Merge branch 'add_4p2z_settings' into development

marbl-ecosys · May 11, 2023 · 75827e2 · 75827e2
2 parents 5a41872 + ea4205e
commit 75827e2
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Showing 11 changed files with 2,930 additions and 104 deletions.
diff --git a/MARBL_tools/MARBL_settings_file_class.py b/MARBL_tools/MARBL_settings_file_class.py
@@ -227,7 +227,7 @@ def _process_variable_value(self, category_name, variable_name):
         # Process derived type!
         # Check to see if PFT_defaults leads to specific PFT declarations
         if (category_name == "PFT_derived_types"):
-            for valid_PFT_default in ["CESM2", "CESM2+cocco"]:
+            for valid_PFT_default in ["CESM2", "CESM2+cocco", "4p2z"]:
                 append_to_keys = 'PFT_defaults == "{}"'.format(valid_PFT_default) in self._config_keyword
                 if append_to_keys:
                     settings_key = '_{}_PFT_keys'.format(valid_PFT_default)
@@ -241,13 +241,15 @@ def _process_variable_value(self, category_name, variable_name):
                 base_name = "%s%s%%" % (variable_name, elem_index)
 
                 if append_to_keys:
+                    if n < len(PFT_keys):
+                        PFT_keys.append('null')
                     # Add key for specific PFT
                     if variable_name == 'zooplankton_settings':
-                      self._config_keyword.append('((zooplankton_sname)) == "%s"' % PFT_keys[n])
+                        self._config_keyword.append('((zooplankton_sname)) == "%s"' % PFT_keys[n])
                     elif variable_name == 'autotroph_settings':
-                      self._config_keyword.append('((autotroph_sname)) == "%s"' % PFT_keys[n])
+                        self._config_keyword.append('((autotroph_sname)) == "%s"' % PFT_keys[n])
                     elif variable_name == 'grazing_relationship_settings':
-                      self._config_keyword.append('((grazer_sname)) == "%s"' % PFT_keys[n])
+                        self._config_keyword.append('((grazer_sname)) == "%s"' % PFT_keys[n])
 
                 for key in _sort_with_specific_suffix_first(this_var["datatype"].keys(),'_cnt'):
                     if key[0] != '_':

diff --git a/defaults/diagnostics_latest.yaml b/defaults/diagnostics_latest.yaml
@@ -464,8 +464,12 @@ pocToFloor :
    longname : POC Flux Hitting Sea Floor
    units : nmol/cm^2/s
    vertical_grid : none
-   frequency : never
-   operator : average
+   frequency :
+      - medium
+      - high
+   operator :
+      - average
+      - average
 pocToSed :
    longname : POC Flux to Sediments
    units : nmol/cm^2/s
@@ -1490,14 +1494,14 @@ graze_((autotroph_sname))_doc_zint_100m :
    vertical_grid : none
    frequency : medium
    operator : average
-graze_((autotroph_sname))_zoo_zint :
-   longname : ((autotroph_lname)) Grazing to ZOO Vertical Integral
+graze_((autotroph_sname))_((zooplankton_sname))_zint :
+   longname : ((autotroph_lname)) Grazing to ((zooplankton_lname)) Vertical Integral
    units : mmol/m^3 cm/s
    vertical_grid : none
    frequency : never
    operator : average
-graze_((autotroph_sname))_zoo_zint_100m :
-   longname : ((autotroph_lname)) Grazing to ZOO Vertical Integral, 0-100m
+graze_((autotroph_sname))_((zooplankton_sname))_zint_100m :
+   longname : ((autotroph_lname)) Grazing to ((zooplankton_lname)) Vertical Integral, 0-100m
    units : mmol/m^3 cm/s
    vertical_grid : none
    frequency : medium
@@ -1859,6 +1863,12 @@ CISO_mui_to_co2star_((autotroph_sname)) :
    vertical_grid : none
    frequency : medium
    operator : average
+((zooplankton_sname))_loss_zint_150m :
+   longname : ((zooplankton_lname)) Loss Vertical Integral, 0-150m
+   units : mmol/m^3 cm/s
+   vertical_grid : none
+   frequency : high
+   operator : average
 ((zooplankton_sname))_loss_basal_zint :
    longname : ((zooplankton_lname)) Basal Respiration Vertical Integral
    units : mmol/m^3 cm/s
@@ -1931,14 +1941,14 @@ graze_((zooplankton_sname))_doc_zint_100m :
    vertical_grid : none
    frequency : never
    operator : average
-graze_((zooplankton_sname))_zoo_zint :
-   longname : ((zooplankton_lname)) Grazing to ZOO Vertical Integral
+graze_((zooplankton_sname))_((zooplankton_sname))_zint :
+   longname : ((zooplankton_lname)) Grazing to ((zooplankton_lname)) Vertical Integral
    units : mmol/m^3 cm/s
    vertical_grid : none
    frequency : never
    operator : average
-graze_((zooplankton_sname))_zoo_zint_100m :
-   longname : ((zooplankton_lname)) Grazing to ZOO Vertical Integral, 0-100m
+graze_((zooplankton_sname))_((zooplankton_sname))_zint_100m :
+   longname : ((zooplankton_lname)) Grazing to ((zooplankton_lname)) Vertical Integral, 0-100m
    units : mmol/m^3 cm/s
    vertical_grid : none
    frequency : never

