import logging
import numpy as np
import pandas as pd
from astropy import units as u
from tardis import constants as const
from numba import jit, prange
from tardis.plasma.properties.base import (
ProcessingPlasmaProperty,
TransitionProbabilitiesProperty,
)
from tardis.plasma.properties.util import macro_atom
logger = logging.getLogger(__name__)
__all__ = [
"StimulatedEmissionFactor",
"TauSobolev",
"BetaSobolev",
"TransitionProbabilities",
"RawRadBoundBoundTransProbs",
"NonMarkovChainTransitionProbabilities",
]
C_EINSTEIN = (
4.0 * (np.pi * const.e.esu) ** 2 / (const.c.cgs * const.m_e.cgs)
).value # See tardis/docs/physics/plasma/macroatom.rst
[docs]class StimulatedEmissionFactor(ProcessingPlasmaProperty):
"""
Attributes
----------
stimulated_emission_factor : Numpy Array, dtype float
Indexed by lines, columns as zones.
"""
outputs = ("stimulated_emission_factor",)
latex_formula = (r"1-\dfrac{g_{lower}n_{upper}}{g_{upper}n_{lower}}",)
def __init__(self, plasma_parent=None, nlte_species=None):
super(StimulatedEmissionFactor, self).__init__(plasma_parent)
self._g_upper = None
self._g_lower = None
self.nlte_species = nlte_species
[docs] def get_g_lower(self, g, lines_lower_level_index):
if self._g_lower is None:
g_lower = np.array(
g.iloc[lines_lower_level_index], dtype=np.float64
)
self._g_lower = g_lower[np.newaxis].T
return self._g_lower
[docs] def get_g_upper(self, g, lines_upper_level_index):
if self._g_upper is None:
g_upper = np.array(
g.iloc[lines_upper_level_index], dtype=np.float64
)
self._g_upper = g_upper[np.newaxis].T
return self._g_upper
[docs] def calculate(
self,
g,
level_number_density,
lines_lower_level_index,
lines_upper_level_index,
metastability,
lines,
):
n_lower = level_number_density.values.take(
lines_lower_level_index, axis=0, mode="raise"
)
n_upper = level_number_density.values.take(
lines_upper_level_index, axis=0, mode="raise"
)
g_lower = self.get_g_lower(g, lines_lower_level_index)
g_upper = self.get_g_upper(g, lines_upper_level_index)
meta_stable_upper = self.get_metastable_upper(
metastability, lines_upper_level_index
)
stimulated_emission_factor = 1 - (
(g_lower * n_upper) / (g_upper * n_lower)
)
stimulated_emission_factor[n_lower == 0.0] = 0.0
stimulated_emission_factor[
np.isneginf(stimulated_emission_factor)
] = 0.0
stimulated_emission_factor[
meta_stable_upper & (stimulated_emission_factor < 0)
] = 0.0
if self.nlte_species:
nlte_lines_mask = (
lines.reset_index()
.apply(
lambda row: (row.atomic_number, row.ion_number)
in self.nlte_species,
axis=1,
)
.values
)
stimulated_emission_factor[
(stimulated_emission_factor < 0) & nlte_lines_mask[np.newaxis].T
] = 0.0
return stimulated_emission_factor
[docs]class TauSobolev(ProcessingPlasmaProperty):
"""
Attributes
----------
tau_sobolev : Pandas DataFrame, dtype float
Sobolev optical depth for each line. Indexed by line.
Columns as zones.
