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[Python] Make more use of Interface.adjacent

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This commit is contained in:
Ray Speth 2024-06-16 21:35:13 -04:00 committed by Ray Speth
parent eec37ffcd8
commit f5a0176c28
8 changed files with 53 additions and 90 deletions
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16
doc/sphinx/userguide/python-tutorial.md
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@ -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
specifications of interfaces (surfaces). Here we import definitions of two bulk phases
and the interface between them from file `diamond.yaml`:
A Cantera input file may contain more than one phase specification, and may contain
specifications of interfaces (surfaces and edges). Here we import a surface phase and
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 = ct.Solution('diamond.yaml', 'diamond')
diamond_surf = ct.Interface('diamond.yaml' , 'diamond_100',
[gas2, diamond])
diamond_surf = ct.Interface('diamond.yaml' , 'diamond_100')
diamond_surf.adjacent
```
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

7
samples/python/reactors/1D_packed_bed.py
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@ -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
gas = ct.Solution(mechfile, "gas")
# Import the model for surface-phase
surf = ct.Interface(mechfile, "Ru_surface", [gas])
# Import the models for surface-phase and gas
surf = ct.Interface(mechfile, "Ru_surface")
gas = surf.adjacent["gas"]
# Other parameters
n_gas = gas.n_species # number of gas species

10
samples/python/reactors/surf_pfr_chain.py
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@ -46,13 +46,11 @@ dt = 1.0
t = tc + 273.15 # convert to Kelvin
# import the gas model and set the initial conditions
gas = ct.Solution(yaml_file, 'gas')
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])
# import the phase models and set the initial conditions
surf = ct.Interface(yaml_file, 'Pt_surf')
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

4
test/python/test_composite.py
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@ -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")
solid = ct.Solution("diamond.yaml", "diamond")
interface = ct.Interface("diamond.yaml", "diamond_100", (gas, solid))
interface = ct.Interface("diamond.yaml", "diamond_100")
with self.assertRaises(NotImplementedError):
with open(self.test_work_path / "interface.pkl", "wb") as pkl:

77
test/python/test_kinetics.py
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@ -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", [gas])
surf1 = ct.Interface("ptcombust.yaml", "Pt_surf")
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", [gas])
surf = ct.Interface("ptcombust.yaml", "Pt_surf")
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
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])
anode_int = ct.Interface("lithium_ion_battery.yaml", "edge_anode_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", [gas])
ct.Interface("sticking_coeff_check.yaml", "Pt_surf")
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,
['gas', 'metal', 'oxide_bulk',])
anode_surf = ct.Interface(mech, 'metal_surface', [gas_a])
oxide_surf_a = ct.Interface(mech, 'oxide_surface', [gas_a, oxide_a])
tpb_a = ct.Interface(mech, 'tpb', [anode_bulk, anode_surf, oxide_surf_a])
tpb_a = ct.Interface(mech, "tpb")
anode_surf = tpb_a.adjacent["metal_surface"]
gas_a = anode_surf.adjacent["gas"]
oxide_surf_a = tpb_a.adjacent["oxide_surface"]
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,
['gas', 'metal', 'oxide_bulk'])
cathode_surf = ct.Interface(mech, 'metal_surface', [gas_c])
oxide_surf_c = ct.Interface(mech, 'oxide_surface', [gas_c, oxide_c])
tpb_c = ct.Interface(mech, 'tpb', [cathode_bulk, cathode_surf,
oxide_surf_c])
tpb_c = ct.Interface(mech, "tpb")
cathode_surf = tpb_c.adjacent["metal_surface"]
gas_c = cathode_surf.adjacent["gas"]
oxide_surf_c = tpb_c.adjacent["oxide_surface"]
oxide_c = oxide_surf_c.adjacent["oxide_bulk"]
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"
# The 'elde' electrode phase is needed as a source/sink for electrons:
anode = ct.Solution(file, "anode")
elect = ct.Solution(file, "electron")
elyte = ct.Solution(file, "electrolyte")
anode_int = ct.Interface(file, "edge_anode_electrolyte", [anode, elect, elyte])
anode_int = ct.Interface("lithium_ion_battery.yaml", "edge_anode_electrolyte")
anode = anode_int.adjacent["anode"]
elect = anode_int.adjacent["electron"]
elyte = anode_int.adjacent["electrolyte"]
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", [gas])
surf1 = ct.Interface("ptcombust.yaml", "Pt_surf")
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", [gas])
surf = ct.Interface("ptcombust.yaml", "Pt_surf")
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", [gas])
surf = ct.Interface("ptcombust.yaml", "Pt_surf")
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", [gas1])
surf1 = ct.Interface("ptcombust.yaml", "Pt_surf")
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", [gas2])
surf2 = ct.Interface("ptcombust-motzwise.yaml", "Pt_surf")
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)
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 = ct.Interface("blowers-masel.yaml", "Pt_surf")
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", [gas2])
surf2 = ct.Interface("blowers-masel.yaml", "Pt_motz_wise")
surf2.TPY = surf1.TPY
k1 = surf1.forward_rate_constants

4
test/python/test_onedim.py
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@ -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.gas])
self.surf_phase = ct.Interface("ptcombust-simple.yaml", "Pt_surf")
self.gas = self.surf_phase.adjacent["gas"]
def create_reacting_surface(self, comp, tsurf, tinlet, width):
self.gas.TPX = tinlet, ct.one_atm, comp

20
test/python/test_reactor.py
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@ -1965,10 +1965,8 @@ class TestSurfaceKinetics(utilities.CanteraTest):
def make_reactors(self):
self.net = ct.ReactorNet()
self.gas = ct.Solution('diamond.yaml', 'gas')
self.solid = ct.Solution('diamond.yaml', 'diamond')
self.interface = ct.Interface('diamond.yaml', 'diamond_100',
(self.gas, self.solid))
self.interface = ct.Interface('diamond.yaml', 'diamond_100')
self.gas = self.interface.adjacent['gas']
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")
solid = ct.Solution("diamond.yaml", "diamond")
interface = ct.Interface("diamond.yaml", "diamond_100", (gas1, solid))
interface = ct.Interface("diamond.yaml", "diamond_100")
gas1 = interface.adjacent["gas"]
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")
solid = ct.Solution("diamond.yaml", "diamond")
interface = ct.Interface("diamond.yaml", "diamond_100", (gas1, solid))
interface = ct.Interface("diamond.yaml", "diamond_100")
gas1 = interface.adjacent["gas"]
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.gas])
self.surf = ct.Interface(model, interface_phase)
self.gas = self.surf.adjacent["gas"]
def test_advance_coverages_parameters(self):
# create gas and interface

5
test/python/test_thermo.py
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@ -1114,10 +1114,7 @@ class TestThermo(utilities.CanteraTest):
class TestInterfacePhase(utilities.CanteraTest):
def setUp(self):
self.gas = ct.Solution("diamond.yaml", "gas")
self.solid = ct.Solution("diamond.yaml", "diamond")
self.interface = ct.Interface("diamond.yaml", "diamond_100",
(self.gas, self.solid))
self.interface = ct.Interface("diamond.yaml", "diamond_100")
def test_properties(self):
self.interface.site_density = 100