Read fates parameters from their own file.

The fates parameter file is now specified via a separate namelist
fates_paramfile. This variable may or may not point to the same netcdf
file as the host parameter file. All fates parameters are read from
this file, including the pft level variables, which are now stored in
EDpftvarcon instead of pftcon. Note that some parameters are shared
between the host and fates. These are 'host' parameters, not fates
parameters and are read from the host file.

Work for NGT-ED Github issue #155

User interface changes?: Yes. Users who have custom parameter files
will need to set namelist varible 'fates_paramfile' to point to their
file instead. Host parameters are still read from the file specified
by namelist variable 'paramfile'. If users have modified host
parameters in addition to fates parameters, they will need to update
both namelist variables.

Code review: andre

Test suite: clm_short
Test baseline: clm4_5_12_r195
Test namelist changes: none
Test answer changes: bit for bit
Test summary: all tests pass

Test suite: ed - yellowstone gnu, intel, pgi
Test baseline: a651a4f
Test namelist changes: yes, new namilest var fates_paramfile
Test answer changes: bit for bit
Test summary: all tests pass

biogeochem/EDCanopyStructureMod.F90

@@ -7,7 +7,7 @@ module EDCanopyStructureMod
 
   use shr_kind_mod          , only : r8 => shr_kind_r8;
   use FatesGlobals          , only : fates_log
-  use pftconMod             , only : pftcon
+  use EDPftvarcon             , only : EDPftvarcon_inst
   use EDGrowthFunctionsMod  , only : c_area
   use EDCohortDynamicsMod   , only : copy_cohort, terminate_cohorts, fuse_cohorts
   use EDtypesMod            , only : ed_site_type, ed_patch_type, ed_cohort_type, ncwd
@@ -617,7 +617,7 @@ subroutine canopy_spread( currentSite )
        currentCohort => currentPatch%tallest
        do while (associated(currentCohort))
           currentCohort%c_area = c_area(currentCohort) 
-          if(pftcon%woody(currentCohort%pft) == 1)then
+          if(EDPftvarcon_inst%woody(currentCohort%pft) == 1)then
              arealayer(currentCohort%canopy_layer) = arealayer(currentCohort%canopy_layer) + currentCohort%c_area
           endif
           currentCohort => currentCohort%shorter
@@ -663,7 +663,7 @@ subroutine canopy_summarization( nsites, sites, bc_in )
     use EDGrowthFunctionsMod , only : tree_lai, c_area
     use EDEcophysConType     , only : EDecophyscon
     use EDtypesMod           , only : area
-    use pftconMod            , only : pftcon
+    use EDPftvarcon            , only : EDPftvarcon_inst
 
     ! !ARGUMENTS    
     integer                 , intent(in)            :: nsites
@@ -727,7 +727,7 @@ subroutine canopy_summarization( nsites, sites, bc_in )
 
              if(currentCohort%canopy_layer==1)then
                 currentPatch%total_canopy_area = currentPatch%total_canopy_area + currentCohort%c_area
-                if(pftcon%woody(ft)==1)then
+                if(EDPftvarcon_inst%woody(ft)==1)then
                    currentPatch%total_tree_area = currentPatch%total_tree_area + currentCohort%c_area
                 endif
              endif
@@ -989,11 +989,11 @@ subroutine leaf_area_profile( currentSite , snow_depth_si, frac_sno_eff_si)
              do iv = 1,currentCohort%NV-1 
 
                 ! what is the height of this layer? (for snow burial purposes...)  
-                ! pftcon%vertical_canopy_frac(ft))! fudge - this should be pft specific but i cant get it to compile. 
+                ! EDPftvarcon_inst%vertical_canopy_frac(ft))! fudge - this should be pft specific but i cant get it to compile. 
                 layer_top_hite = currentCohort%hite-((iv/currentCohort%NV) * currentCohort%hite * &
                       EDecophyscon%crown(currentCohort%pft) )
                 layer_bottom_hite = currentCohort%hite-(((iv+1)/currentCohort%NV) * currentCohort%hite * &
-                      EDecophyscon%crown(currentCohort%pft)) ! pftcon%vertical_canopy_frac(ft))
+                      EDecophyscon%crown(currentCohort%pft)) ! EDPftvarcon_inst%vertical_canopy_frac(ft))
 
                 fraction_exposed =1.0_r8
 
@@ -1022,10 +1022,10 @@ subroutine leaf_area_profile( currentSite , snow_depth_si, frac_sno_eff_si)
 
