Module diskchef.physics.multidust
Module with a definition of multiple dust populations
Expand source code
"""Module with a definition of multiple dust populations"""
from dataclasses import dataclass
from typing import Literal
import numpy as np
from astropy import units as u
from diskchef.engine.other import PathLike
from diskchef.engine.ctable import CTable
from diskchef.engine.exceptions import CHEFRuntimeError
@dataclass
class DustPopulation:
"""
Class with the data on the dust population
Args:
total_dust_density: total density of all dust components, `astropy.units.Quantity` in density units
mass_fraction: multiplier to get the density of this dust population
average_size_for_chemistry: average grain size weighted by surface area, see Vasyunin et al. 2011 Eq. 9
(https://iopscience.iop.org/article/10.1088/0004-637X/727/2/76/pdf)
Usage:
>>> # If the name is not set, use index of the created dust (unsafe!)
>>> dust0 = DustPopulation("some_opacity.inp", total_dust_density=1e-15 * u.g / u.cm ** 3)
>>> dust0.name
'Dust_0'
>>> dust1 = DustPopulation("some_opacity.inp", total_dust_density=1e-15 * u.g / u.cm ** 3)
>>> dust1.name
'Dust_1'
>>> table = CTable()
>>> table["Radius"] = [1, 2, 3] * u.au
>>> table["Dust density"] = [100, 10, 1] * u.g / u.cm ** 3 * 1e-15
>>> table["Dust temperature"] = [100, 50, 25] * u.K
>>> dust = DustPopulation("some_opacity.inp", table=table, name="Default dust")
>>> dust.write_to_table()
>>> table # doctest: +NORMALIZE_WHITESPACE
<CTable length=3>
Radius Dust density Dust temperature Default dust mass fraction Default dust number density Default dust temperature Default dust surface area per volume
AU g / cm3 K 1 / cm3 K 1 / cm
float64 float64 float64 float64 float64 float64 float64
------------ ------------ ---------------- -------------------------- --------------------------- ------------------------ ------------------------------------
1.000000e+00 1.000000e-13 1.000000e+02 1.000000e+00 7.957747e+00 1.000000e+02 1.000000e-08
2.000000e+00 1.000000e-14 5.000000e+01 1.000000e+00 7.957747e-01 5.000000e+01 1.000000e-09
3.000000e+00 1.000000e-15 2.500000e+01 1.000000e+00 7.957747e-02 2.500000e+01 1.000000e-10
>>> table.dust_list[0].name
'Default dust'
>>> dust_large = DustPopulation("large_opacity.inp", table=table, name="Large dust", mass_fraction=0.3, average_size_for_chemistry=1*u.cm)
>>> dust_large.write_to_table()
>>> table # doctest: +NORMALIZE_WHITESPACE
<CTable length=3>
Radius Dust density Dust temperature Default dust mass fraction Default dust number density Default dust temperature Default dust surface area per volume Large dust mass fraction Large dust number density Large dust temperature Large dust surface area per volume
AU g / cm3 K 1 / cm3 K 1 / cm 1 / cm3 K 1 / cm
float64 float64 float64 float64 float64 float64 float64 float64 float64 float64 float64
------------ ------------ ---------------- -------------------------- --------------------------- ------------------------ ------------------------------------ ------------------------ ------------------------- ---------------------- ----------------------------------
1.000000e+00 1.000000e-13 1.000000e+02 1.000000e+00 7.957747e+00 1.000000e+02 1.000000e-08 3.000000e-01 2.387324e-15 1.000000e+02 3.000000e-14
2.000000e+00 1.000000e-14 5.000000e+01 1.000000e+00 7.957747e-01 5.000000e+01 1.000000e-09 3.000000e-01 2.387324e-16 5.000000e+01 3.000000e-15
3.000000e+00 1.000000e-15 2.500000e+01 1.000000e+00 7.957747e-02 2.500000e+01 1.000000e-10 3.000000e-01 2.387324e-17 2.500000e+01 3.000000e-16
>>> [dust.name for dust in table.dust_list]
['Default dust', 'Large dust']
>>> # Now, the total dust population exceeds the total dust mass (sum of mass_fraction != 1)
>>> table.dust_population_fully_set
False
>>> table.normalize_dust()
>>> table.dust_population_fully_set
True
>>> table # doctest: +NORMALIZE_WHITESPACE
<CTable length=3>
Radius Dust density Dust temperature Default dust mass fraction Default dust number density Default dust temperature Default dust surface area per volume Large dust mass fraction Large dust number density Large dust temperature Large dust surface area per volume
AU g / cm3 K 1 / cm3 K 1 / cm 1 / cm3 K 1 / cm
float64 float64 float64 float64 float64 float64 float64 float64 float64 float64 float64
