Merge fates columnization, commit '18613d14', into andre-ed-clm-16x

Runtime error in restarts. Error is at
EDRestVectorMod.F90:1516. Potentiall related merge conflict in
subgridMod.F90::subgrid_get_info_netveg() and how ncohorts is set.

Test suite: ed - yellowstone gnu, intel, pgi
Test baseline: none

Test status - runtime failure in restart tests. all other tests pass.

components/clm/src/ED/biogeochem/EDCohortDynamicsMod.F90

@@ -27,7 +27,7 @@ module EDCohortDynamicsMod
   public :: sort_cohorts
   public :: copy_cohort
   public :: count_cohorts
-  public :: countCohorts
+!  public :: countCohorts
   public :: allocate_live_biomass
 
   logical, parameter :: DEBUG  = .false. ! local debug flag
@@ -1137,46 +1137,46 @@ function count_cohorts( currentPatch ) result ( backcount )
   end function count_cohorts
 
   !-------------------------------------------------------------------------------------!
-  function countCohorts( bounds, ed_allsites_inst ) result ( totNumCohorts ) 
+!  function countCohorts( bounds, ed_allsites_inst ) result ( totNumCohorts ) 
     !
     ! !DESCRIPTION:
     !  counts the total number of cohorts over all p levels (ed_patch_type) so we
     ! can allocate vectors, copy from LL -> vector and read/write restarts.
     !
     ! !USES:
-    use decompMod, only : bounds_type
+!    use decompMod, only : bounds_type
     !
     ! !ARGUMENTS    
-    type(bounds_type)  , intent(in)            :: bounds 
-    type(ed_site_type) , intent(inout), target :: ed_allsites_inst( bounds%begg: )
+!    type(bounds_type)  , intent(in)            :: bounds 
+!    type(ed_site_type) , intent(inout), target :: ed_allsites_inst( bounds%begg: )
     !
     ! !LOCAL VARIABLES:
-    type (ed_patch_type)  , pointer :: currentPatch
-    type (ed_cohort_type) , pointer :: currentCohort
-    integer :: g, totNumCohorts
-    logical :: error
+!    type (ed_patch_type)  , pointer :: currentPatch
+!    type (ed_cohort_type) , pointer :: currentCohort
+!    integer :: g, totNumCohorts
+!    logical :: error
     !----------------------------------------------------------------------
 
-    totNumCohorts = 0
+!    totNumCohorts = 0
 
-    do g = bounds%begg,bounds%endg
+!    do g = bounds%begg,bounds%endg
 
-       if (ed_allsites_inst(g)%istheresoil) then   
+!       if (ed_allsites_inst(g)%istheresoil) then   
 
-          currentPatch => ed_allsites_inst(g)%oldest_patch
-          do while(associated(currentPatch))
+!          currentPatch => ed_allsites_inst(g)%oldest_patch
+!          do while(associated(currentPatch))
 
-             currentCohort => currentPatch%shortest
-             do while(associated(currentCohort))        
-                totNumCohorts = totNumCohorts + 1
-                currentCohort => currentCohort%taller
-             enddo !currentCohort
-             currentPatch => currentPatch%younger
-          end do
+!             currentCohort => currentPatch%shortest
+!             do while(associated(currentCohort))        
+!                totNumCohorts = totNumCohorts + 1
+!                currentCohort => currentCohort%taller
+!             enddo !currentCohort
+!             currentPatch => currentPatch%younger
+!          end do
 
-       end if
-    end do
+!       end if
+!    end do
 
-  end function countCohorts
+!  end function countCohorts
 
 end module EDCohortDynamicsMod

components/clm/src/ED/biogeochem/EDPatchDynamicsMod.F90

@@ -9,7 +9,7 @@ module EDPatchDynamicsMod
   use clm_varctl           , only : iulog 
   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, numPatchesPerGridCell
+  use EDtypesMod           , only : ncwd, n_dbh_bins, ntol, numpft_ed, area, dbhmax, numPatchesPerCol
   use EDTypesMod           , only : ed_site_type, ed_patch_type, ed_cohort_type, udata
   use EDTypesMod           , only : min_patch_area
   !
@@ -1014,7 +1014,7 @@ subroutine fuse_patches( csite )
     !---------------------------------------------------------------------
 
