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fiasco currently only supports version 8 of the CHIANTI database.

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CHIANTI IDL Comparison: Ionization Fraction#

Compare the ionization fraction calculation to that in the CHIANTI IDL routines for a few select ions.

import matplotlib.pyplot as plt
import numpy as np

from astropy.visualization import quantity_support
from jinja2 import Template

import fiasco

from fiasco.tests.idl.helpers import read_idl_test_output

quantity_support()

<astropy.visualization.units.quantity_support.<locals>.MplQuantityConverter object at 0x7f519f9421d0>

Define a function for comparing and plotting the outputs from fiasco and IDL. Note that we have precomputed the IDL outputs.

def plot_idl_comparison(x, y_idl, y_python, fig, n_rows, i_row, quantity_name, thresh=1e-6):
    # Highlight region where value of goft is within some value of the peak
    idx = np.where(y_idl>=y_idl.max()*thresh)
    x_thresh_min, x_thresh_max = x[idx[0][[0,-1]]]
    # Direct comparison
    ax1 = fig.add_subplot(n_rows, 3, i_row+1)
    ax1.plot(x, y_python, label='fiasco')
    ax1.plot(x, y_idl, color='k', marker='o', ls='--', markevery=2, label='IDL')
    ax1.axvspan(x[0], x_thresh_min, color='r', alpha=0.25)
    ax1.axvspan(x_thresh_max, x[-1], color='r', alpha=0.25)
    ax1.set_xscale('log')
    ax1.set_yscale('log')
    if i_row == 0:
        ax1.set_title('Ionization Fraction')
    ax1.set_xlim(x[[0,-1]])
    ax1.set_ylim(y_python.max()*np.array([thresh,2]))
    ax1.set_ylabel(quantity_name)
    # Ratio
    ax2 = fig.add_subplot(n_rows, 3, i_row+2, sharex=ax1)
    ax2.plot(x, (y_python/y_idl).decompose())
    ax2.axvspan(x[0], x_thresh_min, color='r', alpha=0.25)
    ax2.axvspan(x_thresh_max, x[-1], color='r', alpha=0.25)
    ax2.axhline(y=1, color='k', ls=':')
    if i_row == 0:
        ax2.set_title('fiasco / IDL')
    diff_limit = .001
    ax2.set_ylim(1-diff_limit, 1+diff_limit)
    # Normalized difference
    ax3 = fig.add_subplot(n_rows, 3, i_row+3, sharex=ax1)
    ax3.plot(x,  ((y_python - y_idl)/y_idl).decompose())
    ax3.axvspan(x[0], x_thresh_min, color='r', alpha=0.25)
    ax3.axvspan(x_thresh_max, x[-1], color='r', alpha=0.25)
    ax3.axhline(y=0, color='k', ls=':')
    if i_row == 0:
        ax3.set_title('(fiasco - IDL)/IDL')
    ax3.set_ylim(-diff_limit, diff_limit)
    return ax1, ax2, ax3

Next, plot the comparison between the ionization fraction results for a selected number of ions. In the case of fiasco, we will also compute the ionization fraction in addition to reading the tabulated values. The regions highlighted in red denote places where the ionization fraction is less than \(10^{-6}\) times the peak of the ionization fraction. In these regions, the comparison is between the two results is not as critical as differences due to the interpolation schemes may show large deviations between the two approaches. However, the ionization fraction in these regions does not meaningfully contribute to any other derived quantities.

ioneq_files = [
    'ioneq_1_1',
    'ioneq_6_1',
    'ioneq_6_2',
    'ioneq_6_3',
    'ioneq_20_2',
    'ioneq_26_5',
    'ioneq_26_16',
    'ioneq_26_18',
    'ioneq_26_20',
    'ioneq_26_27',
]
fig = plt.figure(figsize=(9,3*len(ioneq_files)), layout='constrained')
for i, name in enumerate(ioneq_files):
    idl_result = read_idl_test_output(name, '8.0.7')
    ion = fiasco.Ion((idl_result['Z'], idl_result['iz']),
                     idl_result['temperature'],
                     ioneq_filename=idl_result['ioneq_filename'])
    element = fiasco.Element(ion.atomic_symbol, ion.temperature)
    ioneq = element.equilibrium_ionization
    print(f'IDL code to produce ioneq result for {ion.ion_name_roman}:')
    print(Template(idl_result['idl_script']).render(**idl_result))
    axes = plot_idl_comparison(ion.temperature, idl_result['ioneq'], ion.ioneq,
                               fig, len(ioneq_files), 3*i, f'{ion.ion_name_roman}')
    axes[0].plot(element.temperature, ioneq[:, ion.charge_state],
                 label='fiasco (rates)', color='C1', ls='-')
    axes[0].legend()
plt.show()
Ionization Fraction, fiasco / IDL, (fiasco - IDL)/IDL
/home/docs/checkouts/readthedocs.org/user_builds/fiasco/conda/latest/lib/python3.11/site-packages/asdf/_asdf.py:359: AsdfWarning: File 'file:///home/docs/checkouts/readthedocs.org/user_builds/fiasco/conda/latest/lib/python3.11/site-packages/fiasco/tests/idl/data/ioneq_1_1_v8.0.7.asdf' was created with extension URI 'asdf://astropy.org/core/extensions/core-1.5.0' (from package asdf-astropy==0.5.0), which is not currently installed
  warnings.warn(msg, AsdfWarning)
IDL code to produce ioneq result for H I:

