musica 0.11.1.4__cp312-cp312-win_amd64.whl → 0.12.1__cp312-cp312-win_amd64.whl

musica/test/{test_parser.py → unit/test_util_full_mechanism.py}

@@ -1,9 +1,270 @@
-import pytest
-from musica.mechanism_configuration import *
-from musica import _ReactionType
+import musica.mechanism_configuration as mc
 
 
-def validate_species(species):
+def get_fully_defined_mechanism():
+    # Chemical species
+    A = mc.Species(name="A", other_properties={"__absolute tolerance": "1.0e-30"})
+    B = mc.Species(name="B", tracer_type="AEROSOL")
+    C = mc.Species(name="C", tracer_type="THIRD_BODY")
+    M = mc.Species(name="M")
+    H2O2 = mc.Species(
+        name="H2O2",
+        HLC_298K_mol_m3_Pa=1.011596348,
+        HLC_exponential_factor_K=6340,
+        diffusion_coefficient_m2_s=1.46e-05,
+        N_star=1.74,
+        molecular_weight_kg_mol=0.0340147,
+        density_kg_m3=1000.0,
+        other_properties={"__absolute tolerance": "1.0e-10"},
+    )
+    ethanol = mc.Species(
+        name="ethanol",
+        diffusion_coefficient_m2_s=0.95e-05,
+        N_star=2.55,
+        molecular_weight_kg_mol=0.04607,
+        other_properties={"__absolute tolerance": "1.0e-20"},
+    )
+    ethanol_aq = mc.Species(
+        name="ethanol_aq",
+        molecular_weight_kg_mol=0.04607,
+        density_kg_m3=1000.0,
+        other_properties={"__absolute tolerance": "1.0e-20"},
+    )
+    H2O2_aq = mc.Species(
+        name="H2O2_aq",
+        molecular_weight_kg_mol=0.0340147,
+        density_kg_m3=1000.0,
+        other_properties={"__absolute tolerance": "1.0e-10"},
+    )
+    H2O_aq = mc.Species(
+        name="H2O_aq",
+        density_kg_m3=1000.0,
+        molecular_weight_kg_mol=0.01801,
+    )
+    aerosol_stuff = mc.Species(
+        name="aerosol stuff",
+        molecular_weight_kg_mol=0.5,
+        density_kg_m3=1000.0,
+        other_properties={"__absolute tolerance": "1.0e-20"},
+    )
+    more_aerosol_stuff = mc.Species(
+        name="more aerosol stuff",
+        molecular_weight_kg_mol=0.2,
+        density_kg_m3=1000.0,
+        other_properties={"__absolute tolerance": "1.0e-20"},
+    )
+
+    # Chemical phases
+    gas = mc.Phase(name="gas", species=[A, B, C, ethanol])
+    aqueous_aerosol = mc.Phase(
+        name="aqueous aerosol",
+        species=[H2O2_aq, H2O_aq, ethanol_aq, A, B, C],
+        other_properties={"__irrelevant": "2"},
+    )
+    surface_reacting_phase = mc.Phase(
+        name="surface reacting phase",
+        species=[aerosol_stuff, more_aerosol_stuff]
+    )
+    cloud = mc.Phase(name="cloud", species=[B, C])
+
+    # Reactions
+    my_arrhenius = mc.Arrhenius(
+        name="my arrhenius",
+        A=32.1, B=-2.3, C=102.3, D=63.4, E=-1.3,
+        gas_phase=gas,
+        reactants=[B],
+        products=[C],
+        other_properties={"__irrelevant": "2"},
+    )
+
+    my_other_arrhenius = mc.Arrhenius(
+        name="my other arrhenius",
+        A=29.3, B=-1.5, Ea=101.2, D=82.6, E=-0.98,
+        gas_phase=gas,
+        reactants=[A],
+        products=[(1.2, B)]
+    )
+
+    my_condensed_arrhenius = mc.CondensedPhaseArrhenius(
+        name="my condensed arrhenius",
+        condensed_phase=aqueous_aerosol,
+        A=123.45,
+        B=1.3,
+        Ea=123.45,
+        D=300.0,
+        E=0.6e-5,
+        reactants=[H2O2_aq, H2O_aq],
+        products=[ethanol_aq],
+        other_properties={"__irrelevant": "2"},
+    )
+
+    my_other_condensed_arrhenius = mc.CondensedPhaseArrhenius(
+        name="my other condensed arrhenius",
+        condensed_phase=aqueous_aerosol,
+        A=123.45,
+        B=1.3,
+        C=123.45,
+        D=300.0,
+        E=0.6e-5,
+        reactants=[H2O2_aq, H2O_aq],
+        products=[ethanol_aq]
+    )
+
+    my_troe = mc.Troe(
+        name="my troe",
+        gas_phase=gas,
+        k0_A=1.2e-12,
+        k0_B=167,
+        k0_C=3,
+        kinf_A=136,
+        kinf_B=5,
+        kinf_C=24,
+        Fc=0.9,
+        N=0.8,
+        reactants=[B, M],
+        products=[C],
+        other_properties={"__irrelevant": "2"},
+    )
+
+    my_ternary = mc.TernaryChemicalActivation(
+        name="my ternary chemical activation",
+        gas_phase=gas,
+        k0_A=32.1,
+        k0_B=-2.3,
+        k0_C=102.3,
+        kinf_A=63.4,
