fungal wood respiration

biogeochem/EDPhysiologyMod.F90

@@ -20,6 +20,7 @@ module EDPhysiologyMod
   use FatesInterfaceTypesMod, only    : hlm_use_nocomp
   use EDParamsMod           , only    : crop_lu_pft_vector
   use EDParamsMod           , only    : GetNVegLayers
+  use EDParamsMod           , only    : cwd_hr_frag_frac
   use FatesInterfaceTypesMod, only    : hlm_use_tree_damage
   use FatesInterfaceTypesMod, only : hlm_use_ed_prescribed_phys
   use FatesConstantsMod, only    : r8 => fates_r8
@@ -490,6 +491,9 @@ subroutine PreDisturbanceLitterFluxes( currentSite, currentPatch, bc_in )
               sum(litt%leaf_fines_frag) + sum(litt%root_fines_frag) + &
               sum(litt%seed_decay) + sum(litt%seed_germ_decay))
 
+         site_mass%funghr_out = site_mass%funghr_out + currentPatch%area * &
+              (sum(litt%ag_cwd_funghr) + sum(litt%bg_cwd_funghr))
+
          ! Track total seed decay diagnostic in [kg/m2/day]
          diag%tot_seed_turnover = diag%tot_seed_turnover + &
               (sum(litt%seed_decay) + sum(litt%seed_germ_decay))*currentPatch%area*area_inv
@@ -562,11 +566,12 @@ subroutine PreDisturbanceIntegrateLitter(currentPatch)
        ! -----------------------------------------------------------------------------------
        nlevsoil = size(litt%bg_cwd,dim=2)
        do c = 1,ncwd
-          litt%ag_cwd(c) = litt%ag_cwd(c)  + litt%ag_cwd_in(c) - litt%ag_cwd_frag(c)
+          litt%ag_cwd(c) = litt%ag_cwd(c)  + litt%ag_cwd_in(c) - litt%ag_cwd_frag(c) - litt%ag_cwd_funghr(c)
           do ilyr=1,nlevsoil
              litt%bg_cwd(c,ilyr) = litt%bg_cwd(c,ilyr) &
                   + litt%bg_cwd_in(c,ilyr) &
-                  - litt%bg_cwd_frag(c,ilyr)
+                  - litt%bg_cwd_frag(c,ilyr) &
+                  - litt%bg_cwd_funghr(c,ilyr)
           enddo
        end do
 
@@ -3269,21 +3274,35 @@ subroutine CWDOut( litt, fragmentation_scaler, nlev_eff_decomp )
     integer :: ilyr                    ! Soil layer index
     integer :: dcmpy                   ! Decomposibility pool indexer
     integer :: soil_layer_index = 1    ! Soil layer index associated with above ground litter
+    real(r8) :: decomp_rate            ! per-mass per-day loss rate due to fragmentation AND fungal HR
+    real(r8) :: cwd_hr_frag_frac_eff   ! Effective (element specific) proportion of
+                                       ! losses due to HR
     !----------------------------------------------------------------------
 
 
     ! Above ground litters are associated with the top soil layer temperature and
     ! moisture scalars and fragmentation scalar associated with specified index value
     ! is used for ag_cwd_frag and root_fines_frag calculations.
 
-    do c = 1,ncwd
 
-       litt%ag_cwd_frag(c)   = litt%ag_cwd(c) * SF_val_max_decomp(c) * &
-             years_per_day * fragmentation_scaler(soil_layer_index)
+    ! Heterotrophic respiration can only be applied to the carbon pool!
+    if( litt%element_id.eq.carbon12_element) then
+       cwd_hr_frag_frac_eff = cwd_hr_frag_frac
+    else
+       cwd_hr_frag_frac_eff = 0._r8
+    end if
+
+
+    do c = 1,ncwd
 
