Clean up marbl_abio_dic_surface_flux_mod

Turned some divisions into multiplications, cleaned up local variable names, and added a new settings variable to control whether we compute the derivative diagnostics. Also fixed a missing-import bug in MARBL_share.py
mnlevy1981 · Oct 13, 2023 · 4f2f6b8 · 4f2f6b8
1 parent 39a008d
commit 4f2f6b8
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Showing 19 changed files with 232 additions and 109 deletions.
diff --git a/MARBL_tools/MARBL_share.py b/MARBL_tools/MARBL_share.py
@@ -221,6 +221,9 @@ def expand_template_value(key_name, MARBL_settings, unit_system, unprocessed_dic
 ################################################################################
 
 def meet_dependencies(input_dict, MARBL_settings):
+    import logging
+    logger = logging.getLogger(__name__)
+
     if "dependencies" in input_dict.keys():
         for dependency in input_dict["dependencies"].keys():
             if dependency not in MARBL_settings.settings_dict.keys():

diff --git a/defaults/diagnostics_latest.yaml b/defaults/diagnostics_latest.yaml
@@ -307,6 +307,7 @@ ABIO_FG_DI14C :
 d_SF_ABIO_DIC_d_ABIO_DIC :
    dependencies :
       abio_dic_on : .true.
+      labio_derivative_diags : .true.
    longname : Derivative of STF_ABIO_DIC wrt ABIO_DIC
    units : cm/s
    vertical_grid : none
@@ -315,6 +316,7 @@ d_SF_ABIO_DIC_d_ABIO_DIC :
 d_SF_ABIO_DI14C_d_ABIO_DIC :
    dependencies :
       abio_dic_on : .true.
+      labio_derivative_diags : .true.
    longname : Derivative of STF_ABIO_DI14C wrt ABIO_DIC
    units : cm/s
    vertical_grid : none
@@ -323,6 +325,7 @@ d_SF_ABIO_DI14C_d_ABIO_DIC :
 d_SF_ABIO_DI14C_d_ABIO_DI14C :
    dependencies :
       abio_dic_on : .true.
+      labio_derivative_diags : .true.
    longname : Derivative of STF_ABIO_DI14C wrt ABIO_DI14C
    units : cm/s
    vertical_grid : none

diff --git a/defaults/json/diagnostics_latest.json b/defaults/json/diagnostics_latest.json
@@ -2363,7 +2363,8 @@
    },
    "d_SF_ABIO_DI14C_d_ABIO_DI14C": {
       "dependencies": {
-         "abio_dic_on": ".true."
+         "abio_dic_on": ".true.",
+         "labio_derivative_diags": ".true."
       },
       "frequency": "never",
       "longname": "Derivative of STF_ABIO_DI14C wrt ABIO_DI14C",
@@ -2373,7 +2374,8 @@
    },
    "d_SF_ABIO_DI14C_d_ABIO_DIC": {
       "dependencies": {
-         "abio_dic_on": ".true."
+         "abio_dic_on": ".true.",
+         "labio_derivative_diags": ".true."
       },
       "frequency": "never",
       "longname": "Derivative of STF_ABIO_DI14C wrt ABIO_DIC",
@@ -2383,7 +2385,8 @@
    },
    "d_SF_ABIO_DIC_d_ABIO_DIC": {
       "dependencies": {
-         "abio_dic_on": ".true."
+         "abio_dic_on": ".true.",
+         "labio_derivative_diags": ".true."
       },
       "frequency": "never",
       "longname": "Derivative of STF_ABIO_DIC wrt ABIO_DIC",

diff --git a/defaults/json/settings_cesm2.0.json b/defaults/json/settings_cesm2.0.json
@@ -1097,6 +1097,14 @@
          "subcategory": "5. general parameters",
          "units": 1
       },
+      "labio_derivative_diags": {
+         "datatype": "logical",
+         "default_value": ".false.",
+         "dependencies": "abio_dic_on",
+         "longname": "Control whether derivative diagnostics are computed in abiotic surface flux (useful for Newton-Krylov)",
+         "subcategory": "3. config flags",
+         "units": "unitless"
+      },
       "ladjust_bury_coeff": {
          "_append_to_config_keywords": true,
          "datatype": "logical",

