MARBL Support

Externals.cfg

@@ -1,8 +1,8 @@
 [mom]
-tag = dev/ncar_240510
+branch = mnlevy1981/add_MARBL
 protocol = git
 local_path = MOM6
-repo_url = https://github.com/NCAR/MOM6.git
+repo_url = https://github.com/mnlevy1981/MOM6.git
 required = True
 externals = ../Externals_MOM.cfg
 

Externals_MOM.cfg

@@ -8,5 +8,12 @@ protocol = git
 from_submodule=True
 required = True
 
+[MARBL]
+protocol = git
+tag = marbl0.47.0
+repo_url = https://github.com/marbl-ecosys/MARBL
+local_path = pkg/MARBL
+required = True
+
 [externals_description]
 schema_version = 1.0.0

cime_config/MARBL_scripts/MARBL_diagnostics.py

@@ -0,0 +1,61 @@
+""" Interface to the marbl_diagnostics_class object
+"""
+
+class MARBL_diagnostics_for_MOM(object):
+    def __init__(self, MARBL_dir, caseroot, MARBL_settings):
+
+        import sys, os
+
+        # Set up arguments for marbl_diagnostics_class constructor
+        # Note that this is a dictionary that will be used to pass named variables to class constructor
+        # Arguments to be passed are
+        # 1. default_diagnostics_file: full path to default_diagnostics.json
+        #      (can be in SourceMods, otherwise comes from MARBL)
+        # 2. MARBL_settings: a MARBL_settings_for_MOM object
+        MARBL_args = dict()
+
+        # User can put default_values.json in SourceMods, otherwise use file provided by MARBL
+        MARBL_args["default_diagnostics_file"] = os.path.join(caseroot,"SourceMods","src.mom","diagnostics_latest.json")
+        if not os.path.isfile(MARBL_args["default_diagnostics_file"]):
+            MARBL_args["default_diagnostics_file"] = os.path.join(MARBL_dir, "defaults", "json", "diagnostics_latest.json")
+
+        MARBL_args["MARBL_settings"] = MARBL_settings._MARBL_settings
+
+        # MARBL can run in mks unit system instead of requiring MOM to convert to / from cgs
+        MARBL_args["unit_system"] = "mks"
+
+        # Import MARBL_diagnostics_file_class, which may come from MARBL_tools or SourceMods/src.mom
+        # (i) need MARBL_dir in path for both branches of this if statement because even if
+        #     MARBL_diagnostics_file_class.py is in SourceMods, it needs to import MARBL_tools itself
+        sys.path.append(MARBL_dir)
+        # (ii) Here's where we import from either MARBL_tools or SourceMods
+        diagnostics_class_dir = os.path.join(caseroot, "SourceMods", "src.mom")
+        if not os.path.isfile(os.path.join(diagnostics_class_dir, "MARBL_diagnostics_file_class.py")):
+            from MARBL_tools import MARBL_diagnostics_file_class
+        else:
+            import imp
+            import logging
+            logger = logging.getLogger(__name__)
+            logging.info('Importing MARBL_diagnostics_file_class.py from %s' % diagnostics_class_dir)
+            diagnostics_class_module = diagnostics_class_dir+'/MARBL_diagnostics_file_class.py'
+            if os.path.isfile(diagnostics_class_module):
+                MARBL_diagnostics_file_class = imp.load_source('MARBL_diagnostics_file_class', diagnostics_class_module)
+            else:
+                logger.error('Can not find %s' % diagnostics_class_module)
+                sys.exit(1)
+
+        # Generate diagnostics object
+        self.MARBL_diagnostic_dict = MARBL_diagnostics_file_class.MARBL_diagnostics_class(**MARBL_args)
+
+    ################################################################################
+    #                             PUBLIC CLASS METHODS                             #
+    ################################################################################
+
+    def write_diagnostics_file(self, diagnostics_file_out, diag_mode, append):
+        """ Add all MARBL diagnostics to file containing MOM diagnostics
+            Also create a list of diagnostics generated by MOM
+        """
+        diag_mode_loc = 'full' if diag_mode == 'test_suite' else diag_mode
+        from MARBL_tools import generate_diagnostics_file
+        generate_diagnostics_file(self.MARBL_diagnostic_dict, diagnostics_file_out, diag_mode_loc, append)
+

