Merge remote-tracking branch 'klindsay/bugfix/253'

marbl-ecosys · Apr 5, 2018 · 21f77a2 · 21f77a2
2 parents 5ce7fe9 + b986d61
commit 21f77a2
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Showing 4 changed files with 32 additions and 32 deletions.
diff --git a/autogenerated_src/default_settings.json b/autogenerated_src/default_settings.json
@@ -52,7 +52,7 @@
                "datatype": "real",
                "default_value": {
                   "((autotroph_sname)) == \"diat\"": 5,
-                  "((autotroph_sname)) == \"diaz\"": 2.2,
+                  "((autotroph_sname)) == \"diaz\"": 2.5,
                   "((autotroph_sname)) == \"sp\"": 5,
                   "default": "1e34"
                },
@@ -133,9 +133,9 @@
             "gQfe_min": {
                "datatype": "real",
                "default_value": {
-                  "((autotroph_sname)) == \"diat\"": "3e-6",
-                  "((autotroph_sname)) == \"diaz\"": "6e-6",
-                  "((autotroph_sname)) == \"sp\"": "3e-6",
+                  "((autotroph_sname)) == \"diat\"": 2.7e-06,
+                  "((autotroph_sname)) == \"diaz\"": 5.4e-06,
+                  "((autotroph_sname)) == \"sp\"": 2.7e-06,
                   "default": "1e34"
                },
                "longname": "Minimum Fe/C ratio for growth",
@@ -471,8 +471,8 @@
             "z_umax_0_per_day": {
                "datatype": "real",
                "default_value": {
-                  "((grazing_sname)) == \"diat_zoo\"": 3.05,
-                  "((grazing_sname)) == \"diaz_zoo\"": 3.1,
+                  "((grazing_sname)) == \"diat_zoo\"": 3.1,
+                  "((grazing_sname)) == \"diaz_zoo\"": 3.25,
                   "((grazing_sname)) == \"sp_zoo\"": 3.3,
                   "default": "1e34"
                },
@@ -899,7 +899,7 @@
       },
       "parm_FeLig_scavenge_rate0": {
          "datatype": "real",
-         "default_value": 1.3,
+         "default_value": 1.4,
          "longname": "Scavenging base rate for bound iron",
          "subcategory": "4. general parameters (scavenging)",
          "units": "unitless"
@@ -920,7 +920,7 @@
       },
       "parm_Fe_scavenge_rate0": {
          "datatype": "real",
-         "default_value": 15,
+         "default_value": 18.0,
          "longname": "Scavenging base rate for Fe",
          "subcategory": "4. general parameters (scavenging)",
          "units": "unitless"
@@ -1040,9 +1040,9 @@
             ],
             "default": [
                1,
-               2.2,
-               4,
-               5
+               3.0,
+               4.5,
+               5.5
             ]
          },
          "longname": "Prescribed scalelen values",

diff --git a/src/default_settings.yaml b/src/default_settings.yaml
@@ -352,7 +352,7 @@ general_parms :
       subcategory : 4. general parameters (scavenging)
       units : unitless
       datatype : real
-      default_value : 15
+      default_value : 18.0
    parm_Lig_scavenge_rate0 :
       longname : Scavenging base rate for bound ligand
       subcategory : 4. general parameters (scavenging)
@@ -364,7 +364,7 @@ general_parms :
       subcategory : 4. general parameters (scavenging)
       units : unitless
       datatype : real
-      default_value : 1.3
+      default_value : 1.4
    parm_Lig_degrade_rate0 :
       longname : Fe-binding ligand bacterial degradation base rate coefficient
       subcategory : 4. general parameters
@@ -437,9 +437,9 @@ general_parms :
       default_value :
          default :
             - 1
-            - 2.2
-            - 4
-            - 5
+            - 3.0
+            - 4.5
+            - 5.5
          GRID == "CESM_x3" :
             - 1
             - 3.3
@@ -676,9 +676,9 @@ PFT_derived_types :
             datatype : real
             default_value :
                default : 1e34
-               ((autotroph_sname)) == "sp" : 3e-6
-               ((autotroph_sname)) == "diat" : 3e-6
-               ((autotroph_sname)) == "diaz" : 6e-6
+               ((autotroph_sname)) == "sp" : 2.7e-6
+               ((autotroph_sname)) == "diat" : 2.7e-6
+               ((autotroph_sname)) == "diaz" : 5.4e-6
          alphaPI_per_day :
             longname : Initial slope of P_I curve (GD98)
             subcategory : 10. autotrophs
@@ -698,7 +698,7 @@ PFT_derived_types :
                default : 1e34
                ((autotroph_sname)) == "sp" : 5
                ((autotroph_sname)) == "diat" : 5
-               ((autotroph_sname)) == "diaz" : 2.2
+               ((autotroph_sname)) == "diaz" : 2.5
          thetaN_max :
             longname : Maximum thetaN (Chl / N)
             subcategory : 10. autotrophs
@@ -892,8 +892,8 @@ PFT_derived_types :
             default_value :
                default : 1e34
                ((grazing_sname)) == "sp_zoo" : 3.3
-               ((grazing_sname)) == "diat_zoo" : 3.05
-               ((grazing_sname)) == "diaz_zoo" : 3.1
+               ((grazing_sname)) == "diat_zoo" : 3.1
+               ((grazing_sname)) == "diaz_zoo" : 3.25
          z_grz :
             longname : Grazing coefficient
             subcategory : 12. grazing

