From b92991601d834ce072eb0f4b6634f12467906ee0 Mon Sep 17 00:00:00 2001
From: "Bryan W. Weber" <bryan.w.weber@gmail.com>
Date: Thu, 23 Jul 2020 17:29:50 -0400
Subject: [PATCH 01/18] [Cython/Examples] Fix extract_submechanism example

When loading reactions from a YAML file, an instance of a Kinetics
object is required so that the species associated with the reactions are
available. The required object is now constructed from the already
loaded species definitions.

Fixes #821, problem introduced in 1866e3542d2bdbaa8f1d4df69923746a3279895c
---
 .../cantera/examples/kinetics/extract_submechanism.py  | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/interfaces/cython/cantera/examples/kinetics/extract_submechanism.py b/interfaces/cython/cantera/examples/kinetics/extract_submechanism.py
index aa52aefea0d..19a7c9b0d81 100644
--- a/interfaces/cython/cantera/examples/kinetics/extract_submechanism.py
+++ b/interfaces/cython/cantera/examples/kinetics/extract_submechanism.py
@@ -14,7 +14,8 @@
 import cantera as ct
 import matplotlib.pyplot as plt
 
-all_species = ct.Species.listFromFile('gri30.yaml')
+input_file = 'gri30.yaml'
+all_species = ct.Species.listFromFile(input_file)
 species = []
 
 # Filter species
@@ -36,7 +37,8 @@
 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.yaml')
+ref_phase = ct.Solution(thermo='ideal-gas', kinetics='gas', species=all_species)
+all_reactions = ct.Reaction.listFromFile(input_file, ref_phase)
 reactions = []
 
 print('\nReactions:')
@@ -51,8 +53,8 @@
     print(R.equation)
 print('\n')
 
-gas1 = ct.Solution('gri30.yaml')
-gas2 = ct.Solution(thermo='IdealGas', kinetics='GasKinetics',
+gas1 = ct.Solution(input_file)
+gas2 = ct.Solution(thermo='ideal-gas', kinetics='gas',
                    species=species, reactions=reactions)
 
 

From 25abfad083d28ece0ffbe06442cbf3e9b688e84d Mon Sep 17 00:00:00 2001
From: "Bryan W. Weber" <bryan.w.weber@gmail.com>
Date: Mon, 27 Jul 2020 10:05:12 -0400
Subject: [PATCH 02/18] Fix infinite loop in diffusion_flame_extinction.py

This change reworks the abortion criteria for the diffusion flame
extinction example. Previously, the loop was only aborted when the flame
temperature was above the inlet temperature, the difference of the flame
temperature in the prior two iterations was less than the threshold, AND
the change in strain rate parameter was less than the threshold.
However, I found that this combination of conditions was never reached,
because the only way to change the strain rate delta was to have an
extinguished flame, and eventually the flame remains extinguished even
if the delta_alpha is reduced. This leads to an infinite loop, since the
abortion criteria check are only done if the flame is burning. This
change moves the abortion criteria check into the case where the flame
is not burning.

In addition, the flame temperature check is modified to use
np.isclose(). I found that on the last burning iteration, the maximum
flame temperature was only just barely above the oxidizer inlet
temperature. Thus, the result printed to the screen was not very useful.
The change to np.isclose() produces a more useful result for the final
burning iteration before extinction. The last non-burning iteration is
also saved to the output file(s) for reference.

Fixes #872
---
 .../onedim/diffusion_flame_extinction.py      | 44 ++++++++++++++-----
 1 file changed, 32 insertions(+), 12 deletions(-)

diff --git a/interfaces/cython/cantera/examples/onedim/diffusion_flame_extinction.py b/interfaces/cython/cantera/examples/onedim/diffusion_flame_extinction.py
index 14b84313ad3..ac168b0d7b3 100644
--- a/interfaces/cython/cantera/examples/onedim/diffusion_flame_extinction.py
+++ b/interfaces/cython/cantera/examples/onedim/diffusion_flame_extinction.py
@@ -130,13 +130,12 @@
         f.solve(loglevel=0)
     except ct.CanteraError as e:
         print('Error: Did not converge at n =', n, e)
-    if np.max(f.T) > temperature_limit_extinction:
+    if not np.isclose(np.max(f.T), temperature_limit_extinction):
         # Flame is still burning, so proceed to next strain rate
         n_last_burning = n
         if hdf_output:
             group = 'extinction/{0:04d}'.format(n)
-            f.write_hdf(file_name, group=group, quiet=False,
-                        description='extinction iteration'.format(n))
+            f.write_hdf(file_name, group=group, quiet=True)
         else:
             file_name = 'extinction_{0:04d}.xml'.format(n)
             f.save(os.path.join(data_directory, file_name),
@@ -145,19 +144,32 @@
                    ', reaction mechanism ' + reaction_mechanism)
         T_max.append(np.max(f.T))
         a_max.append(np.max(np.abs(np.gradient(f.velocity) / np.gradient(f.grid))))
+        print('Flame burning at alpha = {:8.4F}. Proceeding to the next iteration, '
+              'with delta_alpha = {}'.format(alpha[-1], delta_alpha))
+    elif ((T_max[-2] - T_max[-1] < delta_T_min) and (delta_alpha < delta_alpha_min)):
         # If the temperature difference is too small and the minimum relative
-        # strain rate increase is reached, abort
-        if ((T_max[-2] - T_max[-1] < delta_T_min) &
-                (delta_alpha < delta_alpha_min)):
-            print('Flame extinguished at n = {0}.'.format(n),
-                  'Abortion criterion satisfied.')
-            break
+        # strain rate increase is reached, save the last, non-burning, solution
+        # to the output file and break the loop
+        T_max.append(np.max(f.T))
+        a_max.append(np.max(np.abs(np.gradient(f.velocity) / np.gradient(f.grid))))
+        if hdf_output:
+            group = 'extinction/{0:04d}'.format(n)
+            f.write_hdf(file_name, group=group, quiet=True)
+        else:
+            file_name = 'extinction_{0:04d}.xml'.format(n)
+            f.save(os.path.join(data_directory, file_name), name='solution', loglevel=0)
+        print('Flame extinguished at alpha = {0:8.4F}.'.format(alpha[-1]),
+              'Abortion criterion satisfied.')
+        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]))
         # Reduce relative strain rate increase
         delta_alpha = delta_alpha / delta_alpha_factor
+
+        print('Flame extinguished at alpha = {0:8.4F}. Restoring alpha = {1:8.4F} and '
+              'trying delta_alpha = {2}'.format(
+                  alpha[-1], alpha[n_last_burning], delta_alpha))
+
         # Restore last burning solution
         if hdf_output:
             group = 'extinction/{0:04d}'.format(n_last_burning)
@@ -168,7 +180,15 @@
                       name='solution', loglevel=0)
 
 
-# Print some parameters at the extinction point
+# Print some parameters at the extinction point, after restoring the last burning
+# solution
+if hdf_output:
+    group = 'extinction/{0:04d}'.format(n_last_burning)
+    f.read_hdf(file_name, group=group)
+else:
+    file_name = 'extinction_{0:04d}.xml'.format(n_last_burning)
+    f.restore(os.path.join(data_directory, file_name),
+              name='solution', loglevel=0)
 print('----------------------------------------------------------------------')
 print('Parameters at the extinction point:')
 print('Pressure p={0} bar'.format(f.P / 1e5))

From 4f55735f56f10a616edaca20eb95ab6598b6338b Mon Sep 17 00:00:00 2001
From: "Bryan W. Weber" <bryan.w.weber@gmail.com>
Date: Tue, 28 Jul 2020 19:48:12 -0400
Subject: [PATCH 03/18] Typo fixes

---
 data/sofc.yaml                                | 28 +++++++++----------
 include/cantera/kinetics/RateCoeffMgr.h       |  4 +--
 include/cantera/kinetics/RxnRates.h           |  2 +-
 include/cantera/kinetics/StoichManager.h      |  6 ++--
 include/cantera/thermo/EdgePhase.h            |  4 +--
 .../surface_chemistry/catalytic_combustion.py |  4 +--
 .../examples/surface_chemistry/sofc.py        |  6 ++--
 7 files changed, 27 insertions(+), 27 deletions(-)

diff --git a/data/sofc.yaml b/data/sofc.yaml
index cbe0b95e7c9..2421ca57172 100644
--- a/data/sofc.yaml
+++ b/data/sofc.yaml
@@ -5,7 +5,7 @@ description: |-
   species thermochemistry ARE NOT REAL VALUES - they are chosen only
   for the purposes of this example.
 
