import pandas as pd
from logging import debug
from .utils import make_inout_react_graph
[docs]
def read_chemicalscheme(chemistry, **kwargs):
"""Reads a chemical scheme from existing files
Args:
chemistry (pycif.utils.classes.chemistries.Chemistry): the chemical
scheme
Return:
Grid dictionary with characteristics of the chemical scheme
Notes:
"""
debug("Reading Chemistry")
workdir = chemistry.workdir
dirchem_ref = "{}/chemical_scheme/{}/".format(workdir, chemistry.schemeid)
# ACTIVE SPECIES
file_chem = "{}/ACTIVE_SPECIES.{}".format(dirchem_ref, chemistry.schemeid)
acspecies = pd.read_csv(
file_chem, header=None, sep=" ",
names=["ID", "name", "htransport", "vtransport", "bound_dry"]
)
chemistry.acspecies = chemistry.from_dict(
{acspecies.loc[k, "name"]: {
"htransport": acspecies.loc[k, "htransport"],
"vtransport": acspecies.loc[k, "vtransport"],
"bound_dry": bool(acspecies.loc[k, "bound_dry"]),
} for k in acspecies.index}
)
chemistry.nacspecies = len(acspecies)
# OUTPUT SPECIES
file_out = "{}/OUTPUT_SPECIES.{}".format(dirchem_ref, chemistry.schemeid)
outspecies = pd.read_csv(
file_out, header=None, sep=r"\s+", names=["name", "output_frac"]
)
chemistry.outspecies = chemistry.from_dict(
{outspecies.loc[k, "name"]: {
"output_frac": outspecies.loc[k, "output_frac"],
} for k in outspecies.index}
)
# ANTHROPIC
file_chem = "{}/ANTHROPIC.{}".format(dirchem_ref, chemistry.schemeid)
emis_species = pd.read_csv(
file_chem, header=None, sep=" ", usecols=[0, 1], names=["ID", "name"]
)
chemistry.emis_species = chemistry.from_dict(
{s: None for s in emis_species["name"]}
)
chemistry.nemisspec = len(emis_species)
# BIOGENIC
file_chem = "{}/BIOGENIC.{}".format(dirchem_ref, chemistry.schemeid)
bio_species = pd.read_csv(
file_chem, header=None, sep=" ", usecols=[0, 1], names=["ID", "name"]
)
chemistry.bio_species = chemistry.from_dict(
{s: None for s in bio_species["name"]}
)
chemistry.nemisspec_interp = len(bio_species)
# DEPO_SPEC
file_chem = "{}/DEPO_SPEC.{}".format(dirchem_ref, chemistry.schemeid)
dep_species = pd.read_csv(
file_chem, header=None, sep=" ", usecols=[0], names=["name"]
)
chemistry.dep_species = chemistry.from_dict(
{s: None for s in dep_species["name"]}
)
chemistry.ndepspecies = len(dep_species)
# CHEMISTRY
with open(dirchem_ref + "CHEMISTRY." + chemistry.schemeid, "r") as fsp:
ln = fsp.readlines()
chemistry.nreacs = len(ln)
with open(dirchem_ref + "FAMILIES." + chemistry.schemeid, "r") as fsp:
ln = fsp.readlines()
chemistry.nfamilies = len(ln)
# MAKE GRAPH OF PRODUCTS AND REACTIVE SPECIES
chemistry.inout_reaction_graph = make_inout_react_graph(
f"{dirchem_ref}/CHEMISTRY.{chemistry.schemeid}")
# TODO: generalize number of prescribed species
chemistry.nprspecies = 4
