Add nonlinear loss to diags

defaults/diagnostics_latest.yaml

@@ -1863,12 +1863,36 @@ CISO_mui_to_co2star_((autotroph_sname)) :
    vertical_grid : none
    frequency : medium
    operator : average
+((zooplankton_sname))_loss_linear_zint_100m :
+   longname : ((zooplankton_lname)) Loss (linear component) Vertical Integral, 0-100m
+   units : mmol/m^3 cm/s
+   vertical_grid : none
+   frequency : never
+   operator : average
+((zooplankton_sname))_loss_nonlinear_zint_100m :
+   longname : ((zooplankton_lname)) Loss (nonlinear component) Vertical Integral, 0-100m
+   units : mmol/m^3 cm/s
+   vertical_grid : none
+   frequency : medium
+   operator : average
 ((zooplankton_sname))_loss_zint_150m :
    longname : ((zooplankton_lname)) Loss Vertical Integral, 0-150m
    units : mmol/m^3 cm/s
    vertical_grid : none
    frequency : high
    operator : average
+((zooplankton_sname))_loss_linear_zint_150m :
+   longname : ((zooplankton_lname)) Loss (linear component) Vertical Integral, 0-150m
+   units : mmol/m^3 cm/s
+   vertical_grid : none
+   frequency : never
+   operator : average
+((zooplankton_sname))_loss_nonlinear_zint_150m :
+   longname : ((zooplankton_lname)) Loss (nonlinear component) Vertical Integral, 0-150m
+   units : mmol/m^3 cm/s
+   vertical_grid : none
+   frequency : high
+   operator : average
 ((zooplankton_sname))_loss_poc_zint :
    longname : ((zooplankton_lname)) Loss to POC Vertical Integral
    units : mmol/m^3 cm/s
@@ -1960,6 +1984,20 @@ x_graze_((zooplankton_sname))_zint_100m :
    truncate : true
    frequency : never
    operator : average
+((zooplankton_sname))_loss_linear :
+   longname : ((zooplankton_lname)) Loss (linear component)
+   units : mmol/m^3/s
+   vertical_grid : layer_avg
+   truncate : true
+   frequency : never
+   operator : average
+((zooplankton_sname))_loss_nonlinear :
+   longname : ((zooplankton_lname)) Loss (nonlinear component)
+   units : mmol/m^3/s
+   vertical_grid : layer_avg
+   truncate : true
+   frequency : never
+   operator : average
 ((zooplankton_sname))_loss_poc :
    longname : ((zooplankton_lname)) Loss to POC
    units : mmol/m^3/s

defaults/json/diagnostics_latest.json

@@ -293,6 +293,50 @@
       "units": "mmol/m^3 cm/s",
       "vertical_grid": "none"
    },
+   "((zooplankton_sname))_loss_linear": {
+      "frequency": "never",
+      "longname": "((zooplankton_lname)) Loss (linear component)",
+      "operator": "average",
+      "truncate": true,
+      "units": "mmol/m^3/s",
+      "vertical_grid": "layer_avg"
+   },
+   "((zooplankton_sname))_loss_linear_zint_100m": {
+      "frequency": "never",
+      "longname": "((zooplankton_lname)) Loss (linear component) Vertical Integral, 0-100m",
+      "operator": "average",
+      "units": "mmol/m^3 cm/s",
+      "vertical_grid": "none"
+   },
+   "((zooplankton_sname))_loss_linear_zint_150m": {
+      "frequency": "never",
+      "longname": "((zooplankton_lname)) Loss (linear component) Vertical Integral, 0-150m",
+      "operator": "average",
+      "units": "mmol/m^3 cm/s",
+      "vertical_grid": "none"
+   },
+   "((zooplankton_sname))_loss_nonlinear": {
+      "frequency": "never",
+      "longname": "((zooplankton_lname)) Loss (nonlinear component)",
+      "operator": "average",
+      "truncate": true,
+      "units": "mmol/m^3/s",
+      "vertical_grid": "layer_avg"
+   },
+   "((zooplankton_sname))_loss_nonlinear_zint_100m": {
+      "frequency": "medium",
+      "longname": "((zooplankton_lname)) Loss (nonlinear component) Vertical Integral, 0-100m",
+      "operator": "average",
+      "units": "mmol/m^3 cm/s",
+      "vertical_grid": "none"
+   },
+   "((zooplankton_sname))_loss_nonlinear_zint_150m": {
+      "frequency": "high",
+      "longname": "((zooplankton_lname)) Loss (nonlinear component) Vertical Integral, 0-150m",
+      "operator": "average",
+      "units": "mmol/m^3 cm/s",
+      "vertical_grid": "none"
+   },
    "((zooplankton_sname))_loss_poc": {
       "frequency": "never",
       "longname": "((zooplankton_lname)) Loss to POC",