------------ ------------ ---------------- -------------------------- --------------------------- ------------------------ ------------------------------------ ------------------------ ------------------------- ---------------------- ----------------------------------
1.000000e+00 1.000000e-13 1.000000e+02 7.692308e-01 6.121344e+00 1.000000e+02 7.692308e-09 2.307692e-01 1.836403e-15 1.000000e+02 2.307692e-14
2.000000e+00 1.000000e-14 5.000000e+01 7.692308e-01 6.121344e-01 5.000000e+01 7.692308e-10 2.307692e-01 1.836403e-16 5.000000e+01 2.307692e-15
3.000000e+00 1.000000e-15 2.500000e+01 7.692308e-01 6.121344e-02 2.500000e+01 7.692308e-11 2.307692e-01 1.836403e-17 2.500000e+01 2.307692e-16
>>> # Different ratio at different locations, also note that if Dust temperature was not set, it will be set as np.nan
>>> table = CTable()
>>> table["Radius"] = [1, 2, 3] * u.au
>>> table["Dust density"] = [100, 10, 1] * u.g / u.cm ** 3 * 1e-15
>>> dust = DustPopulation("some_opacity.inp", table=table, name="Default dust", mass_fraction=[0.8, 0.7, 0.5])
>>> dust.write_to_table()
>>> dust_large = DustPopulation("large_opacity.inp", table=table, name="Large dust", mass_fraction=[0.2, 0.3, 0.5], average_size_for_chemistry=1*u.cm)
>>> dust_large.write_to_table()
>>> table # doctest: +NORMALIZE_WHITESPACE
<CTable length=3>
Radius Dust density Default dust mass fraction Default dust number density Default dust temperature Default dust surface area per volume Large dust mass fraction Large dust number density Large dust temperature Large dust surface area per volume
AU g / cm3 1 / cm3 K 1 / cm 1 / cm3 K 1 / cm
float64 float64 float64 float64 float64 float64 float64 float64 float64 float64
------------ ------------ -------------------------- --------------------------- ------------------------ ------------------------------------ ------------------------ ------------------------- ---------------------- ----------------------------------
1.000000e+00 1.000000e-13 8.000000e-01 6.366198e+00 nan 8.000000e-09 2.000000e-01 1.591549e-15 nan 2.000000e-14
2.000000e+00 1.000000e-14 7.000000e-01 5.570423e-01 nan 7.000000e-10 3.000000e-01 2.387324e-16 nan 3.000000e-15
3.000000e+00 1.000000e-15 5.000000e-01 3.978874e-02 nan 5.000000e-11 5.000000e-01 3.978874e-17 nan 5.000000e-16
>>> table.dust_population_fully_set
True
>>> # Rescaling also works if mass fractions are given independently
>>> dust_asteroid = DustPopulation("asteroid_opacity.inp", table=table, name="Asteroids", mass_fraction=[0.5, 0.3, 0.5], average_size_for_chemistry=1*u.km)
>>> dust_asteroid.write_to_table()
>>> table.dust_population_fully_set
False
>>> table.normalize_dust()
>>> table.dust_population_fully_set
True
>>> table # doctest: +NORMALIZE_WHITESPACE
<CTable length=3>
Radius Dust density Default dust mass fraction Default dust number density Default dust temperature Default dust surface area per volume Large dust mass fraction Large dust number density Large dust temperature Large dust surface area per volume Asteroids mass fraction Asteroids number density Asteroids temperature Asteroids surface area per volume
AU g / cm3 1 / cm3 K 1 / cm 1 / cm3 K 1 / cm 1 / cm3 K 1 / cm
float64 float64 float64 float64 float64 float64 float64 float64 float64 float64 float64 float64 float64 float64
------------ ------------ -------------------------- --------------------------- ------------------------ ------------------------------------ ------------------------ ------------------------- ---------------------- ---------------------------------- ----------------------- ------------------------ --------------------- ---------------------------------
1.000000e+00 1.000000e-13 5.333333e-01 4.244132e+00 nan 5.333333e-09 1.333333e-01 1.061033e-15 nan 1.333333e-14 3.333333e-01 2.652582e-30 nan 3.333333e-19
2.000000e+00 1.000000e-14 5.384615e-01 4.284941e-01 nan 5.384615e-10 2.307692e-01 1.836403e-16 nan 2.307692e-15 2.307692e-01 1.836403e-31 nan 2.307692e-20
3.000000e+00 1.000000e-15 3.333333e-01 2.652582e-02 nan 3.333333e-11 3.333333e-01 2.652582e-17 nan 3.333333e-16 3.333333e-01 2.652582e-32 nan 3.333333e-21
"""
opacity_file: PathLike
table: CTable = None
total_dust_density: u.g / u.cm ** 3 = None
dust_temperature: u.K = None
mass_fraction: u.dimensionless_unscaled = 1.
