Merge conflicts resolved. Nastiest conflicts were insdie allocate_liv…

…e_biomass() where the day frequency was updated in master and the head had some pretty drastic overhaul on order of operations.

biogeochem/EDCanopyStructureMod.F90

@@ -465,12 +465,12 @@ subroutine canopy_structure( currentSite )
                       endif
                       !call terminate_cohorts(currentPatch) 
                       if(promswitch == 1)then
-                        ! write(fates_log(),*) 'cohort loop',currentCohort%pft,currentCohort%indexnumber,currentPatch%patchno
+                        ! write(fates_log(),*) 'cohort loop',currentCohort%pft,currentPatch%patchno
                       endif
                       !----------- End of cohort splitting ------------------------------!             
                    else
                       if(promswitch == 1)then
-                         ! write(fates_log(),*) 'cohort list',currentCohort%pft,currentCohort%indexnumber, &
+                         ! write(fates_log(),*) 'cohort list',currentCohort%pft, &
                              ! currentCohort%canopy_layer,currentCohort%c_area
                       endif
                    endif
@@ -485,7 +485,7 @@ subroutine canopy_structure( currentSite )
                         !currentPatch%patchno,z,i,lower_cohort_switch
                 endif
                 if(promswitch == 1.and.associated(currentPatch%tallest))then
-                   ! write(fates_log(),*) 'cohorts',currentCohort%pft,currentCohort%indexnumber,currentPatch%patchno, &
+                   ! write(fates_log(),*) 'cohorts',currentCohort%pft,currentPatch%patchno, &
                         !currentCohort%c_area
                 endif
              enddo !arealayer loop

biogeochem/EDCohortDynamicsMod.F90

@@ -6,14 +6,16 @@ module EDCohortDynamicsMod
   ! !USES: 
   use abortutils            , only : endrun
   use FatesGlobals          , only : fates_log
+  use FatesGlobals          , only : freq_day
   use FatesConstantsMod     , only : r8 => fates_r8
+  use FatesConstantsMod     , only : fates_unset_int
   use shr_log_mod           , only : errMsg => shr_log_errMsg
   use pftconMod             , only : pftcon
   use EDEcophysContype      , only : EDecophyscon
   use EDGrowthFunctionsMod  , only : c_area, tree_lai
   use EDTypesMod            , only : ed_site_type, ed_patch_type, ed_cohort_type
   use EDTypesMod            , only : fusetol, cp_nclmax
-  use EDtypesMod            , only : ncwd, maxcohortsperpatch, udata
+  use EDtypesMod            , only : ncwd, maxcohortsperpatch
   use EDtypesMod            , only : sclass_ed,nlevsclass_ed,AREA
   use EDtypesMod            , only : min_npm2, min_nppatch, min_n_safemath
   !
@@ -73,7 +75,6 @@ subroutine create_cohort(patchptr, pft, nn, hite, dbh, &
     !----------------------------------------------------------------------
 
     allocate(new_cohort)
-    udata%cohort_number = udata%cohort_number + 1  !give each cohort a unique number for checking cohort fusing routine.
 
     call nan_cohort(new_cohort)  ! Make everything in the cohort not-a-number
     call zero_cohort(new_cohort) ! Zero things that need to be zeroed. 
@@ -82,7 +83,8 @@ subroutine create_cohort(patchptr, pft, nn, hite, dbh, &
     ! Define cohort state variable
     !**********************/
 
-    new_cohort%indexnumber  = udata%cohort_number
+    new_cohort%indexnumber  = fates_unset_int ! Cohort indexing was not thread-safe, setting
+                                              ! bogus value for the time being (RGK-012017)
     new_cohort%siteptr      => patchptr%siteptr
     new_cohort%patchptr     => patchptr
     new_cohort%pft          = pft     
@@ -109,7 +111,7 @@ subroutine create_cohort(patchptr, pft, nn, hite, dbh, &
 
     if (new_cohort%dbh <= 0.0_r8 .or. new_cohort%n == 0._r8 .or. new_cohort%pft == 0 ) then
              write(fates_log(),*) 'ED: something is zero in create_cohort', &
-                             new_cohort%indexnumber,new_cohort%dbh,new_cohort%n, &
+                             new_cohort%dbh,new_cohort%n, &
                              new_cohort%pft
              call endrun(msg=errMsg(sourcefile, __LINE__))
     endif
@@ -221,6 +223,7 @@ subroutine allocate_live_biomass(cc_p,mode)
     ! Use different proportions if the leaves are on vs off
     if(leaves_off_switch==0)then
 
