def parse_exponential(density_dict, v_inner, v_outer, time_explosion):
time_0 = density_dict.pop('time_0', 19.9999584)
if isinstance(time_0, basestring):
time_0 = parse_quantity(time_0).to('s').value
else:
logger.debug('time_0 not supplied for density branch85 - using sensible default %g', time_0)
try:
rho_0 = density_dict.pop('rho_0')
if isinstance(rho_0, basestring):
rho_0 = parse_quantity(rho_0).to('g/cm^3').value
else:
raise KeyError
except KeyError:
rho_0 = 1e-2
logger.warning('rho_o was not given in the config! Using %g', rho_0)
try:
v_0 = density_dict.pop('v_0')
if isinstance(v_0, basestring):
v_0 = parse_quantity(v_0).to('km/s').value
except KeyError:
v_0 = 1
logger.warning('v_0 was not given in the config file! Using %f km/s', v_0)
velocities = 0.5 * (v_inner + v_outer)
densities = calc_exponential_density(velocities, v_0, rho_0)
densities = u.Quantity(densities, 'g/cm^3')
return densities
def parse_power_law(density_dict, v_inner, v_outer, time_explosion):
time_0 = density_dict.pop('time_0', 19.9999584)
if isinstance(time_0, basestring):
time_0 = parse_quantity(time_0).to('s')
else:
logger.debug('time_0 not supplied for density powerlaw - using sensible default %g', time_0)
try:
rho_0 = density_dict.pop('rho_0')
if isinstance(rho_0, basestring):
rho_0 = parse_quantity(rho_0)
else:
raise KeyError
except KeyError:
rho_0 = parse_quantity('1e-2 g/cm^3')
logger.warning('rho_o was not given in the config! Using %g', rho_0)
try:
exponent = density_dict.pop('exponent')
except KeyError:
exponent = 2
logger.warning('exponent was not given in the config file! Using %f', exponent)
try:
v_0 = density_dict.pop('v_0')
if isinstance(v_0, basestring):
v_0 = parse_quantity(v_0).to('cm/s')
except KeyError:
v_0 = parse_quantity('1 cm/s')
logger.warning('v_0 was not given in the config file! Using %f km/s', v_0)
velocities = 0.5 * (v_inner + v_outer)
densities = calc_power_law_density(velocities, v_0, rho_0, exponent)
densities = calculate_density_after_time(densities, time_0, time_explosion)
return densities
def parse_quantity_linspace(quantity_linspace_dictionary, add_one=True):
"""
parse a dictionary of the following kind
{'start': 5000 km/s,
'stop': 10000 km/s,
'num': 1000}
Parameters
----------
quantity_linspace_dictionary: ~dict
add_one: boolean, default: True
Returns
-------
~np.array
"""
start = parse_quantity(quantity_linspace_dictionary['start'])
stop = parse_quantity(quantity_linspace_dictionary['stop'])
try:
stop = stop.to(start.unit)
except u.UnitsError:
raise ConfigurationError('"start" and "stop" keyword must be compatible quantities')
num = quantity_linspace_dictionary['num']
if add_one:
num += 1
return np.linspace(start.value, stop.value, num=num) * start.unit
def test_spectrum_section(self):
assert_almost_equal(self.config['spectrum']['start'].value,
parse_quantity(self.yaml_data['spectrum']['start']).value)
assert_almost_equal(self.config['spectrum']['end'].value,
parse_quantity(self.yaml_data['spectrum']['stop']).value)
assert self.config['spectrum']['bins'] == self.yaml_data['spectrum']['num']
def test_spectrum_section(self):
assert_almost_equal(self.config['spectrum']['start'],
parse_quantity(self.yaml_data['spectrum']['start']))
assert_almost_equal(self.config['spectrum']['end'],
parse_quantity(self.yaml_data['spectrum']['stop']))
assert self.config['spectrum']['bins'] == self.yaml_data['spectrum']['num']
def parse_spectral_bin(spectral_bin_boundary_1, spectral_bin_boundary_2):
spectral_bin_boundary_1 = parse_quantity(spectral_bin_boundary_1).to('Angstrom', u.spectral())
spectral_bin_boundary_2 = parse_quantity(spectral_bin_boundary_2).to('Angstrom', u.spectral())
spectrum_start_wavelength = min(spectral_bin_boundary_1, spectral_bin_boundary_2)
spectrum_end_wavelength = max(spectral_bin_boundary_1, spectral_bin_boundary_2)
return spectrum_start_wavelength, spectrum_end_wavelength
def parse_artis_density(density_file_dict, time_explosion):
density_file = density_file_dict["name"]
for i, line in enumerate(file(density_file)):
if i == 0:
no_of_shells = np.int64(line.strip())
elif i == 1:
time_of_model = u.Quantity(float(line.strip()), "day").to("s")
elif i == 2:
break
velocities, mean_densities_0 = np.recfromtxt(density_file, skip_header=2, usecols=(1, 2), unpack=True)
# converting densities from log(g/cm^3) to g/cm^3 and stretching it to the current ti
velocities = u.Quantity(np.append([0], velocities), "km/s").to("cm/s")
mean_densities_0 = u.Quantity(10 ** mean_densities_0, "g/cm^3")
mean_densities = calculate_density_after_time(mean_densities_0, time_of_model, time_explosion)
# Verifying information
if len(mean_densities) == no_of_shells:
logger.debug("Verified ARTIS file %s (no_of_shells=length of dataset)", density_file)
else:
raise ConfigurationError(
"Error in ARTIS file %s - Number of shells not the same as dataset length" % density_file
)
min_shell = 1
max_shell = no_of_shells
v_inner = velocities[:-1]
v_outer = velocities[1:]
volumes = (4 * np.pi / 3) * (time_of_model ** 3) * (v_outer ** 3 - v_inner ** 3)
masses = (volumes * mean_densities_0 / constants.M_sun).to(1)
logger.info(
"Read ARTIS configuration file %s - found %d zones with total mass %g Msun",
density_file,
no_of_shells,
sum(masses.value),
)
if "v_lowest" in density_file_dict:
v_lowest = parse_quantity(density_file_dict["v_lowest"]).to("cm/s").value
min_shell = v_inner.value.searchsorted(v_lowest)
else:
min_shell = 1
if "v_highest" in density_file_dict:
v_highest = parse_quantity(density_file_dict["v_highest"]).to("cm/s").value
max_shell = v_outer.value.searchsorted(v_highest)
else:
max_shell = no_of_shells
v_inner = v_inner[min_shell:max_shell]
v_outer = v_outer[min_shell:max_shell]
mean_densities = mean_densities[min_shell:max_shell]
return v_inner, v_outer, mean_densities, min_shell, max_shell
def parse_artis_density(density_file_dict, time_explosion):
density_file = density_file_dict['name']
for i, line in enumerate(file(density_file)):
if i == 0:
no_of_shells = np.int64(line.strip())
elif i == 1:
time_of_model = u.Quantity(float(line.strip()), 'day').to('s')