name: str = None
mean_mass_per_grain: u.g = None
grain_particle_density: u.g / u.cm ** 3 = 3 * u.g / u.cm ** 3
opacity_file_format: Literal['radmc'] = 'radmc'
average_size_for_chemistry: u.cm = 1e-5 * u.cm
_idx = 0
def __post_init__(self):
if self.total_dust_density is None:
if self.table is None:
raise CHEFRuntimeError("table OR total_dust_density must be set for DustPopulation")
self.total_dust_density = self.table["Dust density"]
if self.mean_mass_per_grain is None:
self.mean_mass_per_grain = 4. / 3. * np.pi * self.average_size_for_chemistry ** 3 * self.grain_particle_density
if self.name is None: self.name = f"Dust_{self.__class__._idx}"
self.__class__._idx += 1
@property
@u.quantity_input
def number_density(self) -> u.cm ** (-3):
"""
Number density column of given dust species
"""
return self.total_dust_density * self.mass_fraction / self.mean_mass_per_grain
@property
@u.quantity_input
def surface_area_per_volume(self) -> u.cm ** (-1):
"""
Surface area per volume unit, important for chemistry
Assumes spherical grains in default setup
"""
return 4 * np.pi * self.average_size_for_chemistry ** 2 * self.number_density
@property
@u.quantity_input
def temperature(self) -> u.K:
if self.dust_temperature is not None:
return self.dust_temperature
if self.table is not None:
if "Dust temperature" in self.table.colnames:
return self.table["Dust temperature"]
else:
return np.nan * u.K
def write_to_table(self, table: CTable = None):
"""
Write the dust population in the table
Args:
`table`: if given, writes the data in this table. Else, writes in `self.table`
Adds columns
"{self.name} mass fraction"
"{self.name} number density"
"{self.name} temperature"
"{self.name} surface area per volume"
Also adds `self` to `table.dust_list`
"""
if table is None:
table = self.table
table[f"{self.name} mass fraction"] = self.mass_fraction
table[f"{self.name} number density"] = self.number_density
table[f"{self.name} temperature"] = self.temperature
table[f"{self.name} surface area per volume"] = self.surface_area_per_volume
try:
if self not in table.dust_list:
table.dust_list.append(self)
except KeyError:
table.dust_list = [self]Classes
class DustPopulation (opacity_file: Union[str, os.PathLike], table: CTable = None, total_dust_density: Unit("g / cm3") = None, dust_temperature: Unit("K") = None, mass_fraction: Unit(dimensionless) = 1.0, name: str = None, mean_mass_per_grain: Unit("g") = None, grain_particle_density: Unit("g / cm3") = <Quantity 3. g / cm3>, opacity_file_format: Literal['radmc'] = 'radmc', average_size_for_chemistry: Unit("cm") = <Quantity 1.e-05 cm>)-
Class with the data on the dust population
Args
total_dust_density- total density of all dust components,
astropy.units.Quantityin density units mass_fraction- multiplier to get the density of this dust population
average_size_for_chemistry- average grain size weighted by surface area, see Vasyunin et al. 2011 Eq. 9
(https://iopscience.iop.org/article/10.1088/0004-637X/727/2/76/pdf) Usage:
>>> # If the name is not set, use index of the created dust (unsafe!) >>> dust0 = DustPopulation("some_opacity.inp", total_dust_density=1e-15 * u.g / u.cm ** 3) >>> dust0.name 'Dust_0' >>> dust1 = DustPopulation("some_opacity.inp", total_dust_density=1e-15 * u.g / u.cm ** 3) >>> dust1.name 'Dust_1'>>> table = CTable() >>> table["Radius"] = [1, 2, 3] * u.au >>> table["Dust density"] = [100, 10, 1] * u.g / u.cm ** 3 * 1e-15 >>> table["Dust temperature"] = [100, 50, 25] * u.K >>> dust = DustPopulation("some_opacity.inp", table=table, name="Default dust") >>> dust.write_to_table() >>> table # doctest: +NORMALIZE_WHITESPACE <CTable length=3> Radius Dust density Dust temperature Default dust mass fraction Default dust number density Default dust temperature Default dust surface area per volume AU g / cm3 K 1 / cm3 K 1 / cm float64 float64 float64 float64 float64 float64 float64 ------------ ------------ ---------------- -------------------------- --------------------------- ------------------------ ------------------------------------ 1.000000e+00 1.000000e-13 1.000000e+02 1.000000e+00 7.957747e+00 1.000000e+02 1.000000e-08 2.000000e+00 1.000000e-14 5.000000e+01 1.000000e+00 7.957747e-01 5.000000e+01 1.000000e-09 3.000000e+00 1.000000e-15 2.500000e+01 1.000000e+00 7.957747e-02 2.500000e+01 1.000000e-10 >>> table.dust_list[0].name 'Default dust'>>> dust_large = DustPopulation("large_opacity.inp", table=table, name="Large dust", mass_fraction=0.3, average_size_for_chemistry=1*u.cm) >>> dust_large.write_to_table() >>> table # doctest: +NORMALIZE_WHITESPACE <CTable length=3> Radius Dust density Dust temperature Default dust mass fraction Default dust number density Default dust temperature Default dust surface area per volume Large dust mass fraction Large dust number density Large dust temperature Large dust surface area per volume AU g / cm3 K 1 / cm3 K 1 / cm 1 / cm3 K 1 / cm float64 float64 float64 float64 float64 float64 float64 float64 float64 float64 float64 ------------ ------------ ---------------- -------------------------- --------------------------- ------------------------ ------------------------------------ ------------------------ ------------------------- ---------------------- ---------------------------------- 1.000000e+00 1.000000e-13 1.000000e+02 1.000000e+00 7.957747e+00 1.000000e+02 1.000000e-08 3.000000e-01 2.387324e-15 1.000000e+02 3.000000e-14 2.000000e+00 1.000000e-14 5.000000e+01 1.000000e+00 7.957747e-01 5.000000e+01 1.000000e-09 3.000000e-01 2.387324e-16 5.000000e+01 3.000000e-15 3.000000e+00 1.000000e-15 2.500000e+01 1.000000e+00 7.957747e-02 2.500000e+01 1.000000e-10 3.000000e-01 2.387324e-17 2.500000e+01 3.000000e-16 >>> [dust.name for dust in table.dust_list] ['Default dust', 'Large dust']>>> # Now, the total dust population exceeds the total dust mass (sum of mass_fraction != 1) >>> table.dust_population_fully_set False >>> table.normalize_dust() >>> table.dust_population_fully_set True >>> table # doctest: +NORMALIZE_WHITESPACE <CTable length=3> Radius Dust density Dust temperature Default dust mass fraction Default dust number density Default dust temperature Default dust surface area per volume Large dust mass fraction Large dust number density Large dust temperature Large dust surface area per volume AU g / cm3 K 1 / cm3 K 1 / cm 1 / cm3 K 1 / cm float64 float64 float64 float64 float64 float64 float64 float64 float64 float64 float64 ------------ ------------ ---------------- -------------------------- --------------------------- ------------------------ ------------------------------------ ------------------------ ------------------------- ---------------------- ---------------------------------- 1.000000e+00 1.000000e-13 1.000000e+02 7.692308e-01 6.121344e+00 1.000000e+02 7.692308e-09 2.307692e-01 1.836403e-15 1.000000e+02 2.307692e-14 2.000000e+00 1.000000e-14 5.000000e+01 7.692308e-01 6.121344e-01 5.000000e+01 7.692308e-10 2.307692e-01 1.836403e-16 5.000000e+01 2.307692e-15 3.000000e+00 1.000000e-15 2.500000e+01 7.692308e-01 6.121344e-02 2.500000e+01 7.692308e-11 2.307692e-01 1.836403e-17 2.500000e+01 2.307692e-16>>> # Different ratio at different locations, also note that if Dust temperature was not set, it will be set as np.nan >>> table = CTable() >>> table["Radius"] = [1, 2, 3] * u.au >>> table["Dust density"] = [100, 10, 1] * u.g / u.cm ** 3 * 1e-15 >>> dust = DustPopulation("some_opacity.inp", table=table, name="Default dust", mass_fraction=[0.8, 0.7, 0.5]) >>> dust.write_to_table() >>> dust_large = DustPopulation("large_opacity.inp", table=table, name="Large dust", mass_fraction=[0.2, 0.3, 0.5], average_size_for_chemistry=1*u.cm) >>> dust_large.write_to_table() >>> table # doctest: +NORMALIZE_WHITESPACE <CTable length=3> Radius Dust density Default dust mass