Merge pull request #4 from rgknox/yi-logging-v3

Added disturbance index names and partial addition of logging NL entry
rgknox · Aug 28, 2017 · 65bd080 · 65bd080
2 parents 48b01dd + 113fd8f
commit 65bd080
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Showing 4 changed files with 62 additions and 29 deletions.
diff --git a/biogeochem/EDLoggingMortalityMod.F90 b/biogeochem/EDLoggingMortalityMod.F90
@@ -20,6 +20,9 @@ module EDLoggingMortalityMod
    use EDTypesMod        , only : ncwd
    use EDTypesMod        , only : ed_site_type
    use EDTypesMod        , only : ed_resources_management_type
+   use EDTypesMod        , only : dtype_ilog
+   use EDTypesMod        , only : dtype_ifall
+   use EDTypesMod        , only : dtype_ifire
    use EDPftvarcon       , only : EDPftvarcon_inst
    use EDParamsMod       , only : logging_event_code
    use EDParamsMod       , only : logging_dbhmin
@@ -31,7 +34,7 @@ module EDLoggingMortalityMod
    use FatesInterfaceMod , only : hlm_current_day
    use FatesInterfaceMod , only : hlm_model_day
    use FatesInterfaceMod , only : hlm_day_of_year
-   use FatesConstantsMod , only : itrue
+   use FatesConstantsMod , only : itrue,ifalse
    use FatesGlobals      , only : endrun => fates_endrun 
    use FatesGlobals      , only : fates_log
    use shr_log_mod       , only : errMsg => shr_log_errMsg
@@ -72,6 +75,9 @@ subroutine IsItLoggingTime(is_master)
       logging_time = .false.
       icode = int(logging_event_code)
 
+!      if(hlm_use_logging.eq.ifalse) return     ! Don't turn on until fates-clm adds
+                                                ! this to the interface (RGK 08-2017)
+
       if(icode .eq. 1) then
          ! Logging is turned off
          logging_time = .false.
@@ -239,8 +245,8 @@ subroutine logging_litter_fluxes(cp_Site, cp_target, new_patch_target, patch_sit
          currentCohort => currentPatch%shortest
          do while(associated(currentCohort))       
             p = currentCohort%pft
-            if(currentPatch%disturbance_rates(3) > currentPatch%disturbance_rates(2) .and. &
-                  currentPatch%disturbance_rates(3) > currentPatch%disturbance_rates(1) )then 
+            if(currentPatch%disturbance_rates(dtype_ilog) > currentPatch%disturbance_rates(dtype_ifire) .and. &
+                  currentPatch%disturbance_rates(dtype_ilog) > currentPatch%disturbance_rates(dtype_ifall) )then 
                   !mortality is dominant disturbance 
 
                if(EDPftvarcon_inst%woody(p) == 1)then   

diff --git a/biogeochem/EDPatchDynamicsMod.F90 b/biogeochem/EDPatchDynamicsMod.F90
@@ -13,6 +13,9 @@ module EDPatchDynamicsMod
   use EDTypesMod           , only : min_patch_area
   use EDTypesMod           , only : nclmax
   use EDTypesMod           , only : maxpft
+  use EDTypesMod           , only : dtype_ifall
+  use EDTypesMod           , only : dtype_ilog
+  use EDTypesMod           , only : dtype_ifire
   use FatesInterfaceMod    , only : hlm_use_planthydro
   use FatesInterfaceMod    , only : hlm_numlevgrnd
   use FatesInterfaceMod    , only : hlm_numlevsoil
@@ -128,7 +131,7 @@ subroutine disturbance_rates( site_in)
 
           if(currentCohort%canopy_layer == 1)then
 
-             currentPatch%disturbance_rates(1) = currentPatch%disturbance_rates(1) + &
+             currentPatch%disturbance_rates(dtype_ifall) = currentPatch%disturbance_rates(dtype_ifall) + &
                   fates_mortality_disturbance_fraction * &
                   min(1.0_r8,currentCohort%dmort)*hlm_freq_day*currentCohort%c_area/currentPatch%area
 
@@ -156,7 +159,7 @@ subroutine disturbance_rates( site_in)
 
