Merge branch 'development' into fe_updates_from_uci

.github/workflows/run_test_suite.yml

@@ -7,13 +7,13 @@ jobs:
     strategy:
         matrix:
             python-version:
-                - 3.7
+                - 3.9
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - name: Setup Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
 

MARBL_tools/MARBL_diagnostics_file_class.py

@@ -15,7 +15,7 @@ class MARBL_diagnostics_class(object):
     # CONSTRUCTOR #
     ###############
 
-    def __init__(self, default_diagnostics_file, MARBL_settings):
+    def __init__(self, default_diagnostics_file, MARBL_settings, unit_system):
         """ Class constructor: read the JSON file and then construct self.diagnostics_dict
         """
 
@@ -44,7 +44,7 @@ def __init__(self, default_diagnostics_file, MARBL_settings):
                 self.diagnostics_dict[diag_name] = dict(self._diagnostics[diag_name])
             else:
                 # (Also determine correct frequency if 'frequency' is a dict)
-                self.diagnostics_dict.update(MARBL_tools.expand_template_value(diag_name, MARBL_settings, self._diagnostics[diag_name], check_freq=True))
+                self.diagnostics_dict.update(MARBL_tools.expand_template_value(diag_name, MARBL_settings, unit_system, self._diagnostics[diag_name], check_freq=True))
 
         #    ii. Delete diagnostics where dependencies are not met
         #        (Some diagnostics have already been removed via expand_template_value())
@@ -53,10 +53,26 @@ def __init__(self, default_diagnostics_file, MARBL_settings):
                 diags_to_delete.append(diag_name)
                 continue
 
-            #    iii. frequency and operator should always be lists
+            #    iii. frequency, operator, and diag_mode should always be lists
             if not isinstance(self.diagnostics_dict[diag_name]['frequency'], list):
                 self.diagnostics_dict[diag_name]['frequency'] = [self.diagnostics_dict[diag_name]['frequency']]
                 self.diagnostics_dict[diag_name]['operator'] = [self.diagnostics_dict[diag_name]['operator']]
+                self.diagnostics_dict[diag_name]['diag_mode'] = [self.diagnostics_dict[diag_name]['diag_mode']]
+
+            #    iv. update units
+            fix_units = {}
+            if unit_system == 'cgs':
+                fix_units["mmol/m^3 cm"] = "nmol/cm^2"
+                fix_units["mmol/m^3"] = "nmol/cm^3"
+                fix_units["meq/m^3"] = "neq/cm^3"
+            else:
+                fix_units["mmol/m^3 cm"] = "mmol/m^2"
+                fix_units["nmol/cm^2"] = "mmol/m^2"
+                fix_units["g/cm"] = "kg/m"
+                fix_units["cm"] = "m"
+
+            for key, value in fix_units.items():
+                self.diagnostics_dict[diag_name]["units"] = str(self.diagnostics_dict[diag_name]["units"]).replace(key, value)
 
         for diag_name in diags_to_delete:
             del self.diagnostics_dict[diag_name]

MARBL_tools/MARBL_generate_diagnostics_file.py

@@ -40,16 +40,30 @@
                         (default: None)
   -o DIAGNOSTICS_FILE_OUT, --diagnostics_file_out DIAGNOSTICS_FILE_OUT
                         Name of file to be written (default: marbl.diags)
-
+  -u {cgs,mks}, --unit_system {cgs,mks}
+                        Unit system for parameter values (default: cgs)
+  -a, --append          Append to existing diagnostics file (default: False)
 """
 
+if __name__ == "__main__":
+    # We need marbl_root in python path so we can import MARBL_tools from generate_settings_file()
+    import argparse
+    import os
+    import sys
+    marbl_root = os.path.abspath(os.path.join(os.path.dirname(sys.argv[0]), '..'))
+    sys.path.append(marbl_root)
+    from MARBL_tools import MARBL_settings_class
+    from MARBL_tools import MARBL_diagnostics_class
+
+import logging
+from MARBL_tools.MARBL_utils import valid_diag_modes
+
 #######################################
 
-def generate_diagnostics_file(MARBL_diagnostics, diagnostics_file_out, append=False):
+def generate_diagnostics_file(MARBL_diagnostics, diagnostics_file_out, diag_mode="full", append=False):
     """ Produce a list of MARBL diagnostic frequencies and operators from a JSON parameter file
     """
 
-    import logging
     logger = logging.getLogger(__name__)
 
     if not append:
@@ -82,12 +96,18 @@ def generate_diagnostics_file(MARBL_diagnostics, diagnostics_file_out, append=Fa
     # is also a dictionary containing frequency and operator information. Note that
     # string values of frequency and operator are converted to lists of len 1 when the
     # JSON file that generates this list is processed
+    diag_mode_opts = valid_diag_modes()
+    diag_mode_in = diag_mode_opts.index(diag_mode)
     for diag_name in sorted(MARBL_diagnostics.diagnostics_dict.keys()):
         frequencies = MARBL_diagnostics.diagnostics_dict[diag_name]['frequency']
         operators = MARBL_diagnostics.diagnostics_dict[diag_name]['operator']
+        diag_modes = MARBL_diagnostics.diagnostics_dict[diag_name]['diag_mode']
         freq_op = []
-        for freq, op in zip(frequencies, operators):
-            freq_op.append(freq + '_' + op)
+        for freq, op, dm in zip(frequencies, operators, diag_modes):
+            if diag_mode_in >= diag_mode_opts.index(dm):
+                freq_op.append(freq + '_' + op)
+            elif not freq_op: # Only append "never_{op}" if freq_op is empty list
+                freq_op.append('never_' + op)
         fout.write("%s : %s\n" % (diag_name, ", ".join(freq_op)))
     fout.close()
 