+        kinf_B=-1.3,
+        kinf_C=908.5,
+        Fc=1.3,
+        N=32.1,
+        reactants=[B, M],
+        products=[C],
+        other_properties={"__irrelevant": "2"},
+    )
+
+    my_branched = mc.Branched(
+        name="my branched",
+        gas_phase=gas,
+        reactants=[A],
+        alkoxy_products=[B],
+        nitrate_products=[C],
+        X=1.2e-4,
+        Y=167,
+        a0=0.15,
+        n=9,
+        other_properties={"__irrelevant": "2"},
+    )
+
+    my_tunneling = mc.Tunneling(
+        name="my tunneling",
+        gas_phase=gas,
+        reactants=[B],
+        products=[C],
+        A=123.45,
+        B=1200.0,
+        C=1.0e8,
+        other_properties={"__irrelevant": "2"},
+    )
+
+    my_surface = mc.Surface(
+        name="my surface",
+        gas_phase=gas,
+        gas_phase_species=A,
+        reaction_probability=2.0e-2,
+        gas_phase_products=[B, C],
+        condensed_phase=surface_reacting_phase,
+        other_properties={"__irrelevant": "2"},
+    )
+
+    photo_B = mc.Photolysis(
+        name="photo B",
+        gas_phase=gas,
+        reactants=[B],
+        products=[C],
+        scaling_factor=12.3,
+        other_properties={"__irrelevant": "2"},
+    )
+
+    condensed_photo_B = mc.CondensedPhasePhotolysis(
+        name="condensed photo B",
+        condensed_phase=aqueous_aerosol,
+        reactants=[H2O2_aq],
+        products=[ethanol_aq],
+        scaling_factor=12.3,
+        other_properties={"__irrelevant": "2"},
+    )
+
+    my_emission = mc.Emission(
+        name="my emission",
+        gas_phase=gas,
+        products=[B],
+        scaling_factor=12.3,
+        other_properties={"__irrelevant": "2"},
+    )
+
+    my_first_order_loss = mc.FirstOrderLoss(
+        name="my first order loss",
+        gas_phase=gas,
+        reactants=[C],
+        scaling_factor=12.3,
+        other_properties={"__irrelevant": "2"},
+    )
+
+    my_aqueous_equilibrium = mc.AqueousEquilibrium(
+        name="my aqueous eq",
+        condensed_phase=aqueous_aerosol,
+        condensed_phase_water=H2O_aq,
+        A=1.14e-2,
+        C=2300.0,
+        k_reverse=0.32,
+        reactants=[(2, A)],
+        products=[B, C],
+        other_properties={"__irrelevant": "2"},
+    )
+
+    my_wet_deposition = mc.WetDeposition(
+        name="rxn cloud",
+        condensed_phase=cloud,
+        scaling_factor=12.3,
+        other_properties={"__irrelevant": "2"},
+    )
+
+    my_simpol_phase_transfer = mc.SimpolPhaseTransfer(
+        name="my simpol",
+        gas_phase=gas,
+        gas_phase_species=ethanol,
+        condensed_phase=aqueous_aerosol,
+        condensed_phase_species=ethanol_aq,
+        B=[-1.97e03, 2.91e00, 1.96e-03, -4.96e-01],
+        other_properties={"__irrelevant": "2"},
+    )
+
+    user_defined = mc.UserDefined(
+        name="my user defined",
+        gas_phase=gas,
+        reactants=[A, B],
+        products=[(1.3, C)],
+        scaling_factor=12.3,
+        other_properties={"__irrelevant": "2"}
+    )
+
+    # Mechanism
+    return mc.Mechanism(
+        name="Full Configuration",
+        species=[A, B, C, M, H2O2, ethanol, ethanol_aq, H2O2_aq, H2O_aq,
+                 aerosol_stuff, more_aerosol_stuff],
+        phases=[gas, aqueous_aerosol, surface_reacting_phase, cloud],
+        reactions=[my_arrhenius, my_other_arrhenius, my_condensed_arrhenius,
+                   my_other_condensed_arrhenius, my_troe, my_ternary, my_branched,
+                   my_tunneling, my_surface, photo_B, condensed_photo_B,
+                   my_emission, my_first_order_loss, my_aqueous_equilibrium,
+                   my_wet_deposition, my_simpol_phase_transfer,
+                   user_defined],
+        version=mc.Version(1, 0, 0),
+    )
+
+
+def _validate_species(species):
     # Define the expected species and their required attributes
     expected_species = {
         "A": {"other_properties": {"__absolute tolerance": "1e-30"}},
@@ -79,7 +340,7 @@ def validate_species(species):
             )
 
 
-def validate_phases(phases):
+def _validate_phases(phases):
     # Define the expected phases and their associated species
     expected_phases = {
         "gas": ["A", "B", "C", "ethanol"],
@@ -104,19 +365,19 @@ def validate_phases(phases):
         )
 
