diff --git a/stardis/plasma/base.py b/stardis/plasma/base.py index f0d4cdb7..6941750a 100644 --- a/stardis/plasma/base.py +++ b/stardis/plasma/base.py @@ -20,9 +20,9 @@ helium_lte_properties, ) from stardis.plasma.molecules import ( - MoleculeIonNumberDensities, - AlphaLineValdMolecules, - MoleculePartitionFunctions, + MoleculeIonNumberDensity, + AlphaLineValdMolecule, + MoleculePartitionFunction, ) @@ -546,9 +546,9 @@ def create_stellar_plasma( dilution_factor=np.ones_like(stellar_model.temperatures), ) if config.opacity.line.include_molecules: - plasma_modules.append(MoleculeIonNumberDensities) - plasma_modules.append(MoleculePartitionFunctions) - plasma_modules.append(AlphaLineValdMolecules) + plasma_modules.append(MoleculeIonNumberDensity) + plasma_modules.append(MoleculePartitionFunction) + plasma_modules.append(AlphaLineValdMolecule) return BasePlasma( plasma_properties=plasma_modules, diff --git a/stardis/plasma/molecules.py b/stardis/plasma/molecules.py index c65b5955..d8959f22 100644 --- a/stardis/plasma/molecules.py +++ b/stardis/plasma/molecules.py @@ -12,12 +12,12 @@ logger = logging.getLogger(__name__) -class MoleculeIonNumberDensities(ProcessingPlasmaProperty): +class MoleculeIonNumberDensity(ProcessingPlasmaProperty): # Need to think about negative ions - ignoring for now # applicable for equilibrium constants given by Barklem and Collet 2016, which are given in SI units - outputs = ("molecule_number_densities",) + outputs = ("molecule_number_density",) def calculate(self, ion_number_density, t_electrons, atomic_data): # Preprocessing - split ions into symbol, charge, and number @@ -123,16 +123,16 @@ def calculate(self, ion_number_density, t_electrons, atomic_data): return molecule_densities_df -class MoleculePartitionFunctions(ProcessingPlasmaProperty): +class MoleculePartitionFunction(ProcessingPlasmaProperty): """ Attributes ---------- - molecule_partition_functions : DataFrame + molecule_partition_function : DataFrame A pandas DataFrame with dtype float. This represents the partition function for each molecule at each depth point. """ - outputs = ("molecule_partition_functions",) + outputs = ("molecule_partition_function",) def calculate(self, t_electrons, atomic_data): partition_functions = pd.DataFrame( @@ -152,7 +152,7 @@ def calculate(self, t_electrons, atomic_data): return partition_functions -class AlphaLineValdMolecules(ProcessingPlasmaProperty): +class AlphaLineValdMolecule(ProcessingPlasmaProperty): """ Attributes ---------- @@ -176,9 +176,9 @@ class AlphaLineValdMolecules(ProcessingPlasmaProperty): def calculate( self, atomic_data, - molecule_number_densities, + molecule_number_density, t_electrons, - molecule_partition_functions, + molecule_partition_function, ): # solve n_lower : n_i = N * g_i / U * e ^ (-E_i/kT) # get f_lu : loggf -> use g = 2j+1 @@ -213,8 +213,8 @@ def calculate( ).to(1) ) - molecule_densities_div_partition_function = ( - molecule_number_densities.copy().div(molecule_partition_functions) + molecule_densities_div_partition_function = molecule_number_density.copy().div( + molecule_partition_function ) molecule_densities_div_partition_function.index.name = "molecule" @@ -281,7 +281,7 @@ def calculate( return alphas, linelist -class AlphaLineShortlistValdMolecules(ProcessingPlasmaProperty): +class AlphaLineShortlistValdMolecule(ProcessingPlasmaProperty): """ Attributes ---------- @@ -305,9 +305,9 @@ class AlphaLineShortlistValdMolecules(ProcessingPlasmaProperty): def calculate( self, atomic_data, - molecule_number_densities, + molecule_number_density, t_electrons, - molecule_partition_functions, + molecule_partition_function, ): # solve n_lower : n_i = N * g_i / U * e ^ (-E_i/kT) # get f_lu : loggf -> use g = 2j+1 @@ -347,8 +347,8 @@ def calculate( ).to(1) ) - molecule_densities_div_partition_function = ( - molecule_number_densities.copy().div(molecule_partition_functions) + molecule_densities_div_partition_function = molecule_number_density.copy().div( + molecule_partition_function ) molecule_densities_div_partition_function.index.name = "molecule" diff --git a/stardis/radiation_field/opacities/opacities_solvers/broadening.py b/stardis/radiation_field/opacities/opacities_solvers/broadening.py index a667b6b7..35815d3c 100644 --- a/stardis/radiation_field/opacities/opacities_solvers/broadening.py +++ b/stardis/radiation_field/opacities/opacities_solvers/broadening.py @@ -717,9 +717,7 @@ def calculate_molecule_broadening( (len(lines), len(stellar_model.geometry.no_of_depth_points)), dtype=float ) - ions = stellar_plasma.molecule_number_densities[["ion1", "ion2"]].loc[ - lines.molecule - ] + ions = stellar_plasma.molecule_number_density[["ion1", "ion2"]].loc[lines.molecule] ion1_masses = stellar_model.composition.nuclide_masses.loc[ions.ion1].values ion2_masses = stellar_model.composition.nuclide_masses.loc[ions.ion2].values