Fix examples

.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

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
@@ -26,22 +26,22 @@ 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
   lattice oxygen, and an oxygen vacancy. Again, the density is a
   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

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) {

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.

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

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();

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
  */

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":

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)
 
 

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:

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
 

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))

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

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')