 
-def extract_components(components):
+def _extract_components(components):
     return [
         {"species name": component.species_name, "coefficient": component.coefficient}
         for component in components
     ]
 
 
-def validate_arrhenius(reactions):
-    assert reactions[0].type == ReactionType.Arrhenius
-    assert extract_components(reactions[0].reactants) == [
+def _validate_arrhenius(reactions):
+    assert reactions[0].type == mc.ReactionType.Arrhenius
+    assert _extract_components(reactions[0].reactants) == [
         {"species name": "B", "coefficient": 1}
     ]
-    assert extract_components(reactions[0].products) == [
+    assert _extract_components(reactions[0].products) == [
         {"species name": "C", "coefficient": 1}
     ]
     assert reactions[0].A == 32.1
@@ -125,12 +386,12 @@ def validate_arrhenius(reactions):
     assert reactions[0].D == 63.4
     assert reactions[0].E == -1.3
     assert reactions[0].name == "my arrhenius"
-    assert reactions[0].other_properties == {}
-    assert reactions[1].type == ReactionType.Arrhenius
-    assert extract_components(reactions[1].reactants) == [
+    assert reactions[0].other_properties == {"__irrelevant": "2"}
+    assert reactions[1].type == mc.ReactionType.Arrhenius
+    assert _extract_components(reactions[1].reactants) == [
         {"species name": "A", "coefficient": 1}
     ]
-    assert extract_components(reactions[1].products) == [
+    assert _extract_components(reactions[1].products) == [
         {"species name": "B", "coefficient": 1.2}
     ]
     assert reactions[1].A == 29.3
@@ -142,143 +403,135 @@ def validate_arrhenius(reactions):
     assert reactions[1].other_properties == {}
 
 
-def validate_henrys_law(reactions):
-    assert reactions[0].type == ReactionType.HenrysLaw
-    assert reactions[0].gas_phase == "gas"
-    assert extract_components([reactions[0].gas_phase_species]) == [
-        {"species name": "H2O2", "coefficient": 1}
-    ]
-    assert reactions[0].aerosol_phase == "aqueous aerosol"
-    assert extract_components([reactions[0].aerosol_phase_species]) == [
-        {"species name": "H2O2_aq", "coefficient": 1}
-    ]
-    assert reactions[0].aerosol_phase_water == "H2O_aq"
-    assert reactions[0].name == "my henry's law"
-
-
-def validate_simpol_phase_transfer(reactions):
-    assert reactions[0].type == ReactionType.SimpolPhaseTransfer
+def _validate_simpol_phase_transfer(reactions):
+    assert reactions[0].type == mc.ReactionType.SimpolPhaseTransfer
     assert reactions[0].gas_phase == "gas"
-    assert extract_components([reactions[0].gas_phase_species]) == [
+    assert _extract_components([reactions[0].gas_phase_species]) == [
         {"species name": "ethanol", "coefficient": 1}
     ]
-    assert reactions[0].aerosol_phase == "aqueous aerosol"
-    assert extract_components([reactions[0].aerosol_phase_species]) == [
+    assert reactions[0].condensed_phase == "aqueous aerosol"
+    assert _extract_components([reactions[0].condensed_phase_species]) == [
         {"species name": "ethanol_aq", "coefficient": 1}
     ]
     assert reactions[0].B == [-1.97e03, 2.91e00, 1.96e-03, -4.96e-01]
     assert reactions[0].name == "my simpol"
+    assert reactions[0].other_properties == {"__irrelevant": "2"}
 
 
-def validate_aqueous_equilibrium(reactions):
-    assert reactions[0].type == ReactionType.AqueousEquilibrium
-    assert reactions[0].aerosol_phase == "aqueous aerosol"
-    assert reactions[0].aerosol_phase_water == "H2O_aq"
+def _validate_aqueous_equilibrium(reactions):
+    assert reactions[0].type == mc.ReactionType.AqueousEquilibrium
+    assert reactions[0].condensed_phase == "aqueous aerosol"
+    assert reactions[0].condensed_phase_water == "H2O_aq"
     assert reactions[0].A == 1.14e-2
     assert reactions[0].C == 2300.0
     assert reactions[0].k_reverse == 0.32
-    assert extract_components(reactions[0].reactants) == [
+    assert _extract_components(reactions[0].reactants) == [
         {"species name": "A", "coefficient": 2}
     ]
-    assert extract_components(reactions[0].products) == [
+    assert _extract_components(reactions[0].products) == [
         {"species name": "B", "coefficient": 1},
         {"species name": "C", "coefficient": 1},
     ]
     assert reactions[0].name == "my aqueous eq"
+    assert reactions[0].other_properties == {"__irrelevant": "2"}
 
