import os
from ....utils.path import init_dir
from .utils import create_mandchem, create_optchem, make_inout_react_graph
[docs]
def create_chemicalscheme(self):
"""
Read the mandatory chemistry files, create the optional ones and set the
species attributes
consistently with the data retrieved
"""
# 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("rm -rf {}".format(dirchem_ref))
init_dir(dirchem_ref)
# List of files (for LMDZ)
finf = "{}/chemical_scheme.nml".format(dirchem_ref)
filer = "{}/REACTIONS.{}".format(dirchem_ref, mecachim)
fileps = "{}/PRESCRIBED_SPECIES.{}".format(dirchem_ref, mecachim)
filepl = "{}/PRODLOSS_SPECIES.{}".format(dirchem_ref, mecachim)
filedp = "{}/DEPO_SPEC.{}".format(dirchem_ref, mecachim)
filea = "{}/ANTHROPIC.{}".format(dirchem_ref, mecachim)
fileb = "{}/BIOGENIC.{}".format(dirchem_ref, mecachim)
mandatory_files = [filer, fileps, filepl, filedp]
create_mandchem(self, mandatory_files)
files = "{}/STOICHIOMETRY.{}".format(dirchem_ref, mecachim)
filec = "{}/CHEMISTRY.{}".format(dirchem_ref, mecachim)
filerr = "{}/REACTION_RATES.{}".format(dirchem_ref, mecachim)
filej = "{}/PHOTO_RATES.{}".format(dirchem_ref, mecachim)
filef = "{}/FAMILIES.{}".format(dirchem_ref, mecachim)
fileals = "{}/ALL_SPECIES.{}".format(dirchem_ref, mecachim)
fileas = "{}/ACTIVE_SPECIES.{}".format(dirchem_ref, mecachim)
nallqmax, nphoto_rates = create_optchem(self, filer, fileps)
# MAKE GRAPH OF PRODUCTS AND REACTIVE SPECIES
self.inout_reaction_graph = make_inout_react_graph(
f"{dirchem_ref}/CHEMISTRY.{self.schemeid}")
# Create chemical_scheme.nml namelist
os.system('echo "&args" > {}'.format(finf))
os.system("echo \"fnacspec = '{}'\" >> {}".format(fileas, finf))
os.system("echo \"fnallspec = '{}'\" >> {}".format(fileals, finf))
os.system("echo \"fnprescr = '{}'\" >> {}".format(fileps, finf))
os.system("echo \"fnprodl = '{}'\" >> {}".format(filepl, finf))
os.system("echo \"fndep = '{}'\" >> {}".format(filedp, finf))
os.system("echo \"fnchem = '{}'\" >> {}".format(filec, finf))
os.system("echo \"fnstoi = '{}'\" >> {}".format(files, finf))
os.system("echo \"fnrates = '{}'\" >> {}".format(filerr, finf))
os.system("echo \"fnjrates = '{}'\" >> {}".format(filej, finf))
os.system("echo \"fnfamilies = '{}'\" >> {}".format(filef, finf))
os.system('echo "iqmax = {}" >> {}'.format(self.nspecies, finf))
os.system('echo "iallqmax = {}" >> {}'.format(nallqmax, finf))
os.system('echo "iprescrmax = {}" >> {}'.format(self.nprspecies, finf))
os.system('echo "iprodmax = {}" >> {}'.format(self.nprodspecies, finf))
os.system('echo "idepmax = {}" >> {}'.format(self.ndepspecies, finf))
os.system('echo "nreac = {}" >> {}'.format(self.nreacs, finf))
os.system('echo "ijratesmax = {}" >> {}'.format(nphoto_rates, finf))
os.system('echo "/" >> {}'.format(finf))