-  Defines bulk (i.e., 3D) phases - a gas, a metal, and an oxide.
+  Defines bulk (that is, 3D) phases - a gas, a metal, and an oxide.
   The gas contains only the minimum number of species needed to model
   operation on hydrogen. The species definitions are imported from
   gri30.yaml. The initial composition is set to hydrogen + 5% water, but
@@ -26,14 +26,14 @@ description: |-
   charge balances on the metal, then we would require a more complex
   model. Note that there is no work function for this metal.
 
-  Note: the "const_cp" species thermo model is used throughout this
+  Note: the 'const_cp' species thermo model is used throughout this
   file (with the exception of the gaseous species, which use NASA
-  polynomials imported from gri30.cti). The const_cp model assumes a
+  polynomials imported from gri30.yaml). The const_cp model assumes a
   constant specific heat, which by default is zero. Parameters that
-  can be specified are cp0, t0, h0, and s0. If omitted, t0 = 300 K, h0
-  = 0, and s0 = 0. The thermo properties are computed as follows: h =
-  h0 + cp0*(t - t0), s = s0 + cp0*ln(t/t0). For work at a single
-  temperature, it is sufficient to specify only h0.
+  can be specified are cp0, t0, h0, and s0. If omitted, t0 = 300 K,
+  h0 = 0, and s0 = 0. The thermo properties are computed as follows:
+  h = h0 + cp0*(t - t0), s = s0 + cp0*ln(t/t0).
+  For work at a single temperature, it is sufficient to specify only h0.
 
   The 'oxide_bulk' phase is a very simple model for the bulk phase. We only
   consider the oxygen sublattice. The only species we define are a
@@ -41,7 +41,7 @@ description: |-
   required input, but is not used here, so may be set arbitrarily.
 
   The vacancy will be modeled as truly vacant - it contains no atoms,
-  has no charge, and has zero enthalpy and entropy.  This is different
+  has no charge, and has zero enthalpy and entropy. This is different
   from the usual convention in which the vacancy properties are are
   expressed relative to the perfect crystal lattice. For example, in
   the usual convention, an oxygen vacancy has charge +2. But the
@@ -65,7 +65,7 @@ description: |-
   'mol' and 'cm' were specified in the units directive below as the
   units for quantity and length, respectively.
   2. The 'reactions' field specifies that all reaction entries in this file
-  that have are in the 'metal_surface-reactions' field are reactions belonging
+  that are in the 'metal_surface-reactions' field are reactions belonging
   to this surface mechanism.
 
   On the oxide surface, we consider four species:
@@ -74,11 +74,11 @@ description: |-
       3. OH'(ox)  - a surface hydroxyl with charge -1
       4. H2O(ox)  - physisorbed neutral water
 
-  The 'tpb' phase is th etriple phase boundary between the metal, oxide, and gas. A
-  single species is specified, but it is not used, since all reactions
-  only involve species on either side of the tpb. Note that the site
-  density is in mol/cm. But since no reactions involve TPB species,
-  this parameter is unused.
+  The triple phase boundary (TPB) between the metal, oxide, and gas is
+  specified in the 'tpb' phase. A single species is specified, but it
+  is not used, since all reactions only involve species on either side
+  of the TPB. Note that the site density is in mol/cm. But since no
+  reactions involve TPB species, this parameter is unused.
 
 generator: cti2yaml
 cantera-version: 2.5.0a3
diff --git a/include/cantera/kinetics/RateCoeffMgr.h b/include/cantera/kinetics/RateCoeffMgr.h
index 8449e1b9601..4f89f464a74 100644
--- a/include/cantera/kinetics/RateCoeffMgr.h
+++ b/include/cantera/kinetics/RateCoeffMgr.h
@@ -43,10 +43,10 @@ class Rate1
 
     /**
      * Update the concentration-dependent parts of the rate coefficient, if any.
-     * Used by class SurfaceArrhenius to compute coverage-dependent *
+     * Used by class SurfaceArrhenius to compute coverage-dependent
      * modifications to the Arrhenius parameters. The array c should contain
      * whatever data the particular rate coefficient class needs to update its
-     * rates.  Note that this method does not return anything. To get the
+     * rates. Note that this method does not return anything. To get the
      * updated rates, method update must be called after the call to update_C.
      */
     void update_C(const doublereal* c) {
diff --git a/include/cantera/kinetics/RxnRates.h b/include/cantera/kinetics/RxnRates.h
index 8ade9c2fb37..a4ada5fbd11 100644
--- a/include/cantera/kinetics/RxnRates.h
+++ b/include/cantera/kinetics/RxnRates.h
@@ -162,7 +162,7 @@ class SurfaceArrhenius
     }
 
     /**
-     * Update the value the rate constant.
+     * Update the value of the rate constant.
      *
      * This function returns the actual value of the rate constant. It can be
      * safely called for negative values of the pre-exponential factor.
diff --git a/include/cantera/kinetics/StoichManager.h b/include/cantera/kinetics/StoichManager.h
index 9077ed11edd..66c2a138bae 100644
--- a/include/cantera/kinetics/StoichManager.h
+++ b/include/cantera/kinetics/StoichManager.h
@@ -40,7 +40,7 @@ namespace Cantera
  * \f]
  *
  * where \f$ \nu^{(p)_{k,i}} \f$ is the product-side stoichiometric
- * coefficient of species \a k in reaction \a i. This could be done be
+ * coefficient of species \a k in reaction \a i. This could be done by
  * straightforward matrix multiplication, but would be inefficient, since most
  * of the matrix elements of \f$ \nu^{(p)}_{k,i} \f$ are zero. We could do
  * better by using sparse-matrix algorithms to compute this product.
@@ -61,12 +61,12 @@ namespace Cantera
  * computing quantities that can be written as matrix multiplies.
  *
  * They are designed to explicitly unroll loops over species or reactions for
- * Operations on reactions that require knowing the reaction stoichiometry.
+ * operations on reactions that require knowing the reaction stoichiometry.
  *
  * This module consists of class StoichManager, and classes C1, C2, and C3.
  * Classes C1, C2, and C3 handle operations involving one, two, or three
  * species, respectively, in a reaction. Instances are instantiated with a
- * reaction number, and n species numbers (n = 1 for C1, etc.).  All three
+ * reaction number, and n species numbers (n = 1 for C1, etc.). All three
  * classes have the same interface.
  *
  * These classes are designed for use by StoichManager, and the operations
diff --git a/include/cantera/thermo/EdgePhase.h b/include/cantera/thermo/EdgePhase.h
index 22d982a48f0..2825fde0a58 100644
--- a/include/cantera/thermo/EdgePhase.h
+++ b/include/cantera/thermo/EdgePhase.h
@@ -22,8 +22,8 @@ namespace Cantera
  * thermodynamic object.
  *
  * All of the equations and formulations carry through from SurfPhase to this
- * EdgePhase object. It should be noted however, that dimensional object with
- * length dimensions, have their dimensions reduced by one.
+ * EdgePhase object. It should be noted that dimensional quantities with
+ * dimensions including a length have their dimensions reduced by one.
  *
  * @ingroup thermoprops
  */
diff --git a/interfaces/cython/cantera/examples/surface_chemistry/catalytic_combustion.py b/interfaces/cython/cantera/examples/surface_chemistry/catalytic_combustion.py
index d75e20cabed..8b3566e2164 100644
--- a/interfaces/cython/cantera/examples/surface_chemistry/catalytic_combustion.py
+++ b/interfaces/cython/cantera/examples/surface_chemistry/catalytic_combustion.py
@@ -64,7 +64,7 @@
 # grid
 sim = ct.ImpingingJet(gas=gas, width=width, surface=surf_phase)
 
-# Objects of class StagnationFlow have members that represent the gas inlet
+# Objects of class ImpingingJet have members that represent the gas inlet
 # ('inlet') and the surface ('surface'). Set some parameters of these objects.
 sim.inlet.mdot = mdot
 sim.inlet.T = tinlet
@@ -74,7 +74,7 @@
 # Show the initial solution estimate
 sim.show_solution()
 
-# Solving problems with stiff chemistry coulpled to flow can require a
+# Solving problems with stiff chemistry coupled to flow can require a
 # sequential approach where solutions are first obtained for simpler problems
 # and used as the initial guess for more difficult problems.
 
diff --git a/interfaces/cython/cantera/examples/surface_chemistry/sofc.py b/interfaces/cython/cantera/examples/surface_chemistry/sofc.py
index 883dd074eca..a0c1e6523d2 100644
--- a/interfaces/cython/cantera/examples/surface_chemistry/sofc.py
+++ b/interfaces/cython/cantera/examples/surface_chemistry/sofc.py
@@ -1,7 +1,7 @@
 """
 A simple model of a solid oxide fuel cell.
 
