generate_settings_file sets tracer module logicals

Command line arguments for MARBL_generate_settings_file determine value of base_bio_on and abio_dic_on: by default, base_bio_on=T but running --exclude-base-bio sets it to F. Similarly, abio_dic_on=F but running --include-abio-dic sets it to T.
mnlevy1981 · Mar 1, 2024 · 584ca67 · 584ca67
1 parent d5862c6
commit 584ca67
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Showing 14 changed files with 106 additions and 26 deletions.
diff --git a/MARBL_tools/MARBL_generate_settings_file.py b/MARBL_tools/MARBL_generate_settings_file.py
@@ -81,6 +81,14 @@ def _parse_args(marbl_root):
                         default='settings_file', choices = set(('settings_file', 'GCM')),
                         help="Source of initial value for saved state vars that can come from GCM or settings file")
 
+    # Command line argument to specify resolution (default is None)
+    parser.add_argument('--disable-base-bio', action='store_false', dest='base_bio_on',
+                        help='Turn off base biotic tracer module (default is on)')
+
+    # Command line argument to specify resolution (default is None)
+    parser.add_argument('--enable-abio-dic', action='store_true', dest='abio_dic_on',
+                        help='Turn on abiotic DIC tracer module (default is off)')
+
     # Command line argument to specify resolution (default is None)
     parser.add_argument('-g', '--grid', action='store', dest='grid',
                         help='Some default values are grid-dependent')
@@ -115,7 +123,13 @@ def _parse_args(marbl_root):
     logging.basicConfig(format='%(levelname)s (%(funcName)s): %(message)s', level=logging.DEBUG)
 
     from MARBL_tools import MARBL_settings_class
-    DefaultSettings = MARBL_settings_class(args.default_settings_file, args.saved_state_vars_source, args.grid, args.settings_file_in, args.unit_system)
+    DefaultSettings = MARBL_settings_class(args.default_settings_file,
+                                           args.saved_state_vars_source,
+                                           args.base_bio_on,
+                                           args.abio_dic_on,
+                                           args.grid,
+                                           args.settings_file_in,
+                                           args.unit_system)
 
     # Write the settings file
     generate_settings_file(DefaultSettings, args.settings_file_out)
diff --git a/MARBL_tools/MARBL_settings_file_class.py b/MARBL_tools/MARBL_settings_file_class.py
@@ -13,7 +13,9 @@ class MARBL_settings_class(object):
     # CONSTRUCTOR #
     ###############
 
-    def __init__(self, default_settings_file, saved_state_vars_source="settings_file", grid=None, input_file=None, unit_system='cgs'):
+    def __init__(self, default_settings_file, saved_state_vars_source="settings_file",
+                 base_bio_on=True, abio_dic_on=False, grid=None, input_file=None,
+                 unit_system='cgs'):
         """ Class constructor: set up a dictionary of config keywords for when multiple
             default values are provided, read the JSON file, and then populate
             self.settings_dict and self.tracers_dict.
@@ -23,6 +25,10 @@ def __init__(self, default_settings_file, saved_state_vars_source="settings_file
 
         # 1. List of configuration keywords to match in JSON if default_default is a dictionary
         self._config_keyword = []
+        if not base_bio_on:
+            self._config_keyword.append('EXCLUDE_BASE_BIO')
+        if abio_dic_on:
+            self._config_keyword.append('INCLUDE_ABIO_DIC')
         if grid != None:
             self._config_keyword.append('GRID == "%s"' % grid)
         self._config_keyword.append('SAVED_STATE_VARS_SOURCE == "%s"' % saved_state_vars_source)

diff --git a/defaults/json/settings_cesm2.0.json b/defaults/json/settings_cesm2.0.json
@@ -1519,15 +1519,21 @@
       "abio_dic_on": {
          "_append_to_config_keywords": true,
          "datatype": "logical",
-         "default_value": ".false.",
+         "default_value": {
+            "INCLUDE_ABIO_DIC": ".true.",
+            "default": ".false."
+         },
          "longname": "Control whether abiotic carbon tracer module is active",
          "subcategory": "1. tracer modules",
          "units": "unitless"
       },
       "base_bio_on": {
          "_append_to_config_keywords": true,
          "datatype": "logical",
-         "default_value": ".true.",
+         "default_value": {
+            "EXCLUDE_BASE_BIO": ".false.",
+            "default": ".true."
+         },
          "longname": "Control whether the base ecosystem tracer module is active",
          "subcategory": "1. tracer modules",
          "units": "unitless"