    ioneq_file = FILEPATH('chianti.ioneq', ROOT_DIR=!xuvtop, SUBDIR='ioneq')
    read_ioneq, ioneq_file, temperature, ioneq, ioneq_ref
    ioneq = ioneq[*,0,0]

/home/docs/checkouts/readthedocs.org/user_builds/fiasco/conda/latest/lib/python3.11/site-packages/asdf/_asdf.py:359: AsdfWarning: File 'file:///home/docs/checkouts/readthedocs.org/user_builds/fiasco/conda/latest/lib/python3.11/site-packages/fiasco/tests/idl/data/ioneq_6_1_v8.0.7.asdf' was created with extension URI 'asdf://astropy.org/core/extensions/core-1.5.0' (from package asdf-astropy==0.5.0), which is not currently installed
  warnings.warn(msg, AsdfWarning)
IDL code to produce ioneq result for C I:

    ioneq_file = FILEPATH('chianti.ioneq', ROOT_DIR=!xuvtop, SUBDIR='ioneq')
    read_ioneq, ioneq_file, temperature, ioneq, ioneq_ref
    ioneq = ioneq[*,5,0]

/home/docs/checkouts/readthedocs.org/user_builds/fiasco/conda/latest/lib/python3.11/site-packages/astropy/units/quantity.py:671: RuntimeWarning: invalid value encountered in divide
  result = super().__array_ufunc__(function, method, *arrays, **kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/fiasco/conda/latest/lib/python3.11/site-packages/asdf/_asdf.py:359: AsdfWarning: File 'file:///home/docs/checkouts/readthedocs.org/user_builds/fiasco/conda/latest/lib/python3.11/site-packages/fiasco/tests/idl/data/ioneq_6_2_v8.0.7.asdf' was created with extension URI 'asdf://astropy.org/core/extensions/core-1.5.0' (from package asdf-astropy==0.5.0), which is not currently installed
  warnings.warn(msg, AsdfWarning)
IDL code to produce ioneq result for C II:

    ioneq_file = FILEPATH('chianti.ioneq', ROOT_DIR=!xuvtop, SUBDIR='ioneq')
    read_ioneq, ioneq_file, temperature, ioneq, ioneq_ref
    ioneq = ioneq[*,5,1]

/home/docs/checkouts/readthedocs.org/user_builds/fiasco/conda/latest/lib/python3.11/site-packages/asdf/_asdf.py:359: AsdfWarning: File 'file:///home/docs/checkouts/readthedocs.org/user_builds/fiasco/conda/latest/lib/python3.11/site-packages/fiasco/tests/idl/data/ioneq_6_3_v8.0.7.asdf' was created with extension URI 'asdf://astropy.org/core/extensions/core-1.5.0' (from package asdf-astropy==0.5.0), which is not currently installed
  warnings.warn(msg, AsdfWarning)
IDL code to produce ioneq result for C III:

    ioneq_file = FILEPATH('chianti.ioneq', ROOT_DIR=!xuvtop, SUBDIR='ioneq')
    read_ioneq, ioneq_file, temperature, ioneq, ioneq_ref
    ioneq = ioneq[*,5,2]

/home/docs/checkouts/readthedocs.org/user_builds/fiasco/conda/latest/lib/python3.11/site-packages/asdf/_asdf.py:359: AsdfWarning: File 'file:///home/docs/checkouts/readthedocs.org/user_builds/fiasco/conda/latest/lib/python3.11/site-packages/fiasco/tests/idl/data/ioneq_20_2_v8.0.7.asdf' was created with extension URI 'asdf://astropy.org/core/extensions/core-1.5.0' (from package asdf-astropy==0.5.0), which is not currently installed
  warnings.warn(msg, AsdfWarning)
IDL code to produce ioneq result for Ca II:

    ioneq_file = FILEPATH('chianti.ioneq', ROOT_DIR=!xuvtop, SUBDIR='ioneq')
    read_ioneq, ioneq_file, temperature, ioneq, ioneq_ref
    ioneq = ioneq[*,19,1]

