CHIANTI IDL Comparison: Contribution Functions

Compare the contribution function calculation to that in the CHIANTI IDL routines for a few select ions.

import hissw
import matplotlib.pyplot as plt
import numpy as np

from astropy.visualization import quantity_support

import fiasco

from fiasco.tests.idl.helpers import read_idl_test_output

quantity_support()

<astropy.visualization.units.quantity_support.<locals>.MplQuantityConverter object at 0x7f51c9ad10d0>

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(1e5, 1e8)
    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 = .05
    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. The regions highlighted in red denote places where the contribution function 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 the contribution function is comparatively small in these regions.

goft_files = [
    'goft_20_15_200.972',
    'goft_26_9_171.073',
    'goft_26_11_188.497',
    'goft_26_14_197.862',
    'goft_26_16_262.984',
]
fig = plt.figure(figsize=(9,3*len(goft_files)), layout='constrained')
template_env = hissw.Environment(ssw_home='', idl_home='').env
for i, name in enumerate(goft_files):
    idl_result = read_idl_test_output(name, '8.0.7')
    ion = fiasco.Ion((idl_result['Z'], idl_result['iz']),
                     idl_result['temperature'],
                     abundance_filename=idl_result['abundance'],
                     ioneq_filename=idl_result['ioneq'])
    contribution_func = ion.contribution_function(idl_result['density'])
    transitions = ion.transitions.wavelength[~ion.transitions.is_twophoton]
    idx = np.argmin(np.abs(transitions - idl_result['wavelength']))
    goft = contribution_func[:, 0, idx]
    axes = plot_idl_comparison(ion.temperature, idl_result['contribution_function'], goft,
                               fig, len(goft_files), 3*i, f'{ion.ion_name_roman}')
    axes[0].legend()
    print(f'IDL code to produce {ion.ion_name_roman} contribution function result:')
    print(template_env.from_string(idl_result['idl_script']).render(**idl_result))

/home/docs/checkouts/readthedocs.org/user_builds/fiasco/conda/latest/lib/python3.11/site-packages/astropy/units/format/utils.py:220: UnitsWarning: The unit 'erg' has been deprecated in the VOUnit standard. Suggested: cm**2.g.s**-2.
  warnings.warn(message, UnitsWarning)
/home/docs/checkouts/readthedocs.org/user_builds/fiasco/conda/latest/lib/python3.11/site-packages/astropy/units/format/utils.py:220: UnitsWarning: The unit 'Angstrom' has been deprecated in the VOUnit standard. Suggested: 0.1nm.
  warnings.warn(message, UnitsWarning)
/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/goft_20_15_200.972_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)
/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)
IDL code to produce Ca XV contribution function result:

        abund_file = FILEPATH('sun_coronal_1992_feldman_ext.abund', ROOT_DIR=!xuvtop, SUBDIR='abundance')
        ioneq_file = FILEPATH('chianti.ioneq', ROOT_DIR=!xuvtop, SUBDIR='ioneq')
        density = 10d / 1d
        wave_min = 7035889255347913d / 35184372088832d
        wave_max = 7106257999525577d / 35184372088832d
        contribution_function = g_of_t(20,$
                                       15,$
                                       dens=density,$
                                       abund_file=abund_file,$
                                       ioneq_file=ioneq_file,$
                                       index=297,/quiet,$
                                       wrange=[wave_min, wave_max])
        ; Call this function to get the temperature array
        read_ioneq,ioneq_file,temperature,ioneq,ref

/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/goft_26_9_171.073_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)
WARNING: No proton data available for Fe 9. Not including proton excitation and de-excitation in level populations calculation. [fiasco.ions]
/home/docs/checkouts/readthedocs.org/user_builds/fiasco/conda/latest/lib/python3.11/site-packages/astropy/units/quantity.py:671: RuntimeWarning: divide by zero encountered in divide
  result = super().__array_ufunc__(function, method, *arrays, **kwargs)
IDL code to produce Fe IX contribution function result:

        abund_file = FILEPATH('sun_coronal_1992_feldman_ext.abund', ROOT_DIR=!xuvtop, SUBDIR='abundance')
        ioneq_file = FILEPATH('chianti.ioneq', ROOT_DIR=!xuvtop, SUBDIR='ioneq')
        density = 10d / 1d
        wave_min = 5983911714263925d / 35184372088832d
        wave_max = 6054280458441589d / 35184372088832d
        contribution_function = g_of_t(26,$
                                       9,$
                                       dens=density,$
                                       abund_file=abund_file,$
                                       ioneq_file=ioneq_file,$
                                       index=13946,/quiet,$
                                       wrange=[wave_min, wave_max])
        ; Call this function to get the temperature array
        read_ioneq,ioneq_file,temperature,ioneq,ref

/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/goft_26_11_188.497_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 Fe XI contribution function result:

        abund_file = FILEPATH('sun_coronal_1992_feldman_ext.abund', ROOT_DIR=!xuvtop, SUBDIR='abundance')
        ioneq_file = FILEPATH('chianti.ioneq', ROOT_DIR=!xuvtop, SUBDIR='ioneq')
        density = 10d / 1d
        wave_min = 3298482106769867d / 17592186044416d
        wave_max = 3333666478858699d / 17592186044416d
        contribution_function = g_of_t(26,$
                                       11,$
                                       dens=density,$
                                       abund_file=abund_file,$
                                       ioneq_file=ioneq_file,$
                                       index=22527,/quiet,$
                                       wrange=[wave_min, wave_max])
        ; Call this function to get the temperature array
        read_ioneq,ioneq_file,temperature,ioneq,ref

/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/goft_26_14_197.862_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 Fe XIV contribution function result:

        abund_file = FILEPATH('sun_coronal_1992_feldman_ext.abund', ROOT_DIR=!xuvtop, SUBDIR='abundance')
        ioneq_file = FILEPATH('chianti.ioneq', ROOT_DIR=!xuvtop, SUBDIR='ioneq')
        density = 10d / 1d
        wave_min = 6926465858151645d / 35184372088832d
        wave_max = 6996834602329309d / 35184372088832d
        contribution_function = g_of_t(26,$
                                       14,$
                                       dens=density,$
                                       abund_file=abund_file,$
                                       ioneq_file=ioneq_file,$
                                       index=27964,/quiet,$
                                       wrange=[wave_min, wave_max])
        ; Call this function to get the temperature array
        read_ioneq,ioneq_file,temperature,ioneq,ref

/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/goft_26_16_262.984_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)
WARNING: No proton data available for Fe 16. Not including proton excitation and de-excitation in level populations calculation. [fiasco.ions]
IDL code to produce Fe XVI contribution function result:

        abund_file = FILEPATH('sun_coronal_1992_feldman_ext.abund', ROOT_DIR=!xuvtop, SUBDIR='abundance')
        ioneq_file = FILEPATH('chianti.ioneq', ROOT_DIR=!xuvtop, SUBDIR='ioneq')
        density = 10d / 1d
        wave_min = 4608871268660281d / 17592186044416d
        wave_max = 4644055640749113d / 17592186044416d
        contribution_function = g_of_t(26,$
                                       16,$
                                       dens=density,$
                                       abund_file=abund_file,$
                                       ioneq_file=ioneq_file,$
                                       index=1415,/quiet,$
                                       wrange=[wave_min, wave_max])
        ; Call this function to get the temperature array
        read_ioneq,ioneq_file,temperature,ioneq,ref