Source code for pycif.plugins.chemistries.iconart.make_chemistry

def create_chemicalscheme(self):
    """
    Read the mandatory chemistry files, create the optional ones and set the
    species attributes
    consistently with the data retrieved
    """

    # Derive emitted species
    self.emis_species = []
    for spec in self.acspecies.attributes:
        self.emis_species += self.mapping_active2emi[spec]
    self.emis_species = sorted(list(set(self.emis_species))) 

    # Map the emitted species to the active species
    self.mapping_emi2active = {emspec: [] for emspec in self.emis_species}
    for spec in self.acspecies.attributes:
        for emspec in self.mapping_active2emi[spec]:
            self.mapping_emi2active[emspec] += [spec]

    # Store reference species (for EnSRF)
    self.ref_acspecies = list(set([s.split("__sample#")[0] 
                                  for s in self.acspecies.attributes]))
    self.ref_emis_species = list(set([ems.split("__sample#")[0] 
                                  for ems in self.emis_species]))

    # Create attribute to store tracer information for the xml file
    self.dict_tracers = {}

    default_xml_config = {
        'transport': 'stdchem',
        'unit': 'none',
        'c_solve': 'passive',
        'init_mode': '0',
    }

    self.oem_categories = []
    self.oem_tracers = []
    for spec in self.acspecies.attributes:

        spec_ref = spec.split("__sample#")[0]

        # Create the config for the background tracer
        spec_bg = spec_ref + '_BG'
        if spec_bg not in self.dict_tracers: 
            self.dict_tracers[spec_bg] = {
                'id': spec_bg,
                **default_xml_config
            }

        # Create the emission config for the reference tracer
        emis_species_ref = self.mapping_active2emi_ref[spec_ref]
        if len(emis_species_ref) > 0:
            oem_xml_config = {
                'oem_type': 'emis',
                'oem_tscale': '3',
                'oem_cat': sorted(emis_species_ref),
                'oem_vp': ['ground_emissions'] * len(emis_species_ref),
                'oem_tp': sorted(emis_species_ref)
            }
        else:
            oem_xml_config = {}

        # Create the reference tracer
        if spec_ref not in self.dict_tracers:
            self.dict_tracers[spec_ref] = {
                'id': spec_ref,
                **default_xml_config,
                **oem_xml_config
            }

            # Store the order of categories in tracers.xml
            self.oem_categories += sorted(emis_species_ref)
            self.oem_tracers += [spec_ref]

            # To monitor emissions, add an active tracer for each emitted tracer
            for emi_spec in emis_species_ref:
                self.dict_tracers[emi_spec] = {
                    'id': emi_spec,
                    **default_xml_config,
                    **{
                        'oem_type': 'emis',
                        'oem_tscale': '3',
                        'oem_cat': [emi_spec],
                        'oem_vp': ['ground_emissions'],
                        'oem_tp': [emi_spec]
                    }
                }

        # If ensemble
        if "__sample#" in spec:

            # Create the config for the optimized background tracer
            spec_bg_post = spec_ref + '_BG_POST'
            if spec_bg_post not in self.dict_tracers: 
                self.dict_tracers[spec_bg_post] = {
                    'id': spec_bg_post,
                    **default_xml_config
                }


            # Create the config for the optimized emitted tracers
            for emi_spec in emis_species_ref:
                emi_spec_post = emi_spec + '_POST'
                if emi_spec_post not in self.dict_tracers:
                    self.dict_tracers[emi_spec_post] = {
                        'id': emi_spec_post,
                        **default_xml_config,
                        **{
                            'oem_type': 'emis',
                            'oem_tscale': '3',
                            'oem_cat': [emi_spec + '_POST'],
                            'oem_vp': ['ground_emissions'],
                            'oem_tp': [emi_spec]
                        }
                    }

            # Create the config for the sample active tracer
            self.dict_tracers[spec] = {
                'id': spec,
                **default_xml_config
            }