src/marbl_diagnostics_mod.F90

@@ -1309,7 +1309,11 @@ subroutine marbl_diagnostics_init(  &
       if (.not.ind%lconstructed()) then
         allocate(ind%zoo_loss_zint(zooplankton_cnt))
         allocate(ind%zoo_loss_zint_100m(zooplankton_cnt))
+        allocate(ind%zoo_loss_linear_zint_100m(zooplankton_cnt))
+        allocate(ind%zoo_loss_nonlinear_zint_100m(zooplankton_cnt))
         allocate(ind%zoo_loss_zint_150m(zooplankton_cnt))
+        allocate(ind%zoo_loss_linear_zint_150m(zooplankton_cnt))
+        allocate(ind%zoo_loss_nonlinear_zint_150m(zooplankton_cnt))
         allocate(ind%zoo_loss_poc_zint(zooplankton_cnt))
         allocate(ind%zoo_loss_poc_zint_100m(zooplankton_cnt))
         allocate(ind%zoo_loss_doc_zint(zooplankton_cnt))
@@ -1350,6 +1354,30 @@ subroutine marbl_diagnostics_init(  &
           return
         end if
 
+        lname = trim(zooplankton_settings(n)%lname) // ' Loss (linear component) Vertical Integral, 0-100m'
+        sname = trim(zooplankton_settings(n)%sname) // '_loss_linear_zint_100m'
+        units = 'mmol/m^3 cm/s'
+        vgrid = 'none'
+        truncate = .false.
+        call diags%add_diagnostic(lname, sname, units, vgrid, truncate,  &
+             ind%zoo_loss_linear_zint_100m(n), marbl_status_log)
+        if (marbl_status_log%labort_marbl) then
+          call marbl_logging_add_diagnostics_error(marbl_status_log, sname, subname)
+          return
+        end if
+
+        lname = trim(zooplankton_settings(n)%lname) // ' Loss (nonlinear component) Vertical Integral, 0-100m'
+        sname = trim(zooplankton_settings(n)%sname) // '_loss_nonlinear_zint_100m'
+        units = 'mmol/m^3 cm/s'
+        vgrid = 'none'
+        truncate = .false.
+        call diags%add_diagnostic(lname, sname, units, vgrid, truncate,  &
+             ind%zoo_loss_nonlinear_zint_100m(n), marbl_status_log)
+        if (marbl_status_log%labort_marbl) then
+          call marbl_logging_add_diagnostics_error(marbl_status_log, sname, subname)
+          return
+        end if
+
         lname = trim(zooplankton_settings(n)%lname) // ' Loss Vertical Integral, 0-150m'
         sname = trim(zooplankton_settings(n)%sname) // '_loss_zint_150m'
         units = 'mmol/m^3 cm/s'
@@ -1362,6 +1390,30 @@ subroutine marbl_diagnostics_init(  &
           return
         end if
 
+        lname = trim(zooplankton_settings(n)%lname) // ' Loss (linear component) Vertical Integral, 0-150m'
+        sname = trim(zooplankton_settings(n)%sname) // '_loss_linear_zint_150m'
+        units = 'mmol/m^3 cm/s'
+        vgrid = 'none'
+        truncate = .false.
+        call diags%add_diagnostic(lname, sname, units, vgrid, truncate,  &
+             ind%zoo_loss_linear_zint_150m(n), marbl_status_log)
+        if (marbl_status_log%labort_marbl) then
+          call marbl_logging_add_diagnostics_error(marbl_status_log, sname, subname)
+          return
+        end if
+
+        lname = trim(zooplankton_settings(n)%lname) // ' Loss (nonlinear component) Vertical Integral, 0-150m'
+        sname = trim(zooplankton_settings(n)%sname) // '_loss_nonlinear_zint_150m'
+        units = 'mmol/m^3 cm/s'
+        vgrid = 'none'
+        truncate = .false.
+        call diags%add_diagnostic(lname, sname, units, vgrid, truncate,  &
+             ind%zoo_loss_nonlinear_zint_150m(n), marbl_status_log)
+        if (marbl_status_log%labort_marbl) then
+          call marbl_logging_add_diagnostics_error(marbl_status_log, sname, subname)
+          return
+        end if
+
         lname = trim(zooplankton_settings(n)%lname) // ' Loss to POC Vertical Integral'
         sname = trim(zooplankton_settings(n)%sname) // '_loss_poc_zint'
         units = 'mmol/m^3 cm/s'
@@ -2854,6 +2906,8 @@ subroutine marbl_diagnostics_init(  &
       ! Zooplankton 3D diags
       if (.not.ind%lconstructed()) then
         allocate(ind%zoo_loss(zooplankton_cnt))
+        allocate(ind%zoo_loss_linear(zooplankton_cnt))
+        allocate(ind%zoo_loss_nonlinear(zooplankton_cnt))
         allocate(ind%zoo_loss_poc(zooplankton_cnt))
         allocate(ind%zoo_loss_doc(zooplankton_cnt))
         allocate(ind%zoo_graze(zooplankton_cnt))
@@ -2876,6 +2930,30 @@ subroutine marbl_diagnostics_init(  &
           return
         end if
 
