[Python] Make more use of Interface.adjacent

doc/sphinx/userguide/python-tutorial.md

@@ -202,21 +202,15 @@ ct.add_directory('~/cantera/my_data_files')
 Cantera input files are plain text files, and can be created with any text editor. See
 the page [](input-tutorial) for more information.
 
-A Cantera input file may contain more than one phase specification, or may contain
+A Cantera input file may contain more than one phase specification, and may contain
-specifications of interfaces (surfaces). Here we import definitions of two bulk phases
+specifications of interfaces (surfaces and edges). Here we import a surface phase and
-and the interface between them from file `diamond.yaml`:
+the two adjacent bulk phases from the file `diamond.yaml`:
 
-% TODO: Demonstrate the syntax that starts with creating the Interface
 ```{code-cell} python
-gas2 = ct.Solution('diamond.yaml', 'gas')
+diamond_surf = ct.Interface('diamond.yaml' , 'diamond_100')
-diamond = ct.Solution('diamond.yaml', 'diamond')
+diamond_surf.adjacent
-diamond_surf = ct.Interface('diamond.yaml' , 'diamond_100',
-                            [gas2, diamond])
 ```
 
-Note that the bulk (3D) phases that participate in the surface reactions must also be
-passed as arguments to {py:class}`Interface`.
-
 ## Converting CK-format files
 
 See the page [](ck2yaml-tutorial) for information on how to convert from CK-format to

samples/python/reactors/1D_packed_bed.py

@@ -140,10 +140,9 @@ import matplotlib.pyplot as plt
 
 # Import the reaction mechanism for Ammonia synthesis/decomposition on Ru-Ba/YSZ catalyst
 mechfile = "example_data/ammonia-Ru-Ba-YSZ-CSM-2019.yaml"
-# Import the models for gas-phase
+# Import the models for surface-phase and gas
-gas = ct.Solution(mechfile, "gas")
+surf = ct.Interface(mechfile, "Ru_surface")
-# Import the model for surface-phase
+gas = surf.adjacent["gas"]
-surf = ct.Interface(mechfile, "Ru_surface", [gas])
 
 # Other parameters
 n_gas = gas.n_species  # number of gas species

samples/python/reactors/surf_pfr_chain.py

@@ -46,13 +46,11 @@ dt = 1.0
 
 t = tc + 273.15  # convert to Kelvin
 
-# import the gas model and set the initial conditions
+# import the phase models and set the initial conditions
-gas = ct.Solution(yaml_file, 'gas')
+surf = ct.Interface(yaml_file, 'Pt_surf')
-gas.TPX = t, ct.one_atm, 'CH4:1, O2:1.5, AR:0.1'
-
-# import the surface model
-surf = ct.Interface(yaml_file, 'Pt_surf', [gas])
 surf.TP = t, ct.one_atm
+gas = surf.adjacent['gas']
+gas.TPX = t, ct.one_atm, 'CH4:1, O2:1.5, AR:0.1'
 
 rlen = length/(NReactors-1)
 rvol = area * rlen * porosity

test/python/test_composite.py

@@ -157,9 +157,7 @@ class TestPickle(utilities.CanteraTest):
         self.assertEqual(gas2.transport_model, "multicomponent")
 
     def test_pickle_interface(self):
-        gas = ct.Solution("diamond.yaml", "gas")
+        interface = ct.Interface("diamond.yaml", "diamond_100")
-        solid = ct.Solution("diamond.yaml", "diamond")
-        interface = ct.Interface("diamond.yaml", "diamond_100", (gas, solid))
 
         with self.assertRaises(NotImplementedError):
             with open(self.test_work_path / "interface.pkl", "wb") as pkl:

test/python/test_kinetics.py

@@ -220,8 +220,8 @@ class KineticsFromReactions(utilities.CanteraTest):
                              gas2.net_production_rates)
 
     def test_surface(self):
-        gas = ct.Solution("ptcombust.yaml", "gas")
+        surf1 = ct.Interface("ptcombust.yaml", "Pt_surf")
-        surf1 = ct.Interface("ptcombust.yaml", "Pt_surf", [gas])
+        gas = surf1.adjacent["gas"]
         surf_species = ct.Species.list_from_file("ptcombust.yaml")
         reactions = ct.Reaction.list_from_file("ptcombust.yaml", surf1)
 