fraction Default dust number density Default dust temperature Default dust surface area per volume Large dust mass fraction Large dust number density Large dust temperature Large dust surface area per volume AU g / cm3 1 / cm3 K 1 / cm 1 / cm3 K 1 / cm float64 float64 float64 float64 float64 float64 float64 float64 float64 float64 ------------ ------------ -------------------------- --------------------------- ------------------------ ------------------------------------ ------------------------ ------------------------- ---------------------- ---------------------------------- 1.000000e+00 1.000000e-13 8.000000e-01 6.366198e+00 nan 8.000000e-09 2.000000e-01 1.591549e-15 nan 2.000000e-14 2.000000e+00 1.000000e-14 7.000000e-01 5.570423e-01 nan 7.000000e-10 3.000000e-01 2.387324e-16 nan 3.000000e-15 3.000000e+00 1.000000e-15 5.000000e-01 3.978874e-02 nan 5.000000e-11 5.000000e-01 3.978874e-17 nan 5.000000e-16 >>> table.dust_population_fully_set True>>> # Rescaling also works if mass fractions are given independently >>> dust_asteroid = DustPopulation("asteroid_opacity.inp", table=table, name="Asteroids", mass_fraction=[0.5, 0.3, 0.5], average_size_for_chemistry=1*u.km) >>> dust_asteroid.write_to_table() >>> table.dust_population_fully_set False >>> table.normalize_dust() >>> table.dust_population_fully_set True >>> table # doctest: +NORMALIZE_WHITESPACE <CTable length=3> Radius Dust density Default dust mass fraction Default dust number density Default dust temperature Default dust surface area per volume Large dust mass fraction Large dust number density Large dust temperature Large dust surface area per volume Asteroids mass fraction Asteroids number density Asteroids temperature Asteroids surface area per volume AU g / cm3 1 / cm3 K 1 / cm 1 / cm3 K 1 / cm 1 / cm3 K 1 / cm float64 float64 float64 float64 float64 float64 float64 float64 float64 float64 float64 float64 float64 float64 ------------ ------------ -------------------------- --------------------------- ------------------------ ------------------------------------ ------------------------ ------------------------- ---------------------- ---------------------------------- ----------------------- ------------------------ --------------------- --------------------------------- 1.000000e+00 1.000000e-13 5.333333e-01 4.244132e+00 nan 5.333333e-09 1.333333e-01 1.061033e-15 nan 1.333333e-14 3.333333e-01 2.652582e-30 nan 3.333333e-19 2.000000e+00 1.000000e-14 5.384615e-01 4.284941e-01 nan 5.384615e-10 2.307692e-01 1.836403e-16 nan 2.307692e-15 2.307692e-01 1.836403e-31 nan 2.307692e-20 3.000000e+00 1.000000e-15 3.333333e-01 2.652582e-02 nan 3.333333e-11 3.333333e-01 2.652582e-17 nan 3.333333e-16 3.333333e-01 2.652582e-32 nan 3.333333e-21Expand source code
@dataclass class DustPopulation: """ Class with the data on the dust population Args: total_dust_density: total density of all dust components, `astropy.units.Quantity` in density units mass_fraction: multiplier to get the density of this dust population average_size_for_chemistry: average grain size weighted by surface area, see Vasyunin et al. 2011 Eq. 9 (https://iopscience.iop.org/article/10.1088/0004-637X/727/2/76/pdf) Usage: >>> # If the name is not set, use index of the created dust (unsafe!) >>> dust0 = DustPopulation("some_opacity.inp", total_dust_density=1e-15 * u.g / u.cm ** 3) >>> dust0.name 'Dust_0' >>> dust1 = DustPopulation("some_opacity.inp", total_dust_density=1e-15 * u.g / u.cm ** 3) >>> dust1.name 'Dust_1' >>> table = CTable() >>> table["Radius"] = [1, 2, 3] * u.au >>> table["Dust density"] = [100, 10, 1] * u.g / u.cm ** 3 * 1e-15 >>> table["Dust temperature"] = [100, 50, 25] * u.K >>> dust = DustPopulation("some_opacity.inp", table=table, name="Default dust") >>> dust.write_to_table() >>> table # doctest: +NORMALIZE_WHITESPACE <CTable length=3> Radius Dust density Dust temperature Default dust