+        lname    = trim(zooplankton_settings(n)%lname) // ' Loss (linear component)'
+        sname    = trim(zooplankton_settings(n)%sname) // '_loss_linear'
+        units    = 'mmol/m^3/s'
+        vgrid    = 'layer_avg'
+        truncate = .not. lecovars_full_depth_tavg
+        call diags%add_diagnostic(lname, sname, units, vgrid, truncate,  &
+             ind%zoo_loss_linear(n), marbl_status_log)
+        if (marbl_status_log%labort_marbl) then
+          call marbl_logging_add_diagnostics_error(marbl_status_log, sname, subname)
+          return
+        end if
+
+        lname    = trim(zooplankton_settings(n)%lname) // ' Loss (nonlinear component)'
+        sname    = trim(zooplankton_settings(n)%sname) // '_loss_nonlinear'
+        units    = 'mmol/m^3/s'
+        vgrid    = 'layer_avg'
+        truncate = .not. lecovars_full_depth_tavg
+        call diags%add_diagnostic(lname, sname, units, vgrid, truncate,  &
+             ind%zoo_loss_nonlinear(n), marbl_status_log)
+        if (marbl_status_log%labort_marbl) then
+          call marbl_logging_add_diagnostics_error(marbl_status_log, sname, subname)
+          return
+        end if
+
         lname    = trim(zooplankton_settings(n)%lname) // ' Loss to POC'
         sname    = trim(zooplankton_settings(n)%sname) // '_loss_poc'
         units    = 'mmol/m^3/s'
@@ -3924,6 +4002,8 @@ subroutine store_diagnostics_zooplankton(marbl_domain, &
 
     do n = 1, zooplankton_cnt
        diags(ind%zoo_loss(n))%field_3d(:, 1)      = zooplankton_derived_terms%zoo_loss(n,:)
+       diags(ind%zoo_loss_linear(n))%field_3d(:, 1)    = zooplankton_derived_terms%zoo_loss_linear(n,:)
+       diags(ind%zoo_loss_nonlinear(n))%field_3d(:, 1) = zooplankton_derived_terms%zoo_loss_nonlinear(n,:)
        diags(ind%zoo_loss_poc(n))%field_3d(:, 1)  = zooplankton_derived_terms%zoo_loss_poc(n,:)
        diags(ind%zoo_loss_doc(n))%field_3d(:, 1)  = zooplankton_derived_terms%zoo_loss_doc(n,:)
        diags(ind%zoo_graze(n))%field_3d(:, 1)     = zooplankton_derived_terms%zoo_graze(n,:)
@@ -3942,10 +4022,26 @@ subroutine store_diagnostics_zooplankton(marbl_domain, &
             delta_z, kmt, full_depth_integral=diags(ind%zoo_loss_zint(n))%field_2d(1), &
             near_surface_integral=diags(ind%zoo_loss_zint_100m(n))%field_2d(1))
 