elif i == 2:
break
velocities, mean_densities_0 = np.recfromtxt(density_file, skip_header=2, usecols=(1, 2), unpack=True)
#converting densities from log(g/cm^3) to g/cm^3 and stretching it to the current ti
velocities = u.Quantity(np.append([0], velocities), 'km/s').to('cm/s')
mean_densities_0 = u.Quantity(10 ** mean_densities_0, 'g/cm^3')
mean_densities = calculate_density_after_time(mean_densities_0, time_of_model, time_explosion)
#Verifying information
if len(mean_densities) == no_of_shells:
logger.debug('Verified ARTIS file %s (no_of_shells=length of dataset)', density_file)
else:
raise ConfigurationError(
'Error in ARTIS file %s - Number of shells not the same as dataset length' % density_file)
min_shell = 1
max_shell = no_of_shells
v_inner = velocities[:-1]
v_outer = velocities[1:]
volumes = (4 * np.pi / 3) * (time_of_model ** 3) * ( v_outer ** 3 - v_inner ** 3)
masses = (volumes * mean_densities_0 / constants.M_sun).to(1)
logger.info('Read ARTIS configuration file %s - found %d zones with total mass %g Msun', density_file,
no_of_shells, sum(masses.value))
if 'v_lowest' in density_file_dict:
v_lowest = parse_quantity(density_file_dict['v_lowest']).to('cm/s').value
min_shell = v_inner.value.searchsorted(v_lowest)
else:
min_shell = 1
if 'v_highest' in density_file_dict:
v_highest = parse_quantity(density_file_dict['v_highest']).to('cm/s').value
max_shell = v_outer.value.searchsorted(v_highest)
else:
max_shell = no_of_shells
v_inner = v_inner[min_shell:max_shell]
v_outer = v_outer[min_shell:max_shell]
mean_densities = mean_densities[min_shell:max_shell]
return v_inner, v_outer, mean_densities, min_shell, max_shell
def test_velocities(self):
assert_almost_equal(
parse_quantity(self.yaml_data['model']['structure']['velocity']
['start']).cgs.value,
self.config.structure.v_inner[0].cgs.value)
assert_almost_equal(
parse_quantity(self.yaml_data['model']['structure']['velocity']
['stop']).cgs.value,
self.config.structure.v_outer[-1].cgs.value)
assert len(self.config.structure.v_outer) == (
self.yaml_data['model']['structure']['velocity']['num'])
def parse_supernova_section(supernova_dict):
"""
Parse the supernova section
Parameters
----------
supernova_dict: dict
YAML parsed supernova dict
Returns
-------
config_dict: dict
"""
config_dict = {}
#parse luminosity
luminosity_value, luminosity_unit = supernova_dict[
'luminosity_requested'].strip().split()
if luminosity_unit == 'log_lsun':
config_dict['luminosity_requested'] = 10**(
float(luminosity_value) +
np.log10(constants.L_sun.cgs.value)) * u.erg / u.s
else:
config_dict['luminosity_requested'] = (
float(luminosity_value) * u.Unit(luminosity_unit)).to('erg/s')
config_dict['time_explosion'] = parse_quantity(
supernova_dict['time_explosion']).to('s')
if 'distance' in supernova_dict:
config_dict['distance'] = parse_quantity(supernova_dict['distance'])
else:
config_dict['distance'] = None
if 'luminosity_wavelength_start' in supernova_dict:
config_dict['luminosity_nu_end'] = parse_quantity(supernova_dict['luminosity_wavelength_start']). \
to('Hz', u.spectral())
else:
config_dict['luminosity_nu_end'] = np.inf * u.Hz
if 'luminosity_wavelength_end' in supernova_dict:
config_dict['luminosity_nu_start'] = parse_quantity(supernova_dict['luminosity_wavelength_end']). \
to('Hz', u.spectral())
else:
config_dict['luminosity_nu_start'] = 0.0 * u.Hz
return config_dict
def parse_supernova_section(supernova_dict):
"""
Parse the supernova section
Parameters
----------
supernova_dict: dict
YAML parsed supernova dict
Returns
-------
config_dict: dict
"""
config_dict = {}
# parse luminosity
luminosity_value, luminosity_unit = supernova_dict["luminosity_requested"].strip().split()
if luminosity_unit == "log_lsun":
config_dict["luminosity_requested"] = (
10 ** (float(luminosity_value) + np.log10(constants.L_sun.cgs.value)) * u.erg / u.s
)
else:
config_dict["luminosity_requested"] = (float(luminosity_value) * u.Unit(luminosity_unit)).to("erg/s")
config_dict["time_explosion"] = parse_quantity(supernova_dict["time_explosion"]).to("s")
if "distance" in supernova_dict:
config_dict["distance"] = parse_quantity(supernova_dict["distance"])
else:
config_dict["distance"] = None
if "luminosity_wavelength_start" in supernova_dict:
config_dict["luminosity_nu_end"] = parse_quantity(supernova_dict["luminosity_wavelength_start"]).to(
"Hz", u.spectral()
)
else:
config_dict["luminosity_nu_end"] = np.inf * u.Hz
if "luminosity_wavelength_end" in supernova_dict:
config_dict["luminosity_nu_start"] = parse_quantity(supernova_dict["luminosity_wavelength_end"]).to(
"Hz", u.spectral()
)
else:
config_dict["luminosity_nu_start"] = 0.0 * u.Hz
return config_dict
def parse_supernova_section(supernova_dict):
"""
Parse the supernova section
Parameters
----------
supernova_dict: dict
YAML parsed supernova dict
Returns
-------
config_dict: dict
"""
config_dict = {}
#parse luminosity
luminosity_value, luminosity_unit = supernova_dict['luminosity_requested'].strip().split()
if luminosity_unit == 'log_lsun':
config_dict['luminosity_requested'] = 10 ** (
float(luminosity_value) + np.log10(constants.L_sun.cgs.value)) * u.erg / u.s
else:
config_dict['luminosity_requested'] = (float(luminosity_value) * u.Unit(luminosity_unit)).to('erg/s')
config_dict['time_explosion'] = parse_quantity(supernova_dict['time_explosion']).to('s')
if 'distance' in supernova_dict:
config_dict['distance'] = parse_quantity(supernova_dict['distance'])
else:
config_dict['distance'] = None
if 'luminosity_wavelength_start' in supernova_dict:
config_dict['luminosity_nu_end'] = parse_quantity(supernova_dict['luminosity_wavelength_start']). \
to('Hz', u.spectral())
else:
config_dict['luminosity_nu_end'] = np.inf * u.Hz
if 'luminosity_wavelength_end' in supernova_dict:
config_dict['luminosity_nu_start'] = parse_quantity(supernova_dict['luminosity_wavelength_end']). \
to('Hz', u.spectral())
else:
config_dict['luminosity_nu_start'] = 0.0 * u.Hz
return config_dict
def test_parse_quantity():
q1 = parse_quantity('5 km/s')
assert q1.value == 5.