              !Bottom layer
              iv = currentCohort%NV
-             ! pftcon%vertical_canopy_frac(ft))! fudge - this should be pft specific but i cant get it to compile.
+             ! EDPftvarcon_inst%vertical_canopy_frac(ft))! fudge - this should be pft specific but i cant get it to compile.
              layer_top_hite = currentCohort%hite-((iv/currentCohort%NV) * currentCohort%hite * &
                    EDecophyscon%crown(currentCohort%pft) )
-             ! pftcon%vertical_canopy_frac(ft))
+             ! EDPftvarcon_inst%vertical_canopy_frac(ft))
              layer_bottom_hite = currentCohort%hite-(((iv+1)/currentCohort%NV) * currentCohort%hite * &
                    EDecophyscon%crown(currentCohort%pft))
 

biogeochem/EDCohortDynamicsMod.F90

@@ -8,7 +8,7 @@ module EDCohortDynamicsMod
   use FatesGlobals          , only : fates_log
   use FatesConstantsMod     , only : r8 => fates_r8
   use shr_log_mod           , only : errMsg => shr_log_errMsg
-  use pftconMod             , only : pftcon
+  use EDPftvarcon             , only : EDPftvarcon_inst
   use EDEcophysContype      , only : EDecophyscon
   use EDGrowthFunctionsMod  , only : c_area, tree_lai
   use EDTypesMod            , only : ed_site_type, ed_patch_type, ed_cohort_type
@@ -114,11 +114,11 @@ subroutine create_cohort(patchptr, pft, nn, hite, dbh, &
              call endrun(msg=errMsg(sourcefile, __LINE__))
     endif
 
-    if (new_cohort%siteptr%status==2 .and. pftcon%season_decid(pft) == 1) then
+    if (new_cohort%siteptr%status==2 .and. EDPftvarcon_inst%season_decid(pft) == 1) then
       new_cohort%laimemory = 0.0_r8
     endif
 
-    if (new_cohort%siteptr%dstatus==2 .and. pftcon%stress_decid(pft) == 1) then
+    if (new_cohort%siteptr%dstatus==2 .and. EDPftvarcon_inst%stress_decid(pft) == 1) then
       new_cohort%laimemory = 0.0_r8
     endif
 
@@ -191,27 +191,27 @@ subroutine allocate_live_biomass(cc_p,mode)
 
     currentCohort => cc_p
     ft = currentcohort%pft
-    leaf_frac = 1.0_r8/(1.0_r8 + EDecophyscon%sapwood_ratio(ft) * currentcohort%hite + pftcon%froot_leaf(ft))     
+    leaf_frac = 1.0_r8/(1.0_r8 + EDecophyscon%sapwood_ratio(ft) * currentcohort%hite + EDPftvarcon_inst%froot_leaf(ft))     
 
     !currentcohort%bl = currentcohort%balive*leaf_frac    
     !for deciduous trees, there are no leaves  
 
-    if (pftcon%evergreen(ft) == 1) then
+    if (EDPftvarcon_inst%evergreen(ft) == 1) then
        currentcohort%laimemory = 0._r8
        currentcohort%status_coh    = 2      
     endif    
 
     ! iagnore the root and stem biomass from the functional balance hypothesis. This is used when the leaves are 
     !fully on. 
-    !currentcohort%br  = pftcon%froot_leaf(ft) * (currentcohort%balive + currentcohort%laimemory) * leaf_frac
+    !currentcohort%br  = EDPftvarcon_inst%froot_leaf(ft) * (currentcohort%balive + currentcohort%laimemory) * leaf_frac
     !currentcohort%bsw = EDecophyscon%sapwood_ratio(ft) * currentcohort%hite *(currentcohort%balive + &
     !     currentcohort%laimemory)*leaf_frac 
 
     leaves_off_switch = 0
-    if (currentcohort%status_coh == 1.and.pftcon%stress_decid(ft) == 1.and.currentcohort%siteptr%dstatus==1) then !no leaves 
+    if (currentcohort%status_coh == 1.and.EDPftvarcon_inst%stress_decid(ft) == 1.and.currentcohort%siteptr%dstatus==1) then !no leaves 
       leaves_off_switch = 1 !drought decid
     endif
-    if (currentcohort%status_coh == 1.and.pftcon%season_decid(ft) == 1.and.currentcohort%siteptr%status==1) then !no leaves
+    if (currentcohort%status_coh == 1.and.EDPftvarcon_inst%season_decid(ft) == 1.and.currentcohort%siteptr%status==1) then !no leaves
       leaves_off_switch = 1 !cold decid
     endif
 