/home/docs/checkouts/readthedocs.org/user_builds/fiasco/conda/latest/lib/python3.11/site-packages/asdf/_asdf.py:359: AsdfWarning: File 'file:///home/docs/checkouts/readthedocs.org/user_builds/fiasco/conda/latest/lib/python3.11/site-packages/fiasco/tests/idl/data/ioneq_26_5_v8.0.7.asdf' was created with extension URI 'asdf://astropy.org/core/extensions/core-1.5.0' (from package asdf-astropy==0.5.0), which is not currently installed
  warnings.warn(msg, AsdfWarning)
IDL code to produce ioneq result for Fe V:

    ioneq_file = FILEPATH('chianti.ioneq', ROOT_DIR=!xuvtop, SUBDIR='ioneq')
    read_ioneq, ioneq_file, temperature, ioneq, ioneq_ref
    ioneq = ioneq[*,25,4]

/home/docs/checkouts/readthedocs.org/user_builds/fiasco/conda/latest/lib/python3.11/site-packages/asdf/_asdf.py:359: AsdfWarning: File 'file:///home/docs/checkouts/readthedocs.org/user_builds/fiasco/conda/latest/lib/python3.11/site-packages/fiasco/tests/idl/data/ioneq_26_16_v8.0.7.asdf' was created with extension URI 'asdf://astropy.org/core/extensions/core-1.5.0' (from package asdf-astropy==0.5.0), which is not currently installed
  warnings.warn(msg, AsdfWarning)
IDL code to produce ioneq result for Fe XVI:

    ioneq_file = FILEPATH('chianti.ioneq', ROOT_DIR=!xuvtop, SUBDIR='ioneq')
    read_ioneq, ioneq_file, temperature, ioneq, ioneq_ref
    ioneq = ioneq[*,25,15]

/home/docs/checkouts/readthedocs.org/user_builds/fiasco/conda/latest/lib/python3.11/site-packages/asdf/_asdf.py:359: AsdfWarning: File 'file:///home/docs/checkouts/readthedocs.org/user_builds/fiasco/conda/latest/lib/python3.11/site-packages/fiasco/tests/idl/data/ioneq_26_18_v8.0.7.asdf' was created with extension URI 'asdf://astropy.org/core/extensions/core-1.5.0' (from package asdf-astropy==0.5.0), which is not currently installed
  warnings.warn(msg, AsdfWarning)
IDL code to produce ioneq result for Fe XVIII:

    ioneq_file = FILEPATH('chianti.ioneq', ROOT_DIR=!xuvtop, SUBDIR='ioneq')
    read_ioneq, ioneq_file, temperature, ioneq, ioneq_ref
    ioneq = ioneq[*,25,17]

/home/docs/checkouts/readthedocs.org/user_builds/fiasco/conda/latest/lib/python3.11/site-packages/asdf/_asdf.py:359: AsdfWarning: File 'file:///home/docs/checkouts/readthedocs.org/user_builds/fiasco/conda/latest/lib/python3.11/site-packages/fiasco/tests/idl/data/ioneq_26_20_v8.0.7.asdf' was created with extension URI 'asdf://astropy.org/core/extensions/core-1.5.0' (from package asdf-astropy==0.5.0), which is not currently installed
  warnings.warn(msg, AsdfWarning)
IDL code to produce ioneq result for Fe XX:

    ioneq_file = FILEPATH('chianti.ioneq', ROOT_DIR=!xuvtop, SUBDIR='ioneq')
    read_ioneq, ioneq_file, temperature, ioneq, ioneq_ref
    ioneq = ioneq[*,25,19]

/home/docs/checkouts/readthedocs.org/user_builds/fiasco/conda/latest/lib/python3.11/site-packages/asdf/_asdf.py:359: AsdfWarning: File 'file:///home/docs/checkouts/readthedocs.org/user_builds/fiasco/conda/latest/lib/python3.11/site-packages/fiasco/tests/idl/data/ioneq_26_27_v8.0.7.asdf' was created with extension URI 'asdf://astropy.org/core/extensions/core-1.5.0' (from package asdf-astropy==0.5.0), which is not currently installed
  warnings.warn(msg, AsdfWarning)
IDL code to produce ioneq result for Fe XXVII:

    ioneq_file = FILEPATH('chianti.ioneq', ROOT_DIR=!xuvtop, SUBDIR='ioneq')
    read_ioneq, ioneq_file, temperature, ioneq, ioneq_ref
    ioneq = ioneq[*,25,26]

Total running time of the script: (0 minutes 14.386 seconds)

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