diff --git a/src/marbl_pft_mod.F90 b/src/marbl_pft_mod.F90
@@ -221,7 +221,7 @@ subroutine autotroph_set_to_default(self, autotroph_id, marbl_status_log)
         self%kSiO3           = 0.0_r8            ! CESM USERS - DO NOT CHANGE HERE! POP calls put_setting() for this var, see CESM NOTE in marbl_settings_mod
         self%Qp_fixed        =  Qp_zoo           ! only used for lvariable_PtoC=.false.
         self%gQfe_0          = 35.0e-6_r8
-        self%gQfe_min        = 3.0e-6_r8
+        self%gQfe_min        = 2.7e-6_r8
         self%alphaPI_per_day = 0.39_r8
         self%PCref_per_day   = 5.0_r8
         self%thetaN_max      = 2.5_r8
@@ -248,7 +248,7 @@ subroutine autotroph_set_to_default(self, autotroph_id, marbl_status_log)
         self%kSiO3           = 0.7_r8            ! CESM USERS - DO NOT CHANGE HERE! POP calls put_setting() for this var, see CESM NOTE in marbl_settings_mod
         self%Qp_fixed        =  Qp_zoo           ! only used for lvariable_PtoC=.false.
         self%gQfe_0          = 35.0e-6_r8
-        self%gQfe_min        = 3.0e-6_r8
+        self%gQfe_min        = 2.7e-6_r8
         self%alphaPI_per_day = 0.29_r8
         self%PCref_per_day   = 5.0_r8
         self%thetaN_max      = 4.0_r8
@@ -275,9 +275,9 @@ subroutine autotroph_set_to_default(self, autotroph_id, marbl_status_log)
         self%kSiO3           = 0.0_r8            ! CESM USERS - DO NOT CHANGE HERE! POP calls put_setting() for this var, see CESM NOTE in marbl_settings_mod
         self%Qp_fixed        = 0.32_r8 * Qp_zoo  ! only used for lvariable_PtoC=.false.
         self%gQfe_0          = 70.0e-6_r8
-        self%gQfe_min        = 6.0e-6_r8
+        self%gQfe_min        = 5.4e-6_r8
         self%alphaPI_per_day = 0.39_r8
-        self%PCref_per_day   = 2.2_r8
+        self%PCref_per_day   = 2.5_r8
         self%thetaN_max      = 2.5_r8
         self%loss_thres      = 0.02_r8
         self%loss_thres2     = 0.001_r8
@@ -384,7 +384,7 @@ subroutine grazing_set_to_default(self, grazing_id, marbl_status_log)
         self%lname = 'Grazing of diat by zoo'             ! CESM USERS - DO NOT CHANGE HERE! POP calls put_setting() for this var, see CESM NOTE in marbl_settings_mod
         self%auto_ind_cnt = 1                             ! CESM USERS - DO NOT CHANGE HERE! POP calls put_setting() for this var, see CESM NOTE in marbl_settings_mod
         self%zoo_ind_cnt = 0                              ! CESM USERS - DO NOT CHANGE HERE! POP calls put_setting() for this var, see CESM NOTE in marbl_settings_mod
-        self%z_umax_0_per_day = 3.05_r8                   ! CESM USERS - DO NOT CHANGE HERE! POP calls put_setting() for this var, see CESM NOTE in marbl_settings_mod
+        self%z_umax_0_per_day = 3.1_r8                    ! CESM USERS - DO NOT CHANGE HERE! POP calls put_setting() for this var, see CESM NOTE in marbl_settings_mod
         self%z_grz            = 1.2_r8                    ! CESM USERS - DO NOT CHANGE HERE! POP calls put_setting() for this var, see CESM NOTE in marbl_settings_mod
         self%graze_zoo        = 0.25_r8                   ! CESM USERS - DO NOT CHANGE HERE! POP calls put_setting() for this var, see CESM NOTE in marbl_settings_mod
         self%graze_poc        = 0.38_r8                   ! CESM USERS - DO NOT CHANGE HERE! POP calls put_setting() for this var, see CESM NOTE in marbl_settings_mod
@@ -397,7 +397,7 @@ subroutine grazing_set_to_default(self, grazing_id, marbl_status_log)
         self%lname = 'Grazing of diaz by zoo'             ! CESM USERS - DO NOT CHANGE HERE! POP calls put_setting() for this var, see CESM NOTE in marbl_settings_mod
         self%auto_ind_cnt = 1                             ! CESM USERS - DO NOT CHANGE HERE! POP calls put_setting() for this var, see CESM NOTE in marbl_settings_mod
         self%zoo_ind_cnt = 0                              ! CESM USERS - DO NOT CHANGE HERE! POP calls put_setting() for this var, see CESM NOTE in marbl_settings_mod
-        self%z_umax_0_per_day = 3.1_r8                    ! CESM USERS - DO NOT CHANGE HERE! POP calls put_setting() for this var, see CESM NOTE in marbl_settings_mod
+        self%z_umax_0_per_day = 3.25_r8                   ! CESM USERS - DO NOT CHANGE HERE! POP calls put_setting() for this var, see CESM NOTE in marbl_settings_mod
         self%z_grz            = 1.2_r8                    ! CESM USERS - DO NOT CHANGE HERE! POP calls put_setting() for this var, see CESM NOTE in marbl_settings_mod
         self%graze_zoo        = 0.3_r8                    ! CESM USERS - DO NOT CHANGE HERE! POP calls put_setting() for this var, see CESM NOTE in marbl_settings_mod
         self%graze_poc        = 0.1_r8                    ! CESM USERS - DO NOT CHANGE HERE! POP calls put_setting() for this var, see CESM NOTE in marbl_settings_mod
@@ -457,4 +457,4 @@ end subroutine grazing_constructor
 