mass fraction Default dust number density Default dust temperature Default dust surface area per volume AU g / cm3 K 1 / cm3 K 1 / cm float64 float64 float64 float64 float64 float64 float64 ------------ ------------ ---------------- -------------------------- --------------------------- ------------------------ ------------------------------------ 1.000000e+00 1.000000e-13 1.000000e+02 1.000000e+00 7.957747e+00 1.000000e+02 1.000000e-08 2.000000e+00 1.000000e-14 5.000000e+01 1.000000e+00 7.957747e-01 5.000000e+01 1.000000e-09 3.000000e+00 1.000000e-15 2.500000e+01 1.000000e+00 7.957747e-02 2.500000e+01 1.000000e-10 >>> table.dust_list[0].name 'Default dust' >>> dust_large = DustPopulation("large_opacity.inp", table=table, name="Large dust", mass_fraction=0.3, average_size_for_chemistry=1*u.cm) >>> dust_large.write_to_table() >>> table # doctest: +NORMALIZE_WHITESPACE <CTable length=3> Radius Dust density Dust temperature Default dust mass fraction Default dust number density Default dust temperature Default dust surface area per volume Large dust mass fraction Large dust number density Large dust temperature Large dust surface area per volume AU g / cm3 K 1 / cm3 K 1 / cm 1 / cm3 K 1 / cm float64 float64 float64 float64 float64 float64 float64 float64 float64 float64 float64 ------------ ------------ ---------------- -------------------------- --------------------------- ------------------------ ------------------------------------ ------------------------ ------------------------- ---------------------- ---------------------------------- 1.000000e+00 1.000000e-13 1.000000e+02 1.000000e+00 7.957747e+00 1.000000e+02 1.000000e-08 3.000000e-01 2.387324e-15 1.000000e+02 3.000000e-14 2.000000e+00 1.000000e-14 5.000000e+01 1.000000e+00 7.957747e-01 5.000000e+01 1.000000e-09 3.000000e-01 2.387324e-16 5.000000e+01 3.000000e-15 3.000000e+00 1.000000e-15 2.500000e+01 1.000000e+00 7.957747e-02 2.500000e+01 1.000000e-10 3.000000e-01 2.387324e-17 2.500000e+01 3.000000e-16 >>> [dust.name for dust in table.dust_list] ['Default dust', 'Large dust'] >>> # Now, the total dust population exceeds the total dust mass (sum of mass_fraction != 1) >>> table.dust_population_fully_set False >>> table.normalize_dust() >>> table.dust_population_fully_set True >>> table # doctest: +NORMALIZE_WHITESPACE <CTable length=3> Radius Dust density Dust temperature Default dust mass fraction Default dust number density Default dust temperature Default dust surface area per volume Large dust mass fraction Large dust number density Large dust temperature Large dust surface area per volume AU g / cm3 K 1 / cm3 K 1 / cm 1 / cm3 K 1 / cm float64 float64 float64 float64 float64 float64 float64 float64 float64 float64 float64 ------------ ------------ ---------------- -------------------------- --------------------------- ------------------------ ------------------------------------ ------------------------ ------------------------- ---------------------- ---------------------------------- 1.000000e+00 1.000000e-13 1.000000e+02 7.692308e-01 6.121344e+00 1.000000e+02 7.692308e-09 2.307692e-01 1.836403e-15 1.000000e+02 2.307692e-14 2.000000e+00 1.000000e-14 5.000000e+01 7.692308e-01 6.121344e-01 5.000000e+01 7.692308e-10 2.307692e-01 1.836403e-16 5.000000e+01 2.307692e-15 3.000000e+00 1.000000e-15 2.500000e+01 7.692308e-01 6.121344e-02 2.500000e+01 7.692308e-11 2.307692e-01 1.836403e-17 2.500000e+01 2.307692e-16 >>> # Different ratio at different locations, also note that if Dust temperature was not set, it will be set as np.nan >>> table = CTable() >>> table["Radius"] = [1, 2, 3] * u.au >>> table["Dust density"] = [100, 10, 1] * u.g / u.cm ** 3 * 1e-15 >>> dust = DustPopulation("some_opacity.inp", table=table, name="Default dust", mass_fraction=[0.8, 0.7, 0.5]) >>> dust.write_to_table() >>> dust_large = DustPopulation("large_opacity.inp", table=table, name="Large