[Examples] Formatting changes

Add requirements to all Python examples. Update formatting to resolve
some PEP8 problems.

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

@@ -6,11 +6,12 @@
 To test the submechanism, a premixed CO/H2 flame is simulated using the original
 mechanism and the submechanism, which demonstrates that the submechanism
 contains all of the important species and reactions.
+
+Requires: cantera >= 2.5.0, matplotlib >= 2.0
 """
 
 from timeit import default_timer
 import cantera as ct
-import numpy as np
 import matplotlib.pyplot as plt
 
 all_species = ct.Species.listFromFile('gri30.yaml')
@@ -22,7 +23,7 @@
     if 'C' in comp and 'H' in comp:
         # Exclude all hydrocarbon species
         continue
-    if 'N' in comp and comp != {'N':2}:
+    if 'N' in comp and comp != {'N': 2}:
         # Exclude all nitrogen compounds except for N2
         continue
     if 'Ar' in comp:
@@ -54,19 +55,21 @@
 gas2 = ct.Solution(thermo='IdealGas', kinetics='GasKinetics',
                    species=species, reactions=reactions)
 
+
 def solve_flame(gas):
     gas.TPX = 373, 0.05*ct.one_atm, 'H2:0.4, CO:0.6, O2:1, N2:3.76'
 
     # Create the flame simulation object
     sim = ct.CounterflowPremixedFlame(gas=gas, width=0.2)
 
-    sim.reactants.mdot = 0.12 # kg/m^2/s
-    sim.products.mdot = 0.06 # kg/m^2/s
+    sim.reactants.mdot = 0.12  # kg/m^2/s
+    sim.products.mdot = 0.06  # kg/m^2/s
 
     sim.set_refine_criteria(ratio=3, slope=0.1, curve=0.2)
     sim.solve(0, auto=True)
     return sim
 
+
 t1 = default_timer()
 sim1 = solve_flame(gas1)
 t2 = default_timer()

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

@@ -11,6 +11,8 @@
 and the associated species, and run the simulations again with these mechanisms
 to see whether the reduced mechanisms with a certain number of species are able
 to adequately simulate the ignition delay problem.
+
+Requires: cantera >= 2.5.0, matplotlib >= 2.0
 """
 
 import cantera as ct
@@ -44,8 +46,8 @@
 R = sorted(zip(Rmax, gas.reactions()), key=lambda x: -x[0])
 
 # Test reduced mechanisms with different numbers of reactions
-C = plt.cm.winter(np.linspace(0,1,5))
-for i,N in enumerate([40,50,60,70,80]):
+C = plt.cm.winter(np.linspace(0, 1, 5))
+for i, N in enumerate([40, 50, 60, 70, 80]):
     # Get the N most active reactions
     reactions = [r[1] for r in R[:N]]
 
@@ -77,7 +79,7 @@
         tt.append(1000 * t)
         TT.append(r.T)
 
-    plt.plot(tt,TT, lw=2, color=C[i],
+    plt.plot(tt, TT, lw=2, color=C[i],
              label='K={0}, R={1}'.format(gas2.n_species, N))
     plt.xlabel('Time (ms)')
     plt.ylabel('Temperature (K)')

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

@@ -3,8 +3,10 @@
 
 This script uses Graphviz to generate an image. You must have Graphviz installed
 and the program 'dot' must be on your path for this example to work.
-Graphviz can be obtained from http://www.graphviz.org/ or (possibly) installed
+Graphviz can be obtained from https://www.graphviz.org/ or (possibly) installed
 using your operating system's package manager.
+
+Requires: cantera >= 2.5.0
 """
 
 import os

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

@@ -1,6 +1,8 @@
 """
 Adiabatic flame temperature and equilibrium composition for a fuel/air mixture
 as a function of equivalence ratio, including formation of solid carbon.
+
+Requires: cantera >= 2.5.0, matplotlib >= 2.0
 """
 
 import cantera as ct
@@ -35,7 +37,7 @@
 
 # create some arrays to hold the data
 tad = np.zeros(npoints)
-xeq = np.zeros((mix.n_species,npoints))
+xeq = np.zeros((mix.n_species, npoints))
 
 for i in range(npoints):
     # set the gas state
@@ -51,7 +53,7 @@
 
     tad[i] = mix.T
     print('At phi = {0:12.4g}, Tad = {1:12.4g}'.format(phi[i], tad[i]))
-    xeq[:,i] = mix.species_moles
+    xeq[:, i] = mix.species_moles
 