assert q1.unit == u.Unit('km/s')
with pytest.raises(MalformedQuantityError):
parse_quantity(5)
with pytest.raises(MalformedQuantityError):
parse_quantity('abcd')
with pytest.raises(MalformedQuantityError):
parse_quantity('a abcd')
with pytest.raises(MalformedQuantityError):
parse_quantity('5 abcd')
def test_parse_quantity():
q1 = parse_quantity('5 km/s')
assert q1.value == 5.
assert q1.unit == u.Unit('km/s')
with pytest.raises(MalformedQuantityError):
parse_quantity(5)
with pytest.raises(MalformedQuantityError):
parse_quantity('abcd')
with pytest.raises(MalformedQuantityError):
parse_quantity('a abcd')
with pytest.raises(MalformedQuantityError):
parse_quantity('5 abcd')
def read_cmfgen_density(fname):
"""
Reading a density file of the following structure (example; lines starting with a hash will be ignored):
The first density describes the mean density in the center of the model and is not used.
The file consists of a header row and next row contains unit of the respective attributes
velocity densities electron_densities temperature
km/s g/cm^3 /cm^3 K
871.66905 4.2537191e-09 2.5953807e+14 7.6395577
877.44269 4.2537191e-09 2.5953807e+14 7.6395577
Rest columns contain abundances of elements and isotopes
Parameters
----------
fname: str
filename or path with filename
Returns
-------
time_of_model: ~astropy.units.Quantity
time at which the model is valid
velocity: ~np.ndarray
mean_density: ~np.ndarray
electron_densities: ~np.ndarray
temperature: ~np.ndarray
"""
warnings.warn("The current CMFGEN model parser is deprecated",
DeprecationWarning)
df = pd.read_csv(fname, comment='#', delimiter='\s+', skiprows=[0, 2])
with open(fname) as fh:
for row_index, line in enumerate(fh):
if row_index == 0:
time_of_model_string = line.strip().replace('t0:', '')
time_of_model = parse_quantity(time_of_model_string)
elif row_index == 2:
quantities = line.split()
velocity = u.Quantity(df['velocity'].values, quantities[0]).to('cm/s')
temperature = u.Quantity(df['temperature'].values, quantities[1])[1:]
mean_density = u.Quantity(df['densities'].values, quantities[2])[1:]
electron_densities = u.Quantity(df['electron_densities'].values,
quantities[3])[1:]
return time_of_model, velocity, mean_density, electron_densities, temperature
def parse_branch85(density_dict, v_inner, v_outer, time_explosion):
time_0 = density_dict.pop('time_0', 19.9999584)
if isinstance(time_0, basestring):
time_0 = parse_quantity(time_0).to('s')
else:
time_0 *= u.s
logger.debug('time_0 not supplied for density branch85 - using sensible default %g', time_0)
density_coefficient = density_dict.pop('density_coefficient', None)
if density_coefficient is None:
density_coefficient = 3e29 * u.Unit('g/cm^3')
logger.debug('density_coefficient not supplied for density type branch85 - using sensible default %g',
density_coefficient)
else:
density_coefficient = parse_quantity(density_coefficient)
velocities = 0.5 * (v_inner + v_outer)
densities = density_coefficient * (velocities.value * 1e-5) ** -7
densities = calculate_density_after_time(densities, time_0, time_explosion)
return densities
def parse_exponential(density_dict, v_inner, v_outer, time_explosion):
time_0 = density_dict.pop('time_0', 19.9999584)
if isinstance(time_0, basestring):
time_0 = parse_quantity(time_0).to('s').value
else:
logger.debug('time_0 not supplied for density branch85 - using sensible default %g', time_0)
try:
rho_0 = float(density_dict.pop('rho_0'))
except KeyError:
rho_0 = 1e-2
logger.warning('rho_o was not given in the config! Using %g', rho_0)
try:
exponent = density_dict.pop('exponent')
except KeyError:
exponent = 2
logger.warning('exponent was not given in the config file! Using %f', exponent)
velocities = 0.5 * (v_inner + v_outer)
densities = calculate_exponential_densities(velocities, v_inner[0], rho_0, exponent)
return densities
def read_simple_ascii_density(fname):
"""
Reading a density file of the following structure (example; lines starting with a hash will be ignored):
The first density describes the mean density in the center of the model and is not used.
5 s
#index velocity [km/s] density [g/cm^3]
0 1.1e4 1.6e8
1 1.2e4 1.7e8
Parameters
----------
fname: str
filename or path with filename
Returns
-------
time_of_model: ~astropy.units.Quantity
time at which the model is valid
data: ~pandas.DataFrame
data frame containing index, velocity (in km/s) and density
"""
with open(fname) as fh:
time_of_model_string = fh.readline().strip()
time_of_model = parse_quantity(time_of_model_string)
data = recfromtxt(fname,
skip_header=1,
names=('index', 'velocity', 'density'),
dtype=(int, float, float))
velocity = (data['velocity'] * u.km / u.s).to('cm/s')
v_inner, v_outer = velocity[:-1], velocity[1:]
mean_density = (data['density'] * u.Unit('g/cm^3'))[1:]
return time_of_model, data['index'], v_inner, v_outer, mean_density
def read_simple_ascii_density(fname):
"""
Reading a density file of the following structure (example; lines starting with a hash will be ignored):
The first density describes the mean density in the center of the model and is not used.