diff --git a/defaults/json/settings_cesm2.1+cocco.json b/defaults/json/settings_cesm2.1+cocco.json
@@ -1139,6 +1139,14 @@
          "subcategory": "5. general parameters",
          "units": 1
       },
+      "labio_derivative_diags": {
+         "datatype": "logical",
+         "default_value": ".false.",
+         "dependencies": "abio_dic_on",
+         "longname": "Control whether derivative diagnostics are computed in abiotic surface flux (useful for Newton-Krylov)",
+         "subcategory": "3. config flags",
+         "units": "unitless"
+      },
       "ladjust_bury_coeff": {
          "_append_to_config_keywords": true,
          "datatype": "logical",

diff --git a/defaults/json/settings_cesm2.1.json b/defaults/json/settings_cesm2.1.json
@@ -1097,6 +1097,14 @@
          "subcategory": "5. general parameters",
          "units": 1
       },
+      "labio_derivative_diags": {
+         "datatype": "logical",
+         "default_value": ".false.",
+         "dependencies": "abio_dic_on",
+         "longname": "Control whether derivative diagnostics are computed in abiotic surface flux (useful for Newton-Krylov)",
+         "subcategory": "3. config flags",
+         "units": "unitless"
+      },
       "ladjust_bury_coeff": {
          "_append_to_config_keywords": true,
          "datatype": "logical",

diff --git a/defaults/json/settings_latest+4p2z.json b/defaults/json/settings_latest+4p2z.json
@@ -1192,6 +1192,14 @@
          "subcategory": "5. general parameters",
          "units": 1
       },
+      "labio_derivative_diags": {
+         "datatype": "logical",
+         "default_value": ".false.",
+         "dependencies": "abio_dic_on",
+         "longname": "Control whether derivative diagnostics are computed in abiotic surface flux (useful for Newton-Krylov)",
+         "subcategory": "3. config flags",
+         "units": "unitless"
+      },
       "ladjust_bury_coeff": {
          "_append_to_config_keywords": true,
          "datatype": "logical",

diff --git a/defaults/json/settings_latest+cocco.json b/defaults/json/settings_latest+cocco.json
@@ -1139,6 +1139,14 @@
          "subcategory": "5. general parameters",
          "units": 1
       },
+      "labio_derivative_diags": {
+         "datatype": "logical",
+         "default_value": ".false.",
+         "dependencies": "abio_dic_on",
+         "longname": "Control whether derivative diagnostics are computed in abiotic surface flux (useful for Newton-Krylov)",
+         "subcategory": "3. config flags",
+         "units": "unitless"
+      },
       "ladjust_bury_coeff": {
          "_append_to_config_keywords": true,
          "datatype": "logical",

diff --git a/defaults/json/settings_latest.json b/defaults/json/settings_latest.json
@@ -1103,6 +1103,14 @@
          "subcategory": "5. general parameters",
          "units": 1
       },
+      "labio_derivative_diags": {
+         "datatype": "logical",
+         "default_value": ".false.",
+         "dependencies": "abio_dic_on",
+         "longname": "Control whether derivative diagnostics are computed in abiotic surface flux (useful for Newton-Krylov)",
+         "subcategory": "3. config flags",
+         "units": "unitless"
+      },
       "ladjust_bury_coeff": {
          "_append_to_config_keywords": true,
          "datatype": "logical",
@@ -1519,6 +1527,7 @@
    },
    "tracer_modules": {
       "abio_dic_on": {
+         "_append_to_config_keywords": true,
          "datatype": "logical",
          "default_value": ".false.",
          "longname": "Control whether abiotic carbon tracer module is active",

diff --git a/defaults/settings_cesm2.0.yaml b/defaults/settings_cesm2.0.yaml
@@ -374,6 +374,13 @@ general_parms :
       units : unitless
       datatype : logical
       default_value : .false.
+   labio_derivative_diags :
+      dependencies : abio_dic_on
+      longname : Control whether derivative diagnostics are computed in abiotic surface flux (useful for Newton-Krylov)
+      subcategory : 3. config flags
+      units : unitless
+      datatype : logical
+      default_value : .false.
    bftt_dz_sum_thres:
       dependencies : base_bio_on
       longname : MARBL will abort if abs(1 - sum(bot_flux_to_tend)) exceeds this threshold