+
        new_bl = currentcohort%balive*leaf_frac
 
        new_br = pftcon%froot_leaf(ft) * (currentcohort%balive + currentcohort%laimemory) * leaf_frac
@@ -233,13 +236,13 @@ subroutine allocate_live_biomass(cc_p,mode)
        if(mode==1)then 
 
           currentcohort%npp_leaf = currentcohort%npp_leaf + &
-                max(0.0_r8,new_bl - currentcohort%bl) / udata%deltat
+                max(0.0_r8,new_bl - currentcohort%bl) / freq_day
 
           currentcohort%npp_froot = currentcohort%npp_froot + &
-                max(0._r8,new_br - currentcohort%br) / udata%deltat
-          
-          currentcohort%npp_bsw = max(0._r8,new_bsw - currentcohort%bsw)/udata%deltat
-          
+                max(0._r8,new_br - currentcohort%br) / freq_day
+
+          currentcohort%npp_bsw =  max(0.0_r8, new_bsw - currentcohort%bsw)/freq_day
+
           currentcohort%npp_bdead =  currentCohort%dbdeaddt
 
        end if
@@ -271,9 +274,9 @@ subroutine allocate_live_biomass(cc_p,mode)
        if(mode==1)then
 
           currentcohort%npp_froot = currentcohort%npp_froot + &
-                max(0.0_r8,new_br-currentcohort%br)/udata%deltat
+                max(0.0_r8,new_br-currentcohort%br)/freq_day
 
-          currentcohort%npp_bsw = max(0.0_r8, new_bsw-currentcohort%bsw)/udata%deltat
+          currentcohort%npp_bsw = max(0.0_r8, new_bsw-currentcohort%bsw)/freq_day
 
           currentcohort%npp_bdead =  currentCohort%dbdeaddt
 
@@ -1008,8 +1011,7 @@ subroutine copy_cohort( currentCohort,copyc )
     o => currentCohort
     n => copyc
 
-    udata%cohort_number = udata%cohort_number + 1
-    n%indexnumber       = udata%cohort_number
+    n%indexnumber     = fates_unset_int
 
     ! VEGETATION STRUCTURE
     n%pft             = o%pft

biogeochem/EDGrowthFunctionsMod.F90

@@ -7,7 +7,7 @@ module EDGrowthFunctionsMod
   ! ============================================================================
 
   use shr_kind_mod     , only : r8 => shr_kind_r8
-  use clm_varctl       , only : iulog 
+  use FatesGlobals     , only : fates_log
   use pftconMod        , only : pftcon
   use EDEcophysContype , only : EDecophyscon
   use EDTypesMod       , only : ed_cohort_type, cp_nlevcan, dinc_ed
@@ -76,7 +76,7 @@ real(r8) function Hite( cohort_in )
     c = 0.37_r8       
 
     if(cohort_in%dbh <= 0._r8)then
-       write(iulog,*) 'ED: dbh less than zero problem!',cohort_in%indexnumber
+       write(fates_log(),*) 'ED: dbh less than zero problem!'
        cohort_in%dbh = 0.1_r8
     endif
 
@@ -106,7 +106,7 @@ real(r8) function Bleaf( cohort_in )
     real(r8) :: slascaler ! changes the target biomass according to the SLA
 
     if(cohort_in%dbh < 0._r8.or.cohort_in%pft == 0.or.cohort_in%dbh > 1000.0_r8)then
-       write(iulog,*) 'problems in bleaf',cohort_in%dbh,cohort_in%pft
+       write(fates_log(),*) 'problems in bleaf',cohort_in%dbh,cohort_in%pft
     endif
 
     if(cohort_in%dbh <= EDecophyscon%max_dbh(cohort_in%pft))then
@@ -117,7 +117,7 @@ real(r8) function Bleaf( cohort_in )
     slascaler = 0.03_r8/pftcon%slatop(cohort_in%pft)
     bleaf = bleaf * slascaler
 
-    !write(iulog,*) 'bleaf',bleaf, slascaler,cohort_in%pft
+    !write(fates_log(),*) 'bleaf',bleaf, slascaler,cohort_in%pft
 