 
-def validate_condensed_phase_arrhenius(reactions):
+def _validate_condensed_phase_arrhenius(reactions):
     for reaction in reactions:
-        assert reaction.type == ReactionType.CondensedPhaseArrhenius
-        assert reaction.aerosol_phase == "aqueous aerosol"
-        assert reaction.aerosol_phase_water == "H2O_aq"
+        assert reaction.type == mc.ReactionType.CondensedPhaseArrhenius
+        assert reaction.condensed_phase == "aqueous aerosol"
         assert reaction.A == 123.45
         assert reaction.B == 1.3
         assert reaction.D == 300.0
         assert reaction.E == 0.6e-5
-        assert extract_components(reaction.reactants) == [
+        assert _extract_components(reaction.reactants) == [
             {"species name": "H2O2_aq", "coefficient": 1},
             {"species name": "H2O_aq", "coefficient": 1},
         ]
-        assert extract_components(reaction.products) == [
+        assert _extract_components(reaction.products) == [
             {"species name": "ethanol_aq", "coefficient": 1}
         ]
     assert reactions[0].name == "my condensed arrhenius"
     assert reactions[0].C == -123.45 / 1.380649e-23
+    assert reactions[0].other_properties == {"__irrelevant": "2"}
     assert reactions[1].name == "my other condensed arrhenius"
     assert reactions[1].C == 123.45
 
 
-def validate_condensed_phase_photolysis(reactions):
-    assert reactions[0].type == ReactionType.CondensedPhasePhotolysis
-    assert reactions[0].aerosol_phase == "aqueous aerosol"
-    assert reactions[0].aerosol_phase_water == "H2O_aq"
-    assert extract_components(reactions[0].reactants) == [
+def _validate_condensed_phase_photolysis(reactions):
+    assert reactions[0].type == mc.ReactionType.CondensedPhasePhotolysis
+    assert reactions[0].condensed_phase == "aqueous aerosol"
+    assert _extract_components(reactions[0].reactants) == [
         {"species name": "H2O2_aq", "coefficient": 1}
     ]
-    assert extract_components(reactions[0].products) == [
+    assert _extract_components(reactions[0].products) == [
         {"species name": "ethanol_aq", "coefficient": 1}
     ]
     assert reactions[0].scaling_factor == 12.3
     assert reactions[0].name == "condensed photo B"
+    assert reactions[0].other_properties == {"__irrelevant": "2"}
 
 
-def validate_emission(reactions):
-    assert reactions[0].type == ReactionType.Emission
+def _validate_emission(reactions):
+    assert reactions[0].type == mc.ReactionType.Emission
     assert reactions[0].gas_phase == "gas"
-    assert extract_components(reactions[0].products) == [
+    assert _extract_components(reactions[0].products) == [
         {"species name": "B", "coefficient": 1}
     ]
     assert reactions[0].scaling_factor == 12.3
     assert reactions[0].name == "my emission"
+    assert reactions[0].other_properties == {"__irrelevant": "2"}
 
 
-def validate_first_order_loss(reactions):
-    assert reactions[0].type == ReactionType.FirstOrderLoss
+def _validate_first_order_loss(reactions):
+    assert reactions[0].type == mc.ReactionType.FirstOrderLoss
     assert reactions[0].gas_phase == "gas"
-    assert extract_components(reactions[0].reactants) == [
+    assert _extract_components(reactions[0].reactants) == [
         {"species name": "C", "coefficient": 1}
     ]
     assert reactions[0].scaling_factor == 12.3
     assert reactions[0].name == "my first order loss"
+    assert reactions[0].other_properties == {"__irrelevant": "2"}
 
 
-def validate_photolysis(reactions):
-    assert reactions[0].type == ReactionType.Photolysis
+def _validate_photolysis(reactions):
+    assert reactions[0].type == mc.ReactionType.Photolysis
     assert reactions[0].gas_phase == "gas"
-    assert extract_components(reactions[0].reactants) == [
+    assert _extract_components(reactions[0].reactants) == [
         {"species name": "B", "coefficient": 1}
     ]
-    assert extract_components(reactions[0].products) == [
+    assert _extract_components(reactions[0].products) == [
         {"species name": "C", "coefficient": 1}
     ]
     assert reactions[0].scaling_factor == 12.3
     assert reactions[0].name == "photo B"
+    assert reactions[0].other_properties == {"__irrelevant": "2"}
 
 
-def validate_surface(reactions):
-    assert reactions[0].type == ReactionType.Surface
+def _validate_surface(reactions):
+    assert reactions[0].type == mc.ReactionType.Surface
     assert reactions[0].gas_phase == "gas"
-    assert extract_components([reactions[0].gas_phase_species]) == [
+    assert _extract_components([reactions[0].gas_phase_species]) == [
         {"species name": "A", "coefficient": 1}
     ]
     assert reactions[0].reaction_probability == 2.0e-2
-    assert extract_components(reactions[0].gas_phase_products) == [
+    assert _extract_components(reactions[0].gas_phase_products) == [
         {"species name": "B", "coefficient": 1},
         {"species name": "C", "coefficient": 1},
     ]
-    assert reactions[0].aerosol_phase == "surface reacting phase"
+    assert reactions[0].condensed_phase == "surface reacting phase"
     assert reactions[0].name == "my surface"
+    assert reactions[0].other_properties == {"__irrelevant": "2"}
 