5 s
#index velocity [km/s] density [g/cm^3]
0 1.1e4 1.6e8
1 1.2e4 1.7e8
Parameters
----------
fname: str
filename or path with filename
Returns
-------
time_of_model: ~astropy.units.Quantity
time at which the model is valid
data: ~pandas.DataFrame
data frame containing index, velocity (in km/s) and density
"""
with open(fname) as fh:
time_of_model_string = fh.readline().strip()
time_of_model = parse_quantity(time_of_model_string)
data = recfromtxt(fname, skip_header=1,
names=('index', 'velocity', 'density'),
dtype=(int, float, float))
velocity = (data['velocity'] * u.km / u.s).to('cm/s')
mean_density = (data['density'] * u.Unit('g/cm^3'))[1:]
return time_of_model, velocity, mean_density
def parse_artis_model_setup_files(model_file_section_dict, time_explosion):
###### Reading the structure part of the ARTIS file pair
structure_fname = model_file_section_dict['structure_fname']
for i, line in enumerate(file(structure_fname)):
if i == 0:
no_of_shells = np.int64(line.strip())
elif i == 1:
time_of_model = u.Quantity(float(line.strip()), 'day').to('s')
elif i == 2:
break
artis_model_columns = [
'velocities', 'mean_densities_0', 'ni56_fraction', 'co56_fraction',
'fe52_fraction', 'cr48_fraction'
]
artis_model = np.recfromtxt(structure_fname,
skip_header=2,
usecols=(1, 2, 4, 5, 6, 7),
unpack=True,
dtype=[(item, np.float64)
for item in artis_model_columns])
#converting densities from log(g/cm^3) to g/cm^3 and stretching it to the current ti
velocities = u.Quantity(np.append([0], artis_model['velocities']),
'km/s').to('cm/s')
mean_densities_0 = u.Quantity(10**artis_model['mean_densities_0'],
'g/cm^3')
mean_densities = calculate_density_after_time(mean_densities_0,
time_of_model,
time_explosion)
#Verifying information
if len(mean_densities) == no_of_shells:
logger.debug(
'Verified ARTIS model structure file %s (no_of_shells=length of dataset)',
structure_fname)
else:
raise ConfigurationError(
'Error in ARTIS file %s - Number of shells not the same as dataset length'
% structure_fname)
v_inner = velocities[:-1]
v_outer = velocities[1:]
volumes = (4 * np.pi / 3) * (time_of_model**
3) * (v_outer**3 - v_inner**3)
masses = (volumes * mean_densities_0 / constants.M_sun).to(1)
logger.info(
'Read ARTIS configuration file %s - found %d zones with total mass %g Msun',
structure_fname, no_of_shells, sum(masses.value))
if 'v_lowest' in model_file_section_dict:
v_lowest = parse_quantity(
model_file_section_dict['v_lowest']).to('cm/s').value
min_shell = v_inner.value.searchsorted(v_lowest)
else:
min_shell = 1
if 'v_highest' in model_file_section_dict:
v_highest = parse_quantity(
model_file_section_dict['v_highest']).to('cm/s').value
max_shell = v_outer.value.searchsorted(v_highest)
else:
max_shell = no_of_shells
artis_model = artis_model[min_shell:max_shell]
v_inner = v_inner[min_shell:max_shell]
v_outer = v_outer[min_shell:max_shell]
mean_densities = mean_densities[min_shell:max_shell]
###### Reading the abundance part of the ARTIS file pair
abundances_fname = model_file_section_dict['abundances_fname']
abundances = pd.DataFrame(
np.loadtxt(abundances_fname)[min_shell:max_shell, 1:].transpose(),
index=np.arange(1, 31))
ni_stable = abundances.ix[28] - artis_model['ni56_fraction']
co_stable = abundances.ix[27] - artis_model['co56_fraction']
fe_stable = abundances.ix[26] - artis_model['fe52_fraction']
mn_stable = abundances.ix[25] - 0.0
cr_stable = abundances.ix[24] - artis_model['cr48_fraction']
v_stable = abundances.ix[23] - 0.0
ti_stable = abundances.ix[22] - 0.0
abundances.ix[28] = ni_stable
abundances.ix[28] += artis_model['ni56_fraction'] * np.exp(
-(time_explosion * inv_ni56_efolding_time).to(1).value)
abundances.ix[27] = co_stable
abundances.ix[27] += artis_model['co56_fraction'] * np.exp(
-(time_explosion * inv_co56_efolding_time).to(1).value)
abundances.ix[27] += (inv_ni56_efolding_time * artis_model['ni56_fraction'] /
(inv_ni56_efolding_time - inv_co56_efolding_time)) * \
(np.exp(-(inv_co56_efolding_time * time_explosion).to(1).value) - np.exp(
-(inv_ni56_efolding_time * time_explosion).to(1).value))
abundances.ix[26] = fe_stable
abundances.ix[26] += artis_model['fe52_fraction'] * np.exp(
-(time_explosion * inv_fe52_efolding_time).to(1).value)
abundances.ix[26] += (
(artis_model['co56_fraction'] * inv_ni56_efolding_time -
artis_model['co56_fraction'] * inv_co56_efolding_time +
artis_model['ni56_fraction'] * inv_ni56_efolding_time -
artis_model['ni56_fraction'] * inv_co56_efolding_time -
artis_model['co56_fraction'] * inv_ni56_efolding_time *
np.exp(-(inv_co56_efolding_time * time_explosion).to(1).value) +
artis_model['co56_fraction'] * inv_co56_efolding_time *
np.exp(-(inv_co56_efolding_time * time_explosion).to(1).value) -
artis_model['ni56_fraction'] * inv_ni56_efolding_time *
np.exp(-(inv_co56_efolding_time * time_explosion).to(1).value) +
artis_model['ni56_fraction'] * inv_co56_efolding_time *
np.exp(-(inv_ni56_efolding_time * time_explosion).to(1).value)) /
(inv_ni56_efolding_time - inv_co56_efolding_time))
abundances.ix[25] = mn_stable
abundances.ix[25] += (inv_fe52_efolding_time * artis_model['fe52_fraction'] /
(inv_fe52_efolding_time - inv_mn52_efolding_time)) * \
(np.exp(-(inv_mn52_efolding_time * time_explosion).to(1).value) - np.exp(
-(inv_fe52_efolding_time * time_explosion).to(1).value))
abundances.ix[24] = cr_stable
abundances.ix[24] += artis_model['cr48_fraction'] * np.exp(
-(time_explosion * inv_cr48_efolding_time).to(1).value)
abundances.ix[24] += (
(artis_model['fe52_fraction'] * inv_fe52_efolding_time -
artis_model['fe52_fraction'] * inv_mn52_efolding_time -
artis_model['fe52_fraction'] * inv_fe52_efolding_time *
np.exp(-(inv_mn52_efolding_time * time_explosion).to(1).value) +
artis_model['fe52_fraction'] * inv_mn52_efolding_time *
np.exp(-(inv_fe52_efolding_time * time_explosion).to(1).value)) /
(inv_fe52_efolding_time - inv_mn52_efolding_time))
abundances.ix[23] = v_stable
abundances.ix[23] += (inv_cr48_efolding_time * artis_model['cr48_fraction'] /
(inv_cr48_efolding_time - inv_v48_efolding_time)) * \
(np.exp(-(inv_v48_efolding_time * time_explosion).to(1).value) - np.exp(
-(inv_cr48_efolding_time * time_explosion).to(1).value))
abundances.ix[22] = ti_stable
abundances.ix[22] += (
(artis_model['cr48_fraction'] * inv_cr48_efolding_time -
artis_model['cr48_fraction'] * inv_v48_efolding_time -
artis_model['cr48_fraction'] * inv_cr48_efolding_time *
np.exp(-(inv_v48_efolding_time * time_explosion).to(1).value) +
artis_model['cr48_fraction'] * inv_v48_efolding_time *
np.exp(-(inv_cr48_efolding_time * time_explosion).to(1).value)) /
(inv_cr48_efolding_time - inv_v48_efolding_time))
if 'split_shells' in model_file_section_dict:
split_shells = int(model_file_section_dict['split_shells'])
else:
split_shells = 1
if split_shells > 1:
logger.info('Increasing the number of shells by a factor of %s' %
split_shells)
no_of_shells = len(v_inner)
velocities = quantity_linspace(v_inner[0], v_outer[-1],
no_of_shells * split_shells + 1)
v_inner = velocities[:-1]
v_outer = velocities[1:]
old_mean_densities = mean_densities
mean_densities = np.empty(
no_of_shells * split_shells) * old_mean_densities.unit
new_abundance_data = np.empty(
(abundances.values.shape[0], no_of_shells * split_shells))
for i in xrange(split_shells):
mean_densities[i::split_shells] = old_mean_densities
new_abundance_data[:, i::split_shells] = abundances.values
abundances = pd.DataFrame(new_abundance_data,
index=abundances.index)
#def parser_simple_ascii_model
return v_inner, v_outer, mean_densities, abundances
def test_quantity_parser_normal():
q1 = parse_quantity('5 km/s')
assert q1.value == 5.
