Remove Qn_fixed from autotroph_settings_type

After discussion with Keith L, it looks like Qn_fixed and Qn_zoo were added to the code base so the fixed N:C configuration looked more like the fixed P:C configuration... but it isn't necessary since we want to use the same fixed N:C throughout the code (as opposed to fixed P:C, which really does vary from among the different functional types even when fixed spatially / temporally)
mnlevy1981 · May 30, 2024 · df02542 · df02542
1 parent f771fd6
commit df02542
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Showing 19 changed files with 100 additions and 224 deletions.
diff --git a/defaults/json/settings_cesm2.0.json b/defaults/json/settings_cesm2.0.json
@@ -73,6 +73,7 @@
                   "((autotroph_sname)) == \"sp\"": 0.4,
                   "default": "1e34"
                },
+               "dependencies": "lvariable_NtoC",
                "longname": "N threshold in uptake ratio computations",
                "subcategory": "10. autotrophs",
                "units": "unitless"
@@ -107,22 +108,11 @@
                   "((autotroph_sname)) == \"sp\"": 0.8,
                   "default": "1e34"
                },
+               "dependencies": "lvariable_PtoC",
                "longname": "PO4 threshold in uptake ratio computations",
                "subcategory": "10. autotrophs",
                "units": "unitless"
             },
-            "Qn_fixed": {
-               "datatype": "real",
-               "default_value": {
-                  "((autotroph_sname)) == \"diat\"": "16.0/117",
-                  "((autotroph_sname)) == \"diaz\"": "0.32*(16.0/117)",
-                  "((autotroph_sname)) == \"sp\"": "16.0/117",
-                  "default": "1e34"
-               },
-               "longname": "N/C ratio when using fixed N/C ratios",
-               "subcategory": "10. autotrophs",
-               "units": "unitless"
-            },
             "Qp_fixed": {
                "datatype": "real",
                "default_value": {
@@ -1261,6 +1251,7 @@
          "units": "unitless"
       },
       "lvariable_NtoC": {
+         "_append_to_config_keywords": true,
          "datatype": "logical",
          "default_value": ".false.",
          "dependencies": "base_bio_on",

diff --git a/defaults/json/settings_cesm2.1+cocco.json b/defaults/json/settings_cesm2.1+cocco.json
@@ -76,6 +76,7 @@
                   "((autotroph_sname)) == \"sp\"": 0.4,
                   "default": "1e34"
                },
+               "dependencies": "lvariable_NtoC",
                "longname": "N threshold in uptake ratio computations",
                "subcategory": "10. autotrophs",
                "units": "unitless"
@@ -112,22 +113,11 @@
                   "((autotroph_sname)) == \"sp\"": 0.8,
                   "default": "1e34"
                },
+               "dependencies": "lvariable_PtoC",
                "longname": "PO4 threshold in uptake ratio computations",
                "subcategory": "10. autotrophs",
                "units": "unitless"
             },
-            "Qn_fixed": {
-               "datatype": "real",
-               "default_value": {
-                  "((autotroph_sname)) == \"diat\"": "16.0/117",
-                  "((autotroph_sname)) == \"diaz\"": "0.32*(16.0/117)",
-                  "((autotroph_sname)) == \"sp\"": "16.0/117",
-                  "default": "1e34"
-               },
-               "longname": "N/C ratio when using fixed N/C ratios",
-               "subcategory": "10. autotrophs",
-               "units": "unitless"
-            },
             "Qp_fixed": {
                "datatype": "real",
                "default_value": {
@@ -238,6 +228,7 @@
                   "((autotroph_sname)) == \"sp\"": 0.011,
                   "default": "1e34"
                },
+               "dependencies": "lvariable_PtoC",
                "longname": "Initial P/C ratio for growth",
                "subcategory": "10. autotrophs",
                "units": "unitless"
@@ -251,6 +242,7 @@
                   "((autotroph_sname)) == \"sp\"": 0.0075,
                   "default": "1e34"
                },
+               "dependencies": "lvariable_PtoC",
                "longname": "Minimum P/C ratio for growth",
                "subcategory": "10. autotrophs",
                "units": "unitless"
@@ -1309,6 +1301,7 @@
          "units": "unitless"
       },
       "lvariable_NtoC": {
+         "_append_to_config_keywords": true,
          "datatype": "logical",
          "default_value": ".false.",
          "dependencies": "base_bio_on",