-Unlike most SOFC models, this model does not use semi-empirical Butler- Volmer
+Unlike most SOFC models, this model does not use semi-empirical Butler-Volmer
 kinetics for the charge transfer reactions, but uses elementary, reversible
 reactions obeying mass-action kinetics for all reactions, including charge
 transfer. As this script will demonstrate, this approach allows computing the
@@ -125,7 +125,7 @@ def anode_curr(E):
     w = tpb_a.net_production_rates
 
     # the sign convention is that the current is positive when
-    # electrons are being delivered to the anode - i.e. it is positive
+    # electrons are being delivered to the anode - that is, it is positive
     # for fuel cell operation.
     return ct.faraday * w[0] * TPB_length_per_area
 
@@ -172,7 +172,7 @@ def cathode_curr(E):
     w = tpb_c.net_production_rates
 
     # the sign convention is that the current is positive when electrons are
-    # being drawn from the cathode (i.e, negative production rate).
+    # being drawn from the cathode (that is, negative production rate).
     return -ct.faraday * w[0] * TPB_length_per_area
 
 

From bd78c7b7665a8603c6ccd8d06d486b03d57e6204 Mon Sep 17 00:00:00 2001
From: "Bryan W. Weber" <bryan.w.weber@gmail.com>
Date: Tue, 28 Jul 2020 19:48:52 -0400
Subject: [PATCH 04/18] Fix boundary emissivities deprecation warning

The set_boundary_emissivities method is deprecated and will be removed
after Cantera 2.5.0. This change switches one example to use the new
property. The property was also missing from the FlameBase class.
---
 .../examples/onedim/diffusion_flame.py        |  2 +-
 interfaces/cython/cantera/onedim.py           | 24 +++++++++++++++++--
 interfaces/cython/cantera/onedim.pyx          |  8 +++----
 3 files changed, 27 insertions(+), 7 deletions(-)

diff --git a/interfaces/cython/cantera/examples/onedim/diffusion_flame.py b/interfaces/cython/cantera/examples/onedim/diffusion_flame.py
index e910e74633d..66906e9cfc1 100644
--- a/interfaces/cython/cantera/examples/onedim/diffusion_flame.py
+++ b/interfaces/cython/cantera/examples/onedim/diffusion_flame.py
@@ -41,7 +41,7 @@
 f.oxidizer_inlet.T = tin_o
 
 # Set the boundary emissivities
-f.set_boundary_emissivities(0.0, 0.0)
+f.boundary_emissivities = 0.0, 0.0
 # Turn radiation off
 f.radiation_enabled = False
 
diff --git a/interfaces/cython/cantera/onedim.py b/interfaces/cython/cantera/onedim.py
index a5e2c2e3345..aee12cb5bb3 100644
--- a/interfaces/cython/cantera/onedim.py
+++ b/interfaces/cython/cantera/onedim.py
@@ -2,8 +2,8 @@
 # at https://cantera.org/license.txt for license and copyright information.
 
 from math import erf
-from os import path
 from email.utils import formatdate
+import warnings
 import numpy as np
 
 from ._cantera import *
@@ -253,7 +253,27 @@ def radiation_enabled(self, enable):
         self.flame.radiation_enabled = enable
 
     def set_boundary_emissivities(self, e_left, e_right):
-        self.flame.set_boundary_emissivities(e_left, e_right)
+        """
+        .. deprecated:: 2.5
+
+             To be deprecated with version 2.5, and removed thereafter.
+             Replaced by property `boundary_emissivities`.
+        """
+        warnings.warn("Method 'set_boundary_emissivities' to be removed after "
+                      "Cantera 2.5. Replaced by property "
+                      "'boundary_emissivities'", DeprecationWarning)
+        self.flame.boundary_emissivities = e_left, e_right
+
+    @property
+    def boundary_emissivities(self):
+        """ Set/get boundary emissivities. """
+        return self.flame.boundary_emissivities
+
+    @boundary_emissivities.setter
+    def boundary_emissivities(self, epsilon):
+        if len(epsilon) != 2:
+            raise ValueError("Boundary emissivities must both be set at the same time.")
+        self.flame.boundary_emissivities = epsilon[0], epsilon[1]
 
     @property
     def grid(self):
diff --git a/interfaces/cython/cantera/onedim.pyx b/interfaces/cython/cantera/onedim.pyx
index 86f81dea246..7a5ed20a38c 100644
--- a/interfaces/cython/cantera/onedim.pyx
+++ b/interfaces/cython/cantera/onedim.pyx
@@ -578,10 +578,10 @@ cdef class _FlowBase(Domain1D):
         def __get__(self):
             return self.flow.leftEmissivity(), self.flow.rightEmissivity()
         def __set__(self, tuple epsilon):
-            if len(epsilon) == 2:
-                self.flow.setBoundaryEmissivities(epsilon[0], epsilon[1])
-            else:
-                raise ValueError("Setter requires tuple of length 2.")
+            if len(epsilon) != 2:
+                raise ValueError('Setting the boundary emissivities requires a '
+                                 'tuple of length 2.')
+            self.flow.setBoundaryEmissivities(epsilon[0], epsilon[1])
 
     property radiation_enabled:
         """ Determines whether or not to include radiative heat transfer """

From 4e48f024e8f3ae582e17d62672b20bd756a0e708 Mon Sep 17 00:00:00 2001
From: "Bryan W. Weber" <bryan.w.weber@gmail.com>
Date: Tue, 28 Jul 2020 20:24:17 -0400
Subject: [PATCH 05/18] [Example] Specify data file path in flame_fixed_T

This allows the script to be run from the installed location, or from
the root of the source tree.
---
 interfaces/cython/cantera/examples/onedim/flame_fixed_T.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/interfaces/cython/cantera/examples/onedim/flame_fixed_T.py b/interfaces/cython/cantera/examples/onedim/flame_fixed_T.py
index 7811da192a6..fd2bc54a7ed 100644
--- a/interfaces/cython/cantera/examples/onedim/flame_fixed_T.py
+++ b/interfaces/cython/cantera/examples/onedim/flame_fixed_T.py
@@ -7,6 +7,7 @@
 
 import cantera as ct
 import numpy as np
+from pathlib import Path
 
 ################################################################
 # parameter values
@@ -38,7 +39,9 @@
 
 # read temperature vs. position data from a file.
 # The file is assumed to have one z, T pair per line, separated by a comma.
-zloc, tvalues = np.genfromtxt('tdata.dat', delimiter=',', comments='#').T
+# The data file must be stored in the same folder as this script.
+data_file = Path(__file__).parent.joinpath('tdata.dat')
+zloc, tvalues = np.genfromtxt(str(data_file), delimiter=',', comments='#').T
 zloc /= max(zloc)
 
 # set the temperature profile to the values read in

From 4568d367950545017f95907276850f8383769bca Mon Sep 17 00:00:00 2001
From: "Bryan W. Weber" <bryan.w.weber@gmail.com>
Date: Tue, 28 Jul 2020 20:24:54 -0400
Subject: [PATCH 06/18] [Examples] Replace argon.yaml with air.yaml

argon.yaml is deprecated, use air.yaml and specify the composition
instead.
---
 interfaces/cython/cantera/examples/reactors/reactor2.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/interfaces/cython/cantera/examples/reactors/reactor2.py b/interfaces/cython/cantera/examples/reactors/reactor2.py
index 0b33ffe9a56..168136016ab 100644
--- a/interfaces/cython/cantera/examples/reactors/reactor2.py
+++ b/interfaces/cython/cantera/examples/reactors/reactor2.py
@@ -27,8 +27,8 @@
 # First create each gas needed, and a reactor or reservoir for each one.
 
