Source code for pycif.plugins.models.chimere.perturb_model

import copy




def perturb_model(self, nsamples, transf_mapper):
    """Extend the CHIMERE chemistry scheme to accommodate ensemble members.

    Creates ``nsamples`` copies of each active species (``acspecies``),
    output species (``outspecies``), emitted species (``emis_species``),
    and biogenic species (``bio_species``) in the chemistry plugin, then
    removes the original un-suffixed species.  The copies are named with
    a numeric suffix (e.g. ``CH4000``, ``CH4001``, …).  Also records a
    ``perturbed_species`` mapping from sample name back to original name.

    .. note::
        Reactions in the chemical scheme are not yet supported with
        perturbations; an exception is raised if ``self.reactions`` is set.

    Args:
        self (Plugin): CHIMERE model plugin instance.
        nsamples (int): number of ensemble members.
        transf_mapper (dict): transform mapper (unused; kept for API
            consistency with other model plugins).

    Raises:
        Exception: if the chemical scheme contains reactions.
    """

    if hasattr(self, "reactions"):
        raise Exception("There are reactions in your chemical scheme. "
                        "This is not yet implemented!!")

    # Perturb active species in the chemical scheme
    list_acspecies = copy.deepcopy(self.chemistry.acspecies.attributes[:])
    self.perturbed_species = {}
    for spec in list_acspecies:
        for i in range(nsamples):
            spec_sample = f"{spec}{i:03d}"
            spec_plg = getattr(self.chemistry.acspecies, spec)
            setattr(self.chemistry.acspecies, spec_sample, spec_plg)
            self.chemistry.acspecies.attributes.append(spec_sample)
            self.perturbed_species[spec_sample] = spec

        delattr(self.chemistry.acspecies, spec)
        self.chemistry.acspecies.attributes.remove(spec)

    # Perturb output species in the chemical scheme
    list_outspecies = copy.deepcopy(self.chemistry.outspecies.attributes[:])
    for spec in list_outspecies:
        for i in range(nsamples):
            spec_sample = f"{spec}{i:03d}"
            spec_plg = getattr(self.chemistry.outspecies, spec)
            setattr(self.chemistry.outspecies, spec_sample, spec_plg)
            self.chemistry.outspecies.attributes.append(spec_sample)

        delattr(self.chemistry.outspecies, spec)
        self.chemistry.outspecies.attributes.remove(spec)

    # Perturb emis species in the chemical scheme
    list_emispecies = copy.deepcopy(self.chemistry.emis_species.attributes[:])
    for spec in list_emispecies:
        for i in range(nsamples):
            spec_sample = f"{spec}{i:03d}"
            spec_plg = getattr(self.chemistry.emis_species, spec)
            setattr(self.chemistry.emis_species, spec_sample, spec_plg)
            self.chemistry.emis_species.attributes.append(spec_sample)

        delattr(self.chemistry.emis_species, spec)
        self.chemistry.emis_species.attributes.remove(spec)

    # Perturb bio species in the chemical scheme
    list_biospecies = copy.deepcopy(self.chemistry.bio_species.attributes[:])
    for spec in list_biospecies:
        for i in range(nsamples):
            spec_sample = f"{spec}{i:03d}"
            spec_plg = getattr(self.chemistry.bio_species, spec)
            setattr(self.chemistry.bio_species, spec_sample, spec_plg)
            self.chemistry.bio_species.attributes.append(spec_sample)

        delattr(self.chemistry.bio_species, spec)
        self.chemistry.bio_species.attributes.remove(spec)

    # Dump updated chemical scheme as text files for CHIMERE executable
    self.chemistry.create_chemicalscheme()