 # write output CSV file for importing into Excel
 csv_file = 'adiabatic.csv'

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

@@ -1,6 +1,8 @@
 """
 An equilibrium example with charged species in the gas phase
 and multiple condensed phases.
+
+Requires: cantera >= 2.5.0, matplotlib >= 2.0
 """
 
 import cantera as ct

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

@@ -1,10 +1,11 @@
 """
 A freely-propagating, premixed hydrogen flat flame with multicomponent
 transport properties.
+
+Requires: cantera >= 2.5.0
 """
 
 import cantera as ct
-import numpy as np
 
 # Simulation parameters
 p = ct.one_atm  # pressure [Pa]
@@ -34,10 +35,10 @@
 
 # Solve with multi-component transport properties
 f.transport_model = 'Multi'
-f.solve(loglevel) # don't use 'auto' on subsequent solves
+f.solve(loglevel)  # don't use 'auto' on subsequent solves
 f.show_solution()
 print('multicomponent flamespeed = {0:7f} m/s'.format(f.u[0]))
-f.save('h2_adiabatic.xml','multi', 'solution with multicomponent transport')
+f.save('h2_adiabatic.xml', 'multi', 'solution with multicomponent transport')
 
 # write the velocity, temperature, density, and mole fractions to a CSV file
 f.write_csv('h2_adiabatic.csv', quiet=False)

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

@@ -1,15 +1,16 @@
 """
 A burner-stabilized lean premixed hydrogen-oxygen flame at low pressure.
+
+Requires: cantera >= 2.5.0
 """
 
 import cantera as ct
-import numpy as np
 
 p = 0.05 * ct.one_atm
 tburner = 373.0
 mdot = 0.06
 reactants = 'H2:1.5, O2:1, AR:7'  # premixed gas composition
-width = 0.5 # m
+width = 0.5  # m
 loglevel = 1  # amount of diagnostic output (0 to 5)
 
 gas = ct.Solution('h2o2.yaml')
@@ -25,7 +26,7 @@
 f.save('h2_burner_flame.xml', 'mix', 'solution with mixture-averaged transport')
 
 f.transport_model = 'Multi'
-f.solve(loglevel) # don't use 'auto' on subsequent solves
+f.solve(loglevel)  # don't use 'auto' on subsequent solves
 f.show_solution()
 f.save('h2_burner_flame.xml', 'multi', 'solution with multicomponent transport')
 

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

@@ -1,14 +1,15 @@
 """
 A burner-stabilized lean premixed hydrogen-oxygen flame at low pressure.
+
+Requires: cantera >= 2.5.0
 """
 
 import cantera as ct
-import numpy as np
 
 p = ct.one_atm
 tburner = 600.0
 reactants = 'CH4:1.0, O2:2.0, N2:7.52'  # premixed gas composition
-width = 0.5 # m
+width = 0.5  # m
 loglevel = 1  # amount of diagnostic output (0 to 5)
 
 gas = ct.Solution('gri30_ion.yaml')
@@ -26,4 +27,3 @@
 f.save('CH4_burner_flame.xml', 'mix', 'solution with mixture-averaged transport')
 
 f.write_csv('CH4_burner_flame.csv', quiet=False)
-

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

@@ -1,9 +1,10 @@
 """
 An opposed-flow ethane/air diffusion flame
+
+Requires: cantera >= 2.5.0, matplotlib >= 2.0
 """
 
 import cantera as ct
-import numpy as np
 import matplotlib.pyplot as plt
 
 # Input parameters
@@ -16,7 +17,7 @@
 comp_o = 'O2:0.21, N2:0.78, AR:0.01'  # air composition
 comp_f = 'C2H6:1'  # fuel composition
 
-width = 0.02 # Distance between inlets is 2 cm
+width = 0.02  # Distance between inlets is 2 cm
 
 loglevel = 1  # amount of diagnostic output (0 to 5)
 

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

@@ -1,5 +1,3 @@
-# -*- coding: utf-8 -*-
-
 # This file is part of Cantera. See License.txt in the top-level directory or
 # at https://cantera.org/license.txt for license and copyright information.
 
@@ -14,14 +12,18 @@
 
 This example can, for example, be used to iterate to a counterflow diffusion flame to an
 awkward  pressure and strain rate, or to create the basis for a flamelet table.
+
+Requires: cantera >= 2.5.0, matplotlib >= 2.0
 """
 
-import cantera as ct
 import numpy as np
 import os
 
+import cantera as ct
+import matplotlib.pyplot as plt
+
 
-class FlameExtinguished(Exception): 
+class FlameExtinguished(Exception):
     pass
 
 
@@ -37,7 +39,7 @@ class FlameExtinguished(Exception):
 
 reaction_mechanism = 'h2o2.yaml'
 gas = ct.Solution(reaction_mechanism)
-width = 18e-3 # 18mm wide
+width = 18e-3  # 18mm wide
 f = ct.CounterflowDiffusionFlame(gas, width=width)
 