 # create an argon gas object and set its state
-ar = ct.Solution('argon.yaml')
-ar.TP = 1000.0, 20.0 * ct.one_atm
+ar = ct.Solution('air.yaml')
+ar.TPX = 1000.0, 20.0 * ct.one_atm, "AR:1"
 
 # create a reactor to represent the side of the cylinder filled with argon
 r1 = ct.IdealGasReactor(ar)
@@ -113,4 +113,4 @@
     plt.tight_layout()
     plt.show()
 else:
-    print("""To view a plot of these results, run this script with the option -plot""")
+    print("To view a plot of these results, run this script with the option --plot")

From f2c2ab4476f6ae7a062538fee7f27e85211de1b9 Mon Sep 17 00:00:00 2001
From: "Bryan W. Weber" <bryan.w.weber@gmail.com>
Date: Thu, 30 Jul 2020 14:08:48 -0400
Subject: [PATCH 07/18] [Reactor/1D] Fix gas phase production on surfaces

The calculation for the production of gas phase species from
surface reactions assumed that the gas phase species were stored at the
beginning of the rate-of-production array. This is only the case when
the gas ThermoPhase instance is the first phase in the Kinetics thermo
vector, which is not guaranteed to be the case.

It happens that XML input usually forced the gas phase to be the first
phase in the thermo vector, so everything worked out fine. This was
because the associated phase(s) for a surface phase had to be listed in
an XML file, and the XML initializer reads that list to fill the
Kinetics thermo vector.

In the YAML format, the associated phase does not need to be explicitly
listed. Instead, instances of the appropriate phases are passed to the
constructor when the InterfaceKinetics is created. The gas phase can
then come before or after the surface phase, meaning there is no
guarantee of the order of species.

This change checks for the starting index of the gas phase species in
the InterfaceKinetics species-length arrays to make sure that the
appropriate rates of production are added for the gas phase species.

Fixes #902, #877, #873
---
 src/oneD/Boundary1D.cpp | 12 +++++++++---
 src/zeroD/Reactor.cpp   |  3 ++-
 2 files changed, 11 insertions(+), 4 deletions(-)

diff --git a/src/oneD/Boundary1D.cpp b/src/oneD/Boundary1D.cpp
index fdb336cc311..170956a8851 100644
--- a/src/oneD/Boundary1D.cpp
+++ b/src/oneD/Boundary1D.cpp
@@ -679,12 +679,10 @@ void ReactingSurf1D::eval(size_t jg, double* xg, double* rg,
     size_t ioffset = m_kin->kineticsSpeciesIndex(0, m_surfindex);
 
     if (m_enabled) {
-        double maxx = -1.0;
         for (size_t k = 0; k < m_nsp; k++) {
             r[k] = m_work[k + ioffset] * m_sphase->size(k) * rs0;
             r[k] -= rdt*(x[k] - prevSoln(k,0));
             diag[k] = 1;
-            maxx = std::max(x[k], maxx);
         }
         r[0] = 1.0 - sum;
         diag[0] = 0;
@@ -707,9 +705,17 @@ void ReactingSurf1D::eval(size_t jg, double* xg, double* rg,
         double* xb = x - nc;
         rb[c_offset_T] = xb[c_offset_T] - m_temp; // specified T
         size_t nSkip = m_flow_left->rightExcessSpecies();
+        size_t l_offset = 0;
+        ThermoPhase* left_thermo = &m_flow_left->phase();
+        for (size_t nth = 0; nth < m_kin->nPhases(); nth++) {
+            if (&m_kin->thermo(nth) == left_thermo) {
+                l_offset = m_kin->kineticsSpeciesIndex(0, nth);
+                break;
+            }
+        }
         for (size_t nl = 0; nl < m_left_nsp; nl++) {
             if (nl != nSkip) {
-                rb[c_offset_Y+nl] += m_work[nl]*mwleft[nl];
+                rb[c_offset_Y+nl] += m_work[nl + l_offset]*mwleft[nl];
             }
         }
     }
diff --git a/src/zeroD/Reactor.cpp b/src/zeroD/Reactor.cpp
index 85fd70a3520..da3f985312b 100644
--- a/src/zeroD/Reactor.cpp
+++ b/src/zeroD/Reactor.cpp
@@ -296,9 +296,10 @@ double Reactor::evalSurfaces(double t, double* ydot)
         ydot[loc] = sum;
         loc += nk;
 
+        size_t bulkloc = kin->kineticsSpeciesIndex(m_thermo->speciesName(0));
         double wallarea = S->area();
         for (size_t k = 0; k < m_nsp; k++) {
-            m_sdot[k] += m_work[k]*wallarea;
+            m_sdot[k] += m_work[bulkloc + k] * wallarea;
             mdot_surf += m_sdot[k] * mw[k];
         }
     }

From 8b349cfeafab83bd7d5bd05336f61aee488c91ab Mon Sep 17 00:00:00 2001
From: "Bryan W. Weber" <bryan.w.weber@gmail.com>
Date: Fri, 31 Jul 2020 21:52:53 -0400
Subject: [PATCH 08/18] [1D] Add coverage_enabled getter

Adds a getter function for the coverage_enabled property on the
ReactingSurface1D Python class, and the corresponding C++ method.
---
 include/cantera/oneD/Boundary1D.h      | 4 ++++
 interfaces/cython/cantera/_cantera.pxd | 1 +
 interfaces/cython/cantera/onedim.pyx   | 2 ++
 3 files changed, 7 insertions(+)

diff --git a/include/cantera/oneD/Boundary1D.h b/include/cantera/oneD/Boundary1D.h
index 82dc4e68062..f1a7807b92a 100644
--- a/include/cantera/oneD/Boundary1D.h
+++ b/include/cantera/oneD/Boundary1D.h
@@ -299,6 +299,10 @@ class ReactingSurf1D : public Boundary1D
         m_enabled = docov;
     }
 
+    bool coverageEnabled() {
+        return m_enabled;
+    }
+
     virtual std::string componentName(size_t n) const;
 
     virtual void init();
diff --git a/interfaces/cython/cantera/_cantera.pxd b/interfaces/cython/cantera/_cantera.pxd
index 9a8dcf5eeb8..26ff56dcd3c 100644
--- a/interfaces/cython/cantera/_cantera.pxd
+++ b/interfaces/cython/cantera/_cantera.pxd
@@ -757,6 +757,7 @@ cdef extern from "cantera/oneD/Boundary1D.h":
         CxxRreactingSurf1D()
         void setKineticsMgr(CxxInterfaceKinetics*) except +translate_exception
         void enableCoverageEquations(cbool) except +translate_exception
+        cbool coverageEnabled()
 
 
 cdef extern from "cantera/oneD/StFlow.h":
diff --git a/interfaces/cython/cantera/onedim.pyx b/interfaces/cython/cantera/onedim.pyx
index 7a5ed20a38c..97de224169a 100644
--- a/interfaces/cython/cantera/onedim.pyx
+++ b/interfaces/cython/cantera/onedim.pyx
@@ -432,6 +432,8 @@ cdef class ReactingSurface1D(Boundary1D):
         """Controls whether or not to solve the surface coverage equations."""
         def __set__(self, value):
             self.surf.enableCoverageEquations(<cbool>value)
+        def __get__(self):
+            return self.surf.coverageEnabled()
 
 
 cdef class _FlowBase(Domain1D):

From dde41185aa219996ddd36496667012ac084c0b75 Mon Sep 17 00:00:00 2001
From: "Bryan W. Weber" <bryan.w.weber@gmail.com>
Date: Sat, 1 Aug 2020 20:49:42 -0400
Subject: [PATCH 09/18] [Examples] Fix sofc.py divide-by-zero warning