 
-def validate_troe(reactions):
-    assert reactions[0].type == ReactionType.Troe
+def _validate_troe(reactions):
+    assert reactions[0].type == mc.ReactionType.Troe
     assert reactions[0].gas_phase == "gas"
-    assert extract_components(reactions[0].reactants) == [
+    assert _extract_components(reactions[0].reactants) == [
         {"species name": "B", "coefficient": 1},
         {"species name": "M", "coefficient": 1},
     ]
-    assert extract_components(reactions[0].products) == [
+    assert _extract_components(reactions[0].products) == [
         {"species name": "C", "coefficient": 1}
     ]
     assert reactions[0].k0_A == 1.2e-12
@@ -290,18 +543,63 @@ def validate_troe(reactions):
     assert reactions[0].Fc == 0.9
     assert reactions[0].N == 0.8
     assert reactions[0].name == "my troe"
+    assert reactions[0].other_properties == {"__irrelevant": "2"}
 
 
-def validate_branched_no_ro2(reactions):
-    assert reactions[0].type == ReactionType.Branched
+def _validate_ternary_chemical_activation(reactions):
+    assert reactions[0].type == mc.ReactionType.TernaryChemicalActivation
     assert reactions[0].gas_phase == "gas"
-    assert extract_components(reactions[0].reactants) == [
+    assert _extract_components(reactions[0].reactants) == [
+        {"species name": "B", "coefficient": 1},
+        {"species name": "M", "coefficient": 1},
+    ]
+    assert _extract_components(reactions[0].products) == [
+        {"species name": "C", "coefficient": 1}
+    ]
+    assert reactions[0].k0_A == 32.1
+    assert reactions[0].k0_B == -2.3
+    assert reactions[0].k0_C == 102.3
+    assert reactions[0].kinf_A == 63.4
+    assert reactions[0].kinf_B == -1.3
+    assert reactions[0].kinf_C == 908.5
+    assert reactions[0].Fc == 1.3
+    assert reactions[0].N == 32.1
+    assert reactions[0].name == "my ternary chemical activation"
+    assert reactions[0].other_properties == {"__irrelevant": "2"}
+
+
+def _validate_ternary_chemical_activation(reactions):
+    assert reactions[0].type == mc.ReactionType.TernaryChemicalActivation
+    assert reactions[0].gas_phase == "gas"
+    assert _extract_components(reactions[0].reactants) == [
+        {"species name": "B", "coefficient": 1},
+        {"species name": "M", "coefficient": 1},
+    ]
+    assert _extract_components(reactions[0].products) == [
+        {"species name": "C", "coefficient": 1}
+    ]
+    assert reactions[0].k0_A == 32.1
+    assert reactions[0].k0_B == -2.3
+    assert reactions[0].k0_C == 102.3
+    assert reactions[0].kinf_A == 63.4
+    assert reactions[0].kinf_B == -1.3
+    assert reactions[0].kinf_C == 908.5
+    assert reactions[0].Fc == 1.3
+    assert reactions[0].N == 32.1
+    assert reactions[0].name == "my ternary chemical activation"
+    assert reactions[0].other_properties == {"__irrelevant": "2"}
+
+
+def _validate_branched_no_ro2(reactions):
+    assert reactions[0].type == mc.ReactionType.Branched
+    assert reactions[0].gas_phase == "gas"
+    assert _extract_components(reactions[0].reactants) == [
         {"species name": "A", "coefficient": 1}
     ]
-    assert extract_components(reactions[0].alkoxy_products) == [
+    assert _extract_components(reactions[0].alkoxy_products) == [
         {"species name": "B", "coefficient": 1}
     ]
-    assert extract_components(reactions[0].nitrate_products) == [
+    assert _extract_components(reactions[0].nitrate_products) == [
         {"species name": "C", "coefficient": 1}
     ]
     assert reactions[0].X == 1.2e-4
@@ -309,385 +607,92 @@ def validate_branched_no_ro2(reactions):
     assert reactions[0].a0 == 0.15
     assert reactions[0].n == 9
     assert reactions[0].name == "my branched"
+    assert reactions[0].other_properties == {"__irrelevant": "2"}
 
 
-def validate_tunneling(reactions):
-    assert reactions[0].type == ReactionType.Tunneling
+def _validate_tunneling(reactions):
+    assert reactions[0].type == mc.ReactionType.Tunneling
     assert reactions[0].gas_phase == "gas"
-    assert extract_components(reactions[0].reactants) == [
+    assert _extract_components(reactions[0].reactants) == [
         {"species name": "B", "coefficient": 1}
     ]
-    assert extract_components(reactions[0].products) == [
+    assert _extract_components(reactions[0].products) == [
         {"species name": "C", "coefficient": 1}
     ]
     assert reactions[0].A == 123.45
     assert reactions[0].B == 1200.0
     assert reactions[0].C == 1.0e8
     assert reactions[0].name == "my tunneling"
+    assert reactions[0].other_properties == {"__irrelevant": "2"}
 
 
-def validate_wet_deposition(reactions):
-    assert reactions[0].type == ReactionType.WetDeposition
+def _validate_wet_deposition(reactions):
+    assert reactions[0].type == mc.ReactionType.WetDeposition
     assert reactions[0].name == "rxn cloud"
-    assert reactions[0].aerosol_phase == "cloud"
+    assert reactions[0].condensed_phase == "cloud"
     assert reactions[0].scaling_factor == 12.3
+    assert reactions[0].other_properties == {"__irrelevant": "2"}
 