assert q1.unit == u.Unit('km/s')
def test_quantity_parser_malformed_quantity2():
with pytest.raises(MalformedQuantityError):
q1 = parse_quantity('5 abcd')
def parse_artis_model_setup_files(model_file_section_dict, time_explosion):
###### Reading the structure part of the ARTIS file pair
structure_fname = model_file_section_dict['structure_fname']
for i, line in enumerate(file(structure_fname)):
if i == 0:
no_of_shells = np.int64(line.strip())
elif i == 1:
time_of_model = u.Quantity(float(line.strip()), 'day').to('s')
elif i == 2:
break
artis_model_columns = ['velocities', 'mean_densities_0', 'ni56_fraction', 'co56_fraction', 'fe52_fraction',
'cr48_fraction']
artis_model = np.recfromtxt(structure_fname, skip_header=2, usecols=(1, 2, 4, 5, 6, 7), unpack=True,
dtype=[(item, np.float64) for item in artis_model_columns])
#converting densities from log(g/cm^3) to g/cm^3 and stretching it to the current ti
velocities = u.Quantity(np.append([0], artis_model['velocities']), 'km/s').to('cm/s')
mean_densities_0 = u.Quantity(10 ** artis_model['mean_densities_0'], 'g/cm^3')
mean_densities = calculate_density_after_time(mean_densities_0, time_of_model, time_explosion)
#Verifying information
if len(mean_densities) == no_of_shells:
logger.debug('Verified ARTIS model structure file %s (no_of_shells=length of dataset)', structure_fname)
else:
raise ConfigurationError(
'Error in ARTIS file %s - Number of shells not the same as dataset length' % structure_fname)
v_inner = velocities[:-1]
v_outer = velocities[1:]
volumes = (4 * np.pi / 3) * (time_of_model ** 3) * ( v_outer ** 3 - v_inner ** 3)
masses = (volumes * mean_densities_0 / constants.M_sun).to(1)
logger.info('Read ARTIS configuration file %s - found %d zones with total mass %g Msun', structure_fname,
no_of_shells, sum(masses.value))
if 'v_lowest' in model_file_section_dict:
v_lowest = parse_quantity(model_file_section_dict['v_lowest']).to('cm/s').value
min_shell = v_inner.value.searchsorted(v_lowest)
else:
min_shell = 1
if 'v_highest' in model_file_section_dict:
v_highest = parse_quantity(model_file_section_dict['v_highest']).to('cm/s').value
max_shell = v_outer.value.searchsorted(v_highest)
else:
max_shell = no_of_shells
artis_model = artis_model[min_shell:max_shell]
v_inner = v_inner[min_shell:max_shell]
v_outer = v_outer[min_shell:max_shell]
mean_densities = mean_densities[min_shell:max_shell]
###### Reading the abundance part of the ARTIS file pair
abundances_fname = model_file_section_dict['abundances_fname']
abundances = pd.DataFrame(np.loadtxt(abundances_fname)[min_shell:max_shell, 1:].transpose(),
index=np.arange(1, 31))
ni_stable = abundances.ix[28] - artis_model['ni56_fraction']
co_stable = abundances.ix[27] - artis_model['co56_fraction']
fe_stable = abundances.ix[26] - artis_model['fe52_fraction']
mn_stable = abundances.ix[25] - 0.0
cr_stable = abundances.ix[24] - artis_model['cr48_fraction']
v_stable = abundances.ix[23] - 0.0
ti_stable = abundances.ix[22] - 0.0
abundances.ix[28] = ni_stable
abundances.ix[28] += artis_model['ni56_fraction'] * np.exp(
-(time_explosion * inv_ni56_efolding_time).to(1).value)
abundances.ix[27] = co_stable
abundances.ix[27] += artis_model['co56_fraction'] * np.exp(
-(time_explosion * inv_co56_efolding_time).to(1).value)
abundances.ix[27] += (inv_ni56_efolding_time * artis_model['ni56_fraction'] /
(inv_ni56_efolding_time - inv_co56_efolding_time)) * \
(np.exp(-(inv_co56_efolding_time * time_explosion).to(1).value) - np.exp(
-(inv_ni56_efolding_time * time_explosion).to(1).value))
abundances.ix[26] = fe_stable
abundances.ix[26] += artis_model['fe52_fraction'] * np.exp(
-(time_explosion * inv_fe52_efolding_time).to(1).value)
abundances.ix[26] += ((artis_model['co56_fraction'] * inv_ni56_efolding_time
- artis_model['co56_fraction'] * inv_co56_efolding_time
+ artis_model['ni56_fraction'] * inv_ni56_efolding_time
- artis_model['ni56_fraction'] * inv_co56_efolding_time
- artis_model['co56_fraction'] * inv_ni56_efolding_time * np.exp(
-(inv_co56_efolding_time * time_explosion).to(1).value)
+ artis_model['co56_fraction'] * inv_co56_efolding_time * np.exp(
-(inv_co56_efolding_time * time_explosion).to(1).value)
- artis_model['ni56_fraction'] * inv_ni56_efolding_time * np.exp(
-(inv_co56_efolding_time * time_explosion).to(1).value)
+ artis_model['ni56_fraction'] * inv_co56_efolding_time * np.exp(
-(inv_ni56_efolding_time * time_explosion).to(1).value))
/ (inv_ni56_efolding_time - inv_co56_efolding_time))
abundances.ix[25] = mn_stable
abundances.ix[25] += (inv_fe52_efolding_time * artis_model['fe52_fraction'] /
(inv_fe52_efolding_time - inv_mn52_efolding_time)) * \
(np.exp(-(inv_mn52_efolding_time * time_explosion).to(1).value) - np.exp(
-(inv_fe52_efolding_time * time_explosion).to(1).value))
abundances.ix[24] = cr_stable
abundances.ix[24] += artis_model['cr48_fraction'] * np.exp(
-(time_explosion * inv_cr48_efolding_time).to(1).value)
abundances.ix[24] += ((artis_model['fe52_fraction'] * inv_fe52_efolding_time
- artis_model['fe52_fraction'] * inv_mn52_efolding_time
- artis_model['fe52_fraction'] * inv_fe52_efolding_time * np.exp(
-(inv_mn52_efolding_time * time_explosion).to(1).value)
+ artis_model['fe52_fraction'] * inv_mn52_efolding_time * np.exp(
-(inv_fe52_efolding_time * time_explosion).to(1).value))
/ (inv_fe52_efolding_time - inv_mn52_efolding_time))
abundances.ix[23] = v_stable
abundances.ix[23] += (inv_cr48_efolding_time * artis_model['cr48_fraction'] /
(inv_cr48_efolding_time - inv_v48_efolding_time)) * \
(np.exp(-(inv_v48_efolding_time * time_explosion).to(1).value) - np.exp(
-(inv_cr48_efolding_time * time_explosion).to(1).value))
abundances.ix[22] = ti_stable
abundances.ix[22] += ((artis_model['cr48_fraction'] * inv_cr48_efolding_time
- artis_model['cr48_fraction'] * inv_v48_efolding_time