The switch to the YAML input file revealed that the calculation of the
anode and cathode currents in sofc.py relied on a particular order of
the phases. This change corrects that by finding the index of the
electron "species" in the anode and cathode phases.
---
 .../cantera/examples/surface_chemistry/sofc.py   | 16 ++++++++++------
 1 file changed, 10 insertions(+), 6 deletions(-)

diff --git a/interfaces/cython/cantera/examples/surface_chemistry/sofc.py b/interfaces/cython/cantera/examples/surface_chemistry/sofc.py
index a0c1e6523d2..5877ff1a0c3 100644
--- a/interfaces/cython/cantera/examples/surface_chemistry/sofc.py
+++ b/interfaces/cython/cantera/examples/surface_chemistry/sofc.py
@@ -120,14 +120,16 @@ def anode_curr(E):
     # get the species net production rates due to the anode-side TPB reaction
     # mechanism. The production rate array has the values for the neighbor
     # species in the order listed in the .yaml file, followed by the tpb phase.
-    # Since the first neighbor phase is the bulk metal, species 0 is the
-    # electron.
+    # The kinetics_species_index method finds the index of the species,
+    # accounting for the possibility of species being in different orders in the
+    # arrays.
     w = tpb_a.net_production_rates
+    electron_index = tpb_a.kinetics_species_index('electron')
 
     # the sign convention is that the current is positive when
     # electrons are being delivered to the anode - that is, it is positive
     # for fuel cell operation.
-    return ct.faraday * w[0] * TPB_length_per_area
+    return ct.faraday * w[electron_index] * TPB_length_per_area
 
 
 #####################################################################
@@ -167,13 +169,15 @@ def cathode_curr(E):
     # get the species net production rates due to the cathode-side TPB
     # reaction mechanism. The production rate array has the values for the
     # neighbor species in the order listed in the .yaml file, followed by the
-    # tpb phase. Since the first neighbor phase is the bulk metal, species 0
-    # is the electron.
+    # tpb phase. The kinetics_species_index method finds the index of the species,
+    # accounting for the possibility of species being in different orders in the
+    # arrays.
     w = tpb_c.net_production_rates
+    electron_index = tpb_c.kinetics_species_index('electron')
 
     # the sign convention is that the current is positive when electrons are
     # being drawn from the cathode (that is, negative production rate).
-    return -ct.faraday * w[0] * TPB_length_per_area
+    return -ct.faraday * w[electron_index] * TPB_length_per_area
 
 
 # initialization

From 68df649a222372a612b26d67c274a0150bfca417 Mon Sep 17 00:00:00 2001
From: "Bryan W. Weber" <bryan.w.weber@gmail.com>
Date: Sat, 1 Aug 2020 21:06:35 -0400
Subject: [PATCH 10/18] [Examples] Fix UserWarning in ic_engine.py

Matplotlib issues a UserWarning if the xticklabels are explicitly set
but the xticks are not explicitly set. We choose to set ticks every 360
degrees of crank angle, which corresponds to every 0.02 seconds in the
simulation.
---
 .../cantera/examples/reactors/ic_engine.py    | 25 +++++++++++--------
 1 file changed, 14 insertions(+), 11 deletions(-)

diff --git a/interfaces/cython/cantera/examples/reactors/ic_engine.py b/interfaces/cython/cantera/examples/reactors/ic_engine.py
index 13b75c8fefb..c1260cfd0ee 100644
--- a/interfaces/cython/cantera/examples/reactors/ic_engine.py
+++ b/interfaces/cython/cantera/examples/reactors/ic_engine.py
@@ -191,6 +191,7 @@ def ca_ticks(t):
 t = states.t
 
 # pressure and temperature
+xticks = np.arange(0, 0.18, 0.02)
 fig, ax = plt.subplots(nrows=2)
 ax[0].plot(t, states.P / 1.e5)
 ax[0].set_ylabel('$p$ [bar]')
@@ -199,7 +200,8 @@ def ca_ticks(t):
 ax[1].plot(t, states.T)
 ax[1].set_ylabel('$T$ [K]')
 ax[1].set_xlabel(r'$\phi$ [deg]')
-ax[1].set_xticklabels(ca_ticks(ax[1].get_xticks()))
+ax[1].set_xticks(xticks)
+ax[1].set_xticklabels(ca_ticks(xticks))
 plt.show()
 
 # p-V diagram
@@ -224,7 +226,8 @@ def ca_ticks(t):
 ax.legend(loc=0)
 ax.set_ylabel('[kW]')
 ax.set_xlabel(r'$\phi$ [deg]')
-ax.set_xticklabels(ca_ticks(ax.get_xticks()))
+ax.set_xticks(xticks)
+ax.set_xticklabels(ca_ticks(xticks))
 plt.show()
 
 # gas composition
@@ -236,7 +239,8 @@ def ca_ticks(t):
 ax.legend(loc=0)
 ax.set_ylabel('$X_i$ [-]')
 ax.set_xlabel(r'$\phi$ [deg]')
-ax.set_xticklabels(ca_ticks(ax.get_xticks()))
+ax.set_xticks(xticks)
+ax.set_xticklabels(ca_ticks(xticks))
 plt.show()
 
 ######################################################################
@@ -245,22 +249,21 @@ def ca_ticks(t):
 
 # heat release
 Q = trapz(states.heat_release_rate * states.V, t)
-print('{:45s}{:>4.1f} kW'.format('Heat release rate per cylinder (estimate):',
-                                 Q / t[-1] / 1000.))
+output_str = '{:45s}{:>4.1f} {}'
+print(output_str.format('Heat release rate per cylinder (estimate):',
+                        Q / t[-1] / 1000., 'kW'))
 
 # expansion power
 W = trapz(states.dWv_dt, t)
-print('{:45s}{:>4.1f} kW'.format('Expansion power per cylinder (estimate):',
-                                 W / t[-1] / 1000.))
+print(output_str.format('Expansion power per cylinder (estimate):',
+                        W / t[-1] / 1000., 'kW'))
 
 # efficiency
 eta = W / Q
-print('{:45s}{:>4.1f} %'.format('Efficiency (estimate):',
-                                eta * 100.))
+print(output_str.format('Efficiency (estimate):', eta * 100., '%'))
 
 # CO emissions
 MW = states.mean_molecular_weight
 CO_emission = trapz(MW * states.mdot_out * states('CO').X[:, 0], t)
 CO_emission /= trapz(MW * states.mdot_out, t)
-print('{:45s}{:>4.1f} ppm'.format('CO emission (estimate):',
-                                  CO_emission * 1.e6))
+print(output_str.format('CO emission (estimate):', CO_emission * 1.e6, 'ppm'))

From b727b1d83013354c12a2c75601478746464cc778 Mon Sep 17 00:00:00 2001
From: "Bryan W. Weber" <bryan.w.weber@gmail.com>
Date: Sat, 1 Aug 2020 22:16:50 -0400
Subject: [PATCH 11/18] [Fortran] Add extra_inc_dirs to compile Fortran sample

One of the Fortran samples needs to include the extra_inc_dirs variable
so that system header files in non-standard locations will be found.
---
 samples/f77/SConscript | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/samples/f77/SConscript b/samples/f77/SConscript
index 0cd943c15d3..eb589c89b83 100644
--- a/samples/f77/SConscript
+++ b/samples/f77/SConscript
@@ -10,7 +10,8 @@ samples = [('ctlib', ['ctlib.f']),
            ('isentropic', ['isentropic.f'])]
 
 ftn_demo = localenv.Object('demo_ftnlib.cpp',
-                           CPPPATH=['#include', localenv['boost_inc_dir']])
+                           CPPPATH=['#include', localenv['boost_inc_dir'],
+                                    localenv['extra_inc_dirs']])
 for program_name, fortran_sources in samples:
     buildSample(localenv.Program, program_name,
                 fortran_sources + ftn_demo,

From 3578c0378352c91b3c9ce07296991ad23c044b77 Mon Sep 17 00:00:00 2001
From: "Bryan W. Weber" <bryan.w.weber@gmail.com>
Date: Sat, 1 Aug 2020 22:19:47 -0400
Subject: [PATCH 12/18] [ReactionPath] Fix IO warning about unclosed file

Use pathlib to write the text content to a file in write_dot. This
automatically closes the file handle after the text is written.