@@ -232,8 +232,8 @@ subroutine allocate_live_biomass(cc_p,mode)
        if(mode==1)then
 
           currentcohort%npp_froot = currentcohort%npp_froot + &
-               max(0._r8,pftcon%froot_leaf(ft)*(currentcohort%balive+currentcohort%laimemory)*leaf_frac - currentcohort%br) / &
-               udata%deltat
+               max(0._r8, EDPftvarcon_inst%froot_leaf(ft)*(currentcohort%balive+currentcohort%laimemory)*leaf_frac - &
+               currentcohort%br) / udata%deltat
 
           currentcohort%npp_bsw = max(0._r8,EDecophyscon%sapwood_ratio(ft) * currentcohort%hite *(currentcohort%balive + &
                 currentcohort%laimemory)*leaf_frac - currentcohort%bsw)/udata%deltat
@@ -242,7 +242,7 @@ subroutine allocate_live_biomass(cc_p,mode)
 
        end if
 
-       currentcohort%br  = pftcon%froot_leaf(ft) * (currentcohort%balive + currentcohort%laimemory) * leaf_frac
+       currentcohort%br  = EDPftvarcon_inst%froot_leaf(ft) * (currentcohort%balive + currentcohort%laimemory) * leaf_frac
        currentcohort%bsw = EDecophyscon%sapwood_ratio(ft) * currentcohort%hite *(currentcohort%balive + &
             currentcohort%laimemory)*leaf_frac
 
@@ -257,9 +257,9 @@ subroutine allocate_live_biomass(cc_p,mode)
 
 
        currentcohort%bl  = 0.0_r8
-       ideal_balive      = currentcohort%laimemory * pftcon%froot_leaf(ft) +  &
+       ideal_balive      = currentcohort%laimemory * EDPftvarcon_inst%froot_leaf(ft) +  &
             currentcohort%laimemory*  EDecophyscon%sapwood_ratio(ft) * currentcohort%hite
-       currentcohort%br  = pftcon%froot_leaf(ft) * (ideal_balive + currentcohort%laimemory) * leaf_frac
+       currentcohort%br  = EDPftvarcon_inst%froot_leaf(ft) * (ideal_balive + currentcohort%laimemory) * leaf_frac
        currentcohort%bsw = EDecophyscon%sapwood_ratio(ft) * currentcohort%hite *(ideal_balive + &
             currentcohort%laimemory)*leaf_frac 
 
@@ -271,7 +271,7 @@ subroutine allocate_live_biomass(cc_p,mode)
        if(mode==1)then
 
           currentcohort%npp_froot = currentcohort%npp_froot + &
-                max(0.0_r8,pftcon%froot_leaf(ft)*(ideal_balive + &
+                max(0.0_r8,EDPftvarcon_inst%froot_leaf(ft)*(ideal_balive + &
                 currentcohort%laimemory)*leaf_frac*ratio_balive-currentcohort%br)/udata%deltat
 
           currentcohort%npp_bsw = max(0.0_r8,EDecophyscon%sapwood_ratio(ft) * currentcohort%hite *(ideal_balive + &
@@ -289,7 +289,7 @@ subroutine allocate_live_biomass(cc_p,mode)
             currentcohort%status_coh,currentcohort%balive
        write(fates_log(),*) 'actual vs predicted balive',ideal_balive,currentcohort%balive ,ratio_balive,leaf_frac
        write(fates_log(),*) 'leaf,root,stem',currentcohort%bl,currentcohort%br,currentcohort%bsw
-       write(fates_log(),*) 'pft',ft,pftcon%evergreen(ft),pftcon%season_decid(ft),leaves_off_switch
+       write(fates_log(),*) 'pft',ft,EDPftvarcon_inst%evergreen(ft),EDPftvarcon_inst%season_decid(ft),leaves_off_switch
     endif
     currentCohort%b   = currentCohort%bdead + currentCohort%balive
 

biogeochem/EDGrowthFunctionsMod.F90

@@ -8,7 +8,7 @@ module EDGrowthFunctionsMod
 
   use shr_kind_mod     , only : r8 => shr_kind_r8
   use clm_varctl       , only : iulog 
-  use pftconMod        , only : pftcon
+  use EDPftvarcon        , only : EDPftvarcon_inst
   use EDEcophysContype , only : EDecophyscon
   use EDTypesMod       , only : ed_cohort_type, cp_nlevcan, dinc_ed
 