+       decomp_rate = SF_val_max_decomp(c) * years_per_day * fragmentation_scaler(soil_layer_index)
+       litt%ag_cwd_frag(c)   = litt%ag_cwd(c) * decomp_rate * (1._r8-cwd_hr_frag_frac_eff)
+       litt%ag_cwd_funghr(c) = litt%ag_cwd(c) * decomp_rate * cwd_hr_frag_frac_eff
+
        do ilyr = 1,nlev_eff_decomp
-           litt%bg_cwd_frag(c,ilyr) = litt%bg_cwd(c,ilyr) * SF_val_max_decomp(c) * &
-                years_per_day * fragmentation_scaler(ilyr)
+          decomp_rate = SF_val_max_decomp(c) * years_per_day * fragmentation_scaler(ilyr)
+          litt%bg_cwd_frag(c,ilyr)   = litt%bg_cwd(c,ilyr) * decomp_rate * (1._r8-cwd_hr_frag_frac_eff)
+          litt%bg_cwd_funghr(c,ilyr) = litt%bg_cwd(c,ilyr) * decomp_rate * cwd_hr_frag_frac_eff
        enddo
     end do
 

biogeochem/FatesLitterMod.F90

@@ -101,6 +101,9 @@ module FatesLitterMod
       real(r8),allocatable ::  leaf_fines_frag(:)   ! above ground fines fragmentation flux [kg/m2/day]
       real(r8),allocatable ::  root_fines_frag(:,:) ! kg/m2/day
 
+      real(r8)             ::  ag_cwd_funghr(ncwd)  ! above ground Fungal respiration flux [kg/m2/day]
+      real(r8),allocatable ::  bg_cwd_funghr(:,:)   ! below ground fungal respiration flux [kg/m2/day]
+
       real(r8), allocatable :: seed_decay(:)      ! decay of viable seeds to litter     [kg/m2/day]
       real(r8), allocatable :: seed_germ_decay(:) ! decay of germinated seeds to litter [kg/m2/day]
       real(r8), allocatable :: seed_germ_in(:)    ! flux from viable to germinated seed [kg/m2/day]
@@ -164,13 +167,17 @@ subroutine FuseLitter(this,self_area,donor_area,donor_litt)
                              donor_litt%ag_cwd_in(c) * donor_weight
        this%ag_cwd_frag(c) = this%ag_cwd_frag(c) *self_weight + &
                              donor_litt%ag_cwd_frag(c) * donor_weight
+       this%ag_cwd_funghr(c)  = this%ag_cwd_funghr(c) * self_weight + &
+                              donor_litt%ag_cwd_funghr(c) * donor_weight
        do ilyr = 1,nlevsoil
           this%bg_cwd(c,ilyr)      = this%bg_cwd(c,ilyr) * self_weight + &
                                      donor_litt%bg_cwd(c,ilyr) * donor_weight
           this%bg_cwd_in(c,ilyr)   = this%bg_cwd_in(c,ilyr) * self_weight + &
                                      donor_litt%bg_cwd_in(c,ilyr) * donor_weight
           this%bg_cwd_frag(c,ilyr) = this%bg_cwd_frag(c,ilyr) * self_weight + &
                                      donor_litt%bg_cwd_frag(c,ilyr) * donor_weight
+          this%bg_cwd_funghr(c,ilyr) = this%bg_cwd_funghr(c,ilyr) * self_weight + &
+                                     donor_litt%bg_cwd_funghr(c,ilyr) * donor_weight
        end do
 
     end do
@@ -234,11 +241,13 @@ subroutine CopyLitter(this,donor_litt)
     this%ag_cwd(:)      = donor_litt%ag_cwd(:)
     this%ag_cwd_in(:)   = donor_litt%ag_cwd_in(:)
     this%ag_cwd_frag(:) = donor_litt%ag_cwd_frag(:)
+    this%ag_cwd_funghr(:)  = donor_litt%ag_cwd_funghr(:)
 
     this%bg_cwd(:,:)      = donor_litt%bg_cwd(:,:)
     this%bg_cwd_in(:,:)   = donor_litt%bg_cwd_in(:,:)
     this%bg_cwd_frag(:,:) = donor_litt%bg_cwd_frag(:,:)
-
+    this%bg_cwd_funghr(:,:) = donor_litt%bg_cwd_funghr(:,:)
+
     this%leaf_fines(:)    = donor_litt%leaf_fines(:)
     this%seed(:)          = donor_litt%seed(:)
     this%seed_germ(:)     = donor_litt%seed_germ(:)
@@ -272,7 +281,8 @@ subroutine InitAllocate(this,numpft,numlevsoil,element_id)
     allocate(this%bg_cwd_in(ncwd,numlevsoil))
     allocate(this%bg_cwd(ncwd,numlevsoil))
     allocate(this%bg_cwd_frag(ncwd,numlevsoil))
-
+    allocate(this%bg_cwd_funghr(ncwd,numlevsoil))
+
     allocate(this%leaf_fines(ndcmpy))
     allocate(this%root_fines(ndcmpy,numlevsoil))
     allocate(this%leaf_fines_in(ndcmpy))
@@ -304,7 +314,9 @@ subroutine InitAllocate(this,numpft,numlevsoil,element_id)
     this%seed_in_extern(:)    = fates_unset_r8
 