Also modify the reaction_path.py example to use pathlib and subprocess.
These are available since at least Python 3.5 and represent modern
best-practices in Python scripts.
---
 .../cython/cantera/examples/kinetics/reaction_path.py    | 9 +++++----
 interfaces/cython/cantera/reactionpath.pyx               | 4 +++-
 2 files changed, 8 insertions(+), 5 deletions(-)

diff --git a/interfaces/cython/cantera/examples/kinetics/reaction_path.py b/interfaces/cython/cantera/examples/kinetics/reaction_path.py
index 629ffda619e..544f84c9000 100644
--- a/interfaces/cython/cantera/examples/kinetics/reaction_path.py
+++ b/interfaces/cython/cantera/examples/kinetics/reaction_path.py
@@ -9,8 +9,9 @@
 Requires: cantera >= 2.5.0
 """
 
-import os
+from subprocess import run
 import sys
+from pathlib import Path
 
 import cantera as ct
 
@@ -33,14 +34,14 @@
 
 dot_file = 'rxnpath.dot'
 img_file = 'rxnpath.png'
-img_path = os.path.join(os.getcwd(), img_file)
+img_path = Path.cwd().joinpath(img_file)
 
 diagram.write_dot(dot_file)
 print(diagram.get_data())
 
-print("Wrote graphviz input file to '{0}'.".format(os.path.join(os.getcwd(), dot_file)))
+print("Wrote graphviz input file to '{0}'.".format(Path.cwd().joinpath(dot_file)))
 
-os.system('dot {0} -Tpng -o{1} -Gdpi=200'.format(dot_file, img_file))
+run('dot {0} -Tpng -o{1} -Gdpi=200'.format(dot_file, img_file).split())
 print("Wrote graphviz output file to '{0}'.".format(img_path))
 
 if "-view" in sys.argv:
diff --git a/interfaces/cython/cantera/reactionpath.pyx b/interfaces/cython/cantera/reactionpath.pyx
index afd1929f8a4..d23f1789843 100644
--- a/interfaces/cython/cantera/reactionpath.pyx
+++ b/interfaces/cython/cantera/reactionpath.pyx
@@ -1,6 +1,8 @@
 # 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.
 
+from pathlib import Path
+
 cdef class ReactionPathDiagram:
     def __cinit__(self, *args, **kwargs):
         self._log = new CxxStringStream()
@@ -158,7 +160,7 @@ cdef class ReactionPathDiagram:
         Write the reaction path diagram formatted for use by Graphviz's 'dot'
         program to the file named *filename*.
         """
-        open(filename, 'wb').write(self.get_dot().encode('utf-8'))
+        Path(filename).write_text(self.get_dot())
 
     def get_data(self):
         """

From 7ff4af2060d02b7045742b3d508375035692a23e Mon Sep 17 00:00:00 2001
From: "Bryan W. Weber" <bryan.w.weber@gmail.com>
Date: Sat, 1 Aug 2020 22:28:16 -0400
Subject: [PATCH 13/18] [Examples] Properly close multiprocessing.Pool

The multiprocess.Pool object must be closed properly, or the process can
hang according to the Python docs. The recommended method for short code
blocks is to use the context manager. The format of the arguments to
Pool is chosen to allow the last line to be de-dented to remove
ambiguity about the definition of the context manager and the content.
---
 .../transport/multiprocessing_viscosity.py      | 17 ++++++++---------
 1 file changed, 8 insertions(+), 9 deletions(-)

diff --git a/interfaces/cython/cantera/examples/transport/multiprocessing_viscosity.py b/interfaces/cython/cantera/examples/transport/multiprocessing_viscosity.py
index 4f23ae0b318..835a9178896 100644
--- a/interfaces/cython/cantera/examples/transport/multiprocessing_viscosity.py
+++ b/interfaces/cython/cantera/examples/transport/multiprocessing_viscosity.py
@@ -55,15 +55,14 @@ def parallel(mech, predicate, nProcs, nTemps):
     """
     P = ct.one_atm
     X = 'CH4:1.0, O2:1.0, N2:3.76'
-    pool = multiprocessing.Pool(processes=nProcs,
-                                initializer=init_process,
-                                initargs=(mech,))
-
-    y = pool.map(predicate,
-                 zip(itertools.repeat(mech),
-                     np.linspace(300, 900, nTemps),
-                     itertools.repeat(P),
-                     itertools.repeat(X)))
+    with multiprocessing.Pool(
+        processes=nProcs, initializer=init_process, initargs=(mech,)
+    ) as pool:
+        y = pool.map(predicate,
+                     zip(itertools.repeat(mech),
+                         np.linspace(300, 900, nTemps),
+                         itertools.repeat(P),
+                         itertools.repeat(X)))
     return y
 
 

From 9c3c7cc2332e4216173be1db2e99c10be95bfa75 Mon Sep 17 00:00:00 2001
From: "Bryan W. Weber" <bryan.w.weber@gmail.com>
Date: Sun, 2 Aug 2020 07:52:40 -0400
Subject: [PATCH 14/18] [Examples] Fix FutureWarning in diamond_cvd.py

pandas v1.1.0 issues a FutureWarning when plotting single columns from a
DataFrame using the Matplotlib pyplot API. This can be avoided by using
the pandas plotting API instead.
---
 .../examples/surface_chemistry/diamond_cvd.py      | 14 ++++----------
 1 file changed, 4 insertions(+), 10 deletions(-)

diff --git a/interfaces/cython/cantera/examples/surface_chemistry/diamond_cvd.py b/interfaces/cython/cantera/examples/surface_chemistry/diamond_cvd.py
index 0b75c08d87e..ecf7d2301b4 100644
--- a/interfaces/cython/cantera/examples/surface_chemistry/diamond_cvd.py
+++ b/interfaces/cython/cantera/examples/surface_chemistry/diamond_cvd.py
@@ -9,7 +9,7 @@
 role in diamond CVD, and this example computes the growth rate and surface
 coverages as a function of [H] at the surface for fixed temperature and [CH3].
 
-Requires: cantera >= 2.5.0, pandas >= 0.21.0, matplotlib >= 2.0
+Requires: cantera >= 2.5.0, pandas >= 0.25.0, matplotlib >= 2.0
 """
 
 import csv
@@ -58,19 +58,13 @@
     import pandas as pd
     data = pd.read_csv('diamond.csv')
 
-    plt.figure()
-    plt.plot(data['H mole Fraction'], data['Growth Rate (microns/hour)'])
+    data.plot(x="H mole Fraction", y="Growth Rate (microns/hour)", legend=False)
     plt.xlabel('H Mole Fraction')
     plt.ylabel('Growth Rate (microns/hr)')
     plt.show()
 
-    plt.figure()
-    for name in data:
-        if name.startswith(('H mole', 'Growth')):
-            continue
-        plt.plot(data['H mole Fraction'], data[name], label=name)
-
-    plt.legend()
+    names = [name for name in data.columns if not name.startswith(('H mole', 'Growth'))]
+    data.plot(x='H mole Fraction', y=names, legend=True)
     plt.xlabel('H Mole Fraction')
     plt.ylabel('Coverage')
     plt.show()

From 3e6edb8b55f192d968d0b63ccf785820e6afc700 Mon Sep 17 00:00:00 2001
From: Ingmar Schoegl <ischoegl@lsu.edu>
Date: Mon, 10 Aug 2020 07:59:23 -0500
Subject: [PATCH 15/18] [unittests] Fix ch4_ion.yaml

The content of ch4_ion.yaml now matches ch4_ion.cti (the file was re-created
using cti2yaml)
---
 test/data/ch4_ion.yaml | 207 ++++++++++++++++++++++++++++++-----------
 1 file changed, 151 insertions(+), 56 deletions(-)

diff --git a/test/data/ch4_ion.yaml b/test/data/ch4_ion.yaml
index 617385a5ca0..eaadccf8499 100644
--- a/test/data/ch4_ion.yaml
+++ b/test/data/ch4_ion.yaml
@@ -1,102 +1,186 @@
+generator: cti2yaml
+cantera-version: 2.5.0a4
+date: Mon, 10 Aug 2020 12:55:00 +0000
+input-files: [ch4_ion.cti]
+
 units: {length: cm, quantity: mol, activation-energy: cal/mol}
 
 phases:
 - name: gas
   thermo: ideal-gas
+  elements: [O, H, C, N, E]
+  species:
+  - gri30.yaml/species: [H, O, OH, HO2, H2O2, C, CH, CH2, CH2(S), CH3, HCO,
+      CH2O, CH3O]
+  - species: [H2, O2, H2O, CH4, CO, CO2, N2, HCO+, H3O+, E, O2-]
+  skip-undeclared-third-bodies: true
+  kinetics: gas
+  reactions:
+  - gri30.yaml/reactions: declared-species
+  - reactions: declared-species
   transport: ionized-gas
-  species: [O2, H2O, CO2, N2, H3O+, E, O2-]
-  state: {T: 300, P: 1 atm}
+  state:
+    T: 300.0
+    P: 1.01325e+05
 
