musica 0.11.1.4__cp39-cp39-win32.whl → 0.12.0__cp39-cp39-win32.whl

musica/test/test_util_full_mechanism.py

@@ -0,0 +1,668 @@
+from musica.mechanism_configuration import *
+from musica import _ReactionType
+
+
+def get_fully_defined_mechanism():
+    # 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],
+        other_properties = {"__irrelevant": "2"},
+    )
+    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],
+        other_properties = {"__irrelevant": "2"},
+    )
+
+    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],
+        other_properties = {"__irrelevant": "2"},
+    )
+
+    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],
+        other_properties = {"__irrelevant": "2"},
+    )
+
+    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,
+        other_properties = {"__irrelevant": "2"},
+    )
+
+    my_tunneling = 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 = 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,
+        other_properties = {"__irrelevant": "2"},
+    )
+
+    photo_B = Photolysis(
+        name="photo B",
+        gas_phase=gas,
+        reactants=[B],
+        products=[C],
+        scaling_factor=12.3,
+        other_properties = {"__irrelevant": "2"},
+    )
+
+    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,
+        other_properties = {"__irrelevant": "2"},
+    )
+
+    my_emission = Emission(
+        name="my emission",
+        gas_phase=gas,
+        products=[B],
+        scaling_factor=12.3,
+        other_properties = {"__irrelevant": "2"},
+    )
+
+    my_first_order_loss = FirstOrderLoss(
+        name="my first order loss",
+        gas_phase=gas,
+        reactants=[C],
+        scaling_factor=12.3,
+        other_properties = {"__irrelevant": "2"},
+    )
+
+    my_aqueous_equilibrium = AqueousEquilibrium(
+        name="my aqueous eq",
+        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],
+        other_properties = {"__irrelevant": "2"},
+    )
+
+    my_wet_deposition = WetDeposition(
+        name="rxn cloud",
+        aerosol_phase=cloud,
+        scaling_factor=12.3,
+        other_properties = {"__irrelevant": "2"},
+    )
+
+    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,
+        other_properties = {"__irrelevant": "2"},
+    )
+
+    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],
+        other_properties = {"__irrelevant": "2"},
+    )
+
+    user_defined = 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 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),
+    )
+
+
+def _validate_species(species):
+    # Define the expected species and their required attributes
+    expected_species = {
+        "A": {"other_properties": {"__absolute tolerance": "1e-30"}},
+        "B": {"tracer_type": "AEROSOL"},
+        "C": {"tracer_type": "THIRD_BODY"},
+        "M": {},
+        "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": "1e-10"},
+        },
+        "ethanol": {
+            "diffusion_coefficient_m2_s": 0.95e-05,
+            "N_star": 2.55,
+            "molecular_weight_kg_mol": 0.04607,
+            "other_properties": {"__absolute tolerance": "1e-20"},
+        },
+        "ethanol_aq": {
+            "molecular_weight_kg_mol": 0.04607,
+            "density_kg_m3": 1000.0,
+            "other_properties": {"__absolute tolerance": "1e-20"},
+        },
+        "H2O2_aq": {
+            "molecular_weight_kg_mol": 0.0340147,
+            "density_kg_m3": 1000.0,
+            "other_properties": {"__absolute tolerance": "1e-10"},
+        },
+        "H2O_aq": {
+            "density_kg_m3": 1000.0,
+            "molecular_weight_kg_mol": 0.01801,
+        },
+        "aerosol stuff": {
+            "molecular_weight_kg_mol": 0.5,
+            "density_kg_m3": 1000.0,
+            "other_properties": {"__absolute tolerance": "1e-20"},
+        },
+        "more aerosol stuff": {
+            "molecular_weight_kg_mol": 0.2,
+            "density_kg_m3": 1000.0,
+            "other_properties": {"__absolute tolerance": "1e-20"},
+        },
+    }
+
+    # Create a dictionary for quick lookup of species by name
+    species_dict = {sp.name: sp for sp in species}
+
+    # Validate each expected species
+    for name, attributes in expected_species.items():
+        assert name in species_dict, f"Species '{name}' is missing."
+        for attr, expected_value in attributes.items():
