Merge branch 'master' into enhancement/YAML-diagnostics

marbl-ecosys · Feb 12, 2018 · 6edc61f · 6edc61f
2 parents a80eab2 + 866c376
commit 6edc61f
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Showing 14 changed files with 405 additions and 267 deletions.
diff --git a/autogenerated_src/default_diagnostics.json b/autogenerated_src/default_diagnostics.json
@@ -1633,6 +1633,13 @@
       "units": "mmol/m^3/s",
       "vertical_grid": "layer_avg"
    },
+   "insitu_temp": {
+      "frequency": "medium",
+      "longname": "in situ temperature",
+      "operator": "average",
+      "units": "degC",
+      "vertical_grid": "layer_avg"
+   },
    "pCO2SURF": {
       "frequency": "medium",
       "longname": "surface pCO2",

diff --git a/autogenerated_src/default_settings.json b/autogenerated_src/default_settings.json
@@ -1089,19 +1089,22 @@
                "PO4",
                "NO3",
                "SiO3",
-               "ALK"
+               "ALK",
+               "ALK_ALT_CO2"
             ],
             "GRID = CESM_x1": [
                "PO4",
                "NO3",
                "SiO3",
-               "ALK"
+               "ALK",
+               "ALK_ALT_CO2"
             ],
             "GRID = CESM_x3": [
                "PO4",
                "NO3",
                "SiO3",
-               "ALK"
+               "ALK",
+               "ALK_ALT_CO2"
             ],
             "default": ""
          },

diff --git a/src/default_diagnostics.yaml b/src/default_diagnostics.yaml
@@ -492,6 +492,12 @@ CaCO3_form_zint :
    operator : average
 
 # General 3D diags
+insitu_temp :
+   longname : in situ temperature
+   units : degC
+   vertical_grid : layer_avg
+   frequency : medium
+   operator : average
 CO3 :
    longname : Carbonate Ion Concentration
    units : mmol/m^3

diff --git a/src/default_settings.yaml b/src/default_settings.yaml
@@ -974,6 +974,7 @@ tracer_dependent :
             - 'NO3'
             - 'SiO3'
             - 'ALK'
+            - 'ALK_ALT_CO2'
          GRID = CESM_x3 : *CESM_TRACER_RESTORE
          GRID = CESM_x1 : *CESM_TRACER_RESTORE
 
diff --git a/src/marbl_ciso_mod.F90 b/src/marbl_ciso_mod.F90
@@ -244,7 +244,7 @@ subroutine marbl_ciso_set_interior_forcing( &
     !-----------------------------------------------------------------------
     !  local variables
     !-----------------------------------------------------------------------
-    character(len=*), parameter :: subname = 'marbl_ciso_mod:marbl_ciso_set_interior forcing'
+    character(len=*), parameter :: subname = 'marbl_ciso_mod:marbl_ciso_set_interior_forcing'
 
     logical (log_kind) :: zero_mask
 
@@ -459,6 +459,7 @@ subroutine marbl_ciso_set_interior_forcing( &
        !-----------------------------------------------------------------------
        !  set local 13C/12C ratios, assuming ecosystem carries 12C (C=C12+C13+C14)
        !  If any Carbon boxes are zero, set corresponding 13C to zeros.
+       !  Calculate fraction of CO3
        !-----------------------------------------------------------------------
 
        if (DOC_loc(k) > c0) then
@@ -472,9 +473,11 @@ subroutine marbl_ciso_set_interior_forcing( &
        if (DIC_loc(k) > c0) then
           R13C_DIC(k) = DI13C_loc(k) / DIC_loc(k)
           R14C_DIC(k) = DI14C_loc(k) / DIC_loc(k)
+          frac_co3(k) = CO3(k) / DIC_loc(k)
        else
           R13C_DIC(k) = c0
           R14C_DIC(k) = c0
+          frac_co3(k) = c0
        end if
 
        work1 = sum(zooC_loc(:,k),dim=1)
@@ -504,16 +507,6 @@ subroutine marbl_ciso_set_interior_forcing( &
           end if
        end do
 
-       !-----------------------------------------------------------------------
-       ! Calculate fraction of CO3
-       !-----------------------------------------------------------------------
-
-       if (k > column_kmt) then
-          frac_co3(k) = c0
-       else
-          frac_co3(k) = CO3(k) / DIC_loc(k)
-       end if
-
        !-----------------------------------------------------------------------
        !   discrimination factors of carbone chemistry based on
        !   Zhang et al, 1995, Geochim. et Cosmochim. Acta, 59 (1), 107-114
@@ -1759,8 +1752,9 @@ subroutine marbl_ciso_set_surface_forcing( &
          alpha_k,          & ! eps = ( alpa -1 ) * 1000
          alpha_k_14c         ! for 14C, with fractionation being twice as large for 14C than for 13C
 
-    ! kinetic fraction during gas transfert (per mil) (air-sea CO2 exchange) at 21C, Zhang et al 1995,
-    real(r8), parameter :: eps_k = -0.81_r8  ! eps_k = -0.95 at 5C
+    ! kinetic fraction during gas transfer (per mil) (air-sea CO2 exchange)
+    ! average of Zhang et al 1995 values of -0.81 at 21C and -0.95 at 5C
+    real(r8), parameter :: eps_k = -0.88_r8
     !-----------------------------------------------------------------------
 
     associate(                                                                     &
@@ -1803,9 +1797,11 @@ subroutine marbl_ciso_set_surface_forcing( &
     where ( dic(:) /= c0 ) 
        R13C_dic(:) = surface_vals(:,di13c_ind) / dic(:)
        R14C_dic(:) = surface_vals(:,di14c_ind) / dic(:)
+       frac_co3(:) = CO3_SURF_fields(:) / dic(:)
     elsewhere
        R13C_dic(:) = c0
        R14C_dic(:) = c0
+       frac_co3(:) = c0
     end where
 
     !-----------------------------------------------------------------------
@@ -1833,8 +1829,6 @@ subroutine marbl_ciso_set_surface_forcing( &
     !     the measured e_dic_g_surf of Zhang et al. 1995
     !---------------------------------------------------------------------
 
-    frac_co3(:) = CO3_SURF_fields(:) / dic(:)
-
     eps_dic_g_surf(:) = 0.014_r8 * sst(:) * frac_co3(:) - 0.105_r8 * sst(:) + 10.53_r8
 
     !-----------------------------------------------------------------------