 
-def validate_user_defined(reactions):
-    assert reactions[0].type == ReactionType.UserDefined
+def _validate_user_defined(reactions):
+    assert reactions[0].type == mc.ReactionType.UserDefined
     assert reactions[0].gas_phase == "gas"
-    assert extract_components(reactions[0].reactants) == [
+    assert _extract_components(reactions[0].reactants) == [
         {"species name": "A", "coefficient": 1},
         {"species name": "B", "coefficient": 1},
     ]
-    assert extract_components(reactions[0].products) == [
+    assert _extract_components(reactions[0].products) == [
         {"species name": "C", "coefficient": 1.3}
     ]
     assert reactions[0].scaling_factor == 12.3
     assert reactions[0].name == "my user defined"
-    assert reactions[0].other_properties == {}
+    # assert reactions[0].other_properties == {}
+    assert reactions[0].other_properties == {"__irrelevant": "2"}
 
 
 def validate_full_v1_mechanism(mechanism):
     assert mechanism is not None
     assert mechanism.name == "Full Configuration"
     assert len(mechanism.species) == 11
-    validate_species(mechanism.species)
+    _validate_species(mechanism.species)
     assert len(mechanism.phases) == 4
-    validate_phases(mechanism.phases)
+    _validate_phases(mechanism.phases)
     assert len(mechanism.reactions.aqueous_equilibrium) == 1
-    validate_aqueous_equilibrium(mechanism.reactions.aqueous_equilibrium)
+    _validate_aqueous_equilibrium(mechanism.reactions.aqueous_equilibrium)
     assert len(mechanism.reactions.arrhenius) == 2
-    validate_arrhenius(mechanism.reactions.arrhenius)
+    _validate_arrhenius(mechanism.reactions.arrhenius)
     assert len(mechanism.reactions.branched) == 1
-    validate_branched_no_ro2(mechanism.reactions.branched)
+    _validate_branched_no_ro2(mechanism.reactions.branched)
     assert len(mechanism.reactions.condensed_phase_arrhenius) == 2
-    validate_condensed_phase_arrhenius(mechanism.reactions.condensed_phase_arrhenius)
+    _validate_condensed_phase_arrhenius(mechanism.reactions.condensed_phase_arrhenius)
     assert len(mechanism.reactions.condensed_phase_photolysis) == 1
-    validate_condensed_phase_photolysis(
+    _validate_condensed_phase_photolysis(
         mechanism.reactions.condensed_phase_photolysis
     )
     assert len(mechanism.reactions.emission) == 1
-    validate_emission(mechanism.reactions.emission)
+    _validate_emission(mechanism.reactions.emission)
     assert len(mechanism.reactions.first_order_loss) == 1
-    validate_first_order_loss(mechanism.reactions.first_order_loss)
-    assert len(mechanism.reactions.henrys_law) == 1
-    validate_henrys_law(mechanism.reactions.henrys_law)
+    _validate_first_order_loss(mechanism.reactions.first_order_loss)
     assert len(mechanism.reactions.photolysis) == 1
-    validate_photolysis(mechanism.reactions.photolysis)
+    _validate_photolysis(mechanism.reactions.photolysis)
     assert len(mechanism.reactions.simpol_phase_transfer) == 1
-    validate_simpol_phase_transfer(mechanism.reactions.simpol_phase_transfer)
+    _validate_simpol_phase_transfer(mechanism.reactions.simpol_phase_transfer)
     assert len(mechanism.reactions.surface) == 1
-    validate_surface(mechanism.reactions.surface)
+    _validate_surface(mechanism.reactions.surface)
     assert len(mechanism.reactions.troe) == 1
-    validate_troe(mechanism.reactions.troe)
+    _validate_troe(mechanism.reactions.troe)
+    assert len(mechanism.reactions.ternary_chemical_activation) == 1
+    _validate_ternary_chemical_activation(mechanism.reactions.ternary_chemical_activation)
     assert len(mechanism.reactions.tunneling) == 1
-    validate_tunneling(mechanism.reactions.tunneling)
+    _validate_tunneling(mechanism.reactions.tunneling)
     assert len(mechanism.reactions.wet_deposition) == 1
-    validate_wet_deposition(mechanism.reactions.wet_deposition)
+    _validate_wet_deposition(mechanism.reactions.wet_deposition)
     assert len(mechanism.reactions.user_defined) == 1
-    validate_user_defined(mechanism.reactions.user_defined)
+    _validate_user_defined(mechanism.reactions.user_defined)
     assert mechanism.version.major == 1
     assert mechanism.version.minor == 0
     assert mechanism.version.patch == 0
-    assert len(mechanism.reactions) == 17
+    assert len(mechanism.reactions) == 16
     for reaction in mechanism.reactions:
         assert reaction is not None
-        assert isinstance(reaction.type, _ReactionType)
-
-
