def abundances(self, abundances_dict: Optional[Dict[ParticleLike, Real]]):
"""
Set the elemental (or isotopic) abundances. The elements and
isotopes must be the same as or a superset of the elements whose
ionization states are being tracked.
"""
if abundances_dict is None:
self._pars["abundances"] = {elem: np.nan for elem in self.base_particles}
elif not isinstance(abundances_dict, dict):
raise TypeError(
f"The abundances attribute must be a dict with "
f"elements or isotopes as keys and real numbers "
f"representing relative abundances as values."
)
else:
old_keys = abundances_dict.keys()
try:
new_keys_dict = {}
for old_key in old_keys:
new_keys_dict[particle_symbol(old_key)] = old_key
except Exception:
raise ParticleError(
f"The key {repr(old_key)} in the abundances "
f"dictionary is not a valid element or isotope."
)
new_elements = new_keys_dict.keys()
old_elements_set = set(self.base_particles)
new_elements_set = set(new_elements)
if old_elements_set - new_elements_set:
raise ParticleError(
f"The abundances of the following particles are "
f"missing: {old_elements_set - new_elements_set}"
)
new_abundances_dict = {}
for element in new_elements:
inputted_abundance = abundances_dict[new_keys_dict[element]]
try:
inputted_abundance = float(inputted_abundance)
except Exception:
raise TypeError(
f"The abundance for {element} was provided as"
f"{inputted_abundance}, which cannot be "
f"converted to a real number."
) from None
if inputted_abundance < 0:
raise ParticleError(f"The abundance of {element} is negative.")
new_abundances_dict[element] = inputted_abundance
self._pars["abundances"] = new_abundances_dict
def __getitem__(self, *values) -> IonizationState:
errmsg = f"Invalid indexing for IonizationStates instance: {values[0]}"
one_input = not isinstance(values[0], tuple)
two_inputs = len(values[0]) == 2
if not one_input and not two_inputs:
raise IndexError(errmsg)
try:
arg1 = values[0] if one_input else values[0][0]
int_charge = None if one_input else values[0][1]
particle = arg1 if arg1 in self.base_particles else particle_symbol(arg1)
if int_charge is None:
return IonizationState(
particle=particle,
ionic_fractions=self.ionic_fractions[particle],
T_e=self._pars["T_e"],
n_elem=np.sum(self.number_densities[particle]),
tol=self.tol,
)
else:
if not isinstance(int_charge, Integral):
raise TypeError(
f"{int_charge} is not a valid charge for {particle}."
)
elif not 0 <= int_charge <= atomic_number(particle):
raise ChargeError(
f"{int_charge} is not a valid charge for {particle}."
)
return State(
integer_charge=int_charge,
ionic_fraction=self.ionic_fractions[particle][int_charge],
ionic_symbol=particle_symbol(particle, Z=int_charge),
number_density=self.number_densities[particle][int_charge],
)
except Exception as exc:
raise IndexError(errmsg) from exc
def ionic_fractions(self, inputs: Union[Dict, List, Tuple]):
"""
Set the ionic fractions.
Notes
-----
The ionic fractions are initialized during instantiation of
`~plasmapy.particles.IonizationStateCollection`. After this, the
only way to reset the ionic fractions via the ``ionic_fractions``
attribute is via a `dict` with elements or isotopes that are a
superset of the previous elements or isotopes. However, you may
use item assignment of the `~plasmapy.particles.IonizationState`
instance to assign new ionic fractions one element or isotope
at a time.
Raises
------
`~plasmapy.particles.exceptions.ParticleError`
If the ionic fractions cannot be set.
`TypeError`
If ``inputs`` is not a `list`, `tuple`, or `dict` during
instantiation, or if ``inputs`` is not a `dict` when it is
being set.
"""
# A potential problem is that using item assignment on the
# ionic_fractions attribute could cause the original attributes
# to be overwritten without checks being performed. We might
# eventually want to create a new class or subclass of UserDict
# that goes through these checks. In the meantime, we should
# make it clear to users to set ionic_fractions by using item
# assignment on the IonizationStateCollection instance as a whole. An
# example of the problem is `s = IonizationStateCollection(["He"])` being
# followed by `s.ionic_fractions["He"] = 0.3`.
if hasattr(self, "_ionic_fractions"):
if not isinstance(inputs, dict):
raise TypeError(
"Can only reset ionic_fractions with a dict if "
"ionic_fractions has been set already."