     !Adjust for canopies that have become so deep that their bottom layer is not producing any carbon... 
     !nb this will change the allometry and the effects of this remain untested. RF. April 2014  
@@ -141,7 +141,7 @@ real(r8) function tree_lai( cohort_in )
     real(r8) :: slat               ! the sla of the top leaf layer. m2/kgC
 
     if( cohort_in%bl  <  0._r8 .or. cohort_in%pft  ==  0 ) then
-       write(iulog,*) 'problem in treelai',cohort_in%bl,cohort_in%pft
+       write(fates_log(),*) 'problem in treelai',cohort_in%bl,cohort_in%pft
     endif
 
     if( cohort_in%status_coh  ==  2 ) then ! are the leaves on? 
@@ -162,7 +162,7 @@ real(r8) function tree_lai( cohort_in )
     ! at the moments cp_nlevcan default is 40, which is very large, so exceeding this would clearly illustrate a 
     ! huge error 
     if(cohort_in%treelai > cp_nlevcan*dinc_ed)then
-       write(iulog,*) 'too much lai' , cohort_in%treelai , cohort_in%pft , cp_nlevcan * dinc_ed
+       write(fates_log(),*) 'too much lai' , cohort_in%treelai , cohort_in%pft , cp_nlevcan * dinc_ed
     endif
 
     return
@@ -186,7 +186,7 @@ real(r8) function tree_sai( cohort_in )
     sai_scaler = 0.05_r8 ! here, a high biomass of 20KgC per m2 gives us a high SAI of 1.0. 
 
     if( cohort_in%bdead  <  0._r8 .or. cohort_in%pft  ==  0 ) then
-       write(iulog,*) 'problem in treesai',cohort_in%bdead,cohort_in%pft
+       write(fates_log(),*) 'problem in treesai',cohort_in%bdead,cohort_in%pft
     endif
 
     cohort_in%c_area = c_area(cohort_in) ! call the tree area 
@@ -199,7 +199,7 @@ real(r8) function tree_sai( cohort_in )
     ! at the moments cp_nlevcan default is 40, which is very large, so exceeding this would clearly illustrate a 
     ! huge error 
     if(cohort_in%treesai > cp_nlevcan*dinc_ed)then
-       write(iulog,*) 'too much sai' , cohort_in%treesai , cohort_in%pft , cp_nlevcan * dinc_ed
+       write(fates_log(),*) 'too much sai' , cohort_in%treesai , cohort_in%pft , cp_nlevcan * dinc_ed
     endif
 
     return
@@ -223,13 +223,13 @@ real(r8) function c_area( cohort_in )
     real(r8) :: dbh ! Tree diameter at breat height. cm. 
 
     if (DEBUG_growth) then
-       write(iulog,*) 'z_area 1',cohort_in%dbh,cohort_in%pft
-       write(iulog,*) 'z_area 2',EDecophyscon%max_dbh
-       write(iulog,*) 'z_area 3',pftcon%woody
-       write(iulog,*) 'z_area 4',cohort_in%n
-       write(iulog,*) 'z_area 5',cohort_in%patchptr%spread
-       write(iulog,*) 'z_area 6',cohort_in%canopy_layer
-       write(iulog,*) 'z_area 7',ED_val_grass_spread
+       write(fates_log(),*) 'z_area 1',cohort_in%dbh,cohort_in%pft
+       write(fates_log(),*) 'z_area 2',EDecophyscon%max_dbh
+       write(fates_log(),*) 'z_area 3',pftcon%woody
+       write(fates_log(),*) 'z_area 4',cohort_in%n
+       write(fates_log(),*) 'z_area 5',cohort_in%patchptr%spread
+       write(fates_log(),*) 'z_area 6',cohort_in%canopy_layer
+       write(fates_log(),*) 'z_area 7',ED_val_grass_spread
     end if
 
     dbh = min(cohort_in%dbh,EDecophyscon%max_dbh(cohort_in%pft))
@@ -371,8 +371,8 @@ subroutine mortality_rates( cohort_in,cmort,hmort,bmort )
        endif
 
     else
-       write(iulog,*) 'dbh problem in mortality_rates', &
-            cohort_in%dbh,cohort_in%pft,cohort_in%n,cohort_in%canopy_layer,cohort_in%indexnumber
+       write(fates_log(),*) 'dbh problem in mortality_rates', &
+            cohort_in%dbh,cohort_in%pft,cohort_in%n,cohort_in%canopy_layer
     endif
 