dust", mass_fraction=[0.2, 0.3, 0.5], average_size_for_chemistry=1*u.cm) >>> dust_large.write_to_table() >>> table # doctest: +NORMALIZE_WHITESPACE <CTable length=3> Radius Dust density Default dust mass fraction Default dust number density Default dust temperature Default dust surface area per volume Large dust mass fraction Large dust number density Large dust temperature Large dust surface area per volume AU g / cm3 1 / cm3 K 1 / cm 1 / cm3 K 1 / cm float64 float64 float64 float64 float64 float64 float64 float64 float64 float64 ------------ ------------ -------------------------- --------------------------- ------------------------ ------------------------------------ ------------------------ ------------------------- ---------------------- ---------------------------------- 1.000000e+00 1.000000e-13 8.000000e-01 6.366198e+00 nan 8.000000e-09 2.000000e-01 1.591549e-15 nan 2.000000e-14 2.000000e+00 1.000000e-14 7.000000e-01 5.570423e-01 nan 7.000000e-10 3.000000e-01 2.387324e-16 nan 3.000000e-15 3.000000e+00 1.000000e-15 5.000000e-01 3.978874e-02 nan 5.000000e-11 5.000000e-01 3.978874e-17 nan 5.000000e-16 >>> table.dust_population_fully_set True >>> # Rescaling also works if mass fractions are given independently >>> dust_asteroid = DustPopulation("asteroid_opacity.inp", table=table, name="Asteroids", mass_fraction=[0.5, 0.3, 0.5], average_size_for_chemistry=1*u.km) >>> dust_asteroid.write_to_table() >>> table.dust_population_fully_set False >>> table.normalize_dust() >>> table.dust_population_fully_set True >>> table # doctest: +NORMALIZE_WHITESPACE <CTable length=3> Radius Dust density Default dust mass fraction Default dust number density Default dust temperature Default dust surface area per volume Large dust mass fraction Large dust number density Large dust temperature Large dust surface area per volume Asteroids mass fraction Asteroids number density Asteroids temperature Asteroids surface area per volume AU g / cm3 1 / cm3 K 1 / cm 1 / cm3 K 1 / cm 1 / cm3 K 1 / cm float64 float64 float64 float64 float64 float64 float64 float64 float64 float64 float64 float64 float64 float64 ------------ ------------ -------------------------- --------------------------- ------------------------ ------------------------------------ ------------------------ ------------------------- ---------------------- ---------------------------------- ----------------------- ------------------------ --------------------- --------------------------------- 1.000000e+00 1.000000e-13 5.333333e-01 4.244132e+00 nan 5.333333e-09 1.333333e-01 1.061033e-15 nan 1.333333e-14 3.333333e-01 2.652582e-30 nan 3.333333e-19 2.000000e+00 1.000000e-14 5.384615e-01 4.284941e-01 nan 5.384615e-10 2.307692e-01 1.836403e-16 nan 2.307692e-15 2.307692e-01 1.836403e-31 nan 2.307692e-20 3.000000e+00 1.000000e-15 3.333333e-01 2.652582e-02 nan 3.333333e-11 3.333333e-01 2.652582e-17 nan 3.333333e-16 3.333333e-01 2.652582e-32 nan 3.333333e-21 """ opacity_file: PathLike table: CTable = None total_dust_density: u.g / u.cm ** 3 = None dust_temperature: u.K = None mass_fraction: u.dimensionless_unscaled = 1. name: str = None mean_mass_per_grain: u.g = None grain_particle_density: u.g / u.cm ** 3 = 3 * u.g / u.cm ** 3 opacity_file_format: Literal['radmc'] = 'radmc' average_size_for_chemistry: u.cm = 1e-5 * u.cm _idx = 0 def __post_init__(self): if self.total_dust_density is None: if self.table is None: raise CHEFRuntimeError("table OR total_dust_density must be set for DustPopulation") self.total_dust_density = self.table["Dust density"] if self.mean_mass_per_grain is None: self.mean_mass_per_grain = 4. / 3. * np.pi * self.average_size_for_chemistry ** 3 * self.grain_particle_density if self.name is None: self.name = f"Dust_{self.__class__._idx}" self.