def ingest_levels(self):
logger.info("Ingesting levels from `{}`.".format(
self.data_source.short_name))
for rdr in self.ion_readers:
atomic_number = rdr.ion.Z
ion_charge = rdr.ion.Ion - 1
ion = Ion.as_unique(self.session,
atomic_number=atomic_number,
ion_charge=ion_charge)
try:
bound_levels = rdr.bound_levels
except ChiantiIonReaderError:
logger.info("Levels not found for ion {} {}.".format(
convert_atomic_number2symbol(atomic_number), ion_charge))
continue
logger.info("Ingesting levels for {} {}.".format(
convert_atomic_number2symbol(atomic_number), ion_charge))
# ToDo: Determine parity from configuration
for index, row in bound_levels.iterrows():
level = Level(ion=ion,
data_source=self.data_source,
level_index=index,
configuration=row["configuration"],
term=row["term"],
L=row["L"],
J=row["J"],
spin_multiplicity=row["spin_multiplicity"])
level.energies = []
for column, method in [('energy', 'meas'),
('energy_theoretical', 'theor')]:
if row[column] != -1: # check if the value exists
level.energies.append(
LevelEnergy(quantity=row[column] * u.Unit("cm-1"),
data_source=self.data_source,
method=method), )
self.session.add(level)
def ingest_levels(self, levels=None):
if levels is None:
levels = self.gfall_reader.levels
# Select ions
if self.ions is not None:
levels = levels.reset_index().\
join(self.ions, how="inner",
on=["atomic_number", "ion_charge"]).\
set_index(["atomic_number", "ion_charge", "level_index"])
logger.info("Ingesting levels from `{}`.".format(
self.data_source.short_name))
for ion_index, ion_levels in levels.groupby(
level=["atomic_number", "ion_charge"]):
atomic_number, ion_charge = ion_index
ion = Ion.as_unique(self.session,
atomic_number=atomic_number,
ion_charge=ion_charge)
logger.info("Ingesting levels for {} {}.".format(
convert_atomic_number2symbol(atomic_number), ion_charge))
for index, row in ion_levels.iterrows():
# index: (atomic_number, ion_charge, level_index)
level_index = index[2]
ion.levels.append(
Level(level_index=level_index,
data_source=self.data_source,
J=row["j"],
energies=[
LevelEnergy(quantity=row["energy"] *
u.Unit("cm-1"),
method=row["method"],
data_source=self.data_source)
]))
def ingest_ground_levels(self, ground_levels=None):
if ground_levels is None:
ground_levels = self.parser.prepare_ground_levels()
print("Ingesting ground levels from {}".format(
self.data_source.short_name))
for index, row in ground_levels.iterrows():
atomic_number, ion_charge = index
# Replace nan with None
row = row.where(pd.notnull(row), None)
ion = Ion.as_unique(self.session,
atomic_number=atomic_number,
ion_charge=ion_charge)
try:
spin_multiplicity = int(row["spin_multiplicity"])
except TypeError: # Raised when the variable is None
spin_multiplicity = None
try:
parity = int(row["parity"])
except TypeError: # Raised when the variable is None
parity = None
ion.levels.append(
Level(data_source=self.data_source,
configuration=row["configuration"],
term=row["term"],
L=row["L"],
spin_multiplicity=spin_multiplicity,
parity=parity,
J=row["J"],
energies=[
LevelEnergy(quantity=0, data_source=self.data_source)
]))
def foo_engine():
engine = create_engine(foo_db_url)