     !maxpatch = 4  
-    maxpatch = numPatchesPerGridCell
+    maxpatch = numPatchesPerCol
 
     currentSite => csite 
 
@@ -1353,7 +1353,7 @@ subroutine terminate_patches(cs_pnt)
        areatot = areatot + currentPatch%area
        currentPatch => currentPatch%younger
        if((areatot-area) > 0.0000001_r8)then
-          write(iulog,*) 'ED: areatot too large. end terminate', areatot,currentSite%clmgcell
+          write(iulog,*) 'ED: areatot too large. end terminate', areatot
        endif
     enddo
 
@@ -1427,7 +1427,7 @@ subroutine patch_pft_size_profile(cp_pnt)
   end subroutine patch_pft_size_profile
 
   ! ============================================================================
-  function countPatches( bounds, ed_allsites_inst ) result ( totNumPatches ) 
+  function countPatches( bounds, sites, nsites ) result ( totNumPatches ) 
     !
     ! !DESCRIPTION:
     !  Loop over all Patches to count how many there are
@@ -1439,24 +1439,23 @@ function countPatches( bounds, ed_allsites_inst ) result ( totNumPatches )
     !
     ! !ARGUMENTS:
     type(bounds_type)  , intent(in)            :: bounds
-    type(ed_site_type) , intent(inout), target :: ed_allsites_inst( bounds%begg: )
+    type(ed_site_type) , intent(inout), target :: sites(nsites)
+    integer,             intent(in)            :: nsites
     !
     ! !LOCAL VARIABLES:
     type (ed_patch_type), pointer :: currentPatch
-    integer :: g              ! gridcell
     integer :: totNumPatches  ! total number of patches.  
+    integer :: s
     !---------------------------------------------------------------------
 
     totNumPatches = 0
 
-    do g = bounds%begg,bounds%endg
-       if (ed_allsites_inst(g)%istheresoil) then
-          currentPatch => ed_allsites_inst(g)%oldest_patch
-          do while(associated(currentPatch))
-             totNumPatches = totNumPatches + 1
-             currentPatch => currentPatch%younger
-          enddo
-       endif
+    do s = 1,nsites
+       currentPatch => sites(s)%oldest_patch
+       do while(associated(currentPatch))
+          totNumPatches = totNumPatches + 1
+          currentPatch => currentPatch%younger
+       enddo
     enddo
 
    end function countPatches

components/clm/src/ED/biogeochem/EDPhysiologyMod.F90

@@ -247,6 +247,7 @@ subroutine phenology( currentSite, temperature_inst, waterstate_inst)
     use clm_time_manager, only : get_days_per_year, get_curr_date
     use clm_time_manager, only : get_ref_date, timemgr_datediff 
     use EDTypesMod, only : udata
+    use PatchType , only : patch   
     !
     ! !ARGUMENTS:
     type(ed_site_type)      , intent(inout), target :: currentSite
@@ -255,7 +256,6 @@ subroutine phenology( currentSite, temperature_inst, waterstate_inst)
     !
     ! !LOCAL VARIABLES:
     real(r8), pointer :: t_veg24(:) 
-    integer  :: g            ! grid point  
     integer  :: t            ! day of year
     integer  :: ncolddays    ! no days underneath the threshold for leaf drop
     integer  :: ncolddayslim ! critical no days underneath the threshold for leaf drop
@@ -268,6 +268,8 @@ subroutine phenology( currentSite, temperature_inst, waterstate_inst)
     integer  :: mon                      ! month (1, ..., 12)
     integer  :: day                      ! day of month (1, ..., 31)
     integer  :: sec                      ! seconds of the day
+    integer  :: patchi                   ! the first CLM/ALM patch index of the associated column
+    integer  :: coli                     ! the CLM/ALM column index of the associated site
 
     real(r8) :: gdd_threshold
     real(r8) :: a,b,c        ! params of leaf-pn model from botta et al. 2000. 
@@ -283,10 +285,13 @@ subroutine phenology( currentSite, temperature_inst, waterstate_inst)
 