diff --git a/defaults/json/settings_cesm2.1.json b/defaults/json/settings_cesm2.1.json
@@ -73,6 +73,7 @@
                   "((autotroph_sname)) == \"sp\"": 0.4,
                   "default": "1e34"
                },
+               "dependencies": "lvariable_NtoC",
                "longname": "N threshold in uptake ratio computations",
                "subcategory": "10. autotrophs",
                "units": "unitless"
@@ -107,22 +108,11 @@
                   "((autotroph_sname)) == \"sp\"": 0.8,
                   "default": "1e34"
                },
+               "dependencies": "lvariable_PtoC",
                "longname": "PO4 threshold in uptake ratio computations",
                "subcategory": "10. autotrophs",
                "units": "unitless"
             },
-            "Qn_fixed": {
-               "datatype": "real",
-               "default_value": {
-                  "((autotroph_sname)) == \"diat\"": "16.0/117",
-                  "((autotroph_sname)) == \"diaz\"": "0.32*(16.0/117)",
-                  "((autotroph_sname)) == \"sp\"": "16.0/117",
-                  "default": "1e34"
-               },
-               "longname": "N/C ratio when using fixed N/C ratios",
-               "subcategory": "10. autotrophs",
-               "units": "unitless"
-            },
             "Qp_fixed": {
                "datatype": "real",
                "default_value": {
@@ -1264,6 +1254,7 @@
          "units": "unitless"
       },
       "lvariable_NtoC": {
+         "_append_to_config_keywords": true,
          "datatype": "logical",
          "default_value": ".false.",
          "dependencies": "base_bio_on",

diff --git a/defaults/json/settings_latest+4p2z.json b/defaults/json/settings_latest+4p2z.json
@@ -76,6 +76,7 @@
                   "((autotroph_sname)) == \"sp\"": 0.4,
                   "default": "1e34"
                },
+               "dependencies": "lvariable_NtoC",
                "longname": "N threshold in uptake ratio computations",
                "subcategory": "10. autotrophs",
                "units": "unitless"
@@ -112,23 +113,11 @@
                   "((autotroph_sname)) == \"sp\"": 0.8,
                   "default": "1e34"
                },
+               "dependencies": "lvariable_PtoC",
                "longname": "PO4 threshold in uptake ratio computations",
                "subcategory": "10. autotrophs",
                "units": "unitless"
             },
-            "Qn_fixed": {
-               "datatype": "real",
-               "default_value": {
-                  "((autotroph_sname)) == \"cocco\"": "16.0/117",
-                  "((autotroph_sname)) == \"diat\"": "16.0/117",
-                  "((autotroph_sname)) == \"diaz\"": "0.32*(16.0/117)",
-                  "((autotroph_sname)) == \"sp\"": "16.0/117",
-                  "default": "1e34"
-               },
-               "longname": "N/C ratio when using fixed N/C ratios",
-               "subcategory": "10. autotrophs",
-               "units": "unitless"
-            },
             "Qp_fixed": {
                "datatype": "real",
                "default_value": {
@@ -240,6 +229,7 @@
                   "((autotroph_sname)) == \"sp\"": 0.17,
                   "default": "1e34"
                },
+               "dependencies": "lvariable_NtoC",
                "longname": "Initial N/C ratio for growth",
                "subcategory": "10. autotrophs",
                "units": "unitless"
@@ -253,6 +243,7 @@
                   "((autotroph_sname)) == \"sp\"": 0.11,
                   "default": "1e34"
                },
+               "dependencies": "lvariable_NtoC",
                "longname": "Minimum N/C ratio for growth",
                "subcategory": "10. autotrophs",
                "units": "unitless"
@@ -266,6 +257,7 @@
                   "((autotroph_sname)) == \"sp\"": 0.011,
                   "default": "1e34"
                },
+               "dependencies": "lvariable_PtoC",
                "longname": "Initial P/C ratio for growth",
                "subcategory": "10. autotrophs",
                "units": "unitless"
@@ -279,6 +271,7 @@
                   "((autotroph_sname)) == \"sp\"": 0.0075,
                   "default": "1e34"
                },
+               "dependencies": "lvariable_PtoC",
                "longname": "Minimum P/C ratio for growth",
                "subcategory": "10. autotrophs",
                "units": "unitless"
@@ -1398,6 +1391,7 @@
          "units": "unitless"
       },
       "lvariable_NtoC": {
+         "_append_to_config_keywords": true,
          "datatype": "logical",
          "default_value": ".true.",
          "dependencies": "base_bio_on",
@@ -1406,6 +1400,7 @@
          "units": "unitless"
       },
       "lvariable_PtoC": {
+         "_append_to_config_keywords": true,
          "datatype": "logical",
          "default_value": ".true.",
          "dependencies": "base_bio_on",