+            assert hasattr(
+                species_dict[name], attr
+            ), f"Attribute '{attr}' is missing for species '{name}'."
+            got_value = getattr(species_dict[name], attr)
+            # Handle special cases for floating-point representation
+            if isinstance(got_value, str) and ".0e" in got_value:
+                got_value = got_value.replace(".0e", "e")
+            elif isinstance(got_value, dict):
+                def replace_in_dict(d):
+                    for key, value in d.items():
+                        if isinstance(value, str) and ".0e" in value:
+                            d[key] = value.replace(".0e", "e")
+                        elif isinstance(value, dict):
+                            replace_in_dict(value)
+                replace_in_dict(got_value)
+            assert got_value == expected_value, (
+                f"Attribute '{attr}' for species '{name}' has value "
+                f"{got_value}, expected {expected_value}."
+            )
+
+
+def _validate_phases(phases):
+    # Define the expected phases and their associated species
+    expected_phases = {
+        "gas": ["A", "B", "C", "ethanol"],
+        "aqueous aerosol": ["H2O2_aq", "H2O_aq", "ethanol_aq", "A", "B", "C"],
+        "surface reacting phase": ["aerosol stuff", "more aerosol stuff"],
+        "cloud": ["B", "C"],
+    }
+
+    # Create a dictionary for quick lookup of phases by name
+    phases_dict = {phase.name: phase for phase in phases}
+
+    # Validate each expected phase
+    for name, expected_species in expected_phases.items():
+        assert name in phases_dict, f"Phase '{name}' is missing."
+        assert hasattr(
+            phases_dict[name], "species"
+        ), f"Phase '{name}' does not have a 'species' attribute."
+        phase_species = getattr(phases_dict[name], "species")
+        assert set(phase_species) == set(expected_species), (
+            f"Phase '{name}' has species {phase_species}, "
+            f"expected {expected_species}."
+        )
+
+
+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) == [
+        {"species name": "B", "coefficient": 1}
+    ]
+    assert _extract_components(reactions[0].products) == [
+        {"species name": "C", "coefficient": 1}
+    ]
+    assert reactions[0].A == 32.1
+    assert reactions[0].B == -2.3
+    assert reactions[0].C == 102.3
+    assert reactions[0].D == 63.4
+    assert reactions[0].E == -1.3
+    assert reactions[0].name == "my arrhenius"
+    assert reactions[0].other_properties == {"__irrelevant": "2"}
+    assert reactions[1].type == ReactionType.Arrhenius
+    assert _extract_components(reactions[1].reactants) == [
+        {"species name": "A", "coefficient": 1}
+    ]
+    assert _extract_components(reactions[1].products) == [
+        {"species name": "B", "coefficient": 1.2}
+    ]
+    assert reactions[1].A == 29.3
+    assert reactions[1].B == -1.5
+    assert reactions[1].C == -101.2 / 1.380649e-23
+    assert reactions[1].D == 82.6
+    assert reactions[1].E == -0.98
+    assert reactions[1].name == "my other arrhenius"
+    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"
+    assert reactions[0].other_properties == {"__irrelevant": "2"}
+
+
+def _validate_simpol_phase_transfer(reactions):
+    assert reactions[0].type == ReactionType.SimpolPhaseTransfer
+    assert reactions[0].gas_phase == "gas"
+    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]) == [
+        {"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"
+    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) == [
+        {"species name": "A", "coefficient": 2}
+    ]
+    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):
+    for reaction in reactions:
+        assert reaction.type == ReactionType.CondensedPhaseArrhenius
+        assert reaction.aerosol_phase == "aqueous aerosol"
+        assert reaction.aerosol_phase_water == "H2O_aq"
+        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) == [
+            {"species name": "H2O2_aq", "coefficient": 1},
+            {"species name": "H2O_aq", "coefficient": 1},
+        ]
+        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) == [
+        {"species name": "H2O2_aq", "coefficient": 1}
+    ]
+    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
+    assert reactions[0].gas_phase == "gas"
