MARBL version with explicit calcifiers

defaults/diagnostics_latest.yaml

@@ -958,7 +958,7 @@ CaCO3_PROD :
    longname : CaCO3 Production
    units : mmol/m^3/s
    vertical_grid : layer_avg
-   frequency : low
+   frequency : medium
    operator : average
 CaCO3_REMIN :
    longname : CaCO3 Remineralization
@@ -1348,6 +1348,22 @@ CISO_eps_dic_g :
 # Per-autotroph Diagnostics #
 #############################
 
+((autotroph_sname))_C_lim_surf :
+   dependencies :
+      ((autotroph_calcifier)) : true
+   longname : ((autotroph_lname)) C Limitation, Surface
+   units : 1
+   vertical_grid : none
+   frequency : medium
+   operator : average
+((autotroph_sname))_C_lim_Cweight_avg_100m :
+   dependencies :
+      ((autotroph_calcifier)) : true
+   longname : ((autotroph_lname)) C Limitation, carbon biomass weighted average over 0-100m
+   units : 1
+   vertical_grid : none
+   frequency : medium
+   operator : average
 ((autotroph_sname))_N_lim_surf :
    longname : ((autotroph_lname)) N Limitation, Surface
    units : 1

defaults/json/diagnostics_latest.json

@@ -1,4 +1,24 @@
 {
+   "((autotroph_sname))_C_lim_Cweight_avg_100m": {
+      "dependencies": {
+         "((autotroph_calcifier))": true
+      },
+      "frequency": "medium",
+      "longname": "((autotroph_lname)) C Limitation, carbon biomass weighted average over 0-100m",
+      "operator": "average",
+      "units": 1,
+      "vertical_grid": "none"
+   },
+   "((autotroph_sname))_C_lim_surf": {
+      "dependencies": {
+         "((autotroph_calcifier))": true
+      },
+      "frequency": "medium",
+      "longname": "((autotroph_lname)) C Limitation, Surface",
+      "operator": "average",
+      "units": 1,
+      "vertical_grid": "none"
+   },
    "((autotroph_sname))_CaCO3_form": {
       "dependencies": {
          "((autotroph_calcifier))": true
@@ -1004,7 +1024,7 @@
       "vertical_grid": "layer_avg"
    },
    "CaCO3_PROD": {
-      "frequency": "low",
+      "frequency": "medium",
       "longname": "CaCO3 Production",
       "operator": "average",
       "units": "mmol/m^3/s",

defaults/json/settings_cesm2.0.json

@@ -152,6 +152,18 @@
                "subcategory": "10. autotrophs",
                "units": "non-numeric"
             },
+            "kCO2": {
+               "datatype": "real",
+               "default_value": {
+                  "((autotroph_sname)) == \"diat\"": 0,
+                  "((autotroph_sname)) == \"diaz\"": 0,
+                  "((autotroph_sname)) == \"sp\"": 0,
+                  "default": "1e34"
+               },
+               "longname": "CO2 uptake half-sat constant",
+               "subcategory": "10. autotrophs",
+               "units": "nmol/cm^3"
+            },
             "kDOP": {
                "datatype": "real",
                "default_value": {

defaults/json/settings_latest.json

@@ -152,6 +152,18 @@
                "subcategory": "10. autotrophs",
                "units": "non-numeric"
             },
+            "kCO2": {
+               "datatype": "real",
+               "default_value": {
+                  "((autotroph_sname)) == \"diat\"": 0,
+                  "((autotroph_sname)) == \"diaz\"": 0,
+                  "((autotroph_sname)) == \"sp\"": 0,
+                  "default": "1e34"
+               },
+               "longname": "CO2 uptake half-sat constant",
+               "subcategory": "10. autotrophs",
+               "units": "nmol/cm^3"
+            },
             "kDOP": {
                "datatype": "real",
                "default_value": {

defaults/settings_cesm2.0.yaml

@@ -707,6 +707,16 @@ PFT_derived_types :
                ((autotroph_sname)) == "sp" : 0.03e-3
                ((autotroph_sname)) == "diat" : 0.06e-3
                ((autotroph_sname)) == "diaz" : 0.045e-3
+         kCO2 :
+            longname : CO2 uptake half-sat constant
+            subcategory : 10. autotrophs
+            units : nmol/cm^3
+            datatype : real
+            default_value :
+               default : 1e34
+               ((autotroph_sname)) == "sp" : 0
+               ((autotroph_sname)) == "diat" : 0
+               ((autotroph_sname)) == "diaz" : 0         
          kPO4 :
             longname : PO4 uptake half-sat constant
             subcategory : 10. autotrophs

defaults/settings_latest.yaml

@@ -709,6 +709,16 @@ PFT_derived_types :
                ((autotroph_sname)) == "sp" : 0.03e-3
                ((autotroph_sname)) == "diat" : 0.07e-3
                ((autotroph_sname)) == "diaz" : 0.045e-3
+         kCO2 :
+            longname : CO2 uptake half-sat constant
+            subcategory : 10. autotrophs
+            units : nmol/cm^3
+            datatype : real
+            default_value :
+               default : 1e34
+               ((autotroph_sname)) == "sp" : 0
+               ((autotroph_sname)) == "diat" : 0
+               ((autotroph_sname)) == "diaz" : 0
          kPO4 :
             longname : PO4 uptake half-sat constant
             subcategory : 10. autotrophs

src/marbl_diagnostics_mod.F90

@@ -835,6 +835,8 @@ subroutine marbl_diagnostics_init(  &
         allocate(ind%Fe_lim_Cweight_avg_100m(autotroph_cnt))
         allocate(ind%SiO3_lim_surf(autotroph_cnt))
         allocate(ind%SiO3_lim_Cweight_avg_100m(autotroph_cnt))
+        allocate(ind%C_lim_surf(autotroph_cnt))
+        allocate(ind%C_lim_Cweight_avg_100m(autotroph_cnt))
         allocate(ind%light_lim_surf(autotroph_cnt))
         allocate(ind%light_lim_Cweight_avg_100m(autotroph_cnt))
         allocate(ind%photoC_zint(autotroph_cnt))
@@ -961,6 +963,30 @@ subroutine marbl_diagnostics_init(  &
           ind%SiO3_lim_Cweight_avg_100m(n) = -1
         end if
 