     !------------------------------------------------------------------------
 
-    t_veg24       => temperature_inst%t_veg24_patch ! Input:  [real(r8) (:)]  avg pft vegetation temperature for last 24 hrs    
+    ! INTERF-TODO: THIS IS A BAND-AID, AS I WAS HOPING TO REMOVE CLM_PNO
+    ! ALREADY REMOVED currentSite%clmcolumn, hence the need for these
 
-    g = currentSite%clmgcell
+    patchi = currentSite%oldest_patch%clm_pno-1
+    coli   = patch%column(patchi)
 
+    t_veg24       => temperature_inst%t_veg24_patch ! Input:  [real(r8) (:)]  avg pft vegetation temperature for last 24 hrs    
 
     call get_curr_date(yr, mon, day, sec)
     curdate = yr*10000 + mon*100 + day
@@ -315,7 +320,7 @@ subroutine phenology( currentSite, temperature_inst, waterstate_inst)
     cold_t   = 7.5_r8  ! ed_ph_coldtemp
 
     t  = udata%time_period
-    temp_in_C = t_veg24(currentSite%oldest_patch%clm_pno-1) - tfrz
+    temp_in_C = t_veg24(patchi) - tfrz
 
     !-----------------Cold Phenology--------------------!              
 
@@ -359,7 +364,7 @@ subroutine phenology( currentSite, temperature_inst, waterstate_inst)
     endif
     !
     ! accumulate the GDD using daily mean temperatures
-    if (t_veg24(currentSite%oldest_patch%clm_pno-1) .gt. tfrz) then
+    if (t_veg24(patchi) .gt. tfrz) then
        currentSite%ED_GDD_site = currentSite%ED_GDD_site + t_veg24(currentSite%oldest_patch%clm_pno-1) - tfrz
     endif
 
@@ -437,7 +442,7 @@ subroutine phenology( currentSite, temperature_inst, waterstate_inst)
     ! distinction actually matter??).... 
 
     !Accumulate surface water memory of last 10 days.
-    currentSite%water_memory(1) = waterstate_inst%h2osoi_vol_col(currentSite%clmcolumn,1) 
+    currentSite%water_memory(1) = waterstate_inst%h2osoi_vol_col(coli,1) 
     do i = 1,9 !shift memory along one
        currentSite%water_memory(11-i) = currentSite%water_memory(10-i)
     enddo
@@ -1140,6 +1145,7 @@ subroutine fragmentation_scaler( currentPatch, temperature_inst )
     ! !USES:
     use shr_const_mod      , only : SHR_CONST_PI, SHR_CONST_TKFRZ
     use EDSharedParamsMod  , only : EDParamsShareInst
+    use PatchType , only : patch 
     !
     ! !ARGUMENTS    
     type(ed_patch_type)    , intent(inout) :: currentPatch
@@ -1165,8 +1171,9 @@ subroutine fragmentation_scaler( currentPatch, temperature_inst )
 
     catanf_30 = catanf(30._r8)
 
-    c = currentPatch%siteptr%clmcolumn
+!    c = currentPatch%siteptr%clmcolumn
     p = currentPatch%clm_pno
+    c = patch%column(p)
 
