Use YAML for saving and loading 1D flame simulations

include/cantera/base/AnyMap.h

@@ -659,6 +659,9 @@ class AnyMap : public AnyBase
     static bool addOrderingRules(const std::string& objectType,
                                  const std::vector<std::vector<std::string>>& specs);
 
+    //! Remove the specified file from the input cache if it is present
+    static void clearCachedFile(const std::string& filename);
+
 private:
     //! The stored data
     std::unordered_map<std::string, AnyValue> m_data;

include/cantera/oneD/Boundary1D.h

@@ -133,6 +133,8 @@ class Inlet1D : public Boundary1D
                       integer* diagg, double rdt);
     virtual XML_Node& save(XML_Node& o, const double* const soln);
     virtual void restore(const XML_Node& dom, double* soln, int loglevel);
+    virtual AnyMap serialize(const double* soln) const;
+    virtual void restore(const AnyMap& state, double* soln, int loglevel);
 
 protected:
     int m_ilr;
@@ -163,6 +165,7 @@ class Empty1D : public Boundary1D
 
     virtual XML_Node& save(XML_Node& o, const double* const soln);
     virtual void restore(const XML_Node& dom, double* soln, int loglevel);
+    virtual AnyMap serialize(const double* soln) const;
 };
 
 /**
@@ -184,6 +187,7 @@ class Symm1D : public Boundary1D
 
     virtual XML_Node& save(XML_Node& o, const double* const soln);
     virtual void restore(const XML_Node& dom, double* soln, int loglevel);
+    virtual AnyMap serialize(const double* soln) const;
 };
 
 
@@ -205,6 +209,7 @@ class Outlet1D : public Boundary1D
 
     virtual XML_Node& save(XML_Node& o, const double* const soln);
     virtual void restore(const XML_Node& dom, double* soln, int loglevel);
+    virtual AnyMap serialize(const double* soln) const;
 };
 
 
@@ -233,6 +238,8 @@ class OutletRes1D : public Boundary1D
                       integer* diagg, double rdt);
     virtual XML_Node& save(XML_Node& o, const double* const soln);
     virtual void restore(const XML_Node& dom, double* soln, int loglevel);
+    virtual AnyMap serialize(const double* soln) const;
+    virtual void restore(const AnyMap& state, double* soln, int loglevel);
 
 protected:
     size_t m_nsp;
@@ -261,6 +268,8 @@ class Surf1D : public Boundary1D
 
     virtual XML_Node& save(XML_Node& o, const double* const soln);
     virtual void restore(const XML_Node& dom, double* soln, int loglevel);
+    virtual AnyMap serialize(const double* soln) const;
+    virtual void restore(const AnyMap& state, double* soln, int loglevel);
 
     virtual void showSolution_s(std::ostream& s, const double* x);
 
@@ -296,6 +305,8 @@ class ReactingSurf1D : public Boundary1D
 
     virtual XML_Node& save(XML_Node& o, const double* const soln);
     virtual void restore(const XML_Node& dom, double* soln, int loglevel);
+    virtual AnyMap serialize(const double* soln) const;
+    virtual void restore(const AnyMap& state, double* soln, int loglevel);
 
     virtual void _getInitialSoln(double* x) {
         m_sphase->getCoverages(x);

include/cantera/oneD/Domain1D.h

@@ -27,6 +27,7 @@ const int cPorousType = 109;
 class MultiJac;
 class OneDim;
 class Refiner;
+class AnyMap;
 class XML_Node;
 
 /**
@@ -340,6 +341,21 @@ class Domain1D
      */
     virtual void restore(const XML_Node& dom, doublereal* soln, int loglevel);
 
+    //! Save the state of this domain as an AnyMap
+    /*!
+     * @param soln local solution vector for this domain
+     */
+    virtual AnyMap serialize(const double* soln) const;
+
+    //! Restore the solution for this domain from an AnyMap
+    /*!
+     * @param[in]  state AnyMap defining the state of this domain
+     * @param[out] soln Value of the solution vector, local to this domain
+     * @param[in]  loglevel 0 to suppress all output; 1 to show warnings; 2 for
+     *      verbose output
+     */
+    virtual void restore(const AnyMap& state, double* soln, int loglevel);
+
     size_t size() const {
         return m_nv*m_points;
     }
@@ -511,7 +527,6 @@ class Domain1D
 