diff --git a/defaults/json/settings_cesm2.1+cocco.json b/defaults/json/settings_cesm2.1+cocco.json
@@ -1564,15 +1564,21 @@
       "abio_dic_on": {
          "_append_to_config_keywords": true,
          "datatype": "logical",
-         "default_value": ".false.",
+         "default_value": {
+            "INCLUDE_ABIO_DIC": ".true.",
+            "default": ".false."
+         },
          "longname": "Control whether abiotic carbon tracer module is active",
          "subcategory": "1. tracer modules",
          "units": "unitless"
       },
       "base_bio_on": {
          "_append_to_config_keywords": true,
          "datatype": "logical",
-         "default_value": ".true.",
+         "default_value": {
+            "EXCLUDE_BASE_BIO": ".false.",
+            "default": ".true."
+         },
          "longname": "Control whether the base ecosystem tracer module is active",
          "subcategory": "1. tracer modules",
          "units": "unitless"

diff --git a/defaults/json/settings_cesm2.1.json b/defaults/json/settings_cesm2.1.json
@@ -1522,15 +1522,21 @@
       "abio_dic_on": {
          "_append_to_config_keywords": true,
          "datatype": "logical",
-         "default_value": ".false.",
+         "default_value": {
+            "INCLUDE_ABIO_DIC": ".true.",
+            "default": ".false."
+         },
          "longname": "Control whether abiotic carbon tracer module is active",
          "subcategory": "1. tracer modules",
          "units": "unitless"
       },
       "base_bio_on": {
          "_append_to_config_keywords": true,
          "datatype": "logical",
-         "default_value": ".true.",
+         "default_value": {
+            "EXCLUDE_BASE_BIO": ".false.",
+            "default": ".true."
+         },
          "longname": "Control whether the base ecosystem tracer module is active",
          "subcategory": "1. tracer modules",
          "units": "unitless"

diff --git a/defaults/json/settings_latest+4p2z.json b/defaults/json/settings_latest+4p2z.json
@@ -1617,15 +1617,21 @@
       "abio_dic_on": {
          "_append_to_config_keywords": true,
          "datatype": "logical",
-         "default_value": ".false.",
+         "default_value": {
+            "INCLUDE_ABIO_DIC": ".true.",
+            "default": ".false."
+         },
          "longname": "Control whether abiotic carbon tracer module is active",
          "subcategory": "1. tracer modules",
          "units": "unitless"
       },
       "base_bio_on": {
          "_append_to_config_keywords": true,
          "datatype": "logical",
-         "default_value": ".true.",
+         "default_value": {
+            "EXCLUDE_BASE_BIO": ".false.",
+            "default": ".true."
+         },
          "longname": "Control whether the base ecosystem tracer module is active",
          "subcategory": "1. tracer modules",
          "units": "unitless"

diff --git a/defaults/json/settings_latest+cocco.json b/defaults/json/settings_latest+cocco.json
@@ -1564,15 +1564,21 @@
       "abio_dic_on": {
          "_append_to_config_keywords": true,
          "datatype": "logical",
-         "default_value": ".false.",
+         "default_value": {
+            "INCLUDE_ABIO_DIC": ".true.",
+            "default": ".false."
+         },
          "longname": "Control whether abiotic carbon tracer module is active",
          "subcategory": "1. tracer modules",
          "units": "unitless"
       },
       "base_bio_on": {
          "_append_to_config_keywords": true,
          "datatype": "logical",
-         "default_value": ".true.",
+         "default_value": {
+            "EXCLUDE_BASE_BIO": ".false.",
+            "default": ".true."
+         },
          "longname": "Control whether the base ecosystem tracer module is active",
          "subcategory": "1. tracer modules",
          "units": "unitless"

diff --git a/defaults/json/settings_latest.json b/defaults/json/settings_latest.json
@@ -1528,15 +1528,21 @@
       "abio_dic_on": {
          "_append_to_config_keywords": true,
          "datatype": "logical",
-         "default_value": ".false.",
+         "default_value": {
+            "INCLUDE_ABIO_DIC": ".true.",
+            "default": ".false."
+         },
          "longname": "Control whether abiotic carbon tracer module is active",
          "subcategory": "1. tracer modules",
          "units": "unitless"
       },
       "base_bio_on": {
          "_append_to_config_keywords": true,
          "datatype": "logical",
-         "default_value": ".true.",
+         "default_value": {
+            "EXCLUDE_BASE_BIO": ".false.",
+            "default": ".true."
+         },
          "longname": "Control whether the base ecosystem tracer module is active",
          "subcategory": "1. tracer modules",
          "units": "unitless"