- artis_model['cr48_fraction'] * inv_cr48_efolding_time * np.exp(
-(inv_v48_efolding_time * time_explosion).to(1).value)
+ artis_model['cr48_fraction'] * inv_v48_efolding_time * np.exp(
-(inv_cr48_efolding_time * time_explosion).to(1).value))
/ (inv_cr48_efolding_time - inv_v48_efolding_time))
if 'split_shells' in model_file_section_dict:
split_shells = int(model_file_section_dict['split_shells'])
else:
split_shells = 1
if split_shells > 1:
logger.info('Increasing the number of shells by a factor of %s' % split_shells)
no_of_shells = len(v_inner)
velocities = np.linspace(v_inner[0], v_outer[-1], no_of_shells * split_shells + 1)
v_inner = velocities[:-1]
v_outer = velocities[1:]
old_mean_densities = mean_densities
mean_densities = np.empty(no_of_shells * split_shells) * old_mean_densities.unit
new_abundance_data = np.empty((abundances.values.shape[0], no_of_shells * split_shells))
for i in xrange(split_shells):
mean_densities[i::split_shells] = old_mean_densities
new_abundance_data[:, i::split_shells] = abundances.values
abundances = pd.DataFrame(new_abundance_data, index=abundances.index)
#def parser_simple_ascii_model
return v_inner, v_outer, mean_densities, abundances
def parse_uniform(density_dict, v_inner, v_outer, time_explosion):
no_of_shells = len(v_inner)
return parse_quantity(density_dict['value']).to('g cm^-3') * np.ones(no_of_shells)
def test_quantity_parser_normal():
q1 = parse_quantity('5 km/s')
assert q1.value == 5.
assert q1.unit == u.Unit('km/s')
def test_quantity_parser_malformed_quantity2():
with pytest.raises(MalformedQuantityError):
q1 = parse_quantity('5 abcd')
def test_velocities(self):
assert_almost_equal(parse_quantity(self.yaml_data['model']['structure']['velocity']['start']),
self.config.structure.v_inner[0])
assert_almost_equal(parse_quantity(self.yaml_data['model']['structure']['velocity']['stop']),
self.config.structure.v_outer[-1])
assert len(self.config.structure.v_outer) == (self.yaml_data['model']['structure']['velocity']['num'])
def from_config_dict(cls, raw_dict, atom_data=None, test_parser=False):
"""
Reading in from a YAML file and commandline args. Preferring commandline args when given
Parameters
----------
fname : filename for the yaml file
args : namespace object
Not implemented Yet
Returns
-------
`tardis.config_reader.TARDISConfiguration`
"""
config_dict = {}
raw_dict = copy.deepcopy(raw_dict)
#First let's see if we can find an atom_db anywhere:
if test_parser:
atom_data = None
elif 'atom_data' in raw_dict.keys():
atom_data_fname = raw_dict['atom_data']
config_dict['atom_data_fname'] = atom_data_fname
else:
raise ConfigurationError('No atom_data key found in config or command line')
if atom_data is None and not test_parser:
logger.info('Reading Atomic Data from %s', atom_data_fname)
atom_data = atomic.AtomData.from_hdf5(atom_data_fname)
else:
atom_data = atom_data
#Parsing supernova dictionary
config_dict['supernova'] = parse_supernova_section(raw_dict['supernova'])
#Parsing the model section
model_section = raw_dict.pop('model')
v_inner = None
v_outer = None
mean_densities = None
abundances = None
if 'file' in model_section:
v_inner, v_outer, mean_densities, abundances = parse_model_file_section(model_section.pop('file'),
config_dict['supernova']['time_explosion'])
no_of_shells = len(v_inner)
structure_config_dict = {}
if 'structure' in model_section:
#Trying to figure out the structure (number of shells)
structure_section = model_section.pop('structure')
inner_boundary_index, outer_boundary_index = None, None
try:
structure_section_type = structure_section['type']
except KeyError:
raise ConfigurationError('Structure section requires "type" keyword')
if structure_section_type == 'specific':
velocities = parse_quantity_linspace(structure_section['velocity']).to('cm/s')
v_inner, v_outer = velocities[:-1], velocities[1:]
mean_densities = parse_density_section(structure_section['density'], v_inner, v_outer,
config_dict['supernova']['time_explosion'])
elif structure_section_type == 'file':
v_inner_boundary, v_outer_boundary = structure_section.get('v_inner_boundary', 0 * u.km/u.s), \
structure_section.get('v_outer_boundary', np.inf * u.km/u.s)
if not hasattr(v_inner_boundary, 'unit'):
v_inner_boundary = parse_quantity(v_inner_boundary)
if not hasattr(v_outer_boundary, 'unit'):
v_outer_boundary = parse_quantity(v_outer_boundary)
v_inner, v_outer, mean_densities, inner_boundary_index, outer_boundary_index =\
read_density_file(structure_section['filename'], structure_section['filetype'],
config_dict['supernova']['time_explosion'], v_inner_boundary, v_outer_boundary)
else:
raise ConfigurationError('structure section required in configuration file')
r_inner = config_dict['supernova']['time_explosion'] * v_inner
r_outer = config_dict['supernova']['time_explosion'] * v_outer
r_middle = 0.5 * (r_inner + r_outer)
structure_config_dict['v_inner'] = v_inner
structure_config_dict['v_outer'] = v_outer
structure_config_dict['mean_densities'] = mean_densities
no_of_shells = len(v_inner)
structure_config_dict['no_of_shells'] = no_of_shells
structure_config_dict['r_inner'] = r_inner
structure_config_dict['r_outer'] = r_outer
structure_config_dict['r_middle'] = r_middle
structure_config_dict['volumes'] = (4. / 3) * np.pi * (r_outer ** 3 - r_inner ** 3)
config_dict['structure'] = structure_config_dict
#Now that the structure section is parsed we move on to the abundances
abundances_section = model_section.pop('abundances')
abundances_type = abundances_section.pop('type')
if abundances_type == 'uniform':
abundances = pd.DataFrame(columns=np.arange(no_of_shells),
index=pd.Index(np.arange(1, 120), name='atomic_number'), dtype=np.float64)
for element_symbol_string in abundances_section:
z = element_symbol2atomic_number(element_symbol_string)