@@ -295,8 +295,7 @@ class KineticsFromReactions(utilities.CanteraTest):
                              gas2.net_production_rates)
 
     def test_coverage_dependence_flags(self):
-        gas = ct.Solution("ptcombust.yaml", "gas")
+        surf = ct.Interface("ptcombust.yaml", "Pt_surf")
-        surf = ct.Interface("ptcombust.yaml", "Pt_surf", [gas])
         surf.TP = 900, ct.one_atm
         surf.coverages = {"PT(S)":1}
         with self.assertRaises(NotImplementedError):
@@ -306,11 +305,7 @@ class KineticsFromReactions(utilities.CanteraTest):
         surf.net_rates_of_progress_ddCi
 
     def test_electrochemistry_flags(self):
-        # Phases
+        anode_int = ct.Interface("lithium_ion_battery.yaml", "edge_anode_electrolyte")
-        mech = "lithium_ion_battery.yaml"
-        anode, cathode, metal, electrolyte = ct.import_phases(
-            mech, ["anode", "cathode", "electron", "electrolyte"])
-        anode_int = ct.Interface(mech, "edge_anode_electrolyte", adjacent=[anode, metal, electrolyte])
         with self.assertRaises(NotImplementedError):
             anode_int.net_rates_of_progress_ddCi
         # set skip and try to get jacobian again
@@ -537,8 +532,7 @@ class KineticsRepeatability(utilities.CanteraTest):
 
         for err in err_msg:
             with pytest.warns(UserWarning, match=err):
-                gas = ct.Solution("sticking_coeff_check.yaml")
+                ct.Interface("sticking_coeff_check.yaml", "Pt_surf")
-                ct.Interface("sticking_coeff_check.yaml", "Pt_surf", [gas])
 
 
 def check_raises(yaml, err_msg, line):
@@ -958,19 +952,20 @@ class TestSofcKinetics(utilities.CanteraTest):
                     return x0
 
         # Anode-side phases
-        gas_a, anode_bulk, oxide_a = ct.import_phases(mech,
+        tpb_a = ct.Interface(mech, "tpb")
-                                                      ['gas', 'metal', 'oxide_bulk',])
+        anode_surf = tpb_a.adjacent["metal_surface"]
-        anode_surf = ct.Interface(mech, 'metal_surface', [gas_a])
+        gas_a = anode_surf.adjacent["gas"]
-        oxide_surf_a = ct.Interface(mech, 'oxide_surface', [gas_a, oxide_a])
+        oxide_surf_a = tpb_a.adjacent["oxide_surface"]
-        tpb_a = ct.Interface(mech, 'tpb', [anode_bulk, anode_surf, oxide_surf_a])
+        oxide_a = oxide_surf_a.adjacent["oxide_bulk"]
+        anode_bulk = tpb_a.adjacent["metal"]
 
         # Cathode-side phases
-        gas_c, cathode_bulk, oxide_c = ct.import_phases(mech,
+        tpb_c = ct.Interface(mech, "tpb")
-                                                        ['gas', 'metal', 'oxide_bulk'])
+        cathode_surf = tpb_c.adjacent["metal_surface"]
-        cathode_surf = ct.Interface(mech, 'metal_surface', [gas_c])
+        gas_c = cathode_surf.adjacent["gas"]
-        oxide_surf_c = ct.Interface(mech, 'oxide_surface', [gas_c, oxide_c])
+        oxide_surf_c = tpb_c.adjacent["oxide_surface"]
-        tpb_c = ct.Interface(mech, 'tpb', [cathode_bulk, cathode_surf,
+        oxide_c = oxide_surf_c.adjacent["oxide_bulk"]
-                                                 oxide_surf_c])
+        cathode_bulk = tpb_c.adjacent["metal"]
 
         kElectron_a = tpb_a.kinetics_species_index("electron")
         def anode_curr(E):
@@ -1127,13 +1122,10 @@ class TestLithiumIonBatteryKinetics(utilities.CanteraTest):
         assert np.allclose(data, ref, rtol=1e-7)
 
     def test_interface_current(self):
-        file = "lithium_ion_battery.yaml"
+        anode_int = ct.Interface("lithium_ion_battery.yaml", "edge_anode_electrolyte")
-
+        anode = anode_int.adjacent["anode"]
-        # The 'elde' electrode phase is needed as a source/sink for electrons:
+        elect = anode_int.adjacent["electron"]
-        anode = ct.Solution(file, "anode")
+        elyte = anode_int.adjacent["electrolyte"]
-        elect = ct.Solution(file, "electron")
-        elyte = ct.Solution(file, "electrolyte")
-        anode_int = ct.Interface(file, "edge_anode_electrolyte", [anode, elect, elyte])
 