     this%ag_cwd_frag(:)       = fates_unset_r8
+    this%ag_cwd_funghr(:)     = fates_unset_r8
     this%bg_cwd_frag(:,:)     = fates_unset_r8
+    this%bg_cwd_funghr(:,:)   = fates_unset_r8
     this%leaf_fines_frag(:)   = fates_unset_r8
     this%root_fines_frag(:,:) = fates_unset_r8
 
@@ -383,6 +395,7 @@ subroutine DeallocateLitt(this)
     deallocate(this%seed_in_extern)
 
     deallocate(this%bg_cwd_frag)
+    deallocate(this%bg_cwd_funghr)
     deallocate(this%leaf_fines_frag)
     deallocate(this%root_fines_frag)
 
@@ -407,7 +420,9 @@ subroutine ZeroFlux(this)
     this%seed_in_extern(:)    = 0._r8
 
     this%ag_cwd_frag(:)       = 0._r8
+    this%ag_cwd_funghr(:)     = 0._r8
     this%bg_cwd_frag(:,:)     = 0._r8
+    this%bg_cwd_funghr(:,:)   = 0._r8
     this%leaf_fines_frag(:)   = 0._r8
     this%root_fines_frag(:,:) = 0._r8
 

main/ChecksBalancesMod.F90

@@ -325,13 +325,14 @@ subroutine CheckIntegratedMassPools(site)
                  - ediag%tot_seed_turnover)
 
             ! Flux for litter: veg turnover + seed turnover - "these are tot_litter_input"
-            !                  fragmentation - 
+            !                  fragmentation - fungal respiration
             !                  burned litter
 
             ibal%iflux_litter = ibal%iflux_litter + &
                  tot_litter_input - &
                  (site_mass%frag_out*area_inv - ediag%tot_seed_turnover) - &
-                 (sum(site_mass%burn_flux_to_atm(:))*area_inv - ediag%burned_liveveg)
+                 (sum(site_mass%burn_flux_to_atm(:))*area_inv - ediag%burned_liveveg) - &
+                 site_mass%funghr_out*area_inv
 
 
             ediag%err_liveveg = ibal%iflux_liveveg - ibal%state_liveveg

main/EDMainMod.F90

@@ -1015,6 +1015,7 @@ subroutine TotalBalanceCheck (currentSite, call_index, is_restarting )
                site_mass%seed_out + &
                site_mass%flux_generic_out + &
                site_mass%frag_out + &
+               site_mass%funghr_out + &
                site_mass%aresp_acc + &
                site_mass%herbivory_flux_out
        end if
@@ -1049,6 +1050,7 @@ subroutine TotalBalanceCheck (currentSite, call_index, is_restarting )
           write(fates_log(),*) 'seed_out: ',site_mass%seed_out
           write(fates_log(),*) 'flux_generic_out: ',site_mass%flux_generic_out
           write(fates_log(),*) 'frag_out: ',site_mass%frag_out
+          write(fates_log(),*) 'funghr_out: ',site_mass%funghr_out
           write(fates_log(),*) 'aresp_acc: ',site_mass%aresp_acc
           write(fates_log(),*) 'herbivory_flux_out: ',site_mass%herbivory_flux_out
           write(fates_log(),*) 'error=net_flux-dstock:', error