+       call marbl_diagnostics_share_compute_vertical_integrals(diags(ind%zoo_loss_linear(n))%field_3d(:, 1), &
+            delta_z, kmt, near_surface_integral=diags(ind%zoo_loss_linear_zint_100m(n))%field_2d(1), &
+            shallow_depth=diags(ind%zoo_loss_zint_100m(n))%field_2d(1))
+
+       call marbl_diagnostics_share_compute_vertical_integrals(diags(ind%zoo_loss_nonlinear(n))%field_3d(:, 1), &
+            delta_z, kmt, near_surface_integral=diags(ind%zoo_loss_nonlinear_zint_100m(n))%field_2d(1), &
+            shallow_depth=diags(ind%zoo_loss_zint_100m(n))%field_2d(1))
+
        call marbl_diagnostics_share_compute_vertical_integrals(diags(ind%zoo_loss(n))%field_3d(:, 1), &
             delta_z, kmt, near_surface_integral=diags(ind%zoo_loss_zint_150m(n))%field_2d(1), &
             shallow_depth=150.0e2_r8)
 
+       call marbl_diagnostics_share_compute_vertical_integrals(diags(ind%zoo_loss_linear(n))%field_3d(:, 1), &
+            delta_z, kmt, near_surface_integral=diags(ind%zoo_loss_linear_zint_150m(n))%field_2d(1), &
+            shallow_depth=150.0e2_r8)
+
+       call marbl_diagnostics_share_compute_vertical_integrals(diags(ind%zoo_loss_nonlinear(n))%field_3d(:, 1), &
+            delta_z, kmt, near_surface_integral=diags(ind%zoo_loss_nonlinear_zint_150m(n))%field_2d(1), &
+            shallow_depth=150.0e2_r8)
+
        call marbl_diagnostics_share_compute_vertical_integrals(diags(ind%zoo_loss_poc(n))%field_3d(:, 1), &
             delta_z, kmt, full_depth_integral=diags(ind%zoo_loss_poc_zint(n))%field_2d(1), &
             near_surface_integral=diags(ind%zoo_loss_poc_zint_100m(n))%field_2d(1))

src/marbl_interface_private_types.F90

@@ -115,6 +115,8 @@ module marbl_interface_private_types
     real(r8), allocatable :: zoo_graze_doc(:,:)    ! grazing of zooplankton routed to doc (mmol C/m^3/sec)
     real(r8), allocatable :: zoo_graze_dic(:,:)    ! grazing of zooplankton routed to dic (mmol C/m^3/sec)
     real(r8), allocatable :: zoo_loss(:,:)         ! mortality & higher trophic grazing on zooplankton (mmol C/m^3/sec)
+    real(r8), allocatable :: zoo_loss_linear(:,:)     ! linear component of zoo_loss (mmol C/m^3/sec)
+    real(r8), allocatable :: zoo_loss_nonlinear(:,:)  ! nonlinear component of zoo_loss (mmol C/m^3/sec)
     real(r8), allocatable :: zoo_loss_poc(:,:)     ! zoo_loss routed to poc (mmol C/m^3/sec)
     real(r8), allocatable :: zoo_loss_doc(:,:)     ! zoo_loss routed to doc (mmol C/m^3/sec)
     real(r8), allocatable :: zoo_loss_dic(:,:)     ! zoo_loss routed to dic (mmol C/m^3/sec)
@@ -565,7 +567,11 @@ module marbl_interface_private_types
     ! Zooplankton 2D diags
     integer(int_kind), allocatable :: zoo_loss_zint(:)
     integer(int_kind), allocatable :: zoo_loss_zint_100m(:)
+    integer(int_kind), allocatable :: zoo_loss_linear_zint_100m(:)
+    integer(int_kind), allocatable :: zoo_loss_nonlinear_zint_100m(:)
     integer(int_kind), allocatable :: zoo_loss_zint_150m(:)
+    integer(int_kind), allocatable :: zoo_loss_linear_zint_150m(:)
+    integer(int_kind), allocatable :: zoo_loss_nonlinear_zint_150m(:)
     integer(int_kind), allocatable :: zoo_loss_poc_zint(:)
     integer(int_kind), allocatable :: zoo_loss_poc_zint_100m(:)
     integer(int_kind), allocatable :: zoo_loss_doc_zint(:)
@@ -696,6 +702,8 @@ module marbl_interface_private_types
 