   !*****************************************************************************
 
-end module marbl_pft_mod
+end module marbl_pft_mod
diff --git a/src/marbl_settings_mod.F90 b/src/marbl_settings_mod.F90
@@ -365,9 +365,9 @@ subroutine marbl_settings_set_defaults_general_parms()
     parm_init_POC_bury_coeff      = 1.1_r8          ! CESM USERS - DO NOT CHANGE HERE! POP calls put_setting() for this var, see CESM NOTE above
     parm_init_POP_bury_coeff      = 1.1_r8          ! CESM USERS - DO NOT CHANGE HERE! POP calls put_setting() for this var, see CESM NOTE above
     parm_init_bSi_bury_coeff      = 1.0_r8          ! CESM USERS - DO NOT CHANGE HERE! POP calls put_setting() for this var, see CESM NOTE above
-    parm_Fe_scavenge_rate0        = 15.0_r8         ! CESM USERS - DO NOT CHANGE HERE! POP calls put_setting() for this var, see CESM NOTE above
+    parm_Fe_scavenge_rate0        = 18.0_r8         ! CESM USERS - DO NOT CHANGE HERE! POP calls put_setting() for this var, see CESM NOTE above
     parm_Lig_scavenge_rate0       = 0.015_r8        ! CESM USERS - DO NOT CHANGE HERE! POP calls put_setting() for this var, see CESM NOTE above
-    parm_FeLig_scavenge_rate0     = 1.3_r8          ! CESM USERS - DO NOT CHANGE HERE! POP calls put_setting() for this var, see CESM NOTE above
+    parm_FeLig_scavenge_rate0     = 1.4_r8          ! CESM USERS - DO NOT CHANGE HERE! POP calls put_setting() for this var, see CESM NOTE above
     parm_Lig_degrade_rate0        = 0.000094_r8     ! CESM USERS - DO NOT CHANGE HERE! POP calls put_setting() for this var, see CESM NOTE above
     parm_Fe_desorption_rate0      = 1.0e-6_r8       ! CESM USERS - DO NOT CHANGE HERE! POP calls put_setting() for this var, see CESM NOTE above
     parm_f_prod_sp_CaCO3          = 0.070_r8        ! CESM USERS - DO NOT CHANGE HERE! POP calls put_setting() for this var, see CESM NOTE above
@@ -377,7 +377,7 @@ subroutine marbl_settings_set_defaults_general_parms()
     parm_sed_denitrif_coeff       = 1.0_r8          ! CESM USERS - DO NOT CHANGE HERE! POP calls put_setting() for this var, see CESM NOTE above
     bury_coeff_rmean_timescale_years = 10.0_r8      ! CESM USERS - DO NOT CHANGE HERE! POP calls put_setting() for this var, see CESM NOTE above
     parm_scalelen_z    = (/ 100.0e2_r8, 250.0e2_r8, 500.0e2_r8, 1000.0e2_r8 /)  ! CESM USERS - DO NOT CHANGE HERE! POP calls put_setting() for this var, see CESM NOTE above
-    parm_scalelen_vals = (/     1.0_r8,     2.2_r8,     4.0_r8,      5.0_r8 /)  ! CESM USERS - DO NOT CHANGE HERE! POP calls put_setting() for this var, see CESM NOTE above
+    parm_scalelen_vals = (/     1.0_r8,     3.0_r8,     4.5_r8,      5.5_r8 /)  ! CESM USERS - DO NOT CHANGE HERE! POP calls put_setting() for this var, see CESM NOTE above
 
     caco3_bury_thres_opt   = 'omega_calc'           ! CESM USERS - DO NOT CHANGE HERE! POP calls put_setting() for this var, see CESM NOTE above
     caco3_bury_thres_depth = 3000.0e2               ! CESM USERS - DO NOT CHANGE HERE! POP calls put_setting() for this var, see CESM NOTE above