 # Define the operating pressure and boundary conditions
@@ -186,12 +188,10 @@ def interrupt_extinction(t):
 
 # PART 4: PLOT SOME FIGURES
 
-import matplotlib.pyplot as plt
-
 fig1 = plt.figure()
 fig2 = plt.figure()
-ax1 = fig1.add_subplot(1,1,1)
-ax2 = fig2.add_subplot(1,1,1)
+ax1 = fig1.add_subplot(1, 1, 1)
+ax2 = fig2.add_subplot(1, 1, 1)
 p_selected = p_range[::7]
 
 for p in p_selected:
@@ -218,8 +218,8 @@ def interrupt_extinction(t):
 
 fig3 = plt.figure()
 fig4 = plt.figure()
-ax3 = fig3.add_subplot(1,1,1)
-ax4 = fig4.add_subplot(1,1,1)
+ax3 = fig3.add_subplot(1, 1, 1)
+ax4 = fig4.add_subplot(1, 1, 1)
 n_selected = range(1, n, 5)
 for n in n_selected:
     file_name = 'strain_loop_{0:02d}.xml'.format(n)

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

@@ -1,5 +1,3 @@
-# -*- coding: utf-8 -*-
-
 # This file is part of Cantera. See License.txt in the top-level directory or
 # at https://cantera.org/license.txt for license and copyright information.
 
@@ -10,12 +8,16 @@
 The tutorial makes use of the scaling rules derived by Fiala and Sattelmayer
 (doi:10.1155/2014/484372). Please refer to this publication for a detailed
 explanation. Also, please don't forget to cite it if you make use of it.
+
+Requires: cantera >= 2.5.0, matplotlib >= 2.0
 """
 
-import cantera as ct
 import numpy as np
 import os
 
+import cantera as ct
+import matplotlib.pyplot as plt
+
 # Create directory for output data files
 data_directory = 'diffusion_flame_extinction_data/'
 if not os.path.exists(data_directory):
@@ -28,7 +30,7 @@
 
 reaction_mechanism = 'h2o2.yaml'
 gas = ct.Solution(reaction_mechanism)
-width = 18.e-3 # 18mm wide
+width = 18.e-3  # 18mm wide
 f = ct.CounterflowDiffusionFlame(gas, width=width)
 
 # Define the operating pressure and boundary conditions
@@ -133,8 +135,10 @@
             break
     else:
         # Procedure if flame extinguished but abortion criterion is not satisfied
-        print('Flame extinguished at n = {0}. Restoring n = {1} with alpha = {2}'.format(
-              n, n_last_burning, alpha[n_last_burning]))
+        print(
+            'Flame extinguished at n = {0}. Restoring n = {1} '
+            'with alpha = {2}'.format(n, n_last_burning, alpha[n_last_burning])
+        )
         # Reduce relative strain rate increase
         delta_alpha = delta_alpha / delta_alpha_factor
         # Restore last burning solution
@@ -157,7 +161,6 @@
       f.strain_rate('stoichiometric', fuel='H2')))
 
 # Plot the maximum temperature over the maximum axial velocity gradient
-import matplotlib.pyplot as plt
 plt.figure()
 plt.semilogx(a_max, T_max)
 plt.xlabel(r'$a_{max}$ [1/s]')

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

@@ -1,6 +1,8 @@
 """
 A burner-stabilized, premixed methane/air flat flame with multicomponent
 transport properties and a specified temperature profile.
+
+Requires: cantera >= 2.5.0
 """
 
 import cantera as ct
@@ -14,7 +16,7 @@
 comp = 'CH4:0.65, O2:1, N2:3.76'  # premixed gas composition
 
 # The solution domain is chosen to be 1 cm
-width = 0.01 # m
+width = 0.01  # m
 
 loglevel = 1  # amount of diagnostic output (0 to 5)
 refine_grid = True  # 'True' to enable refinement

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

@@ -2,10 +2,11 @@
 Sensitivity analysis for a freely-propagating, premixed methane-air
 flame. Computes the sensitivity of the laminar flame speed with respect
 to each reaction rate constant.
+
+Requires: cantera >= 2.5.0
 """
 
 import cantera as ct
-import numpy as np
 
 # Simulation parameters
 p = ct.one_atm  # pressure [Pa]
@@ -14,7 +15,7 @@
 
 width = 0.03  # m
 
-# IdealGasMix object used to compute mixture properties
+# Solution object used to compute mixture properties
 gas = ct.Solution('gri30.yaml', transport_model='Mix')
 gas.TPX = Tin, p, reactants