# Copyright (c) 2021-2022 Patricio Cubillos
# Pyrat Bay is open-source software under the GNU GPL-2.0 license (see LICENSE)
__all__ = [
'get_tips_molname',
'tips',
'exomol',
'kurucz',
]
import pickle
import numpy as np
from numpy.core.numeric import isscalar
from ... import io as io
from ... import constants as pc
from ... import tools as pt
import mc3.utils as mu
[docs]def get_tips_molname(molID):
"""
Get the TIPS molecule name for given molecule ID.
Parameters
----------
molID: Integer
HITRAN molecule ID. See for example: https://hitran.org/lbl/
Returns
-------
molname: String
Name of molecule.
Examples
--------
>>> import pyratbay.opacity.partitions as pf
>>> print(pf.get_tips_molname(1), pf.get_tips_molname(6))
H2O CH4
"""
with open(pc.ROOT+'pyratbay/data/tips_2021.pkl', 'rb') as p:
data = pickle.load(p)
if molID not in data['mol_ID']:
raise ValueError(
f'TIPS 2021 database does not contain molecule ID: {molID}')
return data['mol_ID'][molID]
[docs]def tips(molecule, isotopes=None, outfile=None, db_type='as_tips'):
"""
Extract TIPS 2021 partition-function values for given molecule.
If requested, write the partition-function into a file for use
with Pyrat Bay.
References:
Gamache et al. (2017), JQSRT, 203, 70.
Gamache et al. (2021), JQSRT, 271, 107713.
Parameters
----------
molecule: String
Name of the molecule.
isotopes: String or list of strings
If not None, only extract the requested isotopes.
outfile: String
If not None, save output to file.
If outfile == 'default', save output to file named as
PF_tips_molecule.dat
db_type: String
If db_type == 'as_exomol', return isotopic names following
the exomol notation.
Returns
-------
pf: 2D float ndarray
TIPS partition function for input molecule.
isotopes: 1D string list
List of isotopes.
temp: 1D float ndarray
Partition-function temperature samples (K).
Examples
--------
>>> import pyratbay.opacity.partitions as pf
>>> pf_data, isotopes, temp = pf.tips('H2O', outfile='default')
Written partition-function file:
'PF_tips_H2O.dat'
for molecule H2O, with isotopes ['161', '181', '171', '162', '182', '172', '262', '282', '272'],
and temperature range 1--5000 K.
"""
with open(pc.ROOT+'pyratbay/data/tips_2021.pkl', 'rb') as p:
data = pickle.load(p)
if molecule not in data:
raise ValueError(f"Molecule '{molecule}' is not in TIPS database.")
if isotopes is None:
isotopes = list(data[molecule].keys())
isotopes = [isotopes] if isscalar(isotopes) else isotopes
for iso in isotopes:
if iso not in data[molecule]:
raise ValueError(
f"Molecule '{molecule}' does not have isotope '{iso}'")
ntemp = np.amin([
len(data[molecule][iso])
for iso in data[molecule]
])
temp = data['temp'][0:ntemp]
# Compute partition function:
niso = len(isotopes)
pf = np.zeros((niso, ntemp), np.double)
for i,iso in enumerate(isotopes):
pf[i] = data[molecule][iso][0:ntemp]
# Get exomol isotope names if requested:
if db_type == 'as_exomol':
ID, molecs, hitran, exomol, iso_ratio, iso_mass = \
io.read_isotopes(pc.ROOT+'pyratbay/data/isotopes.dat')
iso_map = {
exo:hit
for mol, hit, exo in zip(molecs, exomol, hitran)
if mol==molecule
}
isotopes = [iso_map[iso] for iso in isotopes]
# Write output file:
if outfile == 'default':
outfile = f'PF_tips_{molecule}.dat'
if outfile is not None:
header = f'# Tabulated {molecule} partition-function from TIPS.\n\n'
io.write_pf(outfile, pf, isotopes, temp, header)
print(
f"\nWritten partition-function file:\n '{outfile}'"
f"\nfor molecule {molecule}, with isotopes {isotopes},"
f"\nand temperature range {temp[0]:.0f}--{temp[-1]:.0f} K."
)
return pf, isotopes, temp
[docs]def exomol(pf_files, outfile=None):
"""
Extract ExoMol partition-function values from input files.
If requested, write the partition-function into a file for use
with Pyrat Bay.
Parameters
----------
pf_files: String or List of strings
Input Exomol partition-function filenames. If there are
multiple isotopes, all of them must correspond to the same
molecule.
outfile: String
If not None, save output to file.
If outfile == 'default', save output to file named as
PF_exomol_molecule.dat
Returns
-------
pf: 2D float ndarray
TIPS partition function for input molecule.
isotopes: 1D string list
List of isotopes.
temp: 1D float ndarray
Partition-function temperature samples (K).
Examples
--------
>>> # First, download ExoMol data to current dictory, e.g.:
>>> # wget http://www.exomol.com/db/NH3/14N-1H3/BYTe/14N-1H3__BYTe.pf
>>> # wget http://www.exomol.com/db/NH3/15N-1H3/BYTe-15/15N-1H3__BYTe-15.pf
>>> import pyratbay.opacity.partitions as pf
>>> # A single file:
>>> pf_data, isotopes, temp = pf.exomol('14N-1H3__BYTe.pf',
>>> outfile='default')
Written partition-function file:
'PF_exomol_NH3.dat'
for molecule NH3, with isotopes ['4111'],
and temperature range 1--1600 K.