+    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
+    assert reactions[0].gas_phase == "gas"
+    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
+    assert reactions[0].gas_phase == "gas"
+    assert _extract_components(reactions[0].reactants) == [
+        {"species name": "B", "coefficient": 1}
+    ]
+    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
+    assert reactions[0].gas_phase == "gas"
+    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) == [
+        {"species name": "B", "coefficient": 1},
+        {"species name": "C", "coefficient": 1},
+    ]
+    assert reactions[0].aerosol_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
+    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 == 1.2e-12
+    assert reactions[0].k0_B == 167
+    assert reactions[0].k0_C == 3
+    assert reactions[0].kinf_A == 136
+    assert reactions[0].kinf_B == 5
+    assert reactions[0].kinf_C == 24
+    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
+    assert reactions[0].gas_phase == "gas"
+    assert _extract_components(reactions[0].reactants) == [
+        {"species name": "A", "coefficient": 1}
+    ]
+    assert _extract_components(reactions[0].alkoxy_products) == [
+        {"species name": "B", "coefficient": 1}
+    ]
+    assert _extract_components(reactions[0].nitrate_products) == [
+        {"species name": "C", "coefficient": 1}
+    ]
+    assert reactions[0].X == 1.2e-4
+    assert reactions[0].Y == 167
+    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
+    assert reactions[0].gas_phase == "gas"
+    assert _extract_components(reactions[0].reactants) == [
+        {"species name": "B", "coefficient": 1}
+    ]
+    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
+    assert reactions[0].name == "rxn cloud"
+    assert reactions[0].aerosol_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
+    assert reactions[0].gas_phase == "gas"
+    assert _extract_components(reactions[0].reactants) == [
+        {"species name": "A", "coefficient": 1},
+        {"species name": "B", "coefficient": 1},
+    ]
+    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 == {"__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)
+    assert len(mechanism.phases) == 4
+    _validate_phases(mechanism.phases)
+    assert len(mechanism.reactions.aqueous_equilibrium) == 1
+    _validate_aqueous_equilibrium(mechanism.reactions.aqueous_equilibrium)
+    assert len(mechanism.reactions.arrhenius) == 2
+    _validate_arrhenius(mechanism.reactions.arrhenius)
+    assert len(mechanism.reactions.branched) == 1
+    _validate_branched_no_ro2(mechanism.reactions.branched)
+    assert len(mechanism.reactions.condensed_phase_arrhenius) == 2
+    _validate_condensed_phase_arrhenius(mechanism.reactions.condensed_phase_arrhenius)
+    assert len(mechanism.reactions.condensed_phase_photolysis) == 1
+    _validate_condensed_phase_photolysis(
+        mechanism.reactions.condensed_phase_photolysis
+    )
+    assert len(mechanism.reactions.emission) == 1
+    _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)
+    assert len(mechanism.reactions.photolysis) == 1
+    _validate_photolysis(mechanism.reactions.photolysis)
+    assert len(mechanism.reactions.simpol_phase_transfer) == 1
+    _validate_simpol_phase_transfer(mechanism.reactions.simpol_phase_transfer)
+    assert len(mechanism.reactions.surface) == 1
+    _validate_surface(mechanism.reactions.surface)
+    assert len(mechanism.reactions.troe) == 1
+    _validate_troe(mechanism.reactions.troe)
+    assert len(mechanism.reactions.tunneling) == 1
+    _validate_tunneling(mechanism.reactions.tunneling)
+    assert len(mechanism.reactions.wet_deposition) == 1
+    _validate_wet_deposition(mechanism.reactions.wet_deposition)
+    assert len(mechanism.reactions.user_defined) == 1
+    _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
+    for reaction in mechanism.reactions:
+        assert reaction is not None
+        assert isinstance(reaction.type, _ReactionType)

musica/types.py

@@ -20,10 +20,7 @@ from musica import (
     _user_defined_rate_parameters_ordering,
 )
 import musica.mechanism_configuration as mc
-
-AVOGADRO = 6.02214076e23  # mol^-1
-BOLTZMANN = 1.380649e-23  # J K^-1
-GAS_CONSTANT = AVOGADRO * BOLTZMANN  # J K^-1 mol^-1
+from musica.constants import GAS_CONSTANT
 
 FilePath = Union[str, "PathLike[str]"]