"""
outputs = ("tau_sobolevs",)
latex_name = (r"\tau_{\textrm{sobolev}}",)
latex_formula = (
r"\dfrac{\pi e^{2}}{m_{e} c}f_{lu}\lambda t_{exp}\
n_{lower} \Big(1-\dfrac{g_{lower}n_{upper}}{g_{upper}n_{lower}}\Big)",
)
def __init__(self, plasma_parent):
super(TauSobolev, self).__init__(plasma_parent)
self.sobolev_coefficient = (
(
((np.pi * const.e.gauss**2) / (const.m_e.cgs * const.c.cgs))
* u.cm
* u.s
/ u.cm**3
)
.to(1)
.value
)
[docs] def calculate(
self,
lines,
level_number_density,
lines_lower_level_index,
time_explosion,
stimulated_emission_factor,
j_blues,
f_lu,
wavelength_cm,
):
f_lu = f_lu.values[np.newaxis].T
wavelength = wavelength_cm.values[np.newaxis].T
n_lower = level_number_density.values.take(
lines_lower_level_index, axis=0, mode="raise"
)
tau_sobolevs = (
self.sobolev_coefficient
* f_lu
* wavelength
* time_explosion
* n_lower
* stimulated_emission_factor
)
if np.any(np.isnan(tau_sobolevs)) or np.any(
np.isinf(np.abs(tau_sobolevs))
):
raise ValueError(
"Some tau_sobolevs are nan, inf, -inf in tau_sobolevs."
" Something went wrong!"
)
return pd.DataFrame(
tau_sobolevs,
index=lines.index,
columns=np.array(level_number_density.columns),
)
[docs]class BetaSobolev(ProcessingPlasmaProperty):
"""
Attributes
----------
beta_sobolev : Numpy Array, dtype float
"""
outputs = ("beta_sobolev",)
latex_name = (r"\beta_{\textrm{sobolev}}",)
[docs] def calculate(self, tau_sobolevs):
if getattr(self, "beta_sobolev", None) is None:
initial = 0.0
else:
initial = self.beta_sobolev
beta_sobolev = pd.DataFrame(
initial, index=tau_sobolevs.index, columns=tau_sobolevs.columns
)
self.calculate_beta_sobolev(
tau_sobolevs.values.ravel(), beta_sobolev.values.ravel()
)
return beta_sobolev
[docs] @staticmethod
@jit(nopython=True, parallel=True)
def calculate_beta_sobolev(tau_sobolevs, beta_sobolevs):
for i in prange(len(tau_sobolevs)):
if tau_sobolevs[i] > 1e3:
beta_sobolevs[i] = tau_sobolevs[i] ** -1
elif tau_sobolevs[i] < 1e-4:
beta_sobolevs[i] = 1 - 0.5 * tau_sobolevs[i]
else:
beta_sobolevs[i] = (1 - np.exp(-tau_sobolevs[i])) / (
tau_sobolevs[i]
)
return beta_sobolevs
[docs]class TransitionProbabilities(ProcessingPlasmaProperty):
"""
Attributes
----------
transition_probabilities : Pandas DataFrame, dtype float
"""
outputs = ("transition_probabilities",)
def __init__(self, plasma_parent):
super(TransitionProbabilities, self).__init__(plasma_parent)
self.initialize = True
self.normalize = True
[docs] def calculate(
self,
atomic_data,
beta_sobolev,
j_blues,
stimulated_emission_factor,
tau_sobolevs,
):