+        lname = trim(autotroph_settings(n)%lname) // ' C Limitation, Surface'
+        sname = trim(autotroph_settings(n)%sname) // '_C_lim_surf'
+        units = '1'
+        vgrid = 'none'
+        truncate = .false.
+        call diags%add_diagnostic(lname, sname, units, vgrid, truncate,  &
+             ind%C_lim_surf(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(autotroph_settings(n)%lname) // ' C Limitation, carbon biomass weighted average over 0-100m'
+        sname = trim(autotroph_settings(n)%sname) // '_C_lim_Cweight_avg_100m'
+        units = '1'
+        vgrid = 'none'
+        truncate = .false.
+        call diags%add_diagnostic(lname, sname, units, vgrid, truncate,  &
+             ind%C_lim_Cweight_avg_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(autotroph_settings(n)%lname) // ' Light Limitation, Surface'
         sname = trim(autotroph_settings(n)%sname) // '_light_lim_surf'
         units = '1'
@@ -3477,6 +3503,11 @@ subroutine store_diagnostics_autotrophs(marbl_domain, &
                near_surface_integral=diags(ind%SiO3_lim_Cweight_avg_100m(n))%field_2d(1))
        endif
 
+       diags(ind%C_lim_surf(n))%field_2d(1) = autotroph_derived_terms%VCO2(n,1)
+       limterm = autotroph_derived_terms%VCO2(n,:) * autotrophC_weight(:)
+       call marbl_diagnostics_share_compute_vertical_integrals(limterm, delta_z, kmt, &
+            near_surface_integral=diags(ind%C_lim_Cweight_avg_100m(n))%field_2d(1))
+
        diags(ind%light_lim_surf(n))%field_2d(1) = autotroph_derived_terms%light_lim(n,1)
        limterm = autotroph_derived_terms%light_lim(n,:) * autotrophC_weight(:)
        call marbl_diagnostics_share_compute_vertical_integrals(limterm, delta_z, kmt, &

src/marbl_interface_private_types.F90

@@ -43,6 +43,7 @@ module marbl_interface_private_types
     real(r8), allocatable :: gQsi(:,:)            ! diatom Si/C ratio for growth (new biomass)
     real(r8), allocatable :: VNO3(:,:)            ! NH4 uptake rate (non-dim)
     real(r8), allocatable :: VNH4(:,:)            ! NO3 uptake rate (non-dim)
+    real(r8), allocatable :: VCO2(:,:)            ! CO2 uptake rate (non-dim)
     real(r8), allocatable :: VNtot(:,:)           ! total N uptake rate (non-dim)
     real(r8), allocatable :: NO3_V(:,:)           ! nitrate uptake (mmol NO3/m^3/sec)
     real(r8), allocatable :: NH4_V(:,:)           ! ammonium uptake (mmol NH4/m^3/sec)
@@ -531,6 +532,8 @@ module marbl_interface_private_types
     integer(int_kind), allocatable :: Fe_lim_Cweight_avg_100m(:)
     integer(int_kind), allocatable :: SiO3_lim_surf(:)
     integer(int_kind), allocatable :: SiO3_lim_Cweight_avg_100m(:)
+    integer(int_kind), allocatable :: C_lim_surf(:)
+    integer(int_kind), allocatable :: C_lim_Cweight_avg_100m(:)
     integer(int_kind), allocatable :: light_lim_surf(:)
     integer(int_kind), allocatable :: light_lim_Cweight_avg_100m(:)
     integer(int_kind), allocatable :: photoC_zint(:)
@@ -1008,6 +1011,7 @@ subroutine autotroph_derived_terms_constructor(self, autotroph_cnt, km)
     allocate(self%gQsi(autotroph_cnt, km))
     allocate(self%VNO3(autotroph_cnt, km))
     allocate(self%VNH4(autotroph_cnt, km))
+    allocate(self%VCO2(autotroph_cnt, km))
     allocate(self%VNtot(autotroph_cnt, km))
     allocate(self%NO3_V(autotroph_cnt, km))
     allocate(self%NH4_V(autotroph_cnt, km))
@@ -1061,6 +1065,7 @@ subroutine autotroph_derived_terms_destructor(self)
     deallocate(self%gQsi)
     deallocate(self%VNO3)
     deallocate(self%VNH4)
+    deallocate(self%VCO2)
     deallocate(self%VNtot)
     deallocate(self%NO3_V)
     deallocate(self%NH4_V)
@@ -1858,6 +1863,8 @@ subroutine interior_diag_ind_destructor(this)
       deallocate(this%Fe_lim_Cweight_avg_100m)
       deallocate(this%SiO3_lim_surf)
       deallocate(this%SiO3_lim_Cweight_avg_100m)
+      deallocate(this%C_lim_surf)
+      deallocate(this%C_lim_Cweight_avg_100m)
       deallocate(this%light_lim_surf)
       deallocate(this%light_lim_Cweight_avg_100m)
       deallocate(this%photoC_zint)