                 !May need to change currentCohort%c_area
                 !disturbance_rates will be reset to 0 at the end of spawn_patches
-                currentPatch%disturbance_rates(3) = currentPatch%disturbance_rates(3) + &
+                currentPatch%disturbance_rates(dtype_ilog) = currentPatch%disturbance_rates(dtype_ilog) + &
                       min(1.0_r8, currentCohort%lmort_logging +                         & 
                                   currentCohort%lmort_collateral +                      &
                                   currentCohort%lmort_infra ) *                         &
@@ -175,18 +178,18 @@ subroutine disturbance_rates( site_in)
        ! if fires occur at site 
        ! Fudge - fires can't burn the whole patch, as this causes /0 errors.
        ! This is accumulating the daily fires over the whole 30 day patch generation phase.  
-       currentPatch%disturbance_rates(2) = min(0.99_r8,currentPatch%disturbance_rates(2) + currentPatch%frac_burnt)
+       currentPatch%disturbance_rates(dtype_ifire) = min(0.99_r8,currentPatch%disturbance_rates(dtype_ifire) + currentPatch%frac_burnt)
 
-       if (currentPatch%disturbance_rates(2) > 0.98_r8)then
-          write(fates_log(),*) 'very high fire areas',currentPatch%disturbance_rates(2),currentPatch%frac_burnt
+       if (currentPatch%disturbance_rates(dtype_ifire) > 0.98_r8)then
+          write(fates_log(),*) 'very high fire areas',currentPatch%disturbance_rates(dtype_ifire),currentPatch%frac_burnt
        endif
 
-       if (currentPatch%disturbance_rates(3) > currentPatch%disturbance_rates(1) .and. &
-             currentPatch%disturbance_rates(3) > currentPatch%disturbance_rates(2) ) then 
+       if (currentPatch%disturbance_rates(dtype_ilog) > currentPatch%disturbance_rates(dtype_ifall) .and. &
+             currentPatch%disturbance_rates(dtype_ilog) > currentPatch%disturbance_rates(dtype_ifire) ) then 
 
           ! logging disturbance dominates
           ! Y.X. 3/2017
-          currentPatch%disturbance_rate = currentPatch%disturbance_rates(3)
+          currentPatch%disturbance_rate = currentPatch%disturbance_rates(dtype_ilog)
 
           currentCohort => currentPatch%shortest
           do while(associated(currentCohort))
@@ -200,10 +203,10 @@ subroutine disturbance_rates( site_in)
              currentCohort => currentCohort%taller
           enddo !currentCohort
 
-         elseif (currentPatch%disturbance_rates(2) > currentPatch%disturbance_rates(1) .and. &
-                 currentPatch%disturbance_rates(2) > currentPatch%disturbance_rates(3) ) then  ! DISTURBANCE IS FIRE
+         elseif (currentPatch%disturbance_rates(dtype_ifire) > currentPatch%disturbance_rates(dtype_ifall) .and. &
+                 currentPatch%disturbance_rates(dtype_ifire) > currentPatch%disturbance_rates(dtype_ilog) ) then  ! DISTURBANCE IS FIRE
 
-          currentPatch%disturbance_rate = currentPatch%disturbance_rates(2)
+          currentPatch%disturbance_rate = currentPatch%disturbance_rates(dtype_ifire)
 
           ! RGK 02-18-2014
           ! Since treefall mortality is not actually being applied
@@ -230,9 +233,9 @@ subroutine disturbance_rates( site_in)
              currentCohort => currentCohort%taller
           enddo !currentCohort
 
-       elseif (currentPatch%disturbance_rates(1) > currentPatch%disturbance_rates(2) .and. &
-             currentPatch%disturbance_rates(1) > currentPatch%disturbance_rates(3) ) then
-          currentPatch%disturbance_rate = currentPatch%disturbance_rates(1)            ! DISTURBANCE IS MORTALITY
+       elseif (currentPatch%disturbance_rates(dtype_ifall) > currentPatch%disturbance_rates(dtype_ifire) .and. &
+             currentPatch%disturbance_rates(dtype_ifall) > currentPatch%disturbance_rates(dtype_ilog) ) then
+          currentPatch%disturbance_rate = currentPatch%disturbance_rates(dtype_ifall)            ! DISTURBANCE IS MORTALITY
 
        else
           write(fates_log(),*) 'A dominant disturbance mode was not identified somehow'
@@ -241,11 +244,11 @@ subroutine disturbance_rates( site_in)
        endif
 
        site_in%disturbance_mortality = site_in%disturbance_mortality + &
-            currentPatch%disturbance_rates(1)*currentPatch%area/area  
+            currentPatch%disturbance_rates(dtype_ifall)*currentPatch%area/area  
 