 species:
+- name: H2
+  composition: {H: 2}
+  thermo:
+    model: NASA7
+    temperature-ranges: [200.0, 1000.0, 3500.0]
+    data:
+    - [2.34433112, 7.98052075e-03, -1.9478151e-05, 2.01572094e-08, -7.37611761e-12,
+      -917.935173, 0.683010238]
+    - [3.3372792, -4.94024731e-05, 4.99456778e-07, -1.79566394e-10, 2.00255376e-14,
+      -950.158922, -3.20502331]
+  transport:
+    model: gas
+    geometry: linear
+    diameter: 2.92
+    well-depth: 38.0
+    polarizability: 0.455
+    rotational-relaxation: 280.0
+  note: TPIS78
 - name: O2
   composition: {O: 2}
   thermo:
     model: NASA7
-    temperature-ranges: [200, 1000, 3500]
+    temperature-ranges: [200.0, 1000.0, 3500.0]
     data:
-    - [3.78245636E+00, -2.99673416E-03, 9.84730201E-06, -9.68129509E-09,
-       3.24372837E-12, -1.06394356E+03, 3.65767573E+00]
-    - [3.28253784E+00, 1.48308754E-03, -7.57966669E-07, 2.09470555E-10,
-       -2.16717794E-14, -1.08845772E+03, 5.45323129E+00]
+    - [3.78245636, -2.99673416e-03, 9.84730201e-06, -9.68129509e-09, 3.24372837e-12,
+      -1063.94356, 3.65767573]
+    - [3.28253784, 1.48308754e-03, -7.57966669e-07, 2.09470555e-10, -2.16717794e-14,
+      -1088.45772, 5.45323129]
   transport:
     model: gas
     geometry: linear
     diameter: 3.46
-    well-depth: 107.40
+    well-depth: 107.4
     polarizability: 1.131
-    rotational-relaxation: 3.80
-    note: TPIS89
-
+    rotational-relaxation: 3.8
+  note: TPIS89
 - name: H2O
   composition: {H: 2, O: 1}
   thermo:
     model: NASA7
-    temperature-ranges: [200, 1000, 3500]
+    temperature-ranges: [200.0, 1000.0, 3500.0]
     data:
-    - [4.19864056E+00, -2.03643410E-03, 6.52040211E-06, -5.48797062E-09,
-       1.77197817E-12, -3.02937267E+04, -8.49032208E-01]
-    - [3.03399249E+00, 2.17691804E-03, -1.64072518E-07, -9.70419870E-11,
-       1.68200992E-14, -3.00042971E+04, 4.96677010E+00]
+    - [4.19864056, -2.0364341e-03, 6.52040211e-06, -5.48797062e-09, 1.77197817e-12,
+      -3.02937267e+04, -0.849032208]
+    - [3.03399249, 2.17691804e-03, -1.64072518e-07, -9.7041987e-11, 1.68200992e-14,
+      -3.00042971e+04, 4.9667701]
   transport:
     model: gas
     geometry: nonlinear
-    diameter: 2.60
-    well-depth: 572.40
+    diameter: 2.6
+    well-depth: 572.4
     dipole: 1.84
     polarizability: 1.053
-    rotational-relaxation: 4.00
-    note: L 8/89
-
+    rotational-relaxation: 4.0
+  note: L 8/89
+- name: CH4
+  composition: {C: 1, H: 4}
+  thermo:
+    model: NASA7
+    temperature-ranges: [200.0, 1000.0, 3500.0]
+    data:
+    - [5.14987613, -0.0136709788, 4.91800599e-05, -4.84743026e-08, 1.66693956e-11,
+      -1.02466476e+04, -4.64130376]
+    - [0.074851495, 0.0133909467, -5.73285809e-06, 1.22292535e-09, -1.0181523e-13,
+      -9468.34459, 18.437318]
+  transport:
+    model: gas
+    geometry: nonlinear
+    diameter: 3.75
+    well-depth: 141.4
+    polarizability: 2.6
+    rotational-relaxation: 13.0
+  note: L 8/88
+- name: CO
+  composition: {C: 1, O: 1}
+  thermo:
+    model: NASA7
+    temperature-ranges: [200.0, 1000.0, 3500.0]
+    data:
+    - [3.57953347, -6.1035368e-04, 1.01681433e-06, 9.07005884e-10, -9.04424499e-13,
+      -1.4344086e+04, 3.50840928]
+    - [2.71518561, 2.06252743e-03, -9.98825771e-07, 2.30053008e-10, -2.03647716e-14,
+      -1.41518724e+04, 7.81868772]
+  transport:
+    model: gas
+    geometry: linear
+    diameter: 3.65
+    well-depth: 98.1
+    polarizability: 1.95
+    rotational-relaxation: 1.8
+  note: TPIS79
 - name: CO2
   composition: {C: 1, O: 2}
   thermo:
     model: NASA7
-    temperature-ranges: [200, 1000, 3500]
+    temperature-ranges: [200.0, 1000.0, 3500.0]
     data:
-    - [2.35677352E+00, 8.98459677E-03, -7.12356269E-06, 2.45919022E-09,
-       -1.43699548E-13, -4.83719697E+04, 9.90105222E+00]
-    - [3.85746029E+00, 4.41437026E-03, -2.21481404E-06, 5.23490188E-10,
-       -4.72084164E-14, -4.87591660E+04, 2.27163806E+00]
+    - [2.35677352, 8.98459677e-03, -7.12356269e-06, 2.45919022e-09, -1.43699548e-13,
+      -4.83719697e+04, 9.90105222]
+    - [3.85746029, 4.41437026e-03, -2.21481404e-06, 5.23490188e-10, -4.72084164e-14,
+      -4.8759166e+04, 2.27163806]
   transport:
     model: gas
     geometry: linear
     diameter: 3.76
-    well-depth: 244.00
+    well-depth: 244.0
     polarizability: 2.65
-    rotational-relaxation: 2.10
-    note: L 7/88
-
+    rotational-relaxation: 2.1
+  note: L 7/88
 - name: N2
   composition: {N: 2}
   thermo:
     model: NASA7
-    temperature-ranges: [300, 1000, 5000]
+    temperature-ranges: [300.0, 1000.0, 5000.0]
     data:
-    - [3.29867700E+00, 1.40824040E-03, -3.96322200E-06, 5.64151500E-09,
-       -2.44485400E-12, -1.02089990E+03, 3.95037200E+00]
-    - [2.92664000E+00, 1.48797680E-03, -5.68476000E-07, 1.00970380E-10,
-       -6.75335100E-15, -9.22797700E+02, 5.98052800E+00]
+    - [3.298677, 1.4082404e-03, -3.963222e-06, 5.641515e-09, -2.444854e-12,
+      -1020.8999, 3.950372]
+    - [2.92664, 1.4879768e-03, -5.68476e-07, 1.0097038e-10, -6.753351e-15,
+      -922.7977, 5.980528]
   transport:
     model: gas
     geometry: linear
     diameter: 3.62
     well-depth: 97.53
     polarizability: 1.76
-    rotational-relaxation: 4.00
+    rotational-relaxation: 4.0
     dispersion-coefficient: 2.995
     quadrupole-polarizability: 3.602
   note: '121286'
-
+- name: HCO+
+  composition: {H: 1, C: 1, O: 1, E: -1}
+  thermo:
+    model: NASA7
+    temperature-ranges: [300.0, 1000.0, 5000.0]
+    data:
+    - [2.4739736, 8.671559e-03, -1.00315e-05, 6.7170527e-09, -1.7872674e-12,
+      9.9146608e+04, 8.17571187]
+    - [3.741188, 3.3441517e-03, -1.2397121e-06, 2.1189388e-10, -1.370415e-14,
+      9.8884078e+04, 2.07861357]
+  transport:
+    model: gas
+    geometry: linear
+    diameter: 3.59
+    well-depth: 498.0
+    polarizability: 1.356
+    dispersion-coefficient: 0.416
+  note: J12/70
 - name: H3O+
   composition: {H: 3, O: 1, E: -1}
   thermo:
     model: NASA7
-    temperature-ranges: [298.15, 1000, 6000]
+    temperature-ranges: [298.15, 1000.0, 6000.0]
     data:
-    - [3.79295270E+00, -9.10854000E-04, 1.16363549E-05, -1.21364887E-08,
-       4.26159663E-12, 7.07512401E+04, 1.47156856E+00]
-    - [2.49647716E+00, 5.72844920E-03, -1.83953281E-06, 2.73577439E-10,
-       -1.54093985E-14, 7.09729113E+04, 7.45850779E+00]
+    - [3.7929527, -9.10854e-04, 1.16363549e-05, -1.21364887e-08, 4.26159663e-12,
+      7.07512401e+04, 1.47156856]
+    - [2.49647716, 5.7284492e-03, -1.83953281e-06, 2.73577439e-10, -1.54093985e-14,
+      7.09729113e+04, 7.45850779]
   transport:
     model: gas
     geometry: nonlinear
@@ -104,39 +188,50 @@ species:
     well-depth: 106.2
     dipole: 1.417
     polarizability: 0.897
-    rotational-relaxation: 0.0
-    note: TPIS89
-
+  note: TPIS89
 - name: O2-
   composition: {E: 1, O: 2}
   thermo:
     model: NASA7
-    temperature-ranges: [298.15, 1000.00, 6000]
+    temperature-ranges: [298.15, 1000.0, 6000.0]
     data:
-    - [3.66442522E+00, -9.28741138E-04, 6.45477082E-06, -7.7470338E-09,
-       2.93332662E-12, -6.87076983E+03, 4.35140681E+00]
-    - [3.95666294E+00, 5.98141823E-04, -2.12133905E-07, 3.63267581E-11,
-       -2.24989228E-15, -7.06287229E+03, 2.27871017E+00]
+    - [3.66442522, -9.28741138e-04, 6.45477082e-06, -7.7470338e-09, 2.93332662e-12,
+      -6870.76983, 4.35140681]
+    - [3.95666294, 5.98141823e-04, -2.12133905e-07, 3.63267581e-11, -2.24989228e-15,
+      -7062.87229, 2.27871017]
   transport:
     model: gas
     geometry: linear
     diameter: 3.33
     well-depth: 136.5
     polarizability: 1.424
-    note: L4/89
-
+  note: L4/89
 - name: E
   composition: {E: 1}
   thermo:
     model: NASA7
-    temperature-ranges: [200, 3000]
+    temperature-ranges: [200.0, 1000.0, 6000.0]
     data:
-    - [2.5E+00, 0.0, 0.0, 0.0, 0.0, -7.45375000E+02, -1.17246902E+01]
+    - [2.5, 0.0, 0.0, 0.0, 0.0, -745.375, -11.7246902]
+    - [2.5, 0.0, 0.0, 0.0, 0.0, -745.375, -11.7246902]
   transport:
     model: gas
     geometry: atom
     diameter: 2.05
     well-depth: 145.0
     polarizability: 0.667
-    rotational-relaxation: 0.0
-    note: gas L10/92
+  note: gas L10/92
+
+reactions:
+- equation: CH + O => HCO+ + E  # Reaction 1
+  rate-constant: {A: 2.51e+11, b: 0.0, Ea: 1700}
+- equation: HCO+ + H2O => H3O+ + CO  # Reaction 2
+  rate-constant: {A: 1.51e+15, b: 0.0, Ea: 0.0}
+- equation: H3O+ + E => H2O + H  # Reaction 3
+  rate-constant: {A: 2.29e+18, b: -0.5, Ea: 0.0}
+- equation: H3O+ + E => OH + H + H  # Reaction 4
+  rate-constant: {A: 7.95e+21, b: -1.4, Ea: 0.0}
+- equation: H3O+ + E => H2 + OH  # Reaction 5
+  rate-constant: {A: 1.25e+19, b: -0.5, Ea: 0.0}
+- equation: H3O+ + E =>  O + H2 + H  # Reaction 6
+  rate-constant: {A: 6.0e+17, b: -0.3, Ea: 0.0}

