"""
Module for the accretion luminosity relation.
"""
import os
import h5py
import numpy as np
import pooch
from typeguard import typechecked
from species.core import constants
[docs]
@typechecked
def add_accretion_relation(input_path: str, database: h5py._hl.files.File) -> None:
"""
Function for adding the accretion relation from `Aoyama et al.
(2021) <https://ui. adsabs.harvard.edu/abs/
2021ApJ...917L..30A/abstract>`_ and extrapolation from
`Marleau & Aoyama (2022) <https://ui.adsabs.harvard.edu/abs/
2022RNAAS...6..262M/abstract>`_ to the database. It provides
coefficients to convert line to accretion luminosities.
Parameters
----------
input_path : str
Folder where the data is located.
database : h5py._hl.files.File
Database.
Returns
-------
None
NoneType
"""
if not os.path.exists(input_path):
os.makedirs(input_path)
url = (
"https://home.strw.leidenuniv.nl/~stolker/"
"species/ab-Koeffienzenten_mehrStellen.dat"
)
data_file = os.path.join(input_path, "ab-Koeffienzenten_mehrStellen.dat")
if not os.path.isfile(data_file):
pooch.retrieve(
url=url,
known_hash="941b416e678128648c9ce485016af908f16bfe16ab72e0f8cb57a6bad963429a",
fname="ab-Koeffienzenten_mehrStellen.dat",
path=input_path,
progressbar=True,
)
print("Adding coefficients for accretion relation (2.1 kB)...", end="", flush=True)
data = np.genfromtxt(
data_file,
dtype=None,
skip_header=1,
encoding=None,
names=True,
usecols=[0, 1, 2, 3, 4],
)
line_names = data["name"]
coefficients = np.column_stack([data["a"], data["b"]])
n_init = data["ni"]
n_final = data["nf"]
delta_n_min = {"H": 9, "Pa": 8, "Br": 6}
delta_n_max = {"H": 14, "Pa": 13, "Br": 12}
for i, item in enumerate(["H", "Pa", "Br"]):
for j in range(delta_n_min[item], delta_n_max[item] + 1):
# n_f: Ly=1, H=Ba=2, Pa=3, Br=4
n_f_tmp = i + 2
idx_insert = np.argwhere(line_names == f"{item}{j+n_f_tmp-1}")[0][0] + 1
line_names = np.insert(line_names, idx_insert, f"{item}{j+n_f_tmp}")
n_final = np.insert(n_final, idx_insert, n_f_tmp)
# delta_n = n_i - n_f
n_i_tmp = j + n_f_tmp
n_init = np.insert(n_init, idx_insert, n_i_tmp)
# Relation for extrapolation of coefficients
# See Marleau & Aoyama (2022)
a_coeff = 0.811 - (1.0 / (9.90 * n_f_tmp - 9.5 * n_i_tmp))
b_coeff = (
1.0
+ 1.05 * np.log(n_i_tmp)
+ (1.0 / (n_i_tmp - n_f_tmp))
- (1.0 / n_f_tmp)
) * (1.07 + 0.0694 * n_f_tmp) - 1.41
coefficients = np.insert(
coefficients, idx_insert, [[a_coeff, b_coeff]], axis=0
)
# Rest vacuum wavelength (um) from Rydberg formula,
# which is valid usually to three or four decimal places.
# Exact values, if needed, can be obtained from e.g.
# Wiese & Fuhr (2009):
# http://adsabs.harvard.edu/abs/2009JPCRD..38..565W
# https://www.nist.gov/system/files/documents/srd/jpcrd382009565p.pdf
wavelengths = 1e6 / (constants.RYDBERG * (1.0 / n_final**2 - 1.0 / n_init**2))
# data = np.column_stack(
# [
# line_names,
# wavelengths,
# n_init,
# n_final,
# coefficients[:, 0],
# coefficients[:, 1],
# ]
# )
# np.savetxt("acc_lines.dat", data, delimiter=" ", fmt="%s")
database.create_dataset("accretion/wavelengths", data=wavelengths)
database.create_dataset("accretion/coefficients", data=coefficients)
dtype = h5py.special_dtype(vlen=str)
dset = database.create_dataset(
"accretion/hydrogen_lines", (np.size(line_names),), dtype=dtype
)
dset[...] = line_names
print(" [DONE]")
print(
"Please cite Aoyama et al. (2021) and Marleau & Aoyama "
"(2022) when using the accretion relation in a publication"
)