diff --git a/defaults/json/settings_latest+cocco.json b/defaults/json/settings_latest+cocco.json
@@ -76,6 +76,7 @@
                   "((autotroph_sname)) == \"sp\"": 0.4,
                   "default": "1e34"
                },
+               "dependencies": "lvariable_NtoC",
                "longname": "N threshold in uptake ratio computations",
                "subcategory": "10. autotrophs",
                "units": "unitless"
@@ -112,23 +113,11 @@
                   "((autotroph_sname)) == \"sp\"": 0.8,
                   "default": "1e34"
                },
+               "dependencies": "lvariable_PtoC",
                "longname": "PO4 threshold in uptake ratio computations",
                "subcategory": "10. autotrophs",
                "units": "unitless"
             },
-            "Qn_fixed": {
-               "datatype": "real",
-               "default_value": {
-                  "((autotroph_sname)) == \"cocco\"": "16.0/117",
-                  "((autotroph_sname)) == \"diat\"": "16.0/117",
-                  "((autotroph_sname)) == \"diaz\"": "0.32*(16.0/117)",
-                  "((autotroph_sname)) == \"sp\"": "16.0/117",
-                  "default": "1e34"
-               },
-               "longname": "N/C ratio when using fixed N/C ratios",
-               "subcategory": "10. autotrophs",
-               "units": "unitless"
-            },
             "Qp_fixed": {
                "datatype": "real",
                "default_value": {
@@ -240,6 +229,7 @@
                   "((autotroph_sname)) == \"sp\"": 0.17,
                   "default": "1e34"
                },
+               "dependencies": "lvariable_NtoC",
                "longname": "Initial N/C ratio for growth",
                "subcategory": "10. autotrophs",
                "units": "unitless"
@@ -253,6 +243,7 @@
                   "((autotroph_sname)) == \"sp\"": 0.11,
                   "default": "1e34"
                },
+               "dependencies": "lvariable_NtoC",
                "longname": "Minimum N/C ratio for growth",
                "subcategory": "10. autotrophs",
                "units": "unitless"
@@ -266,6 +257,7 @@
                   "((autotroph_sname)) == \"sp\"": 0.011,
                   "default": "1e34"
                },
+               "dependencies": "lvariable_PtoC",
                "longname": "Initial P/C ratio for growth",
                "subcategory": "10. autotrophs",
                "units": "unitless"
@@ -279,6 +271,7 @@
                   "((autotroph_sname)) == \"sp\"": 0.0075,
                   "default": "1e34"
                },
+               "dependencies": "lvariable_PtoC",
                "longname": "Minimum P/C ratio for growth",
                "subcategory": "10. autotrophs",
                "units": "unitless"
@@ -1345,6 +1338,7 @@
          "units": "unitless"
       },
       "lvariable_NtoC": {
+         "_append_to_config_keywords": true,
          "datatype": "logical",
          "default_value": ".true.",
          "dependencies": "base_bio_on",
@@ -1353,6 +1347,7 @@
          "units": "unitless"
       },
       "lvariable_PtoC": {
+         "_append_to_config_keywords": true,
          "datatype": "logical",
          "default_value": ".true.",
          "dependencies": "base_bio_on",

