add include_protons option to two_photon calculation, default to True

Author: Jeffrey Reep

fiasco/io/sources/continuum_sources.py

@@ -259,7 +259,8 @@ class HSeqParser(GenericParser):
     -----
     * The parameter :math: `\psi_{\text{norm}}` (called :math: `A_{\text{sum}}` in CHIANTI) is a normalization factor of
     the integral of the spectral distribution function :math:`\psi(y)` from 0 to 1, such
-    that :math: `\frac{1}{\psi_{\text{norm}}} \int_{0}^{1} \psi(y) dy = 2`.
+    that :math: `\frac{1}{\psi_{\text{norm}}} \int_{0}^{1} \psi(y) dy = 2`.  This normalization is only used For
+    hydrogenic ions.
     """
     filetype = 'hseq_2photon'
     dtypes = [int, float, int, float, float, float]

fiasco/ions.py

@@ -1469,7 +1469,9 @@ def _karzas_cross_section(self, photon_energy: u.erg, ionization_energy: u.erg,
 
     @needs_dataset('elvlc')
     @u.quantity_input
-    def two_photon(self, wavelength: u.angstrom, electron_density: u.cm**(-3)) -> u.erg * u.cm**3 / u.s / u.angstrom:
+    def two_photon(self, wavelength: u.angstrom,
+                    electron_density: u.cm**(-3),
+                    include_protons=True) -> u.erg * u.cm**3 / u.s / u.angstrom:
         r"""
         Two-photon continuum emission of a hydrogenic or helium-like ion.
 
@@ -1512,7 +1514,8 @@ def two_photon(self, wavelength: u.angstrom, electron_density: u.cm**(-3)) -> u.
         energy_dist = (A_ji * rest_wavelength * psi_interp) / (psi_norm * wavelength**3)
 
         pe_ratio = proton_electron_ratio(self.temperature)
-        level_population = self.level_populations(electron_density)[:,:,1]
+        level_population = self.level_populations(electron_density,
+                                                  include_protons=include_protons)[:,:,1]
 
         # N_j(X+m) = N_j(X+m)/N(X+m) * N(X+m)/N(X) * N(X)/N(H) * N(H)/Ne * Ne
         level_density = level_population * np.outer(self.ioneq * self.abundance * pe_ratio, electron_density)