[YAML] Switch interfaces and examples to use YAML files

interfaces/cython/cantera/examples/kinetics/extract_submechanism.py

@@ -13,7 +13,7 @@
 import numpy as np
 import matplotlib.pyplot as plt
 
-all_species = ct.Species.listFromFile('gri30.xml')
+all_species = ct.Species.listFromFile('gri30.yaml')
 species = []
 
 # Filter species
@@ -35,7 +35,7 @@
 print('Species: {0}'.format(', '.join(S.name for S in species)))
 
 # Filter reactions, keeping only those that only involve the selected species
-all_reactions = ct.Reaction.listFromFile('gri30.xml')
+all_reactions = ct.Reaction.listFromFile('gri30.yaml')
 reactions = []
 
 print('\nReactions:')
@@ -50,7 +50,7 @@
     print(R.equation)
 print('\n')
 
-gas1 = ct.Solution('gri30.xml')
+gas1 = ct.Solution('gri30.yaml')
 gas2 = ct.Solution(thermo='IdealGas', kinetics='GasKinetics',
                    species=species, reactions=reactions)
 

interfaces/cython/cantera/examples/kinetics/mechanism_reduction.py

@@ -17,7 +17,7 @@
 import numpy as np
 import matplotlib.pyplot as plt
 
-gas = ct.Solution('gri30.xml')
+gas = ct.Solution('gri30.yaml')
 initial_state = 1200, 5 * ct.one_atm, 'CH4:0.35, O2:1.0, N2:3.76'
 
 # Run a simulation with the full mechanism

interfaces/cython/cantera/examples/kinetics/reaction_path.py

@@ -14,7 +14,7 @@
 
 # these lines can be replaced by any commands that generate
 # an object of a class derived from class Kinetics in some state.
-gas = ct.Solution('gri30.xml')
+gas = ct.Solution('gri30.yaml')
 gas.TPX = 1300.0, ct.one_atm, 'CH4:0.4, O2:1, N2:3.76'
 r = ct.IdealGasReactor(gas)
 net = ct.ReactorNet([r])

interfaces/cython/cantera/examples/multiphase/adiabatic.py

@@ -16,8 +16,8 @@
 P = 101325.0
 
 # phases
-gas = ct.Solution('gri30.xml')
-carbon = ct.Solution('graphite.xml')
+gas = ct.Solution('gri30.yaml')
+carbon = ct.Solution('graphite.yaml')
 
 # the phases that will be included in the calculation, and their initial moles
 mix_phases = [(gas, 1.0), (carbon, 0.0)]

interfaces/cython/cantera/examples/multiphase/plasma_equilibrium.py

@@ -8,9 +8,9 @@
 
 # create objects representing the gas phase and the condensed phases. The gas
 # is a mixture of multiple species, and the condensed phases are all modeled
-# as incompressible stoichiometric substances. See file KOH.cti for more
+# as incompressible stoichiometric substances. See file KOH.yaml for more
 # information.
-phases = ct.import_phases('KOH.cti', ['K_solid', 'K_liquid', 'KOH_a', 'KOH_b',
+phases = ct.import_phases('KOH.yaml', ['K_solid', 'K_liquid', 'KOH_a', 'KOH_b',
                                       'KOH_liquid', 'K2O2_solid', 'K2O_solid',
                                       'KO2_solid', 'ice', 'liquid_water',
                                       'KOH_plasma'])

interfaces/cython/cantera/examples/onedim/adiabatic_flame.py

@@ -13,9 +13,9 @@
 width = 0.03  # m
 loglevel = 1  # amount of diagnostic output (0 to 8)
 
-# IdealGasMix object used to compute mixture properties, set to the state of the
+# Solution object used to compute mixture properties, set to the state of the
 # upstream fuel-air mixture
-gas = ct.Solution('h2o2.xml')
+gas = ct.Solution('h2o2.yaml')
 gas.TPX = Tin, p, reactants
 