     //! Identity tag for the domain
     std::string m_id;
-    std::string m_desc;
     std::unique_ptr<Refiner> m_refiner;
     std::vector<std::string> m_name;
     int m_bw;

include/cantera/oneD/IonFlow.h

@@ -36,6 +36,7 @@ class IonFlow : public StFlow
     virtual void setSolvingStage(const size_t phase);
 
     virtual void resize(size_t components, size_t points);
+    virtual bool componentActive(size_t n) const;
 
     virtual void _finalize(const double* x);
     //! set to solve electric field on a point

include/cantera/oneD/OneDim.h

@@ -16,6 +16,7 @@ namespace Cantera
 
 class Func1;
 class MultiNewton;
+class AnyMap;
 
 /**
  * Container class for multiple-domain 1D problems. Each domain is
@@ -227,6 +228,8 @@ class OneDim
     void save(const std::string& fname, std::string id,
               const std::string& desc, doublereal* sol, int loglevel);
 
+    AnyMap serialize(const double* soln) const;
+
     // options
     void setMinTimeStep(doublereal tmin) {
         m_tmin = tmin;

include/cantera/oneD/StFlow.h

@@ -137,6 +137,9 @@ class StFlow : public Domain1D
 
     virtual size_t componentIndex(const std::string& name) const;
 
+    //! Returns true if the specified component is an active part of the solver state
+    virtual bool componentActive(size_t n) const;
+
     //! Print the solution.
     virtual void showSolution(const doublereal* x);
 
@@ -155,6 +158,9 @@ class StFlow : public Domain1D
     virtual void restore(const XML_Node& dom, doublereal* soln,
                          int loglevel);
 
+    virtual AnyMap serialize(const double* soln) const;
+    virtual void restore(const AnyMap& state, double* soln, int loglevel);
+
     //! Set flow configuration for freely-propagating flames, using an internal
     //! point with a fixed temperature as the condition to determine the inlet
     //! mass flux.
@@ -173,7 +179,7 @@ class StFlow : public Domain1D
     //! Return the type of flow domain being represented, either "Free Flame" or
     //! "Axisymmetric Stagnation".
     //! @see setFreeFlow setAxisymmetricFlow
-    virtual std::string flowType() {
+    virtual std::string flowType() const {
         if (m_type == cFreeFlow) {
             return "Free Flame";
         } else if (m_type == cAxisymmetricStagnationFlow) {

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

@@ -34,7 +34,7 @@
     f.write_hdf('adiabatic_flame.h5', group='mix', mode='w',
                 description='solution with mixture-averaged transport')
 except ImportError:
-    f.save('adiabatic_flame.xml', 'mix',
+    f.save('adiabatic_flame.yaml', 'mix',
            'solution with mixture-averaged transport')
 
 f.show_solution()
@@ -49,7 +49,7 @@
     f.write_hdf('adiabatic_flame.h5', group='multi',
                 description='solution with multicomponent transport')
 except ImportError:
-    f.save('adiabatic_flame.xml', 'multi',
+    f.save('adiabatic_flame.yaml', 'multi',
            'solution with multicomponent transport')
 
 # write the velocity, temperature, density, and mole fractions to a CSV file

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

@@ -28,7 +28,7 @@
     f.write_hdf('burner_flame.h5', group='mix', mode='w',
                 description='solution with mixture-averaged transport')
 except ImportError:
-    f.save('burner_flame.xml', 'mix', 'solution with mixture-averaged transport')
+    f.save('burner_flame.yaml', 'mix', 'solution with mixture-averaged transport')
 
 f.transport_model = 'Multi'
 f.solve(loglevel)  # don't use 'auto' on subsequent solves
@@ -37,6 +37,6 @@
     f.write_hdf('burner_flame.h5', group='multi',
                 description='solution with multicomponent transport')
 except ImportError:
-    f.save('burner_flame.xml', 'multi', 'solution with multicomponent transport')
+    f.save('burner_flame.yaml', 'multi', 'solution with multicomponent transport')
 
 f.write_csv('burner_flame.csv', quiet=False)

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

@@ -54,7 +54,7 @@
     # save to HDF container file if h5py is installed
     f.write_hdf('diffusion_flame.h5', mode='w')
 except ImportError:
-    f.save('diffusion_flame.xml')
+    f.save('diffusion_flame.yaml')
 
 # write the velocity, temperature, and mole fractions to a CSV file
 f.write_csv('diffusion_flame.csv', quiet=False)

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

@@ -88,10 +88,10 @@ def interrupt_extinction(t):
                 description=('Initial hydrogen-oxygen counterflow flame '
                              'at 1 bar and low strain rate'))
 else:
-    file_name = 'initial_solution.xml'
+    file_name = 'initial_solution.yaml'
     f.save(os.path.join(data_directory, file_name), name='solution',
-           description='Cantera version ' + ct.__version__ +
-           ', reaction mechanism ' + reaction_mechanism)
+           description='Initial hydrogen-oxygen counterflow flame '
+                       'at 1 bar and low strain rate')
 