-def test_parsed_full_v1_configuration():
-    parser = Parser()
-    extensions = [".yaml", ".json"]
-    for extension in extensions:
-        path = f"musica/test/examples/v1/full_configuration/full_configuration{extension}"
-        mechanism = parser.parse(path)
-        validate_full_v1_mechanism(mechanism)
-
-
-def test_parser_reports_bad_files():
-    parser = Parser()
-    extensions = [".yaml", ".json"]
-    for extension in extensions:
-        path = f"musica/test/examples/_missing_configuration{extension}"
-        with pytest.raises(Exception):
-            parser.parse(path)
-
-
-def test_hard_coded_full_v1_configuration():
-
-    # Chemical species
-    A = Species(name="A", other_properties={"__absolute tolerance": "1.0e-30"})
-    B = Species(name="B", tracer_type="AEROSOL")
-    C = Species(name="C", tracer_type="THIRD_BODY")
-    M = Species(name="M")
-    H2O2 = Species(
-        name="H2O2",
-        HLC_298K_mol_m3_Pa=1.011596348,
-        HLC_exponential_factor_K=6340,
-        diffusion_coefficient_m2_s=1.46e-05,
-        N_star=1.74,
-        molecular_weight_kg_mol=0.0340147,
-        density_kg_m3=1000.0,
-        other_properties={"__absolute tolerance": "1.0e-10"},
-    )
-    ethanol = Species(
-        name="ethanol",
-        diffusion_coefficient_m2_s=0.95e-05,
-        N_star=2.55,
-        molecular_weight_kg_mol=0.04607,
-        other_properties={"__absolute tolerance": "1.0e-20"},
-    )
-    ethanol_aq = Species(
-        name="ethanol_aq",
-        molecular_weight_kg_mol=0.04607,
-        density_kg_m3=1000.0,
-        other_properties={"__absolute tolerance": "1.0e-20"},
-    )
-    H2O2_aq = Species(
-        name="H2O2_aq",
-        molecular_weight_kg_mol=0.0340147,
-        density_kg_m3=1000.0,
-        other_properties={"__absolute tolerance": "1.0e-10"},
-    )
-    H2O_aq = Species(
-        name="H2O_aq",
-        density_kg_m3=1000.0,
-        molecular_weight_kg_mol=0.01801,
-    )
-    aerosol_stuff = Species(
-        name="aerosol stuff",
-        molecular_weight_kg_mol=0.5,
-        density_kg_m3=1000.0,
-        other_properties={"__absolute tolerance": "1.0e-20"},
-    )
-    more_aerosol_stuff = Species(
-        name="more aerosol stuff",
-        molecular_weight_kg_mol=0.2,
-        density_kg_m3=1000.0,
-        other_properties={"__absolute tolerance": "1.0e-20"},
-    )
-
-    # Chemical phases
-    gas = Phase(name="gas", species=[A, B, C, ethanol])
-    aqueous_aerosol = Phase(
-        name="aqueous aerosol",
-        species=[H2O2_aq, H2O_aq, ethanol_aq, A, B, C]
-    )
-    surface_reacting_phase = Phase(
-        name="surface reacting phase",
-        species=[aerosol_stuff, more_aerosol_stuff]
-    )
-    cloud = Phase(name="cloud", species=[B, C])
-
-    # Reactions
-    my_arrhenius = Arrhenius(
-        name="my arrhenius",
-        A=32.1, B=-2.3, C=102.3, D=63.4, E=-1.3,
-        gas_phase=gas,
-        reactants=[B],
-        products=[C]
-    )
-
-    my_other_arrhenius = Arrhenius(
-        name="my other arrhenius",
-        A=29.3, B=-1.5, Ea=101.2, D=82.6, E=-0.98,
-        gas_phase=gas,
-        reactants=[A],
-        products=[(1.2, B)]
-    )
-
-    my_condensed_arrhenius = CondensedPhaseArrhenius(
-        name="my condensed arrhenius",
-        aerosol_phase=aqueous_aerosol,
-        aerosol_phase_water=H2O_aq,
-        A=123.45,
-        B=1.3,
-        Ea=123.45,
-        D=300.0,
-        E=0.6e-5,
-        reactants=[H2O2_aq, H2O_aq],
-        products=[ethanol_aq]
-    )
-
-    my_other_condensed_arrhenius = CondensedPhaseArrhenius(
-        name="my other condensed arrhenius",
-        aerosol_phase=aqueous_aerosol,
-        aerosol_phase_water=H2O_aq,
-        A=123.45,
-        B=1.3,
-        C=123.45,
-        D=300.0,
-        E=0.6e-5,
-        reactants=[H2O2_aq, H2O_aq],
-        products=[ethanol_aq]
-    )
-
-    my_troe = Troe(
-        name="my troe",
-        gas_phase=gas,
-        k0_A=1.2e-12,
-        k0_B=167,
-        k0_C=3,
-        kinf_A=136,
-        kinf_B=5,
-        kinf_C=24,
-        Fc=0.9,
-        N=0.8,
-        reactants=[B, M],
-        products=[C]
-    )
-
-    my_branched = Branched(
-        name="my branched",
-        gas_phase=gas,
-        reactants=[A],
-        alkoxy_products=[B],
-        nitrate_products=[C],
-        X=1.2e-4,
-        Y=167,
-        a0=0.15,
-        n=9,
-    )
-
-    my_tunneling = Tunneling(
-        name="my tunneling",
-        gas_phase=gas,