Base.metadata.drop_all(engine)
Base.metadata.create_all(engine)
session = Session(bind=engine)
# atoms
h = Atom(atomic_number=1, symbol='H')
ne = Atom(atomic_number=10, symbol='Ne')
# data sources
nist = DataSource(short_name='nist')
ku = DataSource(short_name='ku')
ch = DataSource(short_name="chianti")
# atomic weights
h.weights = [
AtomWeight(quantity=1.00784 * u.u, data_source=nist, uncert=4e-3),
AtomWeight(quantity=1.00811 * u.u, data_source=ku, uncert=4e-3),
]
# ions
h0 = Ion(atomic_number=1,
ion_charge=0,
ionization_energies=[
IonizationEnergy(quantity=13.5984 * u.eV,
data_source=nist,
method="th")
])
ne1 = Ion(atomic_number=10,
ion_charge=1,
ionization_energies=[
IonizationEnergy(quantity=40.96296 * u.eV,
data_source=nist,
method="th"),
IonizationEnergy(quantity=40.97 * u.eV,
data_source=nist,
method="m")
])
ne2 = Ion(atomic_number=10,
ion_charge=2,
ionization_energies=[
IonizationEnergy(quantity=48.839 * u.eV,
data_source=nist,
method="th")
])
# levels
ne2_lvl0_ku = Level(ion=ne2,
data_source=ku,
level_index=0,
configuration="2s2.2p5",
term="2P1.5",
L="P",
J=1.5,
spin_multiplicity=2,
parity=1,
energies=[
LevelEnergy(quantity=0, data_source=ku,
method="m"),
LevelEnergy(quantity=0,
data_source=ku,
method="th")
])
ne2_lvl1_ku = Level(ion=ne2,
data_source=ku,
level_index=1,
configuration="2s2.2p5",
term="2P0.5",
L="P",
J=0.5,
spin_multiplicity=2,
parity=1,
energies=[
LevelEnergy(quantity=780.4 * u.Unit("cm-1"),
data_source=ku,
method="m"),
LevelEnergy(quantity=780.0 * u.Unit("cm-1"),
data_source=ku,
method="th")
])
ne2_lvl2_ku = Level(ion=ne2,
data_source=ku,
level_index=2,
configuration="2s2.2p5",
term="2D2.5",
L="D",
J=2.5,
spin_multiplicity=2,
parity=0,
energies=[
LevelEnergy(quantity=1366.3 * u.Unit("cm-1"),
data_source=ku,
method="m")
])
ne2_lvl1_ch = Level(ion=ne2,
data_source=ch,
level_index=1,
configuration="2s2.2p5",
term="2P0.5",
L="P",
J=0.5,
spin_multiplicity=2,
parity=1,
energies=[
LevelEnergy(quantity=780.2 * u.Unit("cm-1"),
data_source=ch,
method="m")
])
# lines
ne2_line0_ku = Line(
lower_level=ne2_lvl0_ku,
upper_level=ne2_lvl1_ku,
data_source=ku,
wavelengths=[LineWavelength(quantity=183.571 * u.AA, data_source=ku)],
a_values=[
LineAValue(quantity=5.971e-03 * u.Unit("s-1"), data_source=ku)
],
gf_values=[LineGFValue(quantity=8.792e-01, data_source=ku)])
ne2_line1_ku = Line(
lower_level=ne2_lvl0_ku,
upper_level=ne2_lvl2_ku,
data_source=ku,
wavelengths=[
LineWavelength(quantity=18.4210 * u.nm, medium=1, data_source=ku)
],
a_values=[
LineAValue(quantity=5.587e-03 * u.Unit("s-1"), data_source=ku)
],
gf_values=[LineGFValue(quantity=8.238e-01, data_source=ku)])
# electron collisions
ne2_e_col0_ku = ECollision(
lower_level=ne2_lvl0_ku,
upper_level=ne2_lvl1_ku,
data_source=ku,
bt92_ttype=2,
bt92_cups=11.16,
energies=[
ECollisionEnergy(quantity=0.007108 * u.rydberg, data_source=ku)
],
temp_strengths=[(ECollisionTempStrength(temp=0.0, strength=0.255)),
(ECollisionTempStrength(temp=0.07394,
strength=0.266))])
session.add_all([
h, ne, nist, ku, ch, h0, ne1, ne2_lvl1_ch, ne2_lvl0_ku, ne2_lvl1_ku,
ne2_lvl2_ku, ne2_line0_ku, ne2_line1_ku, ne2_e_col0_ku
])
session.commit()
session.close()
return engine