Bugfix for zeroing data and indexing grperc

Merge branch 'rgknox-bugfix36-bugfix4'

Simple fixes that address issues #36 and #4. The fix to issue #4 was
trivial. In the fix to #36 I also checked through the code to assess
under which conditions zero'ing variables such as tlai and tsai would
affect other non-ed parts of the code. The fix allows the zeroing of
the LAI/SAI variables and htop/hbot variables at the patch level
because ED is the only submodule that will currently touch
them. However, moving forward we must be very careful of how other
modules potentially use these patch vectors. It is possible that a
crop model may exist on the same column, and therefore we don't want
to interact with those patches. Although, as far as I know, ACME for
instance may put crops on another column (now, future). Either way,
the changes here should make that zeroing procedure more future proof
by only zeroing natural vegetation, and should also be more efficient
by not constantly zeroing things that don't need zeroing.

Fixes: #36 #4

User interface changes?: No

Code review: rgknox

Test suite: ed - lawrencium-lr3, intel; yellowstone, gnu, intel, pgi

Test baseline: 5421da5
Test namelist changes: none
Test answer changes: b4b

Test summary: pass except for expected fails, f19 and f09 restarts

biogeochem/EDPhysiologyMod.F90

@@ -187,13 +187,13 @@ subroutine trim_canopy( currentSite )
                    currentCohort%leaf_cost =  1._r8/(pftcon%slatop(currentCohort%pft)*1000.0_r8)
                    currentCohort%leaf_cost = currentCohort%leaf_cost + 1.0_r8/(pftcon%slatop(currentCohort%pft)*1000.0_r8) * &
                         pftcon%froot_leaf(currentCohort%pft) / EDecophyscon%root_long(currentCohort%pft)
-                   currentCohort%leaf_cost = currentCohort%leaf_cost * (ED_val_grperc(1) + 1._r8)
+                   currentCohort%leaf_cost = currentCohort%leaf_cost * (ED_val_grperc(currentCohort%pft) + 1._r8)
                 else !evergreen costs
                    currentCohort%leaf_cost = 1.0_r8/(pftcon%slatop(currentCohort%pft)* &
                         pftcon%leaf_long(currentCohort%pft)*1000.0_r8) !convert from sla in m2g-1 to m2kg-1
                    currentCohort%leaf_cost = currentCohort%leaf_cost + 1.0_r8/(pftcon%slatop(currentCohort%pft)*1000.0_r8) * &
                         pftcon%froot_leaf(currentCohort%pft) / EDecophyscon%root_long(currentCohort%pft)
-                   currentCohort%leaf_cost = currentCohort%leaf_cost * (ED_val_grperc(1) + 1._r8)
+                   currentCohort%leaf_cost = currentCohort%leaf_cost * (ED_val_grperc(currentCohort%pft) + 1._r8)
                 endif
                 if (currentCohort%year_net_uptake(z) < currentCohort%leaf_cost)then
                    if (currentCohort%canopy_trim > trim_limit)then

main/EDCLMLinkMod.F90

@@ -986,6 +986,8 @@ subroutine ed_clm_link( this, bounds, ed_allsites_inst, ed_phenology_inst, &
     real(r8) :: canopy_leaf_area                        ! total amount of leaf area in the vegetated area. m2.  
     integer  :: sitecolumn(bounds%begg:bounds%endg)
     logical  :: istheresoil(bounds%begg:bounds%endg) 
+    integer  :: begp_fp, endp_fp                        ! Valid range of patch indices that are associated with 
+                                                        ! FATES (F) for each parent (P) iteration (grid/column)
     !----------------------------------------------------------------------
 
     if ( DEBUG ) then
@@ -1034,31 +1036,31 @@ subroutine ed_clm_link( this, bounds, ed_allsites_inst, ed_phenology_inst, &
          endif
       enddo
 
-      ! ============================================================================
-      ! Zero the whole variable so we dont have ghost values when patch number declines.
-      ! ============================================================================
-
-      clmpatch%is_veg(begp:endp)        = .false. 
-      clmpatch%is_bareground(begp:endp) = .false. 
-      tlai(begp:endp)                   = 0.0_r8    
-      elai(firstsoilpatch(g))           = 0.0_r8
-      tsai(firstsoilpatch(g))           = 0.0_r8
-      esai(firstsoilpatch(g))           = 0.0_r8
-      htop(begp:endp)                   = 0.0_r8      
-      hbot(begp:endp)                   = 0.0_r8   
-
       do g = begg,endg
 
          if(firstsoilpatch(g) >= 0.and.ed_allsites_inst(g)%istheresoil)then 
             ed_allsites_inst(g)%clmcolumn = sitecolumn(g)
 
             ! ============================================================================
             ! Zero the bare ground tile BGC variables.
+            ! Valid Range for zero'ing here is the soil_patch and non crop patches
+            ! If the crops are not turned on, don't worry, they were zero'd once and should
+            ! not change again (RGK).
+            ! firstsoilpatch(g) + numpft - numcft
             ! ============================================================================
 
-            tlai(firstsoilpatch(g)) = 0.0_r8    
-            htop(firstsoilpatch(g)) = 0.0_r8      
-            hbot(firstsoilpatch(g)) = 0.0_r8      
+            begp_fp = firstsoilpatch(g)
+            endp_fp = firstsoilpatch(g) + numpft - numcft
+
+            clmpatch%is_veg(begp_fp:endp_fp)        = .false. 
+            clmpatch%is_bareground(begp_fp:endp_fp) = .false. 
+            tlai(begp_fp:endp_fp)                   = 0.0_r8    
+            htop(begp_fp:endp_fp)                   = 0.0_r8      
+            hbot(begp_fp:endp_fp)                   = 0.0_r8   
+            elai(begp_fp:endp_fp)                   = 0.0_r8
+            tsai(begp_fp:endp_fp)                   = 0.0_r8
+            esai(begp_fp:endp_fp)                   = 0.0_r8
+
 
             patchn = 0
             total_bare_ground = 0.0_r8