Clean up variable P:C and N:C logic

Some settings in marbl_settings_mod.F90 only need to be defined if lvariable_PtoC (or NtoC) is true. Also, found a couple block in marbl_init_tracer_metadata_mod.F90 that wasn't verifying N_ind > 0 before modifying N tracers (N_ind = 0 if lvariable_NtoC = .false.)
mnlevy1981 · May 25, 2024 · 46a90f6 · 46a90f6
1 parent d3a3cdb
commit 46a90f6
Show file tree

Hide file tree

Showing 4 changed files with 77 additions and 53 deletions.
diff --git a/defaults/json/settings_latest.json b/defaults/json/settings_latest.json
@@ -228,6 +228,7 @@
                   "((autotroph_sname)) == \"sp\"": 0.17,
                   "default": "1e34"
                },
+               "dependencies": "lvariable_NtoC",
                "longname": "Initial N/C ratio for growth",
                "subcategory": "10. autotrophs",
                "units": "unitless"
@@ -240,6 +241,7 @@
                   "((autotroph_sname)) == \"sp\"": 0.11,
                   "default": "1e34"
                },
+               "dependencies": "lvariable_NtoC",
                "longname": "Minimum N/C ratio for growth",
                "subcategory": "10. autotrophs",
                "units": "unitless"
@@ -252,6 +254,7 @@
                   "((autotroph_sname)) == \"sp\"": 0.011,
                   "default": "1e34"
                },
+               "dependencies": "lvariable_PtoC",
                "longname": "Initial P/C ratio for growth",
                "subcategory": "10. autotrophs",
                "units": "unitless"
@@ -264,6 +267,7 @@
                   "((autotroph_sname)) == \"sp\"": 0.0075,
                   "default": "1e34"
                },
+               "dependencies": "lvariable_PtoC",
                "longname": "Minimum P/C ratio for growth",
                "subcategory": "10. autotrophs",
                "units": "unitless"
@@ -1300,6 +1304,7 @@
          "units": "unitless"
       },
       "lvariable_NtoC": {
+         "_append_to_config_keywords": true,
          "datatype": "logical",
          "default_value": ".true.",
          "dependencies": "base_bio_on",
@@ -1308,6 +1313,7 @@
          "units": "unitless"
       },
       "lvariable_PtoC": {
+         "_append_to_config_keywords": true,
          "datatype": "logical",
          "default_value": ".true.",
          "dependencies": "base_bio_on",

diff --git a/defaults/settings_latest.yaml b/defaults/settings_latest.yaml
@@ -363,13 +363,15 @@ general_parms :
       units : unitless
       datatype : logical
       default_value : .true.
+      _append_to_config_keywords : true
    lvariable_NtoC :
       dependencies : base_bio_on
       longname : Control if NtoC ratios in autotrophs vary
       subcategory : 3. config flags
       units : unitless
       datatype : logical
       default_value : .true.
+      _append_to_config_keywords : true
    ladjust_bury_coeff :
       dependencies : base_bio_on
       longname : Control if bury coefficients are adjusted (rather than constant)
@@ -1048,6 +1050,7 @@ PFT_derived_types :
                ((autotroph_sname)) == "diat" : 1.8e-3
                ((autotroph_sname)) == "diaz" : 2.0e-3
          gQp_max :
+            dependencies : lvariable_PtoC
             longname : Initial P/C ratio for growth
             subcategory : 10. autotrophs
             units : unitless
@@ -1058,6 +1061,7 @@ PFT_derived_types :
                ((autotroph_sname)) == "diat" : 1.1e-2
                ((autotroph_sname)) == "diaz" : 8.3e-3
          gQp_min :
+            dependencies : lvariable_PtoC
             longname : Minimum P/C ratio for growth
             subcategory : 10. autotrophs
             units : unitless
@@ -1078,6 +1082,7 @@ PFT_derived_types :
                ((autotroph_sname)) == "diat" : 0.8
                ((autotroph_sname)) == "diaz" : 0.8
          gQn_max :
+            dependencies : lvariable_NtoC
             longname : Initial N/C ratio for growth
             subcategory : 10. autotrophs
             units : unitless
@@ -1088,6 +1093,7 @@ PFT_derived_types :
                ((autotroph_sname)) == "diat" : 1.7e-1
                ((autotroph_sname)) == "diaz" : 1.7e-1
          gQn_min :
+            dependencies : lvariable_NtoC
             longname : Minimum N/C ratio for growth
             subcategory : 10. autotrophs
             units : unitless

diff --git a/src/marbl_init_tracer_metadata_mod.F90 b/src/marbl_init_tracer_metadata_mod.F90
@@ -107,14 +107,16 @@ subroutine marbl_init_tracer_metadata(unit_system, marbl_tracer_indices, marbl_t
         marbl_tracer_metadata(n)%tracer_module_name = 'base_bio'
 