 # Set up flame object

interfaces/cython/cantera/examples/onedim/burner_flame.py

@@ -12,7 +12,7 @@
 width = 0.5 # m
 loglevel = 1  # amount of diagnostic output (0 to 5)
 
-gas = ct.Solution('h2o2.xml')
+gas = ct.Solution('h2o2.yaml')
 gas.TPX = tburner, p, reactants
 
 f = ct.BurnerFlame(gas, width=width)

interfaces/cython/cantera/examples/onedim/burner_ion_flame.py

@@ -11,7 +11,7 @@
 width = 0.5 # m
 loglevel = 1  # amount of diagnostic output (0 to 5)
 
-gas = ct.Solution('gri30_ion.cti')
+gas = ct.Solution('gri30_ion.yaml')
 gas.TPX = tburner, p, reactants
 mdot = 0.15 * gas.density
 

interfaces/cython/cantera/examples/onedim/diffusion_flame.py

@@ -22,7 +22,7 @@
 
 # Create the gas object used to evaluate all thermodynamic, kinetic, and
 # transport properties.
-gas = ct.Solution('gri30.xml', 'gri30_mix')
+gas = ct.Solution('gri30.yaml')
 gas.TP = gas.T, p
 
 # Create an object representing the counterflow flame configuration,

interfaces/cython/cantera/examples/onedim/diffusion_flame_batch.py

@@ -35,7 +35,7 @@ class FlameExtinguished(Exception):
 # Set up an initial hydrogen-oxygen counterflow flame at 1 bar and low strain
 # rate (maximum axial velocity gradient = 2414 1/s)
 
-reaction_mechanism = 'h2o2.xml'
+reaction_mechanism = 'h2o2.yaml'
 gas = ct.Solution(reaction_mechanism)
 width = 18e-3 # 18mm wide
 f = ct.CounterflowDiffusionFlame(gas, width=width)

interfaces/cython/cantera/examples/onedim/diffusion_flame_extinction.py

@@ -26,7 +26,7 @@
 # Set up an initial hydrogen-oxygen counterflow flame at 1 bar and low strain
 # rate (maximum axial velocity gradient = 2414 1/s)
 
-reaction_mechanism = 'h2o2.xml'
+reaction_mechanism = 'h2o2.yaml'
 gas = ct.Solution(reaction_mechanism)
 width = 18.e-3 # 18mm wide
 f = ct.CounterflowDiffusionFlame(gas, width=width)

interfaces/cython/cantera/examples/onedim/flame_fixed_T.py

@@ -25,7 +25,7 @@
 # transport properties. It is created with two transport managers, to enable
 # switching from mixture-averaged to multicomponent transport on the last
 # solution.
-gas = ct.Solution('gri30.xml', 'gri30_mix')
+gas = ct.Solution('gri30.yaml')
 
 # set its state to that of the unburned gas at the burner
 gas.TPX = tburner, p, comp

interfaces/cython/cantera/examples/onedim/flamespeed_sensitivity.py

@@ -14,8 +14,8 @@
 
 width = 0.03  # m
 
-# IdealGasMix object used to compute mixture properties
-gas = ct.Solution('gri30.xml', 'gri30_mix')
+# Solution object used to compute mixture properties
+gas = ct.Solution('gri30.yaml')
 gas.TPX = Tin, p, reactants
 
 # Flame object

interfaces/cython/cantera/examples/onedim/ion_burner_flame.py

@@ -11,7 +11,7 @@
 width = 0.5 # m
 loglevel = 1  # amount of diagnostic output (0 to 5)
 