# I wonder why?
# Not sure who wrote this but the answer is that when the plasma is
# first initialised (before the first iteration, without temperature
# values etc.) there are no j_blues values so this just prevents
# an error. Aoife.
if len(j_blues) == 0:
return None
macro_atom_data = self._get_macro_atom_data(atomic_data)
if self.initialize:
self.initialize_macro_atom_transition_type_filters(
atomic_data, macro_atom_data
)
self.transition_probability_coef = (
self._get_transition_probability_coefs(macro_atom_data)
)
self.initialize = False
transition_probabilities = self._calculate_transition_probability(
macro_atom_data, beta_sobolev, j_blues, stimulated_emission_factor
)
transition_probabilities = pd.DataFrame(
transition_probabilities,
index=macro_atom_data.transition_line_id,
columns=tau_sobolevs.columns,
)
return transition_probabilities
def _calculate_transition_probability(
self, macro_atom_data, beta_sobolev, j_blues, stimulated_emission_factor
):
transition_probabilities = np.empty(
(self.transition_probability_coef.shape[0], beta_sobolev.shape[1])
)
# trans_old = self.calculate_transition_probabilities(macro_atom_data, beta_sobolev, j_blues, stimulated_emission_factor)
transition_type = macro_atom_data.transition_type.values
lines_idx = macro_atom_data.lines_idx.values
tpos = macro_atom_data.transition_probability.values
macro_atom.calculate_transition_probabilities(
tpos,
beta_sobolev.values,
j_blues.values,
stimulated_emission_factor,
transition_type,
lines_idx,
self.block_references,
transition_probabilities,
self.normalize,
)
return transition_probabilities
[docs] def calculate_transition_probabilities(
self, macro_atom_data, beta_sobolev, j_blues, stimulated_emission_factor
):
transition_probabilities = self.prepare_transition_probabilities(
macro_atom_data, beta_sobolev, j_blues, stimulated_emission_factor
)
return transition_probabilities
[docs] def initialize_macro_atom_transition_type_filters(
self, atomic_data, macro_atom_data
):
self.transition_up_filter = macro_atom_data.transition_type.values == 1
self.transition_up_line_filter = macro_atom_data.lines_idx.values[
self.transition_up_filter
]
self.block_references = np.hstack(
(
atomic_data.macro_atom_references.block_references,
len(macro_atom_data),
)
)
@staticmethod
def _get_transition_probability_coefs(macro_atom_data):
return macro_atom_data.transition_probability.values[np.newaxis].T
[docs] def prepare_transition_probabilities(
self, macro_atom_data, beta_sobolev, j_blues, stimulated_emission_factor
):
current_beta_sobolev = beta_sobolev.values.take(
macro_atom_data.lines_idx.values, axis=0, mode="raise"
)
transition_probabilities = (
self.transition_probability_coef * current_beta_sobolev
)
j_blues = j_blues.take(
self.transition_up_line_filter, axis=0, mode="raise"
)
macro_stimulated_emission = stimulated_emission_factor.take(
self.transition_up_line_filter, axis=0, mode="raise"
)
transition_probabilities[self.transition_up_filter] *= (
j_blues * macro_stimulated_emission
)
return transition_probabilities
def _normalize_transition_probabilities(self, transition_probabilities):
macro_atom.normalize_transition_probabilities(
transition_probabilities, self.block_references
)
@staticmethod
def _get_macro_atom_data(atomic_data):
try:
return atomic_data.macro_atom_data
except:
logger.debug(
"Macro Atom Data was not found. Instead returning All Macro Atom Data"
)
return atomic_data.macro_atom_data_all
[docs]class NonMarkovChainTransitionProbabilities(TransitionProbabilities):
outputs = ("non_markov_transition_probabilities",)
[docs]class RawRadBoundBoundTransProbs(
TransitionProbabilities, TransitionProbabilitiesProperty
):
"""
Attributes
----------
p_rad_bb : pandas.DataFrame, dtype float
Unnormalized transition probabilities for radiative bound-bound
transitions
"""
outputs = ("p_rad_bb",)
transition_probabilities_outputs = ("p_rad_bb",)
def __init__(self, plasma_parent):
super(RawRadBoundBoundTransProbs, self).__init__(plasma_parent)
self.normalize = False
[docs] def calculate(
self,
atomic_data,
beta_sobolev,
j_blues,
stimulated_emission_factor,
tau_sobolevs,
continuum_interaction_species,
):
p_rad_bb = super().calculate(
atomic_data,
beta_sobolev,
j_blues,
stimulated_emission_factor,
tau_sobolevs,
)
transition_type = atomic_data.macro_atom_data.transition_type.replace(
1, 0
)
index = pd.MultiIndex.from_arrays(
[
atomic_data.macro_atom_data.source_level_idx,
atomic_data.macro_atom_data.destination_level_idx,
transition_type,
]
)
mask_continuum_species = pd.MultiIndex.from_arrays(
[
atomic_data.macro_atom_data.atomic_number,
atomic_data.macro_atom_data.ion_number,
]
).isin(continuum_interaction_species)
p_rad_bb = p_rad_bb.set_index(index, drop=True)[mask_continuum_species]
# To obtain energy-flow rates in cgs from the precomputed transition
# probabilities in the atomic data, we have to multiply by the
# constant C_EINSTEIN and convert from eV to erg.
# See tardis/docs/physics/plasma/macroatom.rst
p_rad_bb = p_rad_bb * C_EINSTEIN * u.eV.to(u.erg)
return p_rad_bb