.ne11_qu240.I20TRCLM45",
                               "ERS.f09_g16.IMCLM45BC")
                              ),

components/clm/src/biogeochem/CNAllocationMod.F90

@@ -831,8 +831,10 @@ subroutine CNAllocation1_PlantNPDemand (bounds, num_soilc, filter_soilc, num_soi
                   if (peaklai(p) == 1) then ! lai at maximum allowed
                      arepr(p) = 0._r8
                      aleaf(p) = 1.e-5_r8
-                     astem(p) = 0._r8
-                     aroot(p) = 1._r8 - arepr(p) - aleaf(p) - astem(p)
+                     aroot(p) = max(0._r8, min(1._r8, arooti(ivt(p)) -   &
+                          (arooti(ivt(p)) - arootf(ivt(p))) *  &
+                          min(1._r8, hui(p)/gddmaturity(p))))
+                     astem(p) = 1._r8 - arepr(p) - aleaf(p) - aroot(p)
                   else
                      arepr(p) = 0._r8
                      aroot(p) = max(0._r8, min(1._r8, arooti(ivt(p)) -   &
@@ -894,7 +896,7 @@ subroutine CNAllocation1_PlantNPDemand (bounds, num_soilc, filter_soilc, num_soi
                   !would be bypassed altogether, not the intended outcome. I checked several of my output files and
                   !they all seemed to be going through the retranslocation loop for soybean - good news.
 
-                  if (ivt(p) /= nsoybean .or. astem(p) == astemf(ivt(p))) then
+                  if (ivt(p) /= nsoybean .or. astem(p) == astemf(ivt(p)) .or. peaklai(p) == 1._r8) then
                      if (grain_flag(p) == 0._r8) then
                         t1 = 1 / dt
                         leafn_to_retransn(p) = t1 * ((leafc(p) / leafcn(ivt(p))) - (leafc(p) / &
@@ -945,10 +947,11 @@ subroutine CNAllocation1_PlantNPDemand (bounds, num_soilc, filter_soilc, num_soi
 
          else if (ivt(p) >= npcropmin) then ! skip generic crops
             cng = graincn(ivt(p))
+            cpg = graincp(ivt(p))
             c_allometry(p) = (1._r8+g1)*(1._r8+f1+f5+f3*(1._r8+f2))
             n_allometry(p) = 1._r8/cnl + f1/cnfr + f5/cng + (f3*f4*(1._r8+f2))/cnlw + &
                  (f3*(1._r8-f4)*(1._r8+f2))/cndw
-            p_allometry(p) = 1._r8/cpl + f1/cpfr + (f3*f4*(1._r8+f2))/cplw + &
+            p_allometry(p) = 1._r8/cpl + f1/cpfr + f5/cpg + (f3*f4*(1._r8+f2))/cplw + &
                  (f3*(1._r8-f4)*(1._r8+f2))/cpdw
 
          else
@@ -3466,10 +3469,11 @@ subroutine CNAllocation3_PlantCNPAlloc (bounds            , &
 
              else if (ivt(p) >= npcropmin) then ! skip generic crops
                  cng = graincn(ivt(p))
+                 cpg = graincp(ivt(p))
                  c_allometry(p) = (1._r8+g1)*(1._r8+f1+f5+f3*(1._r8+f2))
                  n_allometry(p) = 1._r8/cnl + f1/cnfr + f5/cng + (f3*f4*(1._r8+f2))/cnlw + &
                      (f3*(1._r8-f4)*(1._r8+f2))/cndw
-                 p_allometry(p) = 1._r8/cpl + f1/cpfr + (f3*f4*(1._r8+f2))/cplw + &
+                 p_allometry(p) = 1._r8/cpl + f1/cpfr + f5/cpg + (f3*f4*(1._r8+f2))/cplw + &
                      (f3*(1._r8-f4)*(1._r8+f2))/cpdw
 
              else

components/clm/src/biogeochem/CNCropHarvestPoolsMod.F90

@@ -14,6 +14,8 @@ module CNCropHarvestPoolsMod
   use CNCarbonFluxType    , only : carbonflux_type
   use CNNitrogenStateType , only : nitrogenstate_type
   use CNNitrogenFluxType  , only : nitrogenflux_type
+  use PhosphorusStateType , only : phosphorusstate_type
+  use PhosphorusFluxType  , only : phosphorusflux_type
   !
   implicit none
   save
@@ -27,8 +29,8 @@ module CNCropHarvestPoolsMod
 