__class__._idx += 1 @property @u.quantity_input def number_density(self) -> u.cm ** (-3): """ Number density column of given dust species """ return self.total_dust_density * self.mass_fraction / self.mean_mass_per_grain @property @u.quantity_input def surface_area_per_volume(self) -> u.cm ** (-1): """ Surface area per volume unit, important for chemistry Assumes spherical grains in default setup """ return 4 * np.pi * self.average_size_for_chemistry ** 2 * self.number_density @property @u.quantity_input def temperature(self) -> u.K: if self.dust_temperature is not None: return self.dust_temperature if self.table is not None: if "Dust temperature" in self.table.colnames: return self.table["Dust temperature"] else: return np.nan * u.K def write_to_table(self, table: CTable = None): """ Write the dust population in the table Args: `table`: if given, writes the data in this table. Else, writes in `self.table` Adds columns "{self.name} mass fraction" "{self.name} number density" "{self.name} temperature" "{self.name} surface area per volume" Also adds `self` to `table.dust_list` """ if table is None: table = self.table table[f"{self.name} mass fraction"] = self.mass_fraction table[f"{self.name} number density"] = self.number_density table[f"{self.name} temperature"] = self.temperature table[f"{self.name} surface area per volume"] = self.surface_area_per_volume try: if self not in table.dust_list: table.dust_list.append(self) except KeyError: table.dust_list = [self]Class variables
var average_size_for_chemistry : Unit("cm")var dust_temperature : Unit("K")var grain_particle_density : Unit("g / cm3")var mass_fraction : Unit(dimensionless)var mean_mass_per_grain : Unit("g")var name : strvar opacity_file : Union[str, os.PathLike]var opacity_file_format : Literal['radmc']var table : CTablevar total_dust_density : Unit("g / cm3")
Instance variables
var number_density : Unit("1 / cm3")-
Number density column of given dust species
Expand source code
@property @u.quantity_input def number_density(self) -> u.cm ** (-3): """ Number density column of given dust species """ return self.total_dust_density * self.mass_fraction / self.mean_mass_per_grain var surface_area_per_volume : Unit("1 / cm")-
Surface area per volume unit, important for chemistry
Assumes spherical grains in default setup
Expand source code
@property @u.quantity_input def surface_area_per_volume(self) -> u.cm ** (-1): """ Surface area per volume unit, important for chemistry Assumes spherical grains in default setup """ return 4 * np.pi * self.average_size_for_chemistry ** 2 * self.number_density var temperature : Unit("K")-
Expand source code
@property @u.quantity_input def temperature(self) -> u.K: if self.dust_temperature is not None: return self.dust_temperature if self.table is not None: if "Dust temperature" in self.table.colnames: return self.table["Dust temperature"] else: return np.nan * u.K
Methods
def write_to_table(self, table: CTable = None)-
Write the dust population in the table
Args
table: if given, writes the data in this table. Else, writes inself.tableAdds columns "{self.name} mass fraction" "{self.name} number density" "{self.name} temperature" "{self.name} surface area per volume"Also adds
selftotable.dust_listExpand source code
def write_to_table(self, table: CTable = None): """ Write the dust population in the table Args: `table`: if given, writes the data in this table. Else, writes in `self.table` Adds columns "{self.name} mass fraction" "{self.name} number density" "{self.name} temperature" "{self.name} surface area per volume" Also adds `self` to `table.dust_list` """ if table is None: table = self.table table[f"{self.name} mass fraction"] = self.mass_fraction table[f"{self.name} number density"] = self.number_density table[f"{self.name} temperature"] = self.temperature table[f"{self.name} surface area per volume"] = self.surface_area_per_volume try: if self not in table.dust_list: table.dust_list.append(self) except KeyError: table.dust_list = [self]