          !disturbance_logging
         site_in%disturbance_logging = site_in%disturbance_logging + &
-          currentPatch%disturbance_rates(3)*currentPatch%area/area  
+          currentPatch%disturbance_rates(dtype_ilog)*currentPatch%area/area  
 
        currentPatch => currentPatch%younger
 
@@ -413,8 +416,8 @@ subroutine spawn_patches( currentSite, bc_in)
              nc%canopy_layer_yesterday = 1._r8 
 
              ! treefall mortality is the dominant disturbance
-             if(currentPatch%disturbance_rates(1) > currentPatch%disturbance_rates(2) .and. &
-                    currentPatch%disturbance_rates(1) > currentPatch%disturbance_rates(3))then 
+             if(currentPatch%disturbance_rates(dtype_ifall) > currentPatch%disturbance_rates(dtype_ifire) .and. &
+                    currentPatch%disturbance_rates(dtype_ifall) > currentPatch%disturbance_rates(dtype_ilog))then 
                 if(currentCohort%canopy_layer == 1)then
                    ! In the donor patch we are left with fewer trees because the area has decreased
                    ! the plant density for large trees does not actually decrease in the donor patch
@@ -495,8 +498,8 @@ subroutine spawn_patches( currentSite, bc_in)
                 endif
 
              ! Fire is the dominant disturbance 
-             elseif (currentPatch%disturbance_rates(2) > currentPatch%disturbance_rates(1) .and. &
-                     currentPatch%disturbance_rates(2) > currentPatch%disturbance_rates(3)) then !fire
+             elseif (currentPatch%disturbance_rates(dtype_ifire) > currentPatch%disturbance_rates(dtype_ifall) .and. &
+                     currentPatch%disturbance_rates(dtype_ifire) > currentPatch%disturbance_rates(dtype_ilog)) then !fire
 
                 ! Number of members in the new patch, before we impose fire survivorship
                 nc%n = currentCohort%n * patch_site_areadis/currentPatch%area
@@ -518,8 +521,8 @@ subroutine spawn_patches( currentSite, bc_in)
                 nc%lmort_infra      = 0.0_r8
 
              ! Logging is the dominant disturbance  
-             elseif (currentPatch%disturbance_rates(3) > currentPatch%disturbance_rates(1) .and. &
-                     currentPatch%disturbance_rates(3) > currentPatch%disturbance_rates(2)) then  ! Logging 
+             elseif (currentPatch%disturbance_rates(dtype_ilog) > currentPatch%disturbance_rates(dtype_ifall) .and. &
+                     currentPatch%disturbance_rates(dtype_ilog) > currentPatch%disturbance_rates(dtype_ifire)) then  ! Logging 
 
                 if(EDPftvarcon_inst%woody(currentCohort%pft) == 1)then
                    ! Move the survival trees into new patch
@@ -995,7 +998,7 @@ subroutine mortality_litter_fluxes(currentSite, cp_target, new_patch_target, pat
     currentCohort => currentPatch%shortest
     do while(associated(currentCohort))       
        p = currentCohort%pft
-       if(currentPatch%disturbance_rates(1) > currentPatch%disturbance_rates(2))then !mortality is dominant disturbance 
+       if(currentPatch%disturbance_rates(dtype_ifall) > currentPatch%disturbance_rates(dtype_ifire))then !mortality is dominant disturbance 
           if(currentCohort%canopy_layer == 1)then         
              !currentCohort%dmort = mortality_rates(currentCohort) 
              !the disturbance calculations are done with the previous n, c_area and d_mort. So it's probably &