-        reactants=[B],
-        products=[C],
-        A=123.45,
-        B=1200.0,
-        C=1.0e8,
-    )
-
-    my_surface = Surface(
-        name="my surface",
-        gas_phase=gas,
-        gas_phase_species=A,
-        reaction_probability=2.0e-2,
-        gas_phase_products=[B, C],
-        aerosol_phase=surface_reacting_phase,
-    )
-
-    photo_B = Photolysis(
-        name="photo B",
-        gas_phase=gas,
-        reactants=[B],
-        products=[C],
-        scaling_factor=12.3,
-    )
-
-    condensed_photo_B = CondensedPhasePhotolysis(
-        name="condensed photo B",
-        aerosol_phase=aqueous_aerosol,
-        aerosol_phase_water=H2O_aq,
-        reactants=[H2O2_aq],
-        products=[ethanol_aq],
-        scaling_factor=12.3,
-    )
-
-    my_emission = Emission(
-        name="my emission",
-        gas_phase=gas,
-        products=[B],
-        scaling_factor=12.3,
-    )
-
-    my_first_order_loss = FirstOrderLoss(
-        name="my first order loss",
-        gas_phase=gas,
-        reactants=[C],
-        scaling_factor=12.3,
-    )
-
-    my_aqueous_equilibrium = AqueousEquilibrium(
-        name="my aqueous eq",
-        gas_phase=gas,
-        aerosol_phase=aqueous_aerosol,
-        aerosol_phase_water=H2O_aq,
-        A=1.14e-2,
-        C=2300.0,
-        k_reverse=0.32,
-        reactants=[(2, A)],
-        products=[B, C],
-    )
-
-    my_wet_deposition = WetDeposition(
-        name="rxn cloud",
-        aerosol_phase=cloud,
-        scaling_factor=12.3,
-    )
-
-    my_henrys_law = HenrysLaw(
-        name="my henry's law",
-        gas_phase=gas,
-        gas_phase_species=H2O2,
-        aerosol_phase=aqueous_aerosol,
-        aerosol_phase_species=H2O2_aq,
-        aerosol_phase_water=H2O_aq,
-    )
-
-    my_simpol_phase_transfer = SimpolPhaseTransfer(
-        name="my simpol",
-        gas_phase=gas,
-        gas_phase_species=ethanol,
-        aerosol_phase=aqueous_aerosol,
-        aerosol_phase_species=ethanol_aq,
-        B=[-1.97e03, 2.91e00, 1.96e-03, -4.96e-01],
-    )
-
-    user_defined = UserDefined(
-        name="my user defined",
-        gas_phase=gas,
-        reactants=[A, B],
-        products=[(1.3, C)],
-        scaling_factor=12.3,
-    )
-
-    # Mechanism
-    mechanism = Mechanism(
-        name="Full Configuration",
-        species=[A, B, C, M, H2O2, ethanol, ethanol_aq, H2O2_aq, H2O_aq,
-                 aerosol_stuff, more_aerosol_stuff],
-        phases=[gas, aqueous_aerosol, surface_reacting_phase, cloud],
-        reactions=[my_arrhenius, my_other_arrhenius, my_condensed_arrhenius,
-                   my_other_condensed_arrhenius, my_troe, my_branched,
-                   my_tunneling, my_surface, photo_B, condensed_photo_B,
-                   my_emission, my_first_order_loss, my_aqueous_equilibrium,
-                   my_wet_deposition, my_henrys_law, my_simpol_phase_transfer,
-                   user_defined],
-        version=Version(1, 0, 0),
-    )
-
-    validate_full_v1_mechanism(mechanism)
-
-
-def test_hard_coded_default_constructed_types():
-    arrhenius = Arrhenius()
-    assert arrhenius.type == ReactionType.Arrhenius
-    condensed_phase_arrhenius = CondensedPhaseArrhenius()
-    assert condensed_phase_arrhenius.type == ReactionType.CondensedPhaseArrhenius
-    condensed_phase_photolysis = CondensedPhasePhotolysis()
-    assert condensed_phase_photolysis.type == ReactionType.CondensedPhasePhotolysis
-    emission = Emission()
-    assert emission.type == ReactionType.Emission
-    first_order_loss = FirstOrderLoss()
-    assert first_order_loss.type == ReactionType.FirstOrderLoss
-    henrys_law = HenrysLaw()
-    assert henrys_law.type == ReactionType.HenrysLaw
-    photolysis = Photolysis()
-    assert photolysis.type == ReactionType.Photolysis
-    simpol_phase_transfer = SimpolPhaseTransfer()
-    assert simpol_phase_transfer.type == ReactionType.SimpolPhaseTransfer
-    surface = Surface()
-    assert surface.type == ReactionType.Surface
-    troe = Troe()
-    assert troe.type == ReactionType.Troe
-    tunneling = Tunneling()
-    assert tunneling.type == ReactionType.Tunneling
-    wet_deposition = WetDeposition()
-    assert wet_deposition.type == ReactionType.WetDeposition
-    branched = Branched()
-    assert branched.type == ReactionType.Branched
-    user_defined = UserDefined()
-    assert user_defined.type == ReactionType.UserDefined
+        assert isinstance(reaction.type, mc.ReactionType)