densities -> density

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,

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"
 

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