diff --git a/defaults/json/diagnostics_latest.json b/defaults/json/diagnostics_latest.json
@@ -351,6 +351,13 @@
       "units": "mmol/m^3 cm/s",
       "vertical_grid": "none"
    },
+   "((zooplankton_sname))_loss_zint_150m": {
+      "frequency": "high",
+      "longname": "((zooplankton_lname)) Loss Vertical Integral, 0-150m",
+      "operator": "average",
+      "units": "mmol/m^3 cm/s",
+      "vertical_grid": "none"
+   },
    "AOU": {
       "frequency": "medium",
       "longname": "Apparent O2 Utilization",
@@ -1931,6 +1938,20 @@
       "units": "mmol/m^3/s",
       "vertical_grid": "layer_avg"
    },
+   "graze_((autotroph_sname))_((zooplankton_sname))_zint": {
+      "frequency": "never",
+      "longname": "((autotroph_lname)) Grazing to ((zooplankton_lname)) Vertical Integral",
+      "operator": "average",
+      "units": "mmol/m^3 cm/s",
+      "vertical_grid": "none"
+   },
+   "graze_((autotroph_sname))_((zooplankton_sname))_zint_100m": {
+      "frequency": "medium",
+      "longname": "((autotroph_lname)) Grazing to ((zooplankton_lname)) Vertical Integral, 0-100m",
+      "operator": "average",
+      "units": "mmol/m^3 cm/s",
+      "vertical_grid": "none"
+   },
    "graze_((autotroph_sname))_doc": {
       "frequency": "never",
       "longname": "((autotroph_lname)) Grazing to DOC",
@@ -1989,20 +2010,6 @@
       "units": "mmol/m^3 cm/s",
       "vertical_grid": "none"
    },
-   "graze_((autotroph_sname))_zoo_zint": {
-      "frequency": "never",
-      "longname": "((autotroph_lname)) Grazing to ZOO Vertical Integral",
-      "operator": "average",
-      "units": "mmol/m^3 cm/s",
-      "vertical_grid": "none"
-   },
-   "graze_((autotroph_sname))_zoo_zint_100m": {
-      "frequency": "medium",
-      "longname": "((autotroph_lname)) Grazing to ZOO Vertical Integral, 0-100m",
-      "operator": "average",
-      "units": "mmol/m^3 cm/s",
-      "vertical_grid": "none"
-   },
    "graze_((autotroph_sname))_zootot": {
       "frequency": "medium",
       "longname": "((autotroph_lname)) Grazing to ZOO TOT",
@@ -2027,6 +2034,20 @@
       "units": "mmol/m^3/s",
       "vertical_grid": "layer_avg"
    },
+   "graze_((zooplankton_sname))_((zooplankton_sname))_zint": {
+      "frequency": "never",
+      "longname": "((zooplankton_lname)) Grazing to ((zooplankton_lname)) Vertical Integral",
+      "operator": "average",
+      "units": "mmol/m^3 cm/s",
+      "vertical_grid": "none"
+   },
+   "graze_((zooplankton_sname))_((zooplankton_sname))_zint_100m": {
+      "frequency": "never",
+      "longname": "((zooplankton_lname)) Grazing to ((zooplankton_lname)) Vertical Integral, 0-100m",
+      "operator": "average",
+      "units": "mmol/m^3 cm/s",
+      "vertical_grid": "none"
+   },
    "graze_((zooplankton_sname))_doc": {
       "frequency": "never",
       "longname": "((zooplankton_lname)) grazing loss to DOC",
@@ -2085,20 +2106,6 @@
       "units": "mmol/m^3 cm/s",
       "vertical_grid": "none"
    },
-   "graze_((zooplankton_sname))_zoo_zint": {
-      "frequency": "never",
-      "longname": "((zooplankton_lname)) Grazing to ZOO Vertical Integral",
-      "operator": "average",
-      "units": "mmol/m^3 cm/s",
-      "vertical_grid": "none"
-   },
-   "graze_((zooplankton_sname))_zoo_zint_100m": {
-      "frequency": "never",
-      "longname": "((zooplankton_lname)) Grazing to ZOO Vertical Integral, 0-100m",
-      "operator": "average",
-      "units": "mmol/m^3 cm/s",
-      "vertical_grid": "none"
-   },
    "graze_((zooplankton_sname))_zootot": {
       "frequency": "never",
       "longname": "((zooplankton_lname)) grazing loss to ZOO TOT",
@@ -2266,9 +2273,15 @@
       "vertical_grid": "layer_avg"
    },
    "pocToFloor": {
-      "frequency": "never",
+      "frequency": [
+         "medium",
+         "high"
+      ],
       "longname": "POC Flux Hitting Sea Floor",
-      "operator": "average",
+      "operator": [
+         "average",
+         "average"
+      ],
       "units": "nmol/cm^2/s",
       "vertical_grid": "none"
    },