-gas = ct.Solution('gri30_ion.cti')
+gas = ct.Solution('gri30_ion.yaml')
 gas.TPX = tburner, p, reactants
 mdot = 0.15 * gas.density
 

interfaces/cython/cantera/examples/onedim/ion_free_flame.py

@@ -14,7 +14,7 @@
 
 # IdealGasMix object used to compute mixture properties, set to the state of the
 # upstream fuel-air mixture
-gas = ct.Solution('gri30_ion.xml')
+gas = ct.Solution('gri30_ion.yaml')
 gas.TPX = Tin, p, reactants
 
 # Set up flame object

interfaces/cython/cantera/examples/onedim/premixed_counterflow_flame.py

@@ -12,7 +12,7 @@
 T_in = 373.0  # inlet temperature
 mdot_reactants = 0.12  # kg/m^2/s
 mdot_products = 0.06  # kg/m^2/s
-rxnmech = 'h2o2.cti'  # reaction mechanism file
+rxnmech = 'h2o2.yaml'  # reaction mechanism file
 comp = 'H2:1.6, O2:1, AR:7'  # premixed gas composition
 
 width = 0.2 # m

interfaces/cython/cantera/examples/onedim/premixed_counterflow_twin_flame.py

@@ -74,7 +74,7 @@ def solveOpposedFlame(oppFlame, massFlux=0.12, loglevel=1,
     return np.max(oppFlame.T), K, strainRatePoint
 
 # Select the reaction mechanism
-gas = ct.Solution('gri30.cti')
+gas = ct.Solution('gri30.yaml')
 
 # Create a CH4/Air premixed mixture with equivalence ratio=0.75, and at room
 # temperature and pressure.

interfaces/cython/cantera/examples/onedim/stagnation_flame.py

@@ -28,7 +28,7 @@
 # then that solution will be used for the next mdot
 mdot = [0.06, 0.07, 0.08, 0.09, 0.1, 0.11, 0.12]  # kg/m^2/s
 
-rxnmech = 'h2o2.cti'  # reaction mechanism file
+rxnmech = 'h2o2.yaml'  # reaction mechanism file
 comp = 'H2:1.8, O2:1, AR:7'  # premixed gas composition
 
 # The solution domain is chosen to be 20 cm

interfaces/cython/cantera/examples/reactors/NonIdealShockTube.py

@@ -68,7 +68,7 @@ def ignitionDelay(states, species):
 # Real gas IDT calculation
 
 # Load the real gas mechanism:
-real_gas = ct.Solution('nDodecane_Reitz.cti','nDodecane_RK')
+real_gas = ct.Solution('nDodecane_Reitz.yaml', 'nDodecane_RK')
 
 # Set the state of the gas object:
 real_gas.TP = reactorTemperature, reactorPressure
@@ -109,7 +109,7 @@ def ignitionDelay(states, species):
 
 # Ideal gas IDT calculation
 # Create the ideal gas object:
-ideal_gas = ct.Solution('nDodecane_Reitz.cti','nDodecane_IG')
+ideal_gas = ct.Solution('nDodecane_Reitz.yaml', 'nDodecane_IG')
 
 # Set the state of the gas object:
 ideal_gas.TP = reactorTemperature, reactorPressure

interfaces/cython/cantera/examples/reactors/combustor.py

@@ -15,8 +15,9 @@
 import matplotlib.pyplot as plt
 import cantera as ct
 
-# Use reaction mechanism GRI-Mech 3.0
-gas = ct.Solution('gri30.xml')
+# Use reaction mechanism GRI-Mech 3.0. For 0-D simulations,
+# no transport model is necessary.
+gas = ct.Solution('gri30.yaml')
 
 # Create a Reservoir for the inlet, set to a methane/air mixture at a specified
 # equivalence ratio

interfaces/cython/cantera/examples/reactors/custom.py

@@ -37,7 +37,7 @@ def __call__(self, t, y):
         return np.hstack((dTdt, dYdt))
 
 
-gas = ct.Solution('gri30.xml')
+gas = ct.Solution('gri30.yaml')
 