     ! set "froz_q10" parameter
     froz_q10  = EDParamsShareInst%froz_q10  

components/clm/src/ED/biogeophys/EDAccumulateFluxesMod.F90

@@ -20,7 +20,7 @@ module EDAccumulateFluxesMod
 contains
 
   !------------------------------------------------------------------------------
-  subroutine AccumulateFluxes_ED(bounds, p, ed_allsites_inst, photosyns_inst)
+  subroutine AccumulateFluxes_ED(bounds, p, sites, nsites, hsites , photosyns_inst)
     !
     ! !DESCRIPTION:
     ! see above
@@ -36,14 +36,18 @@ subroutine AccumulateFluxes_ED(bounds, p, ed_allsites_inst, photosyns_inst)
     ! !ARGUMENTS    
     type(bounds_type)    , intent(in)            :: bounds  
     integer              , intent(in)            :: p     !patch/'p'
-    type(ed_site_type)   , intent(inout), target :: ed_allsites_inst( bounds%begg: )
+    type(ed_site_type)   , intent(inout), target :: sites(nsites)
+    integer              , intent(in)            :: nsites
+    integer              , intent(in)            :: hsites(bounds%begc:bounds%endc)
+
     type(photosyns_type) , intent(inout)         :: photosyns_inst
     !
     ! !LOCAL VARIABLES:
     type(ed_cohort_type), pointer  :: currentCohort ! current cohort
     type(ed_patch_type) , pointer  :: currentPatch ! current patch
     integer :: iv !leaf layer
-    integer :: g  !gridcell
+    integer :: c  ! clm/alm column
+    integer :: s  ! ed site
     !----------------------------------------------------------------------
 
     associate(& 
@@ -55,8 +59,10 @@ subroutine AccumulateFluxes_ED(bounds, p, ed_allsites_inst, photosyns_inst)
 
       if (patch%is_veg(p)) then
 
-         g = patch%gridcell(p)
-         currentPatch => map_clmpatch_to_edpatch(ed_allsites_inst(g), p) 
+         c = patch%column(p)
+         s = hsites(c)
+
+         currentPatch => map_clmpatch_to_edpatch(sites(s), p) 
          currentCohort => currentPatch%shortest
 
          do while(associated(currentCohort))

components/clm/src/ED/biogeophys/EDBtranMod.F90

@@ -25,7 +25,7 @@ module EDBtranMod
 contains 
 
   !------------------------------------------------------------------------------
-  subroutine btran_ed( bounds, p, ed_allsites_inst, &
+  subroutine btran_ed( bounds, p, sites, nsites, hsites, &
        soilstate_inst, waterstate_inst, temperature_inst, energyflux_inst)
     !
     ! !DESCRIPTION:
@@ -49,15 +49,17 @@ subroutine btran_ed( bounds, p, ed_allsites_inst, &
     ! !ARGUMENTS    
     type(bounds_type)      , intent(in)            :: bounds  ! clump bounds
     integer                , intent(in)            :: p       ! patch/'p'
-    type(ed_site_type)     , intent(inout), target :: ed_allsites_inst( bounds%begg: )
+    type(ed_site_type)     , intent(inout), target :: sites(nsites)
+    integer                , intent(in)            :: nsites
+    integer                , intent(in)            :: hsites(bounds%begc:bounds%endc)
     type(soilstate_type)   , intent(inout)         :: soilstate_inst
     type(waterstate_type)  , intent(in)            :: waterstate_inst
     type(temperature_type) , intent(in)            :: temperature_inst
     type(energyflux_type)  , intent(inout)         :: energyflux_inst
     !
     ! !LOCAL VARIABLES:
     integer :: iv !leaf layer
-    integer :: g  !gridcell
+    integer :: s  !site
     integer :: c  !column
     integer :: j  !soil layer
     integer :: ft ! plant functional type index
@@ -140,9 +142,10 @@ subroutine btran_ed( bounds, p, ed_allsites_inst, &
       if (patch%is_veg(p)) then
 
          c = patch%column(p)
-         g = patch%gridcell(p)
+         s = hsites(c)
 
