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Py38 mpl313 korg [WIP] #339

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ec306cb
Initialization. Nothing works.
alexji Apr 19, 2024
685c7da
Adding some stuff that I won't touch later
alexji Jun 16, 2024
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16 changes: 16 additions & 0 deletions smh/radiative_transfer/korg/__init__.py
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#!/usr/bin/env python
# -*- coding: utf-8 -*-

""" A standardized interface to the Korg radiative transfer code. """

from __future__ import (division, print_function, absolute_import,
unicode_literals)

__all__ = ["abundance_cog", "synthesize", "RTError"]

# See stackoverflow.com/questions/19913653/no-unicode-in-all-for-a-packages-init
# __all__ = [_.encode("ascii") for _ in __all__]

from .cog import abundance_cog
from .synthesis import synthesize
from .utils import RTError
67 changes: 67 additions & 0 deletions smh/radiative_transfer/korg/cog.py
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#!/usr/bin/env python
# -*- coding: utf-8 -*-

"""
Functionality to derive abundances from a transition's curve-of-growth using the
Korg radiative transfer code.
This doesn't actually work yet, because Korg assumes everything is on the linear part of the COG.
"""

from __future__ import (division, print_function, absolute_import,
unicode_literals)

from juliacall import Main as jl
jl.seval("using Korg")
Korg = jl.Korg

import logging
import numpy as np
import re
import yaml
from pkg_resources import resource_stream

from . import utils
from .utils import RTError
from smh.utils import element_to_species
from smh import linelists

logger = logging.getLogger(__name__)


def abundance_cog(photosphere, transitions, full_output=False, verbose=False,
twd=None, **kwargs):
"""
Calculate atomic line abundances by interpolating the measured
equivalent width from the curve-of-growth.
This doesn't actually work yet, because Korg assumes everything is on the linear part of the COG.

# :param photosphere:
# A formatted photosphere.

# :param transitions:
# A list of atomic transitions with measured equivalent widths.

# :param verbose: [optional]
# Specify verbose flags to MOOG. This is primarily used for debugging.

"""

# Create a temporary directory.
path = utils.twd_path(twd=twd,**kwargs)

# Write out the photosphere.
model_in, lines_in = path("model.in"), path("lines.in")
## TODO
photosphere.write(model_in, format="marcs")
## TODO
transitions.write(lines_in, format="moog")

atm = Korg.read_photosphere(model_in)
MH = TODO
linelist = Korg.read_linelist(lines_in, format="moog")
# The first argument specifies the default [X/H] abundance, the second lets you specify the default [alpha/H] abundance, and the third lets you specify individual abundances.
A_X = Korg.format_A_X(MH) # the need for this should go away after including the new code, which shouldn't need an initialization?
measured_EWs = transition["equivalent_width"]
logeps = Korg.Fit.ews_to_abundances(atm, linelist, A_X, measured_EWs)
# return logeps
raise NotImplementedError
83 changes: 83 additions & 0 deletions smh/radiative_transfer/korg/synthesis.py
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#!/usr/bin/env python
# -*- coding: utf-8 -*-

""" Synthesis functionality with the Korg radiative transfer code. """

from __future__ import (division, print_function, absolute_import,
unicode_literals)


import logging
import numpy as np
import yaml
from pkg_resources import resource_stream

from . import utils

logger = logging.getLogger(__name__)

def synthesize(photosphere, transitions, abundances=None, isotopes=None,
verbose=False, twd=None, **kwargs):
"""
Sythesize a stellar spectrum given the model photosphere and list of
transitions provided with Korg.

:param photosphere:
A formatted photosphere.

:param transitions:
A list of atomic transitions with measured equivalent widths.

:param abundances: [optional]
The non-scaled-Solar abundances to use in the synthesis.

:param isotopes: [optional]
The isotopic fractions to use in the synthesis.

:param verbose: [optional]
Specify verbose flags to Korg. This is primarily used for debugging.

"""

# Create a temporary directory and write out the photoshere and transitions.
path = utils.twd_path(twd=twd,**kwargs)
model_in, lines_in = path("model.in"), path("lines.in")
## TODO: can't currently write a correct MARCS format
photosphere.write(model_in, format="marcs")
transitions.write(lines_in, format="moog")
wavemin, wavemax = transitions[0]-1.0,transitions[-1]+1.0
atm = Korg.read_model_atmosphere(model_in)
## TODO: this doesn't support broadening parameters or dissociation energies
## TODO: Korg will automatically apply isotopic ratios when it reads, need to update this?
linelist = Korg.read_linelist(lines_in, format="moog")
# read_linelist(filename; format="vald", isotopic_abundances=Korg.isotopic_abundances)


# Abundances.
#A_X = Korg.format_A_X(-0.5, Dict("C" => -0.25))
#solution = synthesize(atm, linelist, A_X, 5000, 5100)

#synthesize(atm, linelist, A_X, λ_start, λ_stop, [λ_step=0.01]; kwargs... )
#synthesize(atm, linelist, A_X, wavelength_ranges; kwargs... )

#sol = Korg.synthesize(...)
# sol.flux
# sol.wavelengths
# sol.cntm
#flux: the output spectrum
#cntm: the continuum at each wavelength
#alpha: the linear absorption coefficient at each wavelength and atmospheric layer a Matrix of size (layers x wavelengths)
#number_densities: A dictionary mapping Species to vectors of number densities at each atmospheric layer
#electron_number_density: the electron number density at each atmospheric layer
#wavelengths: The vacuum wavelengths (in Å) over which the synthesis was performed. If air_wavelengths=true this will not be the same as the input wavelengths.
#subspectra: A vector of ranges which can be used to index into flux to extract the spectrum for each range provided in wavelength_ranges. If you use the standard λ_start, λ_stop, λ_step arguments, this will be a vector containing only one range.

spectra = []
all_abundances = []
for abundances in all_abundances:
out = Korg.synthesize(atm, linelist, abundances, wavemin, wavemax)
meta = {}
spectra.append((out.wavelengths, out.flux/out.cntm, meta))

#return spectra
raise NotImplementedError
25 changes: 25 additions & 0 deletions smh/radiative_transfer/korg/utils.py
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#!/usr/bin/env python
# -*- coding: utf-8 -*-

""" Utility functions related to MOOG. """

from __future__ import (division, print_function, absolute_import,
unicode_literals)

import logging
import numpy as np
import os
import signal
import subprocess
#import tempfile

from smh.photospheres.abundances import asplund_2009 as solar_composition
from smh.utils import elems_isotopes_ion_to_species, element_to_atomic_number
from smh.utils import mkdtemp
from six import iteritems, string_types

logger = logging.getLogger(__name__)

class RTError(BaseException):
pass