 # Initial condition
 P = ct.one_atm

interfaces/cython/cantera/examples/reactors/fuel_injection.py

@@ -12,7 +12,7 @@
 import cantera as ct
 
 # Use a reduced n-dodecane mechanism with PAH formation pathways
-gas = ct.Solution('nDodecane_Reitz.cti', 'nDodecane_IG')
+gas = ct.Solution('nDodecane_Reitz.yaml', 'nDodecane_IG')
 
 # Create a Reservoir for the fuel inlet, set to pure dodecane
 gas.TPX = 300, 20*ct.one_atm, 'c12h26:1.0'

interfaces/cython/cantera/examples/reactors/ic_engine.py

@@ -20,7 +20,7 @@
 #########################################################################
 
 # reaction mechanism, kinetics type and compositions
-reaction_mechanism = 'nDodecane_Reitz.xml'
+reaction_mechanism = 'nDodecane_Reitz.yaml'
 phase_name = 'nDodecane_IG'
 comp_air = 'o2:1, n2:3.76'
 comp_fuel = 'c12h26:1'

interfaces/cython/cantera/examples/reactors/mix1.py

@@ -19,15 +19,15 @@
 import cantera as ct
 
 # Use air for stream a.
-gas_a = ct.Solution('air.xml')
+gas_a = ct.Solution('air.yaml')
 gas_a.TPX = 300.0, ct.one_atm, 'O2:0.21, N2:0.78, AR:0.01'
 rho_a = gas_a.density
 
 
 # Use GRI-Mech 3.0 for stream b (methane) and for the mixer. If it is desired
 # to have a pure mixer, with no chemistry, use instead a reaction mechanism
 # for gas_b that has no reactions.
-gas_b = ct.Solution('gri30.xml')
+gas_b = ct.Solution('gri30.yaml')
 gas_b.TPX = 300.0, ct.one_atm, 'CH4:1'
 rho_b = gas_b.density
 

interfaces/cython/cantera/examples/reactors/periodic_cstr.py

@@ -11,7 +11,7 @@
 as soon as a significant amount of water is produced the reaction stops. After
 enough time has passed that the water is exhausted from the reactor, the mixture
 explodes again and the process repeats. This explanation can be verified by
-decreasing the rate for reaction 7 in file 'h2o2.cti' and re-running the
+decreasing the rate for reaction 7 in file h2o2.yaml and re-running the
 example.
 
 Acknowledgments: The idea for this example and an estimate of the conditions
@@ -22,7 +22,7 @@
 import numpy as np
 
 # create the gas mixture
-gas = ct.Solution('h2o2.cti')
+gas = ct.Solution('h2o2.yaml')
 
 # pressure = 60 Torr, T = 770 K
 p = 60.0*133.3

interfaces/cython/cantera/examples/reactors/pfr.py

@@ -20,7 +20,7 @@
 area = 1.e-4  # cross-sectional area [m**2]
 
 # input file containing the reaction mechanism
-reaction_mechanism = 'h2o2.xml'
+reaction_mechanism = 'h2o2.yaml'
 
 # Resolution: The PFR will be simulated by 'n_steps' time steps or by a chain
 # of 'n_steps' stirred reactors.

interfaces/cython/cantera/examples/reactors/piston.py

@@ -27,10 +27,10 @@
                                               'V1 [m^3]', 'V2 [m^3]',
                                               'V1+V2 [m^3]','X(CO)'))
 
-gas1 = ct.Solution('h2o2.cti')
+gas1 = ct.Solution('h2o2.yaml')
 gas1.TPX = 900.0, ct.one_atm, 'H2:2, O2:1, AR:20'
 