diff --git a/defaults/settings_cesm2.1+cocco.yaml b/defaults/settings_cesm2.1+cocco.yaml
@@ -378,6 +378,13 @@ general_parms :
       units : unitless
       datatype : logical
       default_value : .false.
+   labio_derivative_diags :
+      dependencies : abio_dic_on
+      longname : Control whether derivative diagnostics are computed in abiotic surface flux (useful for Newton-Krylov)
+      subcategory : 3. config flags
+      units : unitless
+      datatype : logical
+      default_value : .false.
    bftt_dz_sum_thres:
       dependencies : base_bio_on
       longname : MARBL will abort if abs(1 - sum(bot_flux_to_tend)) exceeds this threshold

diff --git a/defaults/settings_cesm2.1.yaml b/defaults/settings_cesm2.1.yaml
@@ -376,6 +376,13 @@ general_parms :
       units : unitless
       datatype : logical
       default_value : .false.
+   labio_derivative_diags :
+      dependencies : abio_dic_on
+      longname : Control whether derivative diagnostics are computed in abiotic surface flux (useful for Newton-Krylov)
+      subcategory : 3. config flags
+      units : unitless
+      datatype : logical
+      default_value : .false.
    bftt_dz_sum_thres:
       dependencies : base_bio_on
       longname : MARBL will abort if abs(1 - sum(bot_flux_to_tend)) exceeds this threshold

diff --git a/defaults/settings_latest+4p2z.yaml b/defaults/settings_latest+4p2z.yaml
@@ -394,6 +394,13 @@ general_parms :
       units : unitless
       datatype : logical
       default_value : .false.
+   labio_derivative_diags :
+      dependencies : abio_dic_on
+      longname : Control whether derivative diagnostics are computed in abiotic surface flux (useful for Newton-Krylov)
+      subcategory : 3. config flags
+      units : unitless
+      datatype : logical
+      default_value : .false.
    bftt_dz_sum_thres:
       dependencies : base_bio_on
       longname : MARBL will abort if abs(1 - sum(bot_flux_to_tend)) exceeds this threshold

diff --git a/defaults/settings_latest+cocco.yaml b/defaults/settings_latest+cocco.yaml
@@ -378,6 +378,13 @@ general_parms :
       units : unitless
       datatype : logical
       default_value : .false.
+   labio_derivative_diags :
+      dependencies : abio_dic_on
+      longname : Control whether derivative diagnostics are computed in abiotic surface flux (useful for Newton-Krylov)
+      subcategory : 3. config flags
+      units : unitless
+      datatype : logical
+      default_value : .false.
    bftt_dz_sum_thres:
       dependencies : base_bio_on
       longname : MARBL will abort if abs(1 - sum(bot_flux_to_tend)) exceeds this threshold

diff --git a/defaults/settings_latest.yaml b/defaults/settings_latest.yaml
@@ -263,6 +263,7 @@ tracer_modules :
       units : unitless
       datatype : logical
       default_value : .false.
+      _append_to_config_keywords : true
    ciso_on :
       longname : Control whether CISO tracer module is active
       subcategory : 1. tracer modules
@@ -377,6 +378,13 @@ general_parms :
       units : unitless
       datatype : logical
       default_value : .false.
+   labio_derivative_diags :
+      dependencies : abio_dic_on
+      longname : Control whether derivative diagnostics are computed in abiotic surface flux (useful for Newton-Krylov)
+      subcategory : 3. config flags
+      units : unitless
+      datatype : logical
+      default_value : .false.
    bftt_dz_sum_thres:
       dependencies : base_bio_on
       longname : MARBL will abort if abs(1 - sum(bot_flux_to_tend)) exceeds this threshold

diff --git a/src/marbl_abio_dic_diagnostics_mod.F90 b/src/marbl_abio_dic_diagnostics_mod.F90
@@ -8,6 +8,7 @@ module marbl_abio_dic_diagnostics_mod
   use marbl_kinds_mod, only : char_len
 
   use marbl_settings_mod, only : unit_system_type
+  use marbl_settings_mod, only : labio_derivative_diags
 
   use marbl_interface_public_types, only : marbl_diagnostics_type
 
@@ -187,40 +188,42 @@ subroutine marbl_abio_dic_diagnostics_init( &
        return
       end if
 