main/EDParamsMod.F90

@@ -44,6 +44,8 @@ module EDParamsMod
    real(r8),protected, public :: comp_excln_exp                       ! weighting factor (exponent) for canopy layer exclusion and promotion
    real(r8),protected, public :: ED_val_nignitions                    ! number of annual ignitions per square km
    real(r8),protected, public :: ED_val_understorey_death             ! fraction of plants in understorey cohort impacted by overstorey tree-fall
+   real(r8),protected, public :: cwd_hr_frag_frac                     ! fraction of losses from CWD pool that are due to
+                                                                      ! fungal heterotrophic respiration as opposed to fragmentation
    real(r8),protected, public :: ED_val_cwd_fcel                      ! Cellulose fraction for CWD
    real(r8),protected, public :: ED_val_cwd_flig                      ! Lignin fraction of coarse woody debris
    real(r8),protected, public :: maintresp_nonleaf_baserate           ! Base maintenance respiration rate for plant tissues
@@ -227,6 +229,7 @@ subroutine FatesParamsInit()
     comp_excln_exp                        = nan
     ED_val_nignitions                     = nan
     ED_val_understorey_death              = nan
+    cwd_hr_frag_frac                      = nan
     ED_val_cwd_fcel                       = nan
     ED_val_cwd_flig                       = nan
     maintresp_nonleaf_baserate            = nan
@@ -339,6 +342,9 @@ subroutine TransferParamsGeneric(pstruct)
 
     param_p => pstruct%GetParamFromName("fates_frag_cwd_flig")
     ED_val_cwd_flig = param_p%r_data_scalar
+
+    param_p => pstruct%GetParamFromName("fates_cwd_hrfrag_frac")
+    cwd_hr_frag_frac = param_p%r_data_scalar
 
     param_p => pstruct%GetParamFromName("fates_maintresp_nonleaf_baserate")
     maintresp_nonleaf_baserate = param_p%r_data_scalar
@@ -514,6 +520,7 @@ subroutine FatesReportParams(is_master)
         write(fates_log(),fmt0) 'comp_excln_exp = ',comp_excln_exp
         write(fates_log(),fmt0) 'ED_val_nignitions = ',ED_val_nignitions
         write(fates_log(),fmt0) 'ED_val_understorey_death = ',ED_val_understorey_death
+        write(fates_log(),fmt0) 'cwd_hr_frag_frac= ', cwd_hr_frag_frac
         write(fates_log(),fmt0) 'ED_val_cwd_fcel = ',ED_val_cwd_fcel
         write(fates_log(),fmt0) 'ED_val_cwd_flig = ',ED_val_cwd_flig
         write(fates_log(),fmt0) 'fates_maintresp_nonleaf_baserate = ', maintresp_nonleaf_baserate

main/EDTypesMod.F90

@@ -294,6 +294,8 @@ module EDTypesMod
 
      real(r8) :: frag_out         ! Litter and coarse woody debris fragmentation flux [kg/site/day]
 
+     real(r8) :: funghr_out       ! Losses to fungal respiration [kg/site/day]
+
      real(r8) :: wood_product_harvest(maxpft)    ! Total mass exported as wood product from wood harvest [kg/site/day]
 
      real(r8) :: wood_product_landusechange(maxpft)    ! Total mass exported as wood product from land use change [kg/site/day]
@@ -715,6 +717,7 @@ subroutine ZeroMassBalFlux(this)
       this%seed_in           = 0._r8
       this%seed_out          = 0._r8
       this%frag_out          = 0._r8
+      this%funghr_out        = 0._r8
       this%wood_product_harvest(:)        = 0._r8
       this%wood_product_landusechange(:)  = 0._r8
       this%burn_flux_to_atm(:)            = 0._r8

main/FatesConstantsMod.F90

@@ -286,7 +286,6 @@ module FatesConstantsMod
 
   ! Conversion: megajoules per joule
   real(fates_r8), parameter, public :: megajoules_per_joule = 1.0E-6_fates_r8
-
 
   ! Conversion: days per second
   real(fates_r8), parameter, public :: days_per_sec = 1.0_fates_r8/86400.0_fates_r8

main/FatesHistoryInterfaceMod.F90

@@ -402,6 +402,7 @@ module FatesHistoryInterfaceMod
   integer :: ih_tveg_si
   integer :: ih_nep_si
   integer :: ih_hr_si
+  integer :: ih_hr_cwdfung_si
 
   integer :: ih_c_stomata_si
   integer :: ih_c_lblayer_si
@@ -5179,11 +5180,12 @@ subroutine update_history_hifrq_sitelevel(this,nc,nsites,sites,bc_in,dt_tstep)
     real(r8) :: dt_tstep_inv        ! inverse timestep (1/sec)
     real(r8) :: n_perm2             ! number of plants per square meter
     real(r8) :: sum_area_rad        ! sum of patch canopy areas
+    real(r8) :: cwdfung_hr
     real(r8),allocatable :: age_area_rad(:)
 