         anode.X = [0.9, 0.1]
         elyte.X = [0.4, 0.3, 0.15, 0.15]
@@ -1554,8 +1546,8 @@ class TestReaction(utilities.CanteraTest):
 
     def test_interface(self):
         surf_species = ct.Species.list_from_file("ptcombust.yaml")
-        gas = ct.Solution("ptcombust.yaml", "gas")
+        surf1 = ct.Interface("ptcombust.yaml", "Pt_surf")
-        surf1 = ct.Interface("ptcombust.yaml", "Pt_surf", [gas])
+        gas = surf1.adjacent["gas"]
 
         rate = ct.InterfaceArrheniusRate(3.7e20, 0, 67.4e6)
         rate.coverage_dependencies = {'H(S)': (0, 0, -6e6)}
@@ -1733,10 +1725,8 @@ class TestReaction(utilities.CanteraTest):
         self.assertNear(A2 * T**b2 * np.exp(-Ta2 / T), gas.forward_rate_constants[0])
 
     def test_modify_interface(self):
-        gas = ct.Solution("ptcombust.yaml", "gas")
+        surf = ct.Interface("ptcombust.yaml", "Pt_surf")
-        surf = ct.Interface("ptcombust.yaml", "Pt_surf", [gas])
         surf.coverages = 'O(S):0.1, PT(S):0.5, H(S):0.4'
-        gas.TP = surf.TP
 
         R = surf.reaction(1)
         R.rate.coverage_dependencies = {'O(S)': (0.0, 0.0, -3e6)}
@@ -1762,10 +1752,8 @@ class TestReaction(utilities.CanteraTest):
             surf.add_reaction(rxn)
 
     def test_modify_sticking(self):
-        gas = ct.Solution("ptcombust.yaml", "gas")
+        surf = ct.Interface("ptcombust.yaml", "Pt_surf")
-        surf = ct.Interface("ptcombust.yaml", "Pt_surf", [gas])
         surf.coverages = "O(S):0.1, PT(S):0.5, H(S):0.4"
-        gas.TP = surf.TP
 
         R = surf.reaction(2)
         R.rate = ct.StickingArrheniusRate(0.25, 0, 0) # original sticking coefficient = 1.0
@@ -1777,14 +1765,11 @@ class TestReaction(utilities.CanteraTest):
 
     def test_motz_wise(self):
         # Motz & Wise off for all reactions
-        gas1 = ct.Solution("ptcombust.yaml", "gas")
+        surf1 = ct.Interface("ptcombust.yaml", "Pt_surf")
-        surf1 = ct.Interface("ptcombust.yaml", "Pt_surf", [gas1])
         surf1.coverages = 'O(S):0.1, PT(S):0.5, H(S):0.4'
-        gas1.TP = surf1.TP
 
         # Motz & Wise correction on for some reactions
-        gas2 = ct.Solution("ptcombust-motzwise.yaml", "gas")
+        surf2 = ct.Interface("ptcombust-motzwise.yaml", "Pt_surf")
-        surf2 = ct.Interface("ptcombust-motzwise.yaml", "Pt_surf", [gas2])
         surf2.TPY = surf1.TPY
 
         k1 = surf1.forward_rate_constants
@@ -1843,15 +1828,11 @@ class TestReaction(utilities.CanteraTest):
 
     def test_BMmotz_wise(self):
         # Motz & Wise off for all reactions
-        gas1 = ct.Solution("blowers-masel.yaml", "gas", transport_model=None)
+        surf1 = ct.Interface("blowers-masel.yaml", "Pt_surf")
-        gas1.TPX = 300, ct.one_atm, {"CH4": 0.095, "O2": 0.21, "AR": 0.79}
-        surf1 = ct.Interface("blowers-masel.yaml", "Pt_surf", [gas1])
         surf1.coverages = 'O(S):0.1, PT(S):0.5, H(S):0.4'
-        gas1.TP = surf1.TP
 