     !mortality_rates = bmort + hmort + cmort

biogeochem/EDPatchDynamicsMod.F90

@@ -7,10 +7,11 @@ module EDPatchDynamicsMod
   use shr_kind_mod         , only : r8 => shr_kind_r8;
   use shr_infnan_mod       , only : nan => shr_infnan_nan, assignment(=)
   use clm_varctl           , only : iulog 
+  use FatesGlobals         , only : freq_day
   use pftconMod            , only : pftcon
   use EDCohortDynamicsMod  , only : fuse_cohorts, sort_cohorts, insert_cohort
   use EDtypesMod           , only : ncwd, n_dbh_bins, ntol, numpft_ed, area, dbhmax, maxPatchesPerCol
-  use EDTypesMod           , only : ed_site_type, ed_patch_type, ed_cohort_type, udata
+  use EDTypesMod           , only : ed_site_type, ed_patch_type, ed_cohort_type
   use EDTypesMod           , only : min_patch_area, cp_numlevgrnd, cp_numSWb
   !
   implicit none
@@ -45,7 +46,6 @@ subroutine disturbance_rates( site_in)
     !
     ! !USES:
     use EDGrowthFunctionsMod , only : c_area, mortality_rates
-    use EDTypesMod           , only : udata
     !
     ! !ARGUMENTS:
     type(ed_site_type) , intent(inout), target :: site_in
@@ -85,7 +85,7 @@ subroutine disturbance_rates( site_in)
           if(currentCohort%canopy_layer == 1)then
 
              currentPatch%disturbance_rates(1) = currentPatch%disturbance_rates(1) + &
-                  min(1.0_r8,currentCohort%dmort)*udata%deltat*currentCohort%c_area/currentPatch%area
+                  min(1.0_r8,currentCohort%dmort)*freq_day*currentCohort%c_area/currentPatch%area
 
           endif
 
@@ -271,7 +271,7 @@ subroutine spawn_patches( currentSite )
                    ! because this is the part of the original patch where no trees have actually fallen
                    ! The diagnostic cmort,bmort and hmort rates have already been saved         
 
-                   currentCohort%n = currentCohort%n * (1.0_r8 - min(1.0_r8,currentCohort%dmort * udata%deltat))
+                   currentCohort%n = currentCohort%n * (1.0_r8 - min(1.0_r8,currentCohort%dmort * freq_day))
 
                    nc%n = 0.0_r8      ! kill all of the trees who caused the disturbance.         
                    nc%cmort = nan     ! The mortality diagnostics are set to nan because the cohort should dissappear
@@ -298,7 +298,7 @@ subroutine spawn_patches( currentSite )
                       ! so with the number density must come the effective mortality rates.
 
                       nc%fmort = 0.0_r8               ! Should had also been zero in the donor
-                      nc%imort = ED_val_understorey_death/udata%deltat  ! This was zero in the donor
+                      nc%imort = ED_val_understorey_death/freq_day  ! This was zero in the donor
                       nc%cmort = currentCohort%cmort
                       nc%hmort = currentCohort%hmort
                       nc%bmort = currentCohort%bmort
@@ -336,7 +336,7 @@ subroutine spawn_patches( currentSite )
                 ! loss of individual from fire in new patch.
                 nc%n = nc%n * (1.0_r8 - currentCohort%fire_mort) 
 
-                nc%fmort = currentCohort%fire_mort/udata%deltat
+                nc%fmort = currentCohort%fire_mort/freq_day
                 nc%imort = 0.0_r8
                 nc%cmort = currentCohort%cmort
                 nc%hmort = currentCohort%hmort
@@ -716,7 +716,7 @@ subroutine mortality_litter_fluxes(cp_target, new_patch_target, patch_site_aread
              !currentCohort%dmort = mortality_rates(currentCohort) 
              !the disturbance calculations are done with the previous n, c_area and d_mort. So it's probably &
              !not right to recalcualte dmort here.
-             canopy_dead = currentCohort%n * min(1.0_r8,currentCohort%dmort * udata%deltat)
+             canopy_dead = currentCohort%n * min(1.0_r8,currentCohort%dmort * freq_day)
 
              currentPatch%canopy_mortality_woody_litter   = currentPatch%canopy_mortality_woody_litter  + &
                   canopy_dead*(currentCohort%bdead+currentCohort%bsw)