@@ -114,7 +114,7 @@ real(r8) function Bleaf( cohort_in )
     else  
        bleaf = 0.0419_r8 * (EDecophyscon%max_dbh(cohort_in%pft)**1.56) * EDecophyscon%wood_density(cohort_in%pft)**0.55_r8      
     endif  
-    slascaler = 0.03_r8/pftcon%slatop(cohort_in%pft)
+    slascaler = 0.03_r8/EDPftvarcon_inst%slatop(cohort_in%pft)
     bleaf = bleaf * slascaler
 
     !write(iulog,*) 'bleaf',bleaf, slascaler,cohort_in%pft
@@ -145,7 +145,7 @@ real(r8) function tree_lai( cohort_in )
     endif
 
     if( cohort_in%status_coh  ==  2 ) then ! are the leaves on? 
-       slat = 1000.0_r8 * pftcon%slatop(cohort_in%pft) ! m2/g to m2/kg
+       slat = 1000.0_r8 * EDPftvarcon_inst%slatop(cohort_in%pft) ! m2/g to m2/kg
        cohort_in%c_area = c_area(cohort_in) ! call the tree area
        leafc_per_unitarea = cohort_in%bl/(cohort_in%c_area/cohort_in%n) !KgC/m2
        if(leafc_per_unitarea > 0.0_r8)then
@@ -225,15 +225,15 @@ real(r8) function c_area( cohort_in )
     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 3',EDPftvarcon_inst%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
     end if
 
     dbh = min(cohort_in%dbh,EDecophyscon%max_dbh(cohort_in%pft))
-    if(pftcon%woody(cohort_in%pft) == 1)then 
+    if(EDPftvarcon_inst%woody(cohort_in%pft) == 1)then 
        c_area = 3.142_r8 * cohort_in%n * &
             (cohort_in%patchptr%spread(cohort_in%canopy_layer)*dbh)**1.56_r8
     else

biogeochem/EDPatchDynamicsMod.F90

@@ -7,7 +7,7 @@ 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 pftconMod            , only : pftcon
+  use EDPftvarcon            , only : EDPftvarcon_inst
   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
@@ -281,7 +281,7 @@ subroutine spawn_patches( currentSite )
                    nc%imort = nan
                 else
                    ! small trees 
-                   if(pftcon%woody(currentCohort%pft) == 1)then
+                   if(EDPftvarcon_inst%woody(currentCohort%pft) == 1)then
 
                       ! Number of trees in the understory of new patch, before we impose impact mortality and survivorship
                       nc%n = currentCohort%n * patch_site_areadis/currentPatch%area
@@ -566,7 +566,7 @@ subroutine fire_litter_fluxes(cp_target, new_patch_target, patch_site_areadis)
        currentCohort => currentPatch%shortest
        do while(associated(currentCohort))
           p = currentCohort%pft
-          if(pftcon%woody(p) == 1)then !DEAD (FROM FIRE) TREES
+          if(EDPftvarcon_inst%woody(p) == 1)then !DEAD (FROM FIRE) TREES
              !************************************/ 
              ! Number of trees that died because of the fire, per m2 of ground. 
              ! Divide their litter into the four litter streams, and spread evenly across ground surface. 
@@ -649,7 +649,7 @@ subroutine fire_litter_fluxes(cp_target, new_patch_target, patch_site_areadis)
        do while(associated(currentCohort))
 
           currentCohort%c_area = c_area(currentCohort) 
-          if(pftcon%woody(currentCohort%pft) == 1)then
+          if(EDPftvarcon_inst%woody(currentCohort%pft) == 1)then
              burned_leaves = (currentCohort%bl+currentCohort%bsw) * currentCohort%cfa
           else
              burned_leaves = (currentCohort%bl+currentCohort%bsw) * currentPatch%burnt_frac_litter(6)
@@ -726,7 +726,7 @@ subroutine mortality_litter_fluxes(cp_target, new_patch_target, patch_site_aread
                   canopy_dead*(currentCohort%br+currentCohort%bstore)
 
          else 
-             if(pftcon%woody(currentCohort%pft) == 1)then
+             if(EDPftvarcon_inst%woody(currentCohort%pft) == 1)then
 
                 understorey_dead = ED_val_understorey_death * currentCohort%n * (patch_site_areadis/currentPatch%area)  !kgC/site/day
                 currentPatch%canopy_mortality_woody_litter  = currentPatch%canopy_mortality_woody_litter  + &