Refactor isotope mass fraction handling and configuration

- Remove raw_isotope_abundance from Composition class
- Update mass fraction parsing to conditionally apply isotope decay
- Modify default model_isotope_time_0 to -1 s to allow skipping decay
- Update test fixtures to explicitly set model_isotope_time_0
- Simplify mass fraction parsing functions by removing redundant returns

tardis/energy_input/tests/test_gamma_ray_channel.py

@@ -76,7 +76,7 @@ def gamma_ray_test_composition(gamma_ray_simulation_state):
     """
 
     raw_isotopic_mass_fraction = (
-        gamma_ray_simulation_state.composition.raw_isotope_abundance
+        gamma_ray_simulation_state.composition.isotopic_mass_fraction
     )
     composition = gamma_ray_simulation_state.composition
     cell_masses = composition.calculate_cell_masses(

tardis/io/configuration/schemas/model_definitions.yml

@@ -181,7 +181,7 @@ definitions:
           description: filename
         model_isotope_time_0:
           type: quantity
-          default: 0 s
+          default: -1 s
           description: Initial time for isotope decay
 
       required:
@@ -199,7 +199,7 @@ definitions:
           - uniform
         model_isotope_time_0:
           type: quantity
-          default: 0 s
+          default: -1 s
           description: Initial time for isotope decay
       additionalProperties:
         type: number

tardis/io/model/parse_composition_configuration.py

@@ -32,16 +32,14 @@ def parse_composition_from_config(atom_data, config, time_explosion, geometry):
     """
     density, electron_densities = parse_density_from_config(config)
 
-    (
-        nuclide_mass_fractions,
-        raw_isotope_mass_fractions,
-    ) = parse_mass_fractions_from_config(config, geometry, time_explosion)
+    (nuclide_mass_fractions) = parse_mass_fractions_from_config(
+        config, geometry, time_explosion
+    )
 
     return (
         Composition(
             density,
             nuclide_mass_fractions,
-            raw_isotope_mass_fractions,
             atom_data.atom_data.mass.copy(),
         ),
         electron_densities,
@@ -86,15 +84,11 @@ def parse_composition_from_csvy(
         csvy_model_config, csvy_model_data, time_explosion
     )
 
-    (
-        nuclide_mass_fractions,
-        raw_isotope_mass_fractions,
-    ) = parse_mass_fractions_from_csvy(
+    (nuclide_mass_fractions) = parse_mass_fractions_from_csvy(
         csvy_model_config, csvy_model_data, geometry, time_explosion
     )
     return Composition(
         density,
         nuclide_mass_fractions,
-        raw_isotope_mass_fractions,
         atom_data.atom_data.mass.copy(),
     )

tardis/io/model/parse_mass_fraction_configuration.py

@@ -89,18 +89,16 @@ def parse_mass_fractions_from_config(config, geometry, time_explosion):
         isotope_mass_fractions /= norm_factor
     # The next line is if the mass_fractions are given via dict
     # and not gone through the schema validator
-    raw_isotope_mass_fractions = isotope_mass_fractions
-    model_isotope_time_0 = config.model.abundances.get(
-        "model_isotope_time_0", 0.0 * u.day
-    )
-    isotope_mass_fractions = IsotopicMassFraction(
-        isotope_mass_fractions, time_0=model_isotope_time_0
-    ).decay(time_explosion)
+    model_isotope_time_0 = config.model.abundances.model_isotope_time_0
+    if model_isotope_time_0 >= 0 * u.s:
+        isotope_mass_fractions = IsotopicMassFraction(
+            isotope_mass_fractions, time_0=model_isotope_time_0
+        ).decay(time_explosion)
 
     nuclide_mass_fractions = convert_to_nuclide_mass_fractions(
         isotope_mass_fractions, mass_fractions
     )
-    return nuclide_mass_fractions, raw_isotope_mass_fractions
+    return nuclide_mass_fractions
 
 
 def parse_mass_fractions_from_csvy(
@@ -171,16 +169,10 @@ def parse_mass_fractions_from_csvy(
         mass_fractions /= norm_factor
         isotope_mass_fractions /= norm_factor
 
-    raw_isotope_mass_fraction = isotope_mass_fractions
     isotope_mass_fractions = IsotopicMassFraction(
         isotope_mass_fractions, time_0=csvy_model_config.model_isotope_time_0
     ).decay(time_explosion)
-    return (
-        convert_to_nuclide_mass_fractions(
-            isotope_mass_fractions, mass_fractions
-        ),
-        raw_isotope_mass_fraction,
-    )
+    return convert_to_nuclide_mass_fractions(isotope_mass_fractions, mass_fractions)
 
 
 def convert_to_nuclide_mass_fractions(isotopic_mass_fractions, mass_fractions):

tardis/model/matter/composition.py

@@ -69,7 +69,6 @@ def __init__(
         self,
         density,
         nuclide_mass_fraction,
-        raw_isotope_abundance,
         element_masses,
         element_masses_unit=u.g,
     ):
@@ -89,7 +88,6 @@ def __init__(
         isotope_masses = self.assemble_isotope_masses()
 
         self.nuclide_masses = pd.concat([self.nuclide_masses, isotope_masses])
-        self.raw_isotope_abundance = raw_isotope_abundance
 
     def assemble_isotope_masses(self):
         isotope_mass_df = pd.Series(

tardis/model/tests/test_base.py

@@ -403,7 +403,7 @@ def non_uniform_simulation_state(atomic_dataset, example_model_file_dir):
     config = Configuration.from_yaml(
         example_model_file_dir / "tardis_configv1_isotope_iabund.yml"
     )
-
+    config.model.abundances.model_isotope_time_0 = 0 * u.s
     return SimulationState.from_config(config, atom_data=atomic_dataset)
 
 
@@ -435,6 +435,7 @@ def simulation_state(self, example_model_file_dir, atomic_dataset):
         config = Configuration.from_yaml(
             example_model_file_dir / "tardis_configv1_isotope_iabund.yml"
         )
+        config.model.abundances.model_isotope_time_0 = 0 * u.s
         return SimulationState.from_config(config, atom_data=atomic_dataset)
 
     def test_atomic_mass(self, simulation_state):

tardis/model/tests/test_csvy_model.py

@@ -2,6 +2,7 @@
 import numpy.testing as npt
 import pandas as pd
 import pytest
+from astropy import units as u
 
 from tardis.io.configuration.config_reader import Configuration
 from tardis.model import SimulationState
@@ -32,6 +33,7 @@ def test_compare_models(model_config_fnames, atomic_dataset):
     csvy_config_file, old_config_file = model_config_fnames
     tardis_config = Configuration.from_yaml(csvy_config_file)
     tardis_config_old = Configuration.from_yaml(old_config_file)
+    tardis_config_old.model.abundances.model_isotope_time_0 = 0 * u.s
     csvy_simulation_state = SimulationState.from_csvy(
         tardis_config, atom_data=atomic_dataset
     )

tardis/plasma/tests/test_tardis_model_density_config.py

@@ -1,6 +1,7 @@
 import numpy.testing as npt
 import pandas.testing as pdt
 import pytest
+from astropy import units as u
 
 from tardis.io.configuration.config_reader import Configuration
 from tardis.model import SimulationState
@@ -16,6 +17,7 @@ def tardis_model_density_config(example_model_file_dir):
 
 @pytest.fixture
 def raw_simulation_state(tardis_model_density_config, kurucz_atomic_data):
+    tardis_model_density_config.model.abundances.model_isotope_time_0 = 0 * u.s
     return SimulationState.from_config(
         tardis_model_density_config, atom_data=kurucz_atomic_data
     )