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

import copy


def perturb_model(self, nsamples, transf_mapper):

    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 = "{}{:03d}".format(spec, i)
            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 = "{}{:03d}".format(spec, i)
            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 = "{}{:03d}".format(spec, i)
            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 = "{}{:03d}".format(spec, i)
            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()