diff --git a/defaults/settings_cesm2.0.yaml b/defaults/settings_cesm2.0.yaml
@@ -255,14 +255,18 @@ tracer_modules :
       subcategory : 1. tracer modules
       units : unitless
       datatype : logical
-      default_value : .true.
+      default_value :
+         default : .true.
+         EXCLUDE_BASE_BIO : .false.
       _append_to_config_keywords : true
    abio_dic_on :
       longname : Control whether abiotic carbon tracer module is active
       subcategory : 1. tracer modules
       units : unitless
       datatype : logical
-      default_value : .false.
+      default_value :
+         default : .false.
+         INCLUDE_ABIO_DIC : .true.
       _append_to_config_keywords : true
    ciso_on :
       longname : Control whether CISO tracer module is active

diff --git a/defaults/settings_cesm2.1+cocco.yaml b/defaults/settings_cesm2.1+cocco.yaml
@@ -255,14 +255,18 @@ tracer_modules :
       subcategory : 1. tracer modules
       units : unitless
       datatype : logical
-      default_value : .true.
+      default_value :
+         default : .true.
+         EXCLUDE_BASE_BIO : .false.
       _append_to_config_keywords : true
    abio_dic_on :
       longname : Control whether abiotic carbon tracer module is active
       subcategory : 1. tracer modules
       units : unitless
       datatype : logical
-      default_value : .false.
+      default_value :
+         default : .false.
+         INCLUDE_ABIO_DIC : .true.
       _append_to_config_keywords : true
    ciso_on :
       longname : Control whether CISO tracer module is active

diff --git a/defaults/settings_cesm2.1.yaml b/defaults/settings_cesm2.1.yaml
@@ -255,14 +255,18 @@ tracer_modules :
       subcategory : 1. tracer modules
       units : unitless
       datatype : logical
-      default_value : .true.
+      default_value :
+         default : .true.
+         EXCLUDE_BASE_BIO : .false.
       _append_to_config_keywords : true
    abio_dic_on :
       longname : Control whether abiotic carbon tracer module is active
       subcategory : 1. tracer modules
       units : unitless
       datatype : logical
-      default_value : .false.
+      default_value :
+         default : .false.
+         INCLUDE_ABIO_DIC : .true.
       _append_to_config_keywords : true
    ciso_on :
       longname : Control whether CISO tracer module is active

diff --git a/defaults/settings_latest+4p2z.yaml b/defaults/settings_latest+4p2z.yaml
@@ -266,14 +266,18 @@ tracer_modules :
       subcategory : 1. tracer modules
       units : unitless
       datatype : logical
-      default_value : .true.
+      default_value :
+         default : .true.
+         EXCLUDE_BASE_BIO : .false.
       _append_to_config_keywords : true
    abio_dic_on :
       longname : Control whether abiotic carbon tracer module is active
       subcategory : 1. tracer modules
       units : unitless
       datatype : logical
-      default_value : .false.
+      default_value :
+         default : .false.
+         INCLUDE_ABIO_DIC : .true.
       _append_to_config_keywords : true
    ciso_on :
       longname : Control whether CISO tracer module is active

diff --git a/defaults/settings_latest+cocco.yaml b/defaults/settings_latest+cocco.yaml
@@ -255,14 +255,18 @@ tracer_modules :
       subcategory : 1. tracer modules
       units : unitless
       datatype : logical
-      default_value : .true.
+      default_value :
+         default : .true.
+         EXCLUDE_BASE_BIO : .false.
       _append_to_config_keywords : true
    abio_dic_on :
       longname : Control whether abiotic carbon tracer module is active
       subcategory : 1. tracer modules
       units : unitless
       datatype : logical
-      default_value : .false.
+      default_value :
+         default : .false.
+         INCLUDE_ABIO_DIC : .true.
       _append_to_config_keywords : true
    ciso_on :
       longname : Control whether CISO tracer module is active

diff --git a/defaults/settings_latest.yaml b/defaults/settings_latest.yaml
@@ -255,14 +255,18 @@ tracer_modules :
       subcategory : 1. tracer modules
       units : unitless
       datatype : logical
-      default_value : .true.
+      default_value :
+         default : .true.
+         EXCLUDE_BASE_BIO : .false.
       _append_to_config_keywords : true
    abio_dic_on :
       longname : Control whether abiotic carbon tracer module is active
       subcategory : 1. tracer modules
       units : unitless
       datatype : logical
-      default_value : .false.
+      default_value :
+         default : .false.
+         INCLUDE_ABIO_DIC : .true.
       _append_to_config_keywords : true
    ciso_on :
       longname : Control whether CISO tracer module is active