diff --git a/main/EDTypesMod.F90 b/main/EDTypesMod.F90
@@ -65,8 +65,10 @@ module EDTypesMod
   integer , parameter :: external_recruitment = 0          ! external recruitment flag 1=yes  
   integer , parameter :: SENES                = 10         ! Window of time over which we track temp for cold sensecence (days)
   real(r8), parameter :: DINC_ED              = 1.0_r8     ! size of LAI bins. 
-  !integer , parameter :: N_DIST_TYPES         = 2          ! number of disturbance types (mortality, fire)
-  integer , parameter :: N_DIST_TYPES         = 3           ! add selective logging disturbance
+  integer , parameter :: N_DIST_TYPES         = 3          ! Disturbance Modes 1) tree-fall, 2) fire, 3) logging
+  integer , parameter :: dtype_ifall          = 1          ! index for naturally occuring tree-fall generated event
+  integer , parameter :: dtype_ifire          = 2          ! index for fire generated disturbance event
+  integer , parameter :: dtype_ilog           = 3          ! index for logging generated disturbance event
 
   ! SPITFIRE     
   integer,  parameter :: NCWD                 = 4          ! number of coarse woody debris pools (twig,s branch,l branch, trunk)

diff --git a/main/FatesInterfaceMod.F90 b/main/FatesInterfaceMod.F90
@@ -19,7 +19,7 @@ module FatesInterfaceMod
    use EDTypesMod          , only : nlevleaf
    use EDTypesMod          , only : maxpft
    use FatesConstantsMod   , only : r8 => fates_r8
-   use FatesConstantsMod   , only : itrue
+   use FatesConstantsMod   , only : itrue,ifalse
    use FatesGlobals        , only : fates_global_verbose
    use FatesGlobals        , only : fates_log
    use FatesGlobals        , only : endrun => fates_endrun
@@ -121,6 +121,10 @@ module FatesInterfaceMod
    integer, protected :: hlm_use_spitfire  ! This flag signals whether or not to use SPITFIRE
                                            ! 1 = TRUE, 0 = FALSE
 
+
+   integer, protected :: hlm_use_logging       ! This flag signals whether or not to use
+                                               ! the logging module
+
    integer, protected :: hlm_use_planthydro    ! This flag signals whether or not to use
                                                ! plant hydraulics (bchristo/xu methods)
                                                ! 1 = TRUE, 0 = FALSE
@@ -1120,6 +1124,11 @@ subroutine set_fates_ctrlparms(tag,ival,rval,cval)
          hlm_use_vertsoilc = unset_int
          hlm_use_spitfire  = unset_int
          hlm_use_planthydro = unset_int
+         hlm_use_logging   = ifalse          ! (RGK: to allow backwards compatibility
+                                             !  defaulting to FALSE, this will allow
+                                             !  the call from the HLM to not necessarily
+                                             !  be forced to exist. Will set this to unset
+                                             !  along with other non backwards compatible changes
          hlm_use_ed_st3    = unset_int
          hlm_use_ed_prescribed_phys = unset_int
          hlm_use_inventory_init = unset_int
@@ -1161,6 +1170,13 @@ subroutine set_fates_ctrlparms(tag,ival,rval,cval)
             call endrun(msg=errMsg(sourcefile, __LINE__))
          end if
 
+         if ( .not.((hlm_use_logging .eq.1).or.(hlm_use_logging.eq.0))    ) then
+            if (fates_global_verbose()) then
+               write(fates_log(), *) 'The FATES namelist planthydro flag must be 0 or 1, exiting'
+            end if
+            call endrun(msg=errMsg(sourcefile, __LINE__))
+         end if
+
          if (  .not.((hlm_use_ed_st3.eq.1).or.(hlm_use_ed_st3.eq.0))    ) then
             if (fates_global_verbose()) then
                write(fates_log(), *) 'The FATES namelist stand structure flag must be 0 or 1, exiting'
@@ -1392,6 +1408,12 @@ subroutine set_fates_ctrlparms(tag,ival,rval,cval)
                   write(fates_log(),*) 'Transfering hlm_use_planthydro= ',ival,' to FATES'
                end if
 
+            case('use_logging')
+               hlm_use_logging = ival
+               if (fates_global_verbose()) then
+                  write(fates_log(),*) 'Transfering hlm_use_planthydro= ',ival,' to FATES'
+               end if
+
             case('use_ed_st3')
                hlm_use_ed_st3 = ival
                if (fates_global_verbose()) then