     type(fates_patch_type),pointer  :: cpatch
     type(fates_cohort_type),pointer :: ccohort
-
+    type(litter_type), pointer :: litt     ! Generic pointer to any litter pool
 
     associate( hio_gpp_si                   => this%hvars(ih_gpp_si)%r81d, &
          hio_npp_si                   => this%hvars(ih_npp_si)%r81d, &
@@ -5196,6 +5198,7 @@ subroutine update_history_hifrq_sitelevel(this,nc,nsites,sites,bc_in,dt_tstep)
          hio_nir_rad_err_si           => this%hvars(ih_nir_rad_err_si)%r81d, &
          hio_nep_si                   => this%hvars(ih_nep_si)%r81d, &
          hio_hr_si                    => this%hvars(ih_hr_si)%r81d, &
+         hio_hr_cwdfung_si            => this%hvars(ih_hr_cwdfung_si)%r81d, &
          hio_gpp_canopy_si            => this%hvars(ih_gpp_canopy_si)%r81d, &
          hio_ar_canopy_si             => this%hvars(ih_ar_canopy_si)%r81d, &
          hio_gpp_understory_si        => this%hvars(ih_gpp_understory_si)%r81d, &
@@ -5246,6 +5249,17 @@ subroutine update_history_hifrq_sitelevel(this,nc,nsites,sites,bc_in,dt_tstep)
                age_class = get_age_class_index(cpatch%age)
                age_area_rad(age_class) = age_area_rad(age_class) + cpatch%total_canopy_area
             end if
+
+            litt => cpatch%litter(element_pos(carbon12_element))
+
+            ! scale fungal resp to from /m2 patch to /m2 site (ie area weighted average)
+            ! convert time units from kg/m2/day to kg/m2/s
+            cwdfung_hr =  cpatch%area*(sum(litt%ag_cwd_funghr) + sum(litt%bg_cwd_funghr))*area_inv*days_per_sec
+
+            hio_hr_si(io_si)  = hio_hr_si(io_si) + cwdfung_hr
+            hio_nep_si(io_si) = hio_nep_si(io_si) + cwdfung_hr
+            hio_hr_cwdfung_si(io_si) = hio_hr_cwdfung_si(io_si) + cwdfung_hr
+
             cpatch => cpatch%younger
          end do
 
@@ -9108,6 +9122,11 @@ subroutine define_history_vars(this, initialize_variables)
             use_default='active', avgflag='A', vtype=site_r8, hlms='CLM:ALM',     &
             upfreq=group_hifr_simple, ivar=ivar, initialize=initialize_variables, index = ih_hr_si)
 
+       call this%set_history_var(vname='FATES_CWDFUNGAL_HET_RESP', units='kg m-2 s-1',  &
+            long='heterotrophic respiration strictly from fungal activity in CWD',      &
+            use_default='active', avgflag='A', vtype=site_r8, hlms='CLM:ALM',     &
+            upfreq=group_hifr_simple, ivar=ivar, initialize=initialize_variables, index = ih_hr_cwdfung_si)
+
        hydro_active_if0: if(hlm_use_planthydro.eq.itrue) then
           call this%set_history_var(vname='FATES_SAPFLOW', units='kg m-2 s-1',    &
                long='areal sap flow rate in kg per m2 ground area per second',               &

parameter_files/fates_params_default.json

@@ -1640,6 +1640,7 @@
       "units": "yr-1",
       "data": [0.52, 0.383, 0.383, 0.19, 1.0, 999.0]
     },
+
     "fates_frag_cwd_frac": {
       "dtype": "float",
       "dims": ["fates_NCWD"],
@@ -1682,6 +1683,13 @@
       "units": "unitless",
       "data": [0.8]
     },
+    "fates_cwd_hrfrag_frac": {
+	"dtype": "float",
+	"dims": ["scalar"],
+	"long_name": "fraction of cwd losses due to fungal heterotrophic respiration and not fragmentation",
+	"units": "-",
+	"data": [0.5]
+    },
     "fates_cnp_eca_plant_escalar": {
       "dtype": "float",
       "dims": ["scalar"],