abundances.ix[z] = float(abundances_section[element_symbol_string])
elif abundances_type == 'file':
index, abundances = read_abundances_file(abundances_section['filename'], abundances_section['filetype'],
inner_boundary_index, outer_boundary_index)
if len(index) != no_of_shells:
raise ConfigurationError('The abundance file specified has not the same number of cells'
'as the specified density profile')
abundances = abundances.replace(np.nan, 0.0)
abundances = abundances[abundances.sum(axis=1) > 0]
norm_factor = abundances.sum(axis=0)
if np.any(np.abs(norm_factor - 1) > 1e-12):
logger.warning("Abundances have not been normalized to 1. - normalizing")
abundances /= norm_factor
config_dict['abundances'] = abundances
########### DOING PLASMA SECTION ###############
plasma_section = raw_dict.pop('plasma')
plasma_config_dict = {}
if plasma_section['ionization'] not in ('nebular', 'lte'):
raise ConfigurationError('plasma_type only allowed to be "nebular" or "lte"')
plasma_config_dict['ionization'] = plasma_section['ionization']
if plasma_section['excitation'] not in ('dilute-lte', 'lte'):
raise ConfigurationError('plasma_type only allowed to be "nebular" or "lte"')
plasma_config_dict['excitation'] = plasma_section['excitation']
if plasma_section['radiative_rates_type'] not in ('dilute-blackbody', 'detailed'):
raise ConfigurationError('radiative_rates_types must be either "dilute-blackbody" or "detailed"')
plasma_config_dict['radiative_rates_type'] = plasma_section['radiative_rates_type']
if plasma_section['line_interaction_type'] not in ('scatter', 'downbranch', 'macroatom'):
raise ConfigurationError('radiative_rates_types must be either "scatter", "downbranch", or "macroatom"')
plasma_config_dict['line_interaction_type'] = plasma_section['line_interaction_type']
if 'w_epsilon' in plasma_section:
plasma_config_dict['w_epsilon'] = plasma_section['w_epsilon']
else:
logger.warn('"w_epsilon" not specified in plasma section - setting it to 1e-10')
plasma_config_dict['w_epsilon'] = 1e-10
if 'delta_treatment' in plasma_section:
plasma_config_dict['delta_treatment'] = plasma_section['delta_treatment']
else:
logger.warn('"delta_treatment" not specified in plasma section - defaulting to None')
plasma_config_dict['delta_treatment'] = None
if 'initial_t_inner' in plasma_section:
plasma_config_dict['t_inner'] = parse_quantity(plasma_section['initial_t_inner']).to('K')
else:
plasma_config_dict['t_inner'] = (((config_dict['supernova']['luminosity_requested'] / \
(4 * np.pi * r_inner[0]**2 * constants.sigma_sb))**.5)**.5).to('K')
logger.info('"initial_t_inner" is not specified in the plasma section - '
'initializing to %s with given luminosity', plasma_config_dict['t_inner'])
if 'initial_t_rads' in plasma_section:
if isinstance('initial_t_rads', basestring):
uniform_t_rads = parse_quantity(plasma_section['initial_t_rads'])
plasma_config_dict['t_rads'] = u.Quantity(np.ones(no_of_shells) * uniform_t_rads.value, u.K)
elif astropy.utils.isiterable(plasma_section['initial_t_rads']):
assert len(plasma_section['initial_t_rads']) == no_of_shells
plasma_config_dict['t_rads'] = u.Quantity(plasma_section['initial_t_rads'], u.K)
else:
logger.info('No "initial_t_rads" specified - initializing with 10000 K')
plasma_config_dict['t_rads'] = u.Quantity(np.ones(no_of_shells) * 10000., u.K)
##### NLTE subsection of Plasma start
nlte_config_dict = {}
nlte_species = []
if 'nlte' in plasma_section:
nlte_section = plasma_section['nlte']
if 'species' in nlte_section:
nlte_species_list = nlte_section.pop('species')
for species_string in nlte_species_list:
nlte_species.append(species_string_to_tuple(species_string))
nlte_config_dict['species'] = nlte_species
nlte_config_dict['species_string'] = nlte_species_list
nlte_config_dict.update(nlte_section)
if 'coronal_approximation' not in nlte_section:
logger.debug('NLTE "coronal_approximation" not specified in NLTE section - defaulting to False')
nlte_config_dict['coronal_approximation'] = False
if 'classical_nebular' not in nlte_section:
logger.debug('NLTE "classical_nebular" not specified in NLTE section - defaulting to False')
nlte_config_dict['classical_nebular'] = False
elif nlte_section: #checks that the dictionary is not empty
logger.warn('No "species" given - ignoring other NLTE options given:\n%s',
pp.pformat(nlte_section))
if not nlte_config_dict:
nlte_config_dict['species'] = []
plasma_config_dict['nlte'] = nlte_config_dict
#^^^^^^^ NLTE subsection of Plasma end
config_dict['plasma'] = plasma_config_dict
#^^^^^^^^^^^^^^ End of Plasma Section
##### Monte Carlo Section
montecarlo_section = raw_dict.pop('montecarlo')
montecarlo_config_dict = {}
#PARSING convergence section
convergence_variables = ['t_inner', 't_rad', 'w']
convergence_config_dict = {}
if 'convergence_strategy' in montecarlo_section:
convergence_section = montecarlo_section.pop('convergence_strategy')
if 'lock_t_inner_cycles' in convergence_section:
lock_t_inner_cycles = convergence_section['lock_t_inner_cycles']
logger.info('lock_t_inner_cycles set to %d cycles', lock_t_inner_cycles)
else:
lock_t_inner_cycles = None
if 't_inner_update_exponent' in convergence_section:
t_inner_update_exponent = convergence_section['t_inner_update_exponent']
logger.info('t_inner update exponent set to %g', t_inner_update_exponent)
else:
t_inner_update_exponent = None
if convergence_section['type'] == 'damped':
convergence_config_dict['type'] == 'damped'
global_damping_constant = convergence_section['damping_constant']
for convergence_variable in convergence_variables:
convergence_parameter_name = convergence_variable
current_convergence_parameters = {}
convergence_config_dict[convergence_parameter_name] = current_convergence_parameters
if convergence_variable in convergence_section:
current_convergence_parameters['damping_constant'] \
