Merge branch 'let_GCM_specify_tracer_modules' into development

MARBL_tools/MARBL_generate_diagnostics_file.py

@@ -158,7 +158,11 @@ def _parse_args(marbl_root):
 
     from MARBL_tools import MARBL_settings_class
     from MARBL_tools import MARBL_diagnostics_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,
+                                           grid=args.grid,
+                                           input_file=args.settings_file_in,
+                                           unit_system=args.unit_system)
     MARBL_diagnostics = MARBL_diagnostics_class(args.default_diagnostics_file, DefaultSettings, args.unit_system)
 
     # Write the diagnostic file

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 flag to turn off the base biotic tracers
+    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 flag to turn on the abiotic DIC tracers
+    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)

MARBL_tools/MARBL_settings_file_class.py

@@ -13,16 +13,24 @@ 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', exclude_dict={}):
         """ 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.
         """
 
         logger = logging.getLogger(__name__)
 
+        # Check argument types
+        if not (type(base_bio_on) == bool and type(abio_dic_on == bool)):
+          raise ValueError("base_bio_on and abio_dic_on must be type bool")
+
         # 1. List of configuration keywords to match in JSON if default_default is a dictionary
         self._config_keyword = []
+        self._config_keyword.append(f'BASE_BIO_ON == {str(base_bio_on).upper()}')
+        self._config_keyword.append(f'ABIO_DIC_ON == {str(abio_dic_on).upper()}')
         if grid != None:
             self._config_keyword.append('GRID == "%s"' % grid)
         self._config_keyword.append('SAVED_STATE_VARS_SOURCE == "%s"' % saved_state_vars_source)
@@ -38,7 +46,7 @@ def __init__(self, default_settings_file, saved_state_vars_source="settings_file
             MARBL_tools.abort(1)
 
         # 4. Read settings input file
-        self._input_dict = _parse_input_file(input_file)
+        self._input_dict = _parse_input_file(input_file, exclude_dict)
 
         # 5. Use an ordered dictionary for keeping variable, value pairs
         #    Also, tracer information is in its own dictionary (initialized to None)
@@ -602,7 +610,7 @@ def _string_to_substring(str_in, separator):
 
 ################################################################################
 
-def _parse_input_file(input_file):
+def _parse_input_file(input_file, exclude_dict):
     """ 1. Read an input file; ignore blank lines and non-quoted Fortran comments.
         2. Turn lines of the form
               variable = value
@@ -625,6 +633,9 @@ def _parse_input_file(input_file):
             line_list = line_loc.strip().split('=')
             # keys in input_dict are all lowercase to allow case-insensitive match
             var_name = line_list[0].strip().lower()
+            if var_name in exclude_dict:
+                logger.error(exclude_dict[var_name])
+                MARBL_tools.abort(1)
             value = line_list[1].strip()
             val_array = _string_to_substring(value, ',')
             if len(val_array) > 1:
@@ -639,7 +650,7 @@ def _parse_input_file(input_file):
     except TypeError:
         # If inputfile == None then the open will result in TypeError
         pass
-    except:
+    except FileNotFoundError:
         logger.error("input_file '%s' was not found" % input_file)
         MARBL_tools.abort(1)
     return input_dict

MARBL_tools/netcdf_metadata_check.py

@@ -110,9 +110,9 @@ def _parse_args():
     ds = xr.open_dataset(args.netcdf_file)
     DefaultSettings = MARBL_settings_class(args.default_settings_file,
                                            "settings_file",
-                                           None,
-                                           args.settings_file_in,
-                                           args.unit_system
+                                           grid=None,
+                                           input_file=args.settings_file_in,
+                                           unit_system=args.unit_system
                                           )
     MARBL_diagnostics = MARBL_diagnostics_class(args.default_diagnostics_file,
                                                 DefaultSettings,

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": {
+            "ABIO_DIC_ON == TRUE": ".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": {
+            "BASE_BIO_ON == FALSE": ".false.",
+            "default": ".true."
+         },
          "longname": "Control whether the base ecosystem tracer module is active",
          "subcategory": "1. tracer modules",
          "units": "unitless"

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": {
+            "ABIO_DIC_ON == TRUE": ".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": {
+            "BASE_BIO_ON == FALSE": ".false.",
+            "default": ".true."
+         },
          "longname": "Control whether the base ecosystem tracer module is active",
          "subcategory": "1. tracer modules",
          "units": "unitless"

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": {
+            "ABIO_DIC_ON == TRUE": ".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": {
+            "BASE_BIO_ON == FALSE": ".false.",
+            "default": ".true."
+         },
          "longname": "Control whether the base ecosystem tracer module is active",
          "subcategory": "1. tracer modules",
          "units": "unitless"

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": {
+            "ABIO_DIC_ON == TRUE": ".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": {
+            "BASE_BIO_ON == FALSE": ".false.",
+            "default": ".true."
+         },
          "longname": "Control whether the base ecosystem tracer module is active",
          "subcategory": "1. tracer modules",
          "units": "unitless"

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": {
+            "ABIO_DIC_ON == TRUE": ".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": {
+            "BASE_BIO_ON == FALSE": ".false.",
+            "default": ".true."
+         },
          "longname": "Control whether the base ecosystem tracer module is active",
          "subcategory": "1. tracer modules",
          "units": "unitless"

defaults/json/settings_latest.json

@@ -1528,15 +1528,21 @@
       "abio_dic_on": {
          "_append_to_config_keywords": true,
          "datatype": "logical",
-         "default_value": ".false.",
+         "default_value": {
+            "ABIO_DIC_ON == TRUE": ".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": {
+            "BASE_BIO_ON == FALSE": ".false.",
+            "default": ".true."
+         },
          "longname": "Control whether the base ecosystem tracer module is active",
          "subcategory": "1. tracer modules",
          "units": "unitless"

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.
+         BASE_BIO_ON == FALSE : .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.
+         ABIO_DIC_ON == TRUE : .true.
       _append_to_config_keywords : true
    ciso_on :
       longname : Control whether CISO tracer module is active

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.
+         BASE_BIO_ON == FALSE : .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.
+         ABIO_DIC_ON == TRUE : .true.
       _append_to_config_keywords : true
    ciso_on :
       longname : Control whether CISO tracer module is active

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.
+         BASE_BIO_ON == FALSE : .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.
+         ABIO_DIC_ON == TRUE : .true.
       _append_to_config_keywords : true
    ciso_on :
       longname : Control whether CISO tracer module is active

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.
+         BASE_BIO_ON == FALSE : .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.
+         ABIO_DIC_ON == TRUE : .true.
       _append_to_config_keywords : true
    ciso_on :
       longname : Control whether CISO tracer module is active

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.
+         BASE_BIO_ON == FALSE : .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.
+         ABIO_DIC_ON == TRUE : .true.
       _append_to_config_keywords : true
    ciso_on :
       longname : Control whether CISO tracer module is active

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.
+         BASE_BIO_ON == FALSE : .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.
+         ABIO_DIC_ON == TRUE : .true.
       _append_to_config_keywords : true
    ciso_on :
       longname : Control whether CISO tracer module is active