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