)
old_particles = set(self.base_particles)
new_particles = {particle_symbol(key) for key in inputs.keys()}
missing_particles = old_particles - new_particles
if missing_particles:
raise ParticleError(
"Can only reset ionic fractions with a dict if "
"the new base particles are a superset of the "
"prior base particles. To change ionic fractions "
"for one base particle, use item assignment on the "
"IonizationStateCollection instance instead."
)
if isinstance(inputs, dict):
original_keys = inputs.keys()
ionfrac_types = {type(inputs[key]) for key in original_keys}
inputs_have_quantities = u.Quantity in ionfrac_types
if inputs_have_quantities and len(ionfrac_types) != 1:
raise TypeError(
"Ionic fraction information may only be inputted "
"as a Quantity object if all ionic fractions are "
"Quantity arrays with units of inverse volume."
)
try:
particles = {key: Particle(key) for key in original_keys}
except (InvalidParticleError, TypeError) as exc:
raise ParticleError(
"Unable to create IonizationStateCollection instance "
"because not all particles are valid."
) from exc
# The particles whose ionization states are to be recorded
# should be elements or isotopes but not ions or neutrals.
for key in particles.keys():
is_element = particles[key].is_category("element")
has_charge_info = particles[key].is_category(
any_of=["charged", "uncharged"]
)
if not is_element or has_charge_info:
raise ParticleError(
f"{key} is not an element or isotope without "
f"charge information."
)
# We are sorting the elements/isotopes by atomic number and
# mass number since we will often want to plot and analyze
# things and this is the most sensible order.
def _sort_entries_by_atomic_and_mass_numbers(k):
return (
particles[k].atomic_number,
particles[k].mass_number if particles[k].isotope else 0,
)
sorted_keys = sorted(
original_keys, key=_sort_entries_by_atomic_and_mass_numbers
)
_elements_and_isotopes = []
_particle_instances = []
new_ionic_fractions = {}
if inputs_have_quantities:
n_elems = {}
for key in sorted_keys:
new_key = particles[key].symbol
_particle_instances.append(particles[key])
if new_key in _elements_and_isotopes:
raise ParticleError(
"Repeated particles in IonizationStateCollection."
)
nstates_input = len(inputs[key])
nstates = particles[key].atomic_number + 1
if nstates != nstates_input:
raise ParticleError(
f"The ionic fractions array for {key} must "
f"have a length of {nstates}."
)
_elements_and_isotopes.append(new_key)
if inputs_have_quantities:
try:
number_densities = inputs[key].to(u.m ** -3)
n_elem = np.sum(number_densities)
new_ionic_fractions[new_key] = np.array(
number_densities / n_elem
)
n_elems[key] = n_elem
except u.UnitConversionError as exc:
raise ParticleError("Units are not inverse volume.") from exc
elif (
isinstance(inputs[key], np.ndarray)
and inputs[key].dtype.kind == "f"
):
new_ionic_fractions[particles[key].symbol] = inputs[key]
else:
try:
new_ionic_fractions[particles[key].symbol] = np.array(
inputs[key], dtype=np.float
)
except ValueError as exc:
raise ParticleError(
f"Inappropriate ionic fractions for {key}."
) from exc
for key in _elements_and_isotopes:
fractions = new_ionic_fractions[key]
if not np.all(np.isnan(fractions)):
if np.min(fractions) < 0 or np.max(fractions) > 1:
raise ParticleError(
f"Ionic fractions for {key} are not between 0 and 1."
)
if not np.isclose(np.sum(fractions), 1, atol=self.tol, rtol=0):
raise ParticleError(
f"Ionic fractions for {key} are not normalized to 1."
)
# When the inputs provide the densities, the abundances must
# not have been provided because that would be redundant
# or contradictory information. The number density scaling
# factor might or might not have been provided. Have the
# number density scaling factor default to the total number
# of neutrals and ions across all elements and isotopes, if
# it was not provided. Then go ahead and calculate the
# abundances based on that. However, we need to be careful
# that the abundances are not overwritten during the
# instantiation of the class.
if inputs_have_quantities:
if np.isnan(self.n0):
new_n = 0 * u.m ** -3
for key in _elements_and_isotopes:
new_n += n_elems[key]
self.n0 = new_n
new_abundances = {}
for key in _elements_and_isotopes:
new_abundances[key] = np.float(n_elems[key] / self.n0)
self._pars["abundances"] = new_abundances
elif isinstance(inputs, (list, tuple)):
try:
_particle_instances = [Particle(particle) for particle in inputs]
except (InvalidParticleError, TypeError) as exc:
raise ParticleError(
"Invalid inputs to IonizationStateCollection."