@@ -97,8 +117,6 @@ def _parse_args(marbl_root):
     """ Parse command line arguments
     """
 
-    import argparse
-
     parser = argparse.ArgumentParser(description="Generate a MARBL settings file from a JSON file",
                                      formatter_class=argparse.ArgumentDefaultsHelpFormatter)
 
@@ -114,7 +132,7 @@ def _parse_args(marbl_root):
 
     # Is the GCM providing initial bury coefficients via saved state?
     parser.add_argument('-v', '--saved_state_vars_source', action='store', dest='saved_state_vars_source',
-                        default='settings_file', choices = set(('settings_file', 'GCM')),
+                        default='settings_file', choices=['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)
@@ -129,30 +147,40 @@ def _parse_args(marbl_root):
     parser.add_argument('-o', '--diagnostics_file_out', action='store', dest='diagnostics_file_out', default='marbl.diags',
                         help='Name of file to be written')
 
+    # Command line argument to where to write the settings file being generated
+    parser.add_argument('-u', '--unit_system', action='store', dest='unit_system', default='cgs',
+                        choices=['cgs', 'mks'], help='Unit system for parameter values')
+
+    # Diagnostic mode (level of output to include)
+    parser.add_argument('-m', '--diag-mode', action='store', dest='diag_mode', default='full',
+                        choices=valid_diag_modes(),
+                        help='Level of output to include')
+
     # Append to existing diagnostics file?
     parser.add_argument('-a', '--append', action='store_true', dest='append',
                         help='Append to existing diagnostics file')
+
     return parser.parse_args()
 
 #######################################
 
 if __name__ == "__main__":
-    # We need marbl_root in python path so we can import MARBL_tools from generate_settings_file()
-    import sys, os
     marbl_root = os.path.abspath(os.path.join(os.path.dirname(sys.argv[0]), '..'))
     sys.path.append(marbl_root)
 
     # Parse command-line arguments (marbl_root is used to set default for JSON file location)
     args = _parse_args(marbl_root)
 
     # Set up logging
-    import logging
     logging.basicConfig(format='%(levelname)s (%(funcName)s): %(message)s', level=logging.DEBUG)
 
-    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)
-    MARBL_diagnostics = MARBL_diagnostics_class(args.default_diagnostics_file, DefaultSettings)
+    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
-    generate_diagnostics_file(MARBL_diagnostics, args.diagnostics_file_out, args.append)
+    generate_diagnostics_file(MARBL_diagnostics, args.diagnostics_file_out, args.diag_mode, args.append)

MARBL_tools/MARBL_generate_settings_file.py

@@ -33,7 +33,8 @@
                         A file that overrides values in JSON (default: None)
   -o SETTINGS_FILE_OUT, --settings_file_out SETTINGS_FILE_OUT
                         Name of file to be written (default: marbl.settings)
-
+  -u {cgs,mks}, --unit_system {cgs,mks}
+                        Unit system for parameter values (default: cgs)
 """
 
 #######################################
@@ -44,12 +45,19 @@ def generate_settings_file(MARBL_settings, settings_file_out):
 
     fout = open(settings_file_out,"w")
     # Sort variables by subcategory
+    written_any = False
     for subcat_name in MARBL_settings.get_subcategory_names():
-        fout.write("! %s\n" % subcat_name.split('. ')[1])
+        header = "! %s\n" % subcat_name.split('. ')[1]
+        var_values = []
         for varname in MARBL_settings.get_settings_dict_variable_names(subcat_name):
-            fout.write("%s = %s\n" % (varname, MARBL_settings.settings_dict[varname]['value']))
-        if subcat_name != MARBL_settings.get_subcategory_names()[-1]:
-            fout.write("\n")
+            var_values.append("%s = %s\n" % (varname, MARBL_settings.settings_dict[varname]['value']))
+        if len(var_values) > 0:
+            if written_any:
+                fout.write("\n")
+            written_any = True
+            fout.write(header)
+            for line in var_values:
+                fout.write(line)
     fout.close()
 
 #######################################
@@ -73,6 +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')
@@ -85,6 +101,10 @@ def _parse_args(marbl_root):
     parser.add_argument('-o', '--settings_file_out', action='store', dest='settings_file_out', default='marbl.settings',
                         help='Name of file to be written')
 
+    # Command line argument to where to write the settings file being generated
+    parser.add_argument('-u', '--unit_system', action='store', dest='unit_system', default='cgs',
+                        choices=['cgs', 'mks'], help='Unit system for parameter values')
+
     return parser.parse_args()
 
 #######################################
@@ -103,7 +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)
+    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)