         n = marbl_tracer_indices%auto_inds(auto_ind)%N_ind
-        marbl_tracer_metadata(n)%lfull_depth_tavg = lecovars_full_depth_tavg
-        marbl_tracer_metadata(n)%tracer_module_name = 'base_bio'
+        if (n > 0) then
+            marbl_tracer_metadata(n)%lfull_depth_tavg = lecovars_full_depth_tavg
+            marbl_tracer_metadata(n)%tracer_module_name = 'base_bio'
+        endif
 
         n = marbl_tracer_indices%auto_inds(auto_ind)%P_ind
         if (n > 0) then
             marbl_tracer_metadata(n)%lfull_depth_tavg = lecovars_full_depth_tavg
             marbl_tracer_metadata(n)%tracer_module_name = 'base_bio'
-          endif
+        endif
 
         n = marbl_tracer_indices%auto_inds(auto_ind)%Fe_ind
         marbl_tracer_metadata(n)%lfull_depth_tavg = lecovars_full_depth_tavg
@@ -263,11 +265,13 @@ subroutine init_autotroph_tracer_metadata(marbl_tracer_metadata,      &
        marbl_tracer_metadata(n)%flux_units = unit_system%conc_flux_units
 
        n = marbl_tracer_indices%auto_inds(auto_ind)%N_ind
-       marbl_tracer_metadata(n)%short_name = trim(autotroph_settings(auto_ind)%sname) // 'N'
-       marbl_tracer_metadata(n)%long_name  = trim(autotroph_settings(auto_ind)%lname) // ' Nitrogen'
-       marbl_tracer_metadata(n)%units      = unit_system%conc_units
-       marbl_tracer_metadata(n)%tend_units = unit_system%conc_tend_units
-       marbl_tracer_metadata(n)%flux_units = unit_system%conc_flux_units
+       if (n.gt.0) then
+           marbl_tracer_metadata(n)%short_name = trim(autotroph_settings(auto_ind)%sname) // 'N'
+           marbl_tracer_metadata(n)%long_name  = trim(autotroph_settings(auto_ind)%lname) // ' Nitrogen'
+           marbl_tracer_metadata(n)%units      = unit_system%conc_units
+           marbl_tracer_metadata(n)%tend_units = unit_system%conc_tend_units
+           marbl_tracer_metadata(n)%flux_units = unit_system%conc_flux_units
+       endif
 
        n = marbl_tracer_indices%auto_inds(auto_ind)%P_ind
        if (n.gt.0) then
@@ -344,4 +348,4 @@ end subroutine init_autotroph_tracer_metadata
 
   !***********************************************************************
 
-end module marbl_init_tracer_metadata_mod
+end module marbl_init_tracer_metadata_mod
diff --git a/src/marbl_settings_mod.F90 b/src/marbl_settings_mod.F90
@@ -1548,26 +1548,6 @@ subroutine marbl_settings_define_PFT_derived_types(this, marbl_status_log)
                         nondefault_required=(PFT_defaults .eq. 'user-specified'))
       call check_and_log_add_var_error(marbl_status_log, sname, subname, labort_marbl_loc)
 
-      write(sname, "(2A)") trim(prefix), 'Qp_fixed'
-      lname    = 'P/C ratio when using fixed P/C ratios'
-      units    = 'unitless'
-      datatype = 'real'
-      rptr     => autotroph_settings(n)%Qp_fixed
-      call this%add_var(sname, lname, units, datatype, category,     &
-                        marbl_status_log, rptr=rptr,                 &
-                        nondefault_required=(PFT_defaults .eq. 'user-specified'))
-      call check_and_log_add_var_error(marbl_status_log, sname, subname, labort_marbl_loc)
-
-      write(sname, "(2A)") trim(prefix), 'Qn_fixed'
-      lname    = 'P/C ratio when using fixed N/C ratios'
-      units    = 'unitless'
-      datatype = 'real'
-      rptr     => autotroph_settings(n)%Qn_fixed
-      call this%add_var(sname, lname, units, datatype, category,     &
-                        marbl_status_log, rptr=rptr,                 &
-                        nondefault_required=(PFT_defaults .eq. 'user-specified'))
-      call check_and_log_add_var_error(marbl_status_log, sname, subname, labort_marbl_loc)
-
       write(sname, "(2A)") trim(prefix), 'SiOpt'
       lname    = 'Si threshold in uptake ratio computations'
       units    = 'nM'
@@ -1608,21 +1588,35 @@ subroutine marbl_settings_define_PFT_derived_types(this, marbl_status_log)
                         nondefault_required=(PFT_defaults .eq. 'user-specified'))
       call check_and_log_add_var_error(marbl_status_log, sname, subname, labort_marbl_loc)
 