cime_config/MARBL_scripts/MARBL_settings.py

@@ -0,0 +1,133 @@
+""" Interface to the marbl_settings_class object
+"""
+
+class MARBL_settings_for_MOM(object):
+    def __init__(self, MARBL_dir, caseroot, base_bio_on, abio_dic_on, ocn_grid, run_type, continue_run, ocn_bgc_config):
+
+        import sys, os
+
+        # Set up arguments for marbl_settings_class constructor
+        # Note that this is a dictionary that will be used to pass named variables to class constructor
+        # Arguments to be passed are
+        # 1. default_settings_file: full path to default_settings.json; can be in SourceMods, otherwise comes from MARBL
+        # 2. grid: CESM_MOM (until we come up with resolution-dependent tunings)
+        # 3. saved_state_vars_source: "settings_file" for startup run, otherwise GCM
+        MARBL_args = dict()
+
+        settings_file = "settings_"+ocn_bgc_config+".json"
+
+        # Users CAN NOT provide these variables in user_nl_marbl
+        MARBL_args["exclude_dict"] = {}
+        for var in ['base_bio_on', 'abio_dic_on']:
+          MARBL_args["exclude_dict"][var] = f'ERROR: {var} can not be set in user_nl_marbl -- ' + \
+                                             'it is controlled by MARBL_TRACER_OPTS in env_run.xml'
+        for var in ['ciso_on', 'ladjust_bury_coeff']:
+          MARBL_args["exclude_dict"][var] = f'ERROR: running with {var} is not supported in CESM+MOM6 yet'
+
+        # User can put settings_file in SourceMods, otherwise use file provided by MARBL
+        MARBL_args["default_settings_file"] = os.path.join(caseroot,"SourceMods","src.mom", settings_file)
+        if not os.path.isfile(MARBL_args["default_settings_file"]):
+            MARBL_args["default_settings_file"] = os.path.join(MARBL_dir, "defaults", "json", settings_file)
+
+        # User can modify user_nl_marbl (or user_nl_marbl_####) in caseroot
+        MARBL_args["input_file"] = os.path.join(caseroot, "user_nl_marbl")
+        if not os.path.isfile(MARBL_args["input_file"]):
+            MARBL_args["input_file"] = None
+
+        # Specify MARBL tracer opts
+        MARBL_args["base_bio_on"] = base_bio_on
+        MARBL_args["abio_dic_on"] = abio_dic_on
+
+        # Specify grid
+        MARBL_args["grid"] = "CESM_MOM"
+
+        # MARBL can run in mks unit system instead of requiring MOM to convert to / from cgs
+        MARBL_args["unit_system"] = "mks"
+
+        # If not a startup run, MARBL may want initial bury coefficient from restart file
+        if run_type == "startup" and not continue_run:
+            MARBL_args["saved_state_vars_source"] = "settings_file"
+        else:
+            MARBL_args["saved_state_vars_source"] = "GCM"
+
+        # Import MARBL_settings_file_class, which may come from MARBL_tools or SourceMods/src.mom
+        # (i) need MARBL_dir in path for both branches of this if statement because even if
+        #     MARBL_settings_file_class.py is in SourceMods, it needs to import MARBL_tools itself
+        sys.path.append(MARBL_dir)
+        # (ii) Here's where we import from either MARBL_tools or SourceMods
+        settings_class_dir = os.path.join(caseroot, "SourceMods", "src.mom")
+        if not os.path.isfile(os.path.join(settings_class_dir, "MARBL_settings_file_class.py")):
+            from MARBL_tools import MARBL_settings_file_class
+        else:
+            import imp
+            import logging
+            logger = logging.getLogger(__name__)
+            logging.info('Importing MARBL_settings_file_class.py from %s' % settings_class_dir)
+            settings_class_module = settings_class_dir+'/MARBL_settings_file_class.py'
+            if os.path.isfile(settings_class_module):
+                MARBL_settings_file_class = imp.load_source('MARBL_settings_file_class', settings_class_module)
+            else:
+                logger.error('Can not find %s' % settings_class_module)
+                sys.exit(1)
+
+        # Generate settings object
+        self._MARBL_settings = MARBL_settings_file_class.MARBL_settings_class(**MARBL_args)
+
+    ################################################################################
+    #                             PUBLIC CLASS METHODS                             #
+    ################################################################################
+
+    def get_tracer_names(self):
+        """ Returns a list of all tracers in current configuration
+        """
+        return self._MARBL_settings.get_tracer_names()
+
+    #######################################
+
+    def get_autotroph_names(self, calcifier_only=False):
+        """ Returns a list of all autotrophs in current configuration
+        """
+        autotroph_list = []
+        try:
+          for n in range(1, self._MARBL_settings.settings_dict['autotroph_cnt']['value']+1):
+              autotroph_name = self._MARBL_settings.settings_dict['autotroph_settings(%d)%%sname' % n]['value'].strip('"')
+              imp_calcifier = (self._MARBL_settings.settings_dict['autotroph_settings(%d)%%imp_calcifier' % n]['value'].strip('"') == '.true.')
+              exp_calcifier = (self._MARBL_settings.settings_dict['autotroph_settings(%d)%%exp_calcifier' % n]['value'].strip('"') == '.true.')
+              if imp_calcifier or exp_calcifier or (not calcifier_only):
+                  autotroph_list.append(autotroph_name)
+        except:
+            print('autotroph_cnt not found, treating as 0')
+        return autotroph_list
+
+    #######################################
+
+    def get_zooplankton_names(self):
+        """ Returns a list of all zooplankton in current configuration
+        """
+        zooplankton_list = []
+        try:
+          for n in range(1, self._MARBL_settings.settings_dict['zooplankton_cnt']['value']+1):
+              zooplankton_name = self._MARBL_settings.settings_dict['zooplankton_settings(%d)%%sname' % n]['value'].strip('"')
+              zooplankton_list.append(zooplankton_name)
+        except:
+            print('zooplankton_cnt not found, treating as 0')
+        return zooplankton_list
+
+    #######################################
+
+    def get_ladjust_bury_coeff(self):
+        """ Returns True if ladjust_bury_coeff = .true.
+        """
+        try:
+            return (self._MARBL_settings.settings_dict['ladjust_bury_coeff']['value'].strip('"') == '.true.')
+        except:
+            print('ladjust_bury_coeff not found, treating as False')
+            return False
+
+    #######################################
+
+    def write_settings_file(self, settings_file_out):
+        """ Write a settings file containing all MARBL settings
+        """
+        from MARBL_tools import generate_settings_file
+        generate_settings_file(self._MARBL_settings, settings_file_out)