>>> # Multiple files (isotopes) for a molecule:
>>> pf_data, isotopes, temp = pf.exomol(
>>> ['14N-1H3__BYTe.pf', '15N-1H3__BYTe-15.pf'], outfile='default')
::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
Warning:
Length of PF files do not match. Trimming to shorter size.
::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
Written partition-function file:
'PF_exomol_NH3.dat'
for molecule NH3, with isotopes ['4111', '5111'],
and temperature range 1--1600 K.
"""
# Put into list if necessary:
if isinstance(pf_files, str):
pf_files = [pf_files]
# Read and extract data from files:
isotopes = []
data, temps = [], []
molecule = ''
for pf_file in pf_files:
# Get info from file name:
mol, iso = pt.get_exomol_mol(pf_file)
# Check all files correspond to the same molecule.
if molecule == '':
molecule = mol
elif molecule != mol:
raise ValueError('All files must correspond to the same molecule.')
isotopes.append(iso)
# Read data:
temp, z = np.loadtxt(pf_file).T
data.append(z)
temps.append(temp)
# Number of isotopes:
niso = len(isotopes)
# Check temp sampling:
minlen = min(len(temp) for temp in temps)
maxlen = max(len(temp) for temp in temps)
ntemp = minlen
if minlen != maxlen:
for temp in temps:
if np.any(temp[0:minlen] - temps[0][0:minlen] != 0):
raise ValueError(
'Temperature sampling in PF files are not compatible.')
with mu.Log() as log:
log.warning('Length of PF files do not match. Trimming to '
'shorter size.')
pf = np.zeros((niso, ntemp), np.double)
for i,z in enumerate(data):
pf[i] = z[0:minlen]
temp = temps[i][0:minlen]
# Write output file:
if outfile == 'default':
outfile = f'PF_exomol_{molecule}.dat'
if outfile is not None:
header = (f'# This file incorporates the tabulated {molecule} '
'partition-function data\n# from Exomol\n\n')
io.write_pf(outfile, pf, isotopes, temp, header)
print("\nWritten partition-function file:\n '{:s}'\nfor molecule "
"{:s}, with isotopes {},\nand temperature range {:.0f}--{:.0f} "
"K.".format(outfile, molecule, isotopes, temp[0], temp[-1]))
return pf, isotopes, temp
[docs]def kurucz(pf_file, outfile=None, type_flag='as_exomol'):
"""
Extract Kurucz partition-function values from input file.
If requested, write the partition-function into a file for use
with Pyrat Bay.
Parameters
----------
pf_file: String
Input partition-function from Kurucz webpage. Currently only H2O
and TiO are available (probably there's no need for any other support).
Files can be downloaded from these links:
http://kurucz.harvard.edu/molecules/h2o/h2opartfn.dat
http://kurucz.harvard.edu/molecules/tio/tiopart.dat
outfile: String
If not None, save output to file.
If outfile == 'default', save output to file named as
PF_kurucz_molecule.dat
Returns
-------
pf: 2D float ndarray
TIPS partition function for input molecule.
isotopes: 1D string list
List of isotopes.
temp: 1D float ndarray
Partition-function temperature samples (K).
Examples
--------
>>> # First, download kurucz data to current dictory, e.g.:
>>> # wget http://kurucz.harvard.edu/molecules/h2o/h2opartfn.dat
>>> # wget http://kurucz.harvard.edu/molecules/tio/tiopart.dat
>>> import pyratbay.opacity.partitions as pf
>>> pf_data, isotopes, temp = pf.kurucz('h2opartfn.dat', outfile='default')
Written partition-function file:
'PF_kurucz_H2O.dat'
for molecule H2O, with isotopes ['1H1H16O', '1H1H17O', '1H1H18O', '1H2H16O'],
and temperature range 10--6000 K.
>>> pf_data, isotopes, temp = pf.kurucz('tiopart.dat', outfile='default')
Written partition-function file:
'PF_kurucz_TiO.dat'
for molecule TiO, with isotopes ['66', '76', '86', '96', '06'],
and temperature range 10--6000 K.
"""
if 'h2o' in pf_file:
molecule = 'H2O'
url = 'http://kurucz.harvard.edu/molecules/h2o/h2opartfn.dat'
isotopes = ['1H1H16O', '1H1H17O', '1H1H18O', '1H2H16O']
skiprows = 6
elif 'tio' in pf_file:
molecule = 'TiO'
url = 'http://kurucz.harvard.edu/molecules/tio/tiopart.dat'
isotopes = ['66', '76', '86', '96', '06']
skiprows = 1
else:
print('Invalid Kurucz partition-function file.')
# Read and extract data from files:
data = np.loadtxt(pf_file, skiprows=skiprows, unpack=True)
# Allocate arrays:
temp = data[0]
pf = data[1:]
# Write output file:
if outfile == 'default':
outfile = 'PF_kurucz_{:s}.dat'.format(molecule)
if outfile is not None:
header = ('# This file incorporates the tabulated {:s} '
'partition-function data\n# from {:s}\n\n'.
format(molecule, url))
io.write_pf(outfile, pf, isotopes, temp, header)
print("\nWritten partition-function file:\n '{:s}'\nfor molecule "
"{:s}, with isotopes {},\nand temperature range {:.0f}--{:.0f} "
"K.".format(outfile, molecule, isotopes, temp[0], temp[-1]))
return pf, isotopes, temp