-      write(sname, "(2A)") trim(prefix), 'gQp_max'
-      lname    = 'initial P/C ratio for growth'
-      units    = 'unitless'
-      datatype = 'real'
-      rptr     => autotroph_settings(n)%gQp_max
-      call this%add_var(sname, lname, units, datatype, category,     &
-                        marbl_status_log, rptr=rptr,                 &
-                        nondefault_required=(PFT_defaults .eq. 'user-specified'))
-      call check_and_log_add_var_error(marbl_status_log, sname, subname, labort_marbl_loc)
+      if (lvariable_PtoC) then
+        write(sname, "(2A)") trim(prefix), 'gQp_max'
+        lname    = 'initial P/C ratio for growth'
+        units    = 'unitless'
+        datatype = 'real'
+        rptr     => autotroph_settings(n)%gQp_max
+        call this%add_var(sname, lname, units, datatype, category,     &
+                          marbl_status_log, rptr=rptr,                 &
+                          nondefault_required=(PFT_defaults .eq. 'user-specified'))
+        call check_and_log_add_var_error(marbl_status_log, sname, subname, labort_marbl_loc)
 
-      write(sname, "(2A)") trim(prefix), 'gQp_min'
-      lname    = 'minimum P/C ratio for growth'
+        write(sname, "(2A)") trim(prefix), 'gQp_min'
+        lname    = 'minimum P/C ratio for growth'
+        units    = 'unitless'
+        datatype = 'real'
+        rptr     => autotroph_settings(n)%gQp_min
+        call this%add_var(sname, lname, units, datatype, category,     &
+                          marbl_status_log, rptr=rptr,                 &
+                          nondefault_required=(PFT_defaults .eq. 'user-specified'))
+        call check_and_log_add_var_error(marbl_status_log, sname, subname, labort_marbl_loc)
+      endif
+
+      ! This is only used when lvariable_PtoC = .false., but settings_file_class always includes it
+      ! in the setting file because it doesn't (yet) have logic to check for false logical vars
+      write(sname, "(2A)") trim(prefix), 'Qp_fixed'
+      lname    = 'P/C ratio when using fixed P/C ratios'
       units    = 'unitless'
       datatype = 'real'
-      rptr     => autotroph_settings(n)%gQp_min
+      rptr     => autotroph_settings(n)%Qp_fixed
       call this%add_var(sname, lname, units, datatype, category,     &
                         marbl_status_log, rptr=rptr,                 &
                         nondefault_required=(PFT_defaults .eq. 'user-specified'))
@@ -1638,21 +1632,35 @@ subroutine marbl_settings_define_PFT_derived_types(this, marbl_status_log)
                         nondefault_required=(PFT_defaults .eq. 'user-specified'))
       call check_and_log_add_var_error(marbl_status_log, sname, subname, labort_marbl_loc)
 
-      write(sname, "(2A)") trim(prefix), 'gQn_max'
-      lname    = 'initial N/C ratio for growth'
-      units    = 'unitless'
-      datatype = 'real'
-      rptr     => autotroph_settings(n)%gQn_max
-      call this%add_var(sname, lname, units, datatype, category,     &
-                        marbl_status_log, rptr=rptr,                 &
-                        nondefault_required=(PFT_defaults .eq. 'user-specified'))
-      call check_and_log_add_var_error(marbl_status_log, sname, subname, labort_marbl_loc)
+      if (lvariable_NtoC) then
+        write(sname, "(2A)") trim(prefix), 'gQn_max'
+        lname    = 'initial N/C ratio for growth'
+        units    = 'unitless'
+        datatype = 'real'
+        rptr     => autotroph_settings(n)%gQn_max
+        call this%add_var(sname, lname, units, datatype, category,     &
+                          marbl_status_log, rptr=rptr,                 &
+                          nondefault_required=(PFT_defaults .eq. 'user-specified'))
+        call check_and_log_add_var_error(marbl_status_log, sname, subname, labort_marbl_loc)
+
+        write(sname, "(2A)") trim(prefix), 'gQn_min'
+        lname    = 'minimum N/C ratio for growth'
+        units    = 'unitless'
+        datatype = 'real'
+        rptr     => autotroph_settings(n)%gQn_min
+        call this%add_var(sname, lname, units, datatype, category,     &
+                          marbl_status_log, rptr=rptr,                 &
+                          nondefault_required=(PFT_defaults .eq. 'user-specified'))
+        call check_and_log_add_var_error(marbl_status_log, sname, subname, labort_marbl_loc)
+      endif
 
-      write(sname, "(2A)") trim(prefix), 'gQn_min'
-      lname    = 'minimum N/C ratio for growth'
+      ! This is only used when lvariable_NtoC = .false., but settings_file_class always includes it
+      ! in the setting file because it doesn't (yet) have logic to check for false logical vars
+      write(sname, "(2A)") trim(prefix), 'Qn_fixed'
+      lname    = 'P/C ratio when using fixed N/C ratios'
       units    = 'unitless'
       datatype = 'real'
-      rptr     => autotroph_settings(n)%gQn_min
+      rptr     => autotroph_settings(n)%Qn_fixed
       call this%add_var(sname, lname, units, datatype, category,     &
                         marbl_status_log, rptr=rptr,                 &
                         nondefault_required=(PFT_defaults .eq. 'user-specified'))