= convergence_section[convergence_variable]['damping_constant']
else:
current_convergence_parameters['damping_constant'] = global_damping_constant
elif convergence_section['type'] == 'specific':
convergence_config_dict['type'] = 'specific'
global_convergence_parameters = {}
global_convergence_parameters['damping_constant'] = convergence_section['damping_constant']
global_convergence_parameters['threshold'] = convergence_section['threshold']
global_convergence_parameters['fraction'] = convergence_section['fraction']
for convergence_variable in convergence_variables:
convergence_parameter_name = convergence_variable
current_convergence_parameters = {}
convergence_config_dict[convergence_parameter_name] = current_convergence_parameters
if convergence_variable in convergence_section:
for param in global_convergence_parameters.keys():
if param == 'fraction' and convergence_variable == 't_inner':
continue
if param in convergence_section[convergence_variable]:
current_convergence_parameters[param] = convergence_section[convergence_variable][param]
else:
current_convergence_parameters[param] = global_convergence_parameters[param]
else:
convergence_config_dict[convergence_parameter_name] = global_convergence_parameters.copy()
global_convergence_parameters['hold'] = convergence_section['hold']
convergence_config_dict['global_convergence_parameters'] = global_convergence_parameters
else:
raise ValueError("convergence criteria unclear %s", convergence_section['type'])
else:
lock_t_inner_cycles = None
t_inner_update_exponent = None
logger.warning('No convergence criteria selected - just damping by 0.5 for w, t_rad and t_inner')
convergence_config_dict['type'] = 'damped'
for convergence_variable in convergence_variables:
convergence_parameter_name = convergence_variable
convergence_config_dict[convergence_parameter_name] = dict(damping_constant=0.5)
if lock_t_inner_cycles is None:
logger.warning('t_inner update lock cycles not set - defaulting to 1')
lock_t_inner_cycles = 1
if t_inner_update_exponent is None:
logger.warning('t_inner update exponent not set - defaulting to -0.5')
t_inner_update_exponent = -0.5
convergence_config_dict['lock_t_inner_cycles'] = lock_t_inner_cycles
convergence_config_dict['t_inner_update_exponent'] = t_inner_update_exponent
montecarlo_config_dict['convergence'] = convergence_config_dict
###### END of convergence section reading
if 'last_no_of_packets' not in montecarlo_section:
montecarlo_section['last_no_of_packets'] = None
if 'no_of_virtual_packets' not in montecarlo_section:
montecarlo_section['no_of_virtual_packets'] = 0
montecarlo_config_dict.update(montecarlo_section)
disable_electron_scattering = plasma_section.get('disable_electron_scattering', False)
if disable_electron_scattering is False:
logger.info("Electron scattering switched on")
montecarlo_config_dict['sigma_thomson'] =6.652486e-25 / (u.cm**2)
else:
logger.warn('Disabling electron scattering - this is not physical')
montecarlo_config_dict['sigma_thomson'] = 1e-200 / (u.cm**2)
montecarlo_config_dict['enable_reflective_inner_boundary'] = False
montecarlo_config_dict['inner_boundary_albedo'] = 0.0
if 'inner_boundary_albedo' in montecarlo_section:
montecarlo_config_dict['inner_boundary_albedo'] = montecarlo_section['inner_boundary_albedo']
if 'enable_reflective_inner_boundary' not in montecarlo_section:
logger.warn('inner_boundary_albedo set, however enable_reflective_inner_boundary option not specified '
'- defaulting to reflective inner boundary')
montecarlo_config_dict['enable_reflective_inner_boundary'] = True
if 'enable_reflective_inner_boundary' in montecarlo_section:
montecarlo_config_dict['enable_reflective_inner_boundary'] = montecarlo_section['enable_reflective_inner_boundary']
if montecarlo_section['enable_reflective_inner_boundary'] == True and 'inner_boundary_albedo' not in montecarlo_section:
logger.warn('enabled reflective inner boundary, but "inner_boundary_albedo" not set - defaulting to 0.5')
montecarlo_config_dict['inner_boundary_albedo'] = 0.5
if 'black_body_sampling' in montecarlo_section:
black_body_sampling_section = montecarlo_section.pop('black_body_sampling')
sampling_start, sampling_end = parse_spectral_bin(black_body_sampling_section['start'],
black_body_sampling_section['stop'])
montecarlo_config_dict['black_body_sampling']['start'] = sampling_start
montecarlo_config_dict['black_body_sampling']['end'] = sampling_end
montecarlo_config_dict['black_body_sampling']['samples'] = np.int64(black_body_sampling_section['num'])
else:
logger.warn('No "black_body_sampling" section in config file - using defaults of '
'50 - 200000 Angstrom (1e6 samples)')
montecarlo_config_dict['black_body_sampling'] = {}
montecarlo_config_dict['black_body_sampling']['start'] = 50 * u.angstrom
montecarlo_config_dict['black_body_sampling']['end'] = 200000 * u.angstrom
montecarlo_config_dict['black_body_sampling']['samples'] = np.int64(1e6)
config_dict['montecarlo'] = montecarlo_config_dict
##### End of MonteCarlo section
##### spectrum section ######
spectrum_section = raw_dict.pop('spectrum')
spectrum_config_dict = {}
spectrum_frequency = parse_quantity_linspace(spectrum_section).to('Hz', u.spectral())
if spectrum_frequency[0] > spectrum_frequency[1]:
spectrum_frequency = spectrum_frequency[::-1]
spectrum_config_dict['start'] = parse_quantity(spectrum_section['start'])
spectrum_config_dict['end'] = parse_quantity(spectrum_section['stop'])
spectrum_config_dict['bins'] = spectrum_section['num']
spectrum_frequency = np.linspace(spectrum_config_dict['end'].to('Hz', u.spectral()).value,
spectrum_config_dict['start'].to('Hz', u.spectral()).value,
num=spectrum_config_dict['bins'] + 1) * u.Hz
spectrum_config_dict['frequency'] = spectrum_frequency.to('Hz')
config_dict['spectrum'] = spectrum_config_dict
return cls(config_dict, atom_data)