   !-----------------------------------------------------------------------
   subroutine CNCropHarvestPools(num_soilc, filter_soilc, &
-       carbonstate_vars, c13_carbonstate_vars, c14_carbonstate_vars, nitrogenstate_vars, &
-       carbonflux_vars, c13_carbonflux_vars, c14_carbonflux_vars, nitrogenflux_vars)
+       carbonstate_vars, c13_carbonstate_vars, c14_carbonstate_vars, nitrogenstate_vars, phosphorusstate_vars,&
+       carbonflux_vars, c13_carbonflux_vars, c14_carbonflux_vars, nitrogenflux_vars, phosphorusflux_vars)
     !
     ! !DESCRIPTION:
     ! Update all loss fluxes from crop harvest pools, and update harvest pool state variables
@@ -42,10 +44,12 @@ subroutine CNCropHarvestPools(num_soilc, filter_soilc, &
     type(carbonstate_type)   , intent(in)    :: c13_carbonstate_vars
     type(carbonstate_type)   , intent(in)    :: c14_carbonstate_vars
     type(nitrogenstate_type) , intent(in)    :: nitrogenstate_vars
+    type(phosphorusstate_type), intent(in)   :: phosphorusstate_vars
     type(carbonflux_type)    , intent(inout) :: carbonflux_vars
     type(carbonflux_type)    , intent(inout) :: c13_carbonflux_vars
     type(carbonflux_type)    , intent(inout) :: c14_carbonflux_vars
     type(nitrogenflux_type)  , intent(inout) :: nitrogenflux_vars
+    type(phosphorusflux_type), intent(inout) :: phosphorusflux_vars
     !
     ! !LOCAL VARIABLES:
     integer :: fc        ! lake filter indices
@@ -75,6 +79,7 @@ subroutine CNCropHarvestPools(num_soilc, filter_soilc, &
        endif
 
        nitrogenflux_vars%prod1n_loss_col(c)    = nitrogenstate_vars%prod1n_col(c)    * kprod1
+       phosphorusflux_vars%prod1p_loss_col(c)  = phosphorusstate_vars%prod1p_col(c)  * kprod1
     end do
 
     ! set time steps
@@ -100,6 +105,8 @@ subroutine CNCropHarvestPools(num_soilc, filter_soilc, &
 
        nitrogenstate_vars%prod1n_col(c)    = nitrogenstate_vars%prod1n_col(c)    + &
             nitrogenflux_vars%hrv_cropn_to_prod1n_col(c)*dt
+       phosphorusstate_vars%prod1p_col(c)    = phosphorusstate_vars%prod1p_col(c)    + &
+            phosphorusflux_vars%hrv_cropp_to_prod1p_col(c)*dt
 
        ! fluxes out of wood product pools, from decomposition
        carbonstate_vars%prod1c_col(c)    = carbonstate_vars%prod1c_col(c)    - &
@@ -117,6 +124,8 @@ subroutine CNCropHarvestPools(num_soilc, filter_soilc, &
 
        nitrogenstate_vars%prod1n_col(c)    = nitrogenstate_vars%prod1n_col(c)    - &
             nitrogenflux_vars%prod1n_loss_col(c)*dt
+       phosphorusstate_vars%prod1p_col(c)  = phosphorusstate_vars%prod1p_col(c)  - &
+            phosphorusflux_vars%prod1p_loss_col(c)*dt
 
     end do ! end of column loop
 

components/clm/src/biogeochem/CNEcosystemDynMod.F90

@@ -794,7 +794,8 @@ subroutine CNEcosystemDynNoLeaching2(bounds,                                  &
 
        call CNCropHarvestPools(num_soilc, filter_soilc, &
             carbonstate_vars, c13_carbonstate_vars, c14_carbonstate_vars, nitrogenstate_vars, &
-            carbonflux_vars, c13_carbonflux_vars, c14_carbonflux_vars, nitrogenflux_vars)
+            phosphorusstate_vars, carbonflux_vars, c13_carbonflux_vars, c14_carbonflux_vars, &
+            nitrogenflux_vars, phosphorusflux_vars)
 
        call CNFireArea(bounds, num_soilc, filter_soilc, num_soilp, filter_soilp, &
             atm2lnd_vars, temperature_vars, energyflux_vars, soilhydrology_vars, waterstate_vars, &