diff --git a/defaults/json/settings_latest.json b/defaults/json/settings_latest.json
@@ -76,6 +76,7 @@
                   "((autotroph_sname)) == \"sp\"": 0.4,
                   "default": "1e34"
                },
+               "dependencies": "lvariable_NtoC",
                "longname": "N threshold in uptake ratio computations",
                "subcategory": "10. autotrophs",
                "units": "unitless"
@@ -110,22 +111,11 @@
                   "((autotroph_sname)) == \"sp\"": 0.8,
                   "default": "1e34"
                },
+               "dependencies": "lvariable_PtoC",
                "longname": "PO4 threshold in uptake ratio computations",
                "subcategory": "10. autotrophs",
                "units": "unitless"
             },
-            "Qn_fixed": {
-               "datatype": "real",
-               "default_value": {
-                  "((autotroph_sname)) == \"diat\"": "16.0/117",
-                  "((autotroph_sname)) == \"diaz\"": "0.32*(16.0/117)",
-                  "((autotroph_sname)) == \"sp\"": "16.0/117",
-                  "default": "1e34"
-               },
-               "longname": "N/C ratio when using fixed N/C ratios",
-               "subcategory": "10. autotrophs",
-               "units": "unitless"
-            },
             "Qp_fixed": {
                "datatype": "real",
                "default_value": {

diff --git a/defaults/settings_cesm2.0.yaml b/defaults/settings_cesm2.0.yaml
@@ -363,6 +363,7 @@ general_parms :
       units : unitless
       datatype : logical
       default_value : .false.
+      _append_to_config_keywords : true
    ladjust_bury_coeff :
       dependencies : base_bio_on
       longname : Control if bury coefficients are adjusted (rather than constant)
@@ -985,16 +986,6 @@ PFT_derived_types :
                ((autotroph_sname)) == "sp" : 1.0/117
                ((autotroph_sname)) == "diat" : 1.0/117
                ((autotroph_sname)) == "diaz" : 0.32*(1.0/117)
-         Qn_fixed :
-            longname : N/C ratio when using fixed N/C ratios
-            subcategory : 10. autotrophs
-            units : unitless
-            datatype : real
-            default_value :
-               default : 1e34
-               ((autotroph_sname)) == "sp" : 16.0/117
-               ((autotroph_sname)) == "diat" : 16.0/117
-               ((autotroph_sname)) == "diaz" : 0.32*(16.0/117)
          SiOpt :
             longname : Si threshold in uptake ratio computations
             subcategory : 10. autotrophs
@@ -1058,6 +1049,7 @@ PFT_derived_types :
                ((autotroph_sname)) == "diat" : 8.3e-3
                ((autotroph_sname)) == "diaz" : 3.7e-3
          POpt :
+            dependencies : lvariable_PtoC
             longname : PO4 threshold in uptake ratio computations
             subcategory : 10. autotrophs
             units : unitless
@@ -1068,6 +1060,7 @@ PFT_derived_types :
                ((autotroph_sname)) == "diat" : 0.8
                ((autotroph_sname)) == "diaz" : 0.8
          NOpt :
+            dependencies : lvariable_NtoC
             longname : N threshold in uptake ratio computations
             subcategory : 10. autotrophs
             units : unitless