     ! Zooplankton 3D diags
     integer(int_kind), allocatable :: zoo_loss(:)
+    integer(int_kind), allocatable :: zoo_loss_linear(:)
+    integer(int_kind), allocatable :: zoo_loss_nonlinear(:)
     integer(int_kind), allocatable :: zoo_loss_poc(:)
     integer(int_kind), allocatable :: zoo_loss_doc(:)
     integer(int_kind), allocatable :: zoo_graze(:)
@@ -1210,6 +1218,8 @@ subroutine zooplankton_derived_terms_constructor(self, zooplankton_cnt, km)
     allocate(self%zoo_graze_doc(zooplankton_cnt, km))
     allocate(self%zoo_graze_dic(zooplankton_cnt, km))
     allocate(self%zoo_loss(zooplankton_cnt, km))
+    allocate(self%zoo_loss_linear(zooplankton_cnt, km))
+    allocate(self%zoo_loss_nonlinear(zooplankton_cnt, km))
     allocate(self%zoo_loss_poc(zooplankton_cnt, km))
     allocate(self%zoo_loss_doc(zooplankton_cnt, km))
     allocate(self%zoo_loss_dic(zooplankton_cnt, km))
@@ -1232,6 +1242,8 @@ subroutine zooplankton_derived_terms_destructor(self)
     deallocate(self%zoo_graze_doc)
     deallocate(self%zoo_graze_dic)
     deallocate(self%zoo_loss)
+    deallocate(self%zoo_loss_linear)
+    deallocate(self%zoo_loss_nonlinear)
     deallocate(self%zoo_loss_poc)
     deallocate(self%zoo_loss_doc)
     deallocate(self%zoo_loss_dic)
@@ -1934,7 +1946,11 @@ subroutine interior_diag_ind_destructor(this)
       deallocate(this%auto_agg_zint_100m)
       deallocate(this%zoo_loss_zint)
       deallocate(this%zoo_loss_zint_100m)
+      deallocate(this%zoo_loss_linear_zint_100m)
+      deallocate(this%zoo_loss_nonlinear_zint_100m)
       deallocate(this%zoo_loss_zint_150m)
+      deallocate(this%zoo_loss_linear_zint_150m)
+      deallocate(this%zoo_loss_nonlinear_zint_150m)
       deallocate(this%zoo_loss_poc_zint)
       deallocate(this%zoo_loss_poc_zint_100m)
       deallocate(this%zoo_loss_doc_zint)

src/marbl_interior_tendency_mod.F90

@@ -1749,9 +1749,11 @@ subroutine compute_Zprime(km, zt, zooC, Tfunc_zoo, zooplankton_derived_terms)
     real(r8) :: C_loss_thres(km)
     !-----------------------------------------------------------------------
 
-    associate(                                               &
-         Zprime   => zooplankton_derived_terms%Zprime(:,:),  & !(zooplankton_cnt)
-         zoo_loss => zooplankton_derived_terms%zoo_loss(:,:) & !(zooplankton_cnt) output
+    associate(                                                                    &
+         Zprime             => zooplankton_derived_terms%Zprime(:,:),             & !(zooplankton_cnt)
+         zoo_loss_linear    => zooplankton_derived_terms%zoo_loss_linear(:,:),    & !(zooplankton_cnt) output
+         zoo_loss_nonlinear => zooplankton_derived_terms%zoo_loss_nonlinear(:,:), & !(zooplankton_cnt) output
+         zoo_loss           => zooplankton_derived_terms%zoo_loss(:,:)            & !(zooplankton_cnt) output
          )
 
       !  calculate the loss threshold interpolation factor
@@ -1761,8 +1763,11 @@ subroutine compute_Zprime(km, zt, zooC, Tfunc_zoo, zooplankton_derived_terms)
         C_loss_thres(:) = f_loss_thres(:) * zooplankton_settings(zoo_ind)%loss_thres
         Zprime(zoo_ind,:) = max(zooC(zoo_ind,:) - C_loss_thres, c0)
 
-        zoo_loss(zoo_ind,:) = (zooplankton_settings(zoo_ind)%z_mort2_0 * Zprime(zoo_ind,:)**zoo_mort2_exp &
-                               + zooplankton_settings(zoo_ind)%z_mort_0  * Zprime(zoo_ind,:)) * Tfunc_zoo(zoo_ind,:)
+        zoo_loss_linear(zoo_ind,:) = zooplankton_settings(zoo_ind)%z_mort_0  * Zprime(zoo_ind,:) &
+                                   * Tfunc_zoo(zoo_ind,:)
+        zoo_loss_nonlinear(zoo_ind,:) = zooplankton_settings(zoo_ind)%z_mort2_0 * Zprime(zoo_ind,:)**zoo_mort2_exp &
+                                      * Tfunc_zoo(zoo_ind,:)
+        zoo_loss(zoo_ind,:) = zoo_loss_linear(zoo_ind,:) + zoo_loss_nonlinear(zoo_ind,:)
       end do
 
     end associate