-         currentPatch => map_clmpatch_to_edpatch(ed_allsites_inst(g), p) 
+         currentPatch => map_clmpatch_to_edpatch(sites(s), p) 
+
          do FT = 1,numpft_ed
             currentPatch%btran_ft(FT) = 0.0_r8
             do j = 1,nlevgrnd

components/clm/src/ED/biogeophys/EDPhotosynthesisMod.F90

@@ -20,7 +20,7 @@ module EDPhotosynthesisMod
 
   !---------------------------------------------------------
   subroutine Photosynthesis_ED (bounds, fn, filterp, esat_tv, eair, oair, cair, &
-       rb, dayl_factor, ed_allsites_inst, &
+       rb, dayl_factor, sites, nsites, hsites, &
        atm2lnd_inst, temperature_inst, canopystate_inst, photosyns_inst)
     !
     ! !DESCRIPTION:
@@ -61,7 +61,9 @@ subroutine Photosynthesis_ED (bounds, fn, filterp, esat_tv, eair, oair, cair, &
     real(r8)               , intent(in)            :: cair( bounds%begp: )        ! Atmospheric CO2 partial pressure (Pa)
     real(r8)               , intent(inout)         :: rb( bounds%begp: )          ! boundary layer resistance (s/m)
     real(r8)               , intent(in)            :: dayl_factor( bounds%begp: ) ! scalar (0-1) for daylength
-    type(ed_site_type)     , intent(inout), target :: ed_allsites_inst( bounds%begg: )
+    type(ed_site_type)     , intent(inout), target :: sites(nsites)
+    integer                , intent(in)            :: nsites
+    integer                , intent(in)            :: hsites(bounds%begc:bounds%endc)
     type(atm2lnd_type)     , intent(in)            :: atm2lnd_inst
     type(temperature_type) , intent(in)            :: temperature_inst
     type(canopystate_type) , intent(inout)         :: canopystate_inst
@@ -145,7 +147,7 @@ subroutine Photosynthesis_ED (bounds, fn, filterp, esat_tv, eair, oair, cair, &
     real(r8) :: theta_ip                          ! empirical curvature parameter for ap photosynthesis co-limitation
 
     ! Other
-    integer  :: c,CL,f,g,iv,j,p,ps,ft             ! indices
+    integer  :: c,CL,f,s,iv,j,p,ps,ft             ! indices
     integer  :: NCL_p                             ! number of canopy layers in patch
     real(r8) :: cf                                ! s m**2/umol -> s/m
     real(r8) :: rsmax0                            ! maximum stomatal resistance [s/m]
@@ -323,10 +325,11 @@ subroutine Photosynthesis_ED (bounds, fn, filterp, esat_tv, eair, oair, cair, &
          gccanopy(p)  = 0._r8  
 
          if (patch%is_veg(p)) then
-            g = patch%gridcell(p)
+
             c = patch%column(p)
+            s = hsites(c)
 
-            currentPatch => map_clmpatch_to_edpatch(ed_allsites_inst(g), p) 
+            currentPatch => map_clmpatch_to_edpatch(sites(s), p) 
 
             currentPatch%ncan(:,:) = 0
             !redo the canopy structure algorithm to get round a bug that is happening for site 125, FT13. 
@@ -401,10 +404,11 @@ subroutine Photosynthesis_ED (bounds, fn, filterp, esat_tv, eair, oair, cair, &
       do f = 1,fn
          p = filterp(f)
          c = patch%column(p)
+         s = hsites(c)
 
          if (patch%is_veg(p)) then
-            g = patch%gridcell(p)
-            currentPatch => map_clmpatch_to_edpatch(ed_allsites_inst(g), p) 
+
+            currentPatch => map_clmpatch_to_edpatch(sites(s), p) 
 
             do FT = 1,numpft_ed
                if (nint(c3psn(FT)) == 1)then