From 0767e5453d8a63bc4c8bfdede85a7fa08dfb1f86 Mon Sep 17 00:00:00 2001
From: Ingmar Schoegl <ischoegl@lsu.edu>
Date: Mon, 10 Aug 2020 08:02:27 -0500
Subject: [PATCH 16/18] [examples] Apply band-aid fix to ion_burner_flame.py

A reduction of domain size makes the example more stable.
---
 interfaces/cython/cantera/examples/onedim/ion_burner_flame.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/interfaces/cython/cantera/examples/onedim/ion_burner_flame.py b/interfaces/cython/cantera/examples/onedim/ion_burner_flame.py
index cb7c744a559..e480dffc91c 100644
--- a/interfaces/cython/cantera/examples/onedim/ion_burner_flame.py
+++ b/interfaces/cython/cantera/examples/onedim/ion_burner_flame.py
@@ -9,7 +9,7 @@
 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 = 0.05  # m
 loglevel = 1  # amount of diagnostic output (0 to 5)
 
 gas = ct.Solution('gri30_ion.yaml')

From 148a6c7a7723a752ed7ce709616b5ee45f0d3086 Mon Sep 17 00:00:00 2001
From: Ingmar Schoegl <ischoegl@lsu.edu>
Date: Mon, 10 Aug 2020 13:00:23 -0500
Subject: [PATCH 17/18] [1D] Fix export of _other columns for IonFlow based
 classes

---
 interfaces/cython/cantera/onedim.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/interfaces/cython/cantera/onedim.py b/interfaces/cython/cantera/onedim.py
index aee12cb5bb3..3232f4e1466 100644
--- a/interfaces/cython/cantera/onedim.py
+++ b/interfaces/cython/cantera/onedim.py
@@ -51,7 +51,7 @@ def other_components(self, domain=None):
         if isinstance(dom, Inlet1D):
             return tuple([e for e in self._other
                           if e not in {'grid', 'lambda', 'eField'}])
-        elif isinstance(dom, IdealGasFlow):
+        elif isinstance(dom, (IdealGasFlow, IonFlow)):
             return self._other
         else:
             return ()

From 42fbd1d61ac19cc2f07da2b583a837bd7ea93eeb Mon Sep 17 00:00:00 2001
From: "Bryan W. Weber" <bryan.w.weber@gmail.com>
Date: Tue, 28 Jul 2020 20:33:04 -0400
Subject: [PATCH 18/18] [CI] Run the Python examples using Bash

---
 .github/workflows/main.yml | 38 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 38 insertions(+)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 7f1c8d127e1..8b060ca8147 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -174,6 +174,44 @@ jobs:
       - name: Test Cantera
         run: scons test
 
+  run-examples:
+    name: Run the Python examples using bash
+    runs-on: ubuntu-18.04
+    steps:
+      - uses: actions/checkout@v2
+        name: Checkout the repository
+        with:
+          submodules: recursive
+      - name: Setup Python
+        uses: actions/setup-python@v1
+        with:
+          python-version: '3.8'
+          architecture: x64
+      - name: Install Apt dependencies
+        run: sudo apt-get install libboost-dev gfortran graphviz liblapack-dev libblas-dev
+      - name: Upgrade pip
+        run: python3 -m pip install -U pip setuptools wheel
+      - name: Install Python dependencies
+        run: python3 -m pip install ruamel.yaml scons numpy cython h5py pandas matplotlib scipy
+      - name: Build Cantera
+        run: python3 `which scons` build -j2
+      - name: Run the examples
+        # See https://unix.stackexchange.com/a/392973 for an explanation of the -exec part
+        run: |
+          find interfaces/cython/cantera/examples -type f -iname "*.py" \
+          -exec sh -c 'for n; do echo "$n" | tee -a results.txt && python3 "$n" >> results.txt || exit 1; done' sh {} +
+        env:
+          PYTHONPATH: build/python
+          PYTHONWARNINGS: error
+          MPLBACKEND: Agg
+      - name: Save the results file for inspection
+        uses: actions/upload-artifact@v2
+        with:
+          path: results.txt
+        # Run this step if the job was successful or failed, but not if it was cancelled
+        # Using always() would run this step if the job was cancelled as well.
+        if: failure() || success()
+
   multiple-sundials:
     name: Sundials ${{ matrix.sundials-ver }}
     runs-on: ubuntu-latest