         # Motz & Wise correction on for some reactions
-        gas2 = ct.Solution("blowers-masel.yaml", "gas")
+        surf2 = ct.Interface("blowers-masel.yaml", "Pt_motz_wise")
-        surf2 = ct.Interface("blowers-masel.yaml", "Pt_motz_wise", [gas2])
         surf2.TPY = surf1.TPY
 
         k1 = surf1.forward_rate_constants

test/python/test_onedim.py

@@ -1713,8 +1713,8 @@ class TestStagnationFlame(utilities.CanteraTest):
 
 class TestImpingingJet(utilities.CanteraTest):
     def setUp(self):
-        self.gas = ct.Solution("ptcombust-simple.yaml", "gas")
+        self.surf_phase = ct.Interface("ptcombust-simple.yaml", "Pt_surf")
-        self.surf_phase = ct.Interface("ptcombust-simple.yaml", "Pt_surf", [self.gas])
+        self.gas = self.surf_phase.adjacent["gas"]
 
     def create_reacting_surface(self, comp, tsurf, tinlet, width):
         self.gas.TPX = tinlet, ct.one_atm, comp

test/python/test_reactor.py

@@ -1965,10 +1965,8 @@ class TestSurfaceKinetics(utilities.CanteraTest):
     def make_reactors(self):
         self.net = ct.ReactorNet()
 
-        self.gas = ct.Solution('diamond.yaml', 'gas')
+        self.interface = ct.Interface('diamond.yaml', 'diamond_100')
-        self.solid = ct.Solution('diamond.yaml', 'diamond')
+        self.gas = self.interface.adjacent['gas']
-        self.interface = ct.Interface('diamond.yaml', 'diamond_100',
-                                      (self.gas, self.solid))
         self.gas.TPX = None, 1.0e3, 'H:0.002, H2:1, CH4:0.01, CH3:0.0002'
         self.r1 = ct.IdealGasReactor(self.gas)
         self.r1.volume = 0.01
@@ -2094,9 +2092,8 @@ class TestReactorSensitivities(utilities.CanteraTest):
     def test_sensitivities2(self):
         net = ct.ReactorNet()
 
-        gas1 = ct.Solution("diamond.yaml", "gas")
+        interface = ct.Interface("diamond.yaml", "diamond_100")
-        solid = ct.Solution("diamond.yaml", "diamond")
+        gas1 = interface.adjacent["gas"]
-        interface = ct.Interface("diamond.yaml", "diamond_100", (gas1, solid))
         r1 = ct.IdealGasReactor(gas1)
         net.add_reactor(r1)
         net.atol_sensitivity = 1e-10
@@ -2256,9 +2253,8 @@ class TestReactorSensitivities(utilities.CanteraTest):
     @utilities.slow_test
     def test_parameter_order3(self):
         # Test including reacting surfaces
-        gas1 = ct.Solution("diamond.yaml", "gas")
+        interface = ct.Interface("diamond.yaml", "diamond_100")
-        solid = ct.Solution("diamond.yaml", "diamond")
+        gas1 = interface.adjacent["gas"]
-        interface = ct.Interface("diamond.yaml", "diamond_100", (gas1, solid))
 
         gas2 = ct.Solution('h2o2.yaml', transport_model=None)
 
@@ -2659,8 +2655,8 @@ class PureFluidReactorTest(utilities.CanteraTest):
 class AdvanceCoveragesTest(utilities.CanteraTest):
     def setup(self, model="ptcombust.yaml", gas_phase="gas", interface_phase="Pt_surf"):
         # create gas and interface
-        self.gas = ct.Solution(model, gas_phase)
+        self.surf = ct.Interface(model, interface_phase)
-        self.surf = ct.Interface(model, interface_phase, [self.gas])
+        self.gas = self.surf.adjacent["gas"]
 
     def test_advance_coverages_parameters(self):
         # create gas and interface

test/python/test_thermo.py

@@ -1114,10 +1114,7 @@ class TestThermo(utilities.CanteraTest):
 
 class TestInterfacePhase(utilities.CanteraTest):
     def setUp(self):
-        self.gas = ct.Solution("diamond.yaml", "gas")
+        self.interface = ct.Interface("diamond.yaml", "diamond_100")
-        self.solid = ct.Solution("diamond.yaml", "diamond")
-        self.interface = ct.Interface("diamond.yaml", "diamond_100",
-                                      (self.gas, self.solid))
 
     def test_properties(self):
         self.interface.site_density = 100