-gas2 = ct.Solution('gri30.xml')
+gas2 = ct.Solution('gri30.yaml')
 gas2.TPX = 900.0, ct.one_atm, 'CO:2, H2O:0.01, O2:5'
 
 r1 = ct.IdealGasReactor(gas1)

interfaces/cython/cantera/examples/reactors/reactor1.py

@@ -9,7 +9,7 @@
 
 import cantera as ct
 
-gas = ct.Solution('gri30.xml')
+gas = ct.Solution('gri30.yaml')
 gas.TPX = 1001.0, ct.one_atm, 'H2:2,O2:1,N2:4'
 r = ct.IdealGasConstPressureReactor(gas)
 

interfaces/cython/cantera/examples/reactors/reactor2.py

@@ -28,17 +28,17 @@
 #-----------------------------------------------------------------------
 
 # create an argon gas object and set its state
-ar = ct.Solution('argon.xml')
+ar = ct.Solution('argon.yaml')
 ar.TP = 1000.0, 20.0 * ct.one_atm
 
 # create a reactor to represent the side of the cylinder filled with argon
 r1 = ct.IdealGasReactor(ar)
 
 # create a reservoir for the environment, and fill it with air.
-env = ct.Reservoir(ct.Solution('air.xml'))
+env = ct.Reservoir(ct.Solution('air.yaml'))
 
 # use GRI-Mech 3.0 for the methane/air mixture, and set its initial state
-gas = ct.Solution('gri30.xml')
+gas = ct.Solution('gri30.yaml')
 gas.TP = 500.0, 0.2 * ct.one_atm
 gas.set_equivalence_ratio(1.1, 'CH4:1.0', 'O2:2, N2:7.52')
 

interfaces/cython/cantera/examples/reactors/sensitivity1.py

@@ -7,7 +7,7 @@
 
 import cantera as ct
 
-gas = ct.Solution('gri30.xml')
+gas = ct.Solution('gri30.yaml')
 temp = 1500.0
 pres = ct.one_atm
 

interfaces/cython/cantera/examples/reactors/surf_pfr.py

@@ -24,7 +24,7 @@
 porosity = 0.3  # Catalyst bed porosity
 
 # input file containing the surface reaction mechanism
-cti_file = 'methane_pox_on_pt.cti'
+yaml_file = 'methane_pox_on_pt.yaml'
 
 output_filename = 'surf_pfr_output.csv'
 
@@ -37,11 +37,11 @@
 t = tc + 273.15  # convert to Kelvin
 
 # import the gas model and set the initial conditions
-gas = ct.Solution(cti_file, 'gas')
+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(cti_file,'Pt_surf', [gas])
+surf = ct.Interface(yaml_file, 'Pt_surf', [gas])
 surf.TP = t, ct.one_atm
 
 rlen = length/(NReactors-1)

interfaces/cython/cantera/examples/surface_chemistry/catalytic_combustion.py

@@ -39,19 +39,19 @@
 #
 # This object will be used to evaluate all thermodynamic, kinetic, and
 # transport properties. The gas phase will be taken from the definition of
-# phase 'gas' in input file 'ptcombust.cti,' which is a stripped-down version
+# phase 'gas' in input file 'ptcombust.yaml,' which is a stripped-down version
 # of GRI-Mech 3.0.
-gas = ct.Solution('ptcombust.cti', 'gas')
+gas = ct.Solution('ptcombust.yaml', 'gas', transport_model=transport)
 gas.TPX = tinlet, p, comp1
 
 ################ create the interface object ##################
 #
 # This object will be used to evaluate all surface chemical production rates.
 # It will be created from the interface definition 'Pt_surf' in input file
-# 'ptcombust.cti,' which implements the reaction mechanism of Deutschmann et
+# 'ptcombust.yaml,' which implements the reaction mechanism of Deutschmann et
 # al., 1995 for catalytic combustion on platinum.
 #
-surf_phase = ct.Interface('ptcombust.cti', 'Pt_surf', [gas])
+surf_phase = ct.Interface('ptcombust.yaml', 'Pt_surf', [gas])
 surf_phase.TP = tsurf, p
 
 # integrate the coverage equations in time for 1 s, holding the gas