Source code for pycif.plugins.chemistries.TM5.make_chemistry

import os

from ....utils.path import init_dir
from .utils import create_mandchem, create_optchem




def create_chemicalscheme(self):
    """Generate TM5 chemical-scheme files from the YAML configuration.

    Functionally identical to the CHIMERE ``create_chemicalscheme`` but
    uses ``DEPO_SPECIES`` instead of ``DEPO_SPEC`` for the deposition file.
    Calls :func:`~pycif.plugins.chemistries.TM5.utils.create_mandchem` and
    :func:`~pycif.plugins.chemistries.TM5.utils.create_optchem` to write:

    * ``REACTIONS`` / ``CHEMISTRY`` / ``STOICHIOMETRY`` / ``REACTION_RATES``
    * ``ACTIVE_SPECIES`` / ``ALL_SPECIES`` / ``ANTHROPIC`` / ``BIOGENIC``
    * ``PHOTO_RATES`` / ``FAMILIES``
    * ``chemical_scheme.nml``

    Args:
        self: TM5 chemistry plugin instance with all species lists and
            ``schemeid`` / ``dirchem_ref`` set.
    """

    # Common variables
    workdir = self.workdir
    mecachim = self.schemeid
    dirchem_ref = self.dirchem_ref

    # Initializes number of species and reactions
    self.nacspecies = (
        len(self.acspecies.attributes) if hasattr(self, "acspecies") else 0
    )
    self.nemisspec = (
        len(self.emis_species.attributes)
        if hasattr(self, "emis_species")
        else 0
    )
    self.nemisspec_interp = (
        len(self.emis_species_interp.attributes)
        if hasattr(self, "emis_species_interp")
        else 0
    )
    self.nprspecies = (
        len(self.prescrconcs.attributes) if hasattr(self, "prescrconcs") else 0
    )
    self.nprodspecies = (
        len(self.prodloss3d.attributes) if hasattr(self, "prodloss3d") else 0
    )
    self.ndepspecies = (
        len(self.deposition.attributes) if hasattr(self, "deposition") else 0
    )
    self.nreacs = (
        len(self.reactions.attributes) if hasattr(self, "reactions") else 0
    )
    self.nfamilies = (
        len(self.families.attributes) if hasattr(self, "families") else 0
    )

    # Cleaning the target directory
    os.system(f"rm -rf  {dirchem_ref}")
    init_dir(dirchem_ref)

    # List of files
    finf = f"{dirchem_ref}/chemical_scheme.nml"
    filer = f"{dirchem_ref}/REACTIONS.{mecachim}"
    fileps = f"{dirchem_ref}/PRESCRIBED_SPECIES.{mecachim}"
    filepl = f"{dirchem_ref}/PRODLOSS_SPECIES.{mecachim}"
    filedp = f"{dirchem_ref}/DEPO_SPECIES.{mecachim}"
    filea = f"{dirchem_ref}/ANTHROPIC.{mecachim}"
    fileb = f"{dirchem_ref}/BIOGENIC.{mecachim}"

    mandatory_files = [filer, fileps, filepl, filedp]
    create_mandchem(self, mandatory_files)

    files = f"{dirchem_ref}/STOICHIOMETRY.{mecachim}"
    filec = f"{dirchem_ref}/CHEMISTRY.{mecachim}"
    filerr = f"{dirchem_ref}/REACTION_RATES.{mecachim}"
    filej = f"{dirchem_ref}/PHOTO_RATES.{mecachim}"
    filef = f"{dirchem_ref}/FAMILIES.{mecachim}"
    fileals = f"{dirchem_ref}/ALL_SPECIES.{mecachim}"
    fileas = f"{dirchem_ref}/ACTIVE_SPECIES.{mecachim}"

    nallqmax, nphoto_rates = create_optchem(self, filer, fileps)

    # Create chemical_scheme.nml namelist
    os.system(f'echo "&args" > {finf}')
    os.system(f"echo \"fnacspec = '{fileas}'\" >> {finf}")
    os.system(f"echo \"fnallspec = '{fileals}'\" >> {finf}")
    os.system(f"echo \"fnprescr = '{fileps}'\" >> {finf}")
    os.system(f"echo \"fnprodl = '{filepl}'\" >> {finf}")
    os.system(f"echo \"fndep = '{filedp}'\" >> {finf}")
    os.system(f"echo \"fnchem = '{filec}'\" >> {finf}")
    os.system(f"echo \"fnstoi = '{files}'\" >> {finf}")
    os.system(f"echo \"fnrates = '{filerr}'\" >> {finf}")
    os.system(f"echo \"fnjrates = '{filej}'\" >> {finf}")
    os.system(f"echo \"fnfamilies = '{filef}'\" >> {finf}")
    os.system(f'echo "iqmax = {self.nspecies}" >> {finf}')
    os.system(f'echo "iallqmax = {nallqmax}" >> {finf}')
    os.system(f'echo "iprescrmax = {self.nprspecies}" >> {finf}')
    os.system(f'echo "iprodmax = {self.nprodspecies}" >> {finf}')
    os.system(f'echo "idepmax = {self.ndepspecies}" >> {finf}')
    os.system(f'echo "nreac = {self.nreacs}" >> {finf}')
    os.system(f'echo "ijratesmax = {nphoto_rates}" >> {finf}')
    os.system(f'echo "/" >> {finf}')