-      lname    = 'Derivative of STF_ABIO_DIC wrt ABIO_DIC'
-      sname    = 'd_SF_ABIO_DIC_d_ABIO_DIC'
-      units    = vel_units
-      vgrid    = 'none'
-      truncate = .false.
-      call diags%add_diagnostic(lname, sname, units, vgrid, truncate,  &
-          ind%d_SF_ABIO_DIC_d_ABIO_DIC, 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    = 'Derivative of STF_ABIO_DI14C wrt ABIO_DIC'
-      sname    = 'd_SF_ABIO_DI14C_d_ABIO_DIC'
-      units    = vel_units
-      vgrid    = 'none'
-      truncate = .false.
-      call diags%add_diagnostic(lname, sname, units, vgrid, truncate,  &
-          ind%d_SF_ABIO_DI14C_d_ABIO_DIC, 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    = 'Derivative of STF_ABIO_DI14C wrt ABIO_DI14C'
-      sname    = 'd_SF_ABIO_DI14C_d_ABIO_DI14C'
-      units    = vel_units
-      vgrid    = 'none'
-      truncate = .false.
-      call diags%add_diagnostic(lname, sname, units, vgrid, truncate,  &
-          ind%d_SF_ABIO_DI14C_d_ABIO_DI14C, marbl_status_log)
-      if (marbl_status_log%labort_marbl) then
-       call marbl_logging_add_diagnostics_error(marbl_status_log, sname, subname)
-       return
+      if (labio_derivative_diags) then
+        lname    = 'Derivative of STF_ABIO_DIC wrt ABIO_DIC'
+        sname    = 'd_SF_ABIO_DIC_d_ABIO_DIC'
+        units    = vel_units
+        vgrid    = 'none'
+        truncate = .false.
+        call diags%add_diagnostic(lname, sname, units, vgrid, truncate,  &
+             ind%d_SF_ABIO_DIC_d_ABIO_DIC, 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    = 'Derivative of STF_ABIO_DI14C wrt ABIO_DIC'
+        sname    = 'd_SF_ABIO_DI14C_d_ABIO_DIC'
+        units    = vel_units
+        vgrid    = 'none'
+        truncate = .false.
+        call diags%add_diagnostic(lname, sname, units, vgrid, truncate,  &
+             ind%d_SF_ABIO_DI14C_d_ABIO_DIC, 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    = 'Derivative of STF_ABIO_DI14C wrt ABIO_DI14C'
+        sname    = 'd_SF_ABIO_DI14C_d_ABIO_DI14C'
+        units    = vel_units
+        vgrid    = 'none'
+        truncate = .false.
+        call diags%add_diagnostic(lname, sname, units, vgrid, truncate,  &
+             ind%d_SF_ABIO_DI14C_d_ABIO_DI14C, marbl_status_log)
+        if (marbl_status_log%labort_marbl) then
+          call marbl_logging_add_diagnostics_error(marbl_status_log, sname, subname)
+          return
+        end if
       end if
 
     end associate
@@ -297,9 +300,11 @@ subroutine marbl_abio_dic_diagnostics_surface_flux_compute( &
     diags(ind%ABIO_ALK_SURF)%field_2d(:) = alk_surf(:)
     diags(ind%ABIO_FG_DIC)%field_2d(:) = fg_dic(:)
     diags(ind%ABIO_FG_DI14C)%field_2d(:) = fg_di14c(:)
-    diags(ind%d_SF_ABIO_DIC_d_ABIO_DIC)%field_2d(:) = derivative_terms(:,1)
-    diags(ind%d_SF_ABIO_DI14C_d_ABIO_DIC)%field_2d(:) = derivative_terms(:,2)
-    diags(ind%d_SF_ABIO_DI14C_d_ABIO_DI14C)%field_2d(:) = derivative_terms(:,3)
+    if (labio_derivative_diags) then
+      diags(ind%d_SF_ABIO_DIC_d_ABIO_DIC)%field_2d(:) = derivative_terms(:,1)
+      diags(ind%d_SF_ABIO_DI14C_d_ABIO_DIC)%field_2d(:) = derivative_terms(:,2)
+      diags(ind%d_SF_ABIO_DI14C_d_ABIO_DI14C)%field_2d(:) = derivative_terms(:,3)
+    end if
 
     end associate