) from exc
_particle_instances.sort(key=_atomic_number_and_mass_number)
_elements_and_isotopes = [
particle.symbol for particle in _particle_instances
]
new_ionic_fractions = {
particle.symbol: np.full(
particle.atomic_number + 1, fill_value=np.nan, dtype=np.float64
)
for particle in _particle_instances
}
else:
raise TypeError("Incorrect inputs to set ionic_fractions.")
for i in range(1, len(_particle_instances)):
if _particle_instances[i - 1].element == _particle_instances[i].element:
if (
not _particle_instances[i - 1].isotope
and _particle_instances[i].isotope
):
raise ParticleError(
"Cannot have an element and isotopes of that element."
)
self._particle_instances = _particle_instances
self._base_particles = _elements_and_isotopes
self._ionic_fractions = new_ionic_fractions
def __setitem__(self, key, value):
errmsg = (
f"Cannot set item for this IonizationStateCollection instance for "
f"key = {repr(key)} and value = {repr(value)}"
)
try:
particle = particle_symbol(key)
self.ionic_fractions[key]
except (ParticleError, TypeError):
raise KeyError(
f"{errmsg} because {repr(key)} is an invalid particle."
) from None
except KeyError:
raise KeyError(
f"{errmsg} because {repr(key)} is not one of the base "
f"particles whose ionization state is being kept track "
f"of."
) from None
if isinstance(value, u.Quantity) and value.unit != u.dimensionless_unscaled:
try:
new_number_densities = value.to(u.m ** -3)
except u.UnitConversionError:
raise ValueError(
f"{errmsg} because the units of value do not "
f"correspond to a number density."
) from None
old_n_elem = np.sum(self.number_densities[particle])
new_n_elem = np.sum(new_number_densities)
density_was_nan = np.all(np.isnan(self.number_densities[particle]))
same_density = u.quantity.allclose(old_n_elem, new_n_elem, rtol=self.tol)
if not same_density and not density_was_nan:
raise ValueError(
f"{errmsg} because the old element number density "
f"of {old_n_elem} is not approximately equal to "
f"the new element number density of {new_n_elem}."
)
value = (new_number_densities / new_n_elem).to(u.dimensionless_unscaled)
# If the abundance of this particle has not been defined,
# then set the abundance if there is enough (but not too
# much) information to do so.
abundance_is_undefined = np.isnan(self.abundances[particle])
isnan_of_abundance_values = np.isnan(list(self.abundances.values()))
all_abundances_are_nan = np.all(isnan_of_abundance_values)
n_is_defined = not np.isnan(self.n0)
if abundance_is_undefined:
if n_is_defined:
self._pars["abundances"][particle] = new_n_elem / self.n0
elif all_abundances_are_nan:
self.n0 = new_n_elem
self._pars["abundances"][particle] = 1
else:
raise ParticleError(
f"Cannot set number density of {particle} to "
f"{value * new_n_elem} when the number density "
f"scaling factor is undefined, the abundance "
f"of {particle} is undefined, and some of the "
f"abundances of other elements/isotopes is "
f"defined."
)
try:
new_fractions = np.array(value, dtype=np.float64)
except Exception as exc:
raise TypeError(
f"{errmsg} because value cannot be converted into an "
f"array that represents ionic fractions."
) from exc
# TODO: Create a separate function that makes sure ionic
# TODO: fractions are valid to reduce code repetition. This
# TODO: would probably best go as a private function in
# TODO: ionization_state.py.
required_nstates = atomic_number(particle) + 1
new_nstates = len(new_fractions)
if new_nstates != required_nstates:
raise ValueError(
f"{errmsg} because value must have {required_nstates} "
f"ionization levels but instead corresponds to "
f"{new_nstates} levels."
)
all_nans = np.all(np.isnan(new_fractions))
if not all_nans and (new_fractions.min() < 0 or new_fractions.max() > 1):
raise ValueError(
f"{errmsg} because the new ionic fractions are not "
f"all between 0 and 1."
)
normalized = np.isclose(np.sum(new_fractions), 1, rtol=self.tol)
if not normalized and not all_nans:
raise ValueError(
f"{errmsg} because the ionic fractions are not normalized to one."
)
self._ionic_fractions[particle][:] = new_fractions[:]