 
 # PART 2: BATCH PRESSURE LOOP
@@ -142,10 +142,9 @@ def interrupt_extinction(t):
             f.write_hdf(file_name, group=group, quiet=False,
                         description='pressure = {0} bar'.format(p))
         else:
-            file_name = 'pressure_loop_' + format(p, '05.1f') + '.xml'
+            file_name = 'pressure_loop_' + format(p, '05.1f') + '.yaml'
             f.save(os.path.join(data_directory, file_name), name='solution', loglevel=1,
-                   description='Cantera version ' + ct.__version__ +
-                   ', reaction mechanism ' + reaction_mechanism)
+                   description='pressure = {0} bar'.format(p))
         p_previous = p
     except ct.CanteraError as e:
         print('Error occurred while solving:', e, 'Try next pressure level')
@@ -176,7 +175,7 @@ def interrupt_extinction(t):
 if hdf_output:
     f.read_hdf(file_name, group='initial_solution')
 else:
-    file_name = 'initial_solution.xml'
+    file_name = 'initial_solution.yaml'
     f.restore(filename=os.path.join(data_directory, file_name), name='solution', loglevel=0)
 
 # Counter to identify the loop
@@ -207,10 +206,9 @@ def interrupt_extinction(t):
             f.write_hdf(file_name, group=group, quiet=False,
                         description='strain rate iteration {}'.format(n))
         else:
-            file_name = 'strain_loop_' + format(n, '02d') + '.xml'
+            file_name = 'strain_loop_' + format(n, '02d') + '.yaml'
             f.save(os.path.join(data_directory, file_name), name='solution', loglevel=1,
-                   description='Cantera version ' + ct.__version__ +
-                   ', reaction mechanism ' + reaction_mechanism)
+                   description='strain rate iteration {}'.format(n))
     except FlameExtinguished:
         print('Flame extinguished')
         break
@@ -232,7 +230,7 @@ def interrupt_extinction(t):
         group = 'pressure_loop/{0:05.1f}'.format(p)
         f.read_hdf(file_name, group=group)
     else:
-        file_name = 'pressure_loop_{0:05.1f}.xml'.format(p)
+        file_name = 'pressure_loop_{0:05.1f}.yaml'.format(p)
         f.restore(filename=os.path.join(data_directory, file_name), name='solution', loglevel=0)
 
     # Plot the temperature profiles for selected pressures
@@ -263,7 +261,7 @@ def interrupt_extinction(t):
         group = 'strain_loop/{0:02d}'.format(n)
         f.read_hdf(file_name, group=group)
     else:
-        file_name = 'strain_loop_{0:02d}.xml'.format(n)
+        file_name = 'strain_loop_{0:02d}.yaml'.format(n)
         f.restore(filename=os.path.join(data_directory, file_name),
                   name='solution', loglevel=0)
     a_max = f.strain_rate('max')  # the maximum axial strain rate

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

@@ -65,10 +65,9 @@
                 description=('Initial solution'))
 else:
     # Save to data directory
-    file_name = 'initial_solution.xml'
+    file_name = 'initial_solution.yaml'
     f.save(os.path.join(data_directory, file_name), name='solution',
-           description='Cantera version ' + ct.__version__ +
-           ', reaction mechanism ' + reaction_mechanism)
+           description="Initial solution")
 
 
 # PART 2: COMPUTE EXTINCTION STRAIN
@@ -138,11 +137,10 @@
             group = 'extinction/{0:04d}'.format(n)
             f.write_hdf(file_name, group=group, quiet=True)
         else:
-            file_name = 'extinction_{0:04d}.xml'.format(n)
+            file_name = 'extinction_{0:04d}.yaml'.format(n)
             f.save(os.path.join(data_directory, file_name),
                    name='solution', loglevel=0,
-                   description='Cantera version ' + ct.__version__ +
-                   ', reaction mechanism ' + reaction_mechanism)
+                   description=f"Solution at alpha = {alpha[-1]}")
         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, '
@@ -157,7 +155,7 @@
             group = 'extinction/{0:04d}'.format(n)
             f.write_hdf(file_name, group=group, quiet=True)
         else:
-            file_name = 'extinction_{0:04d}.xml'.format(n)
+            file_name = 'extinction_{0:04d}.yaml'.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.')
@@ -176,7 +174,7 @@
             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)
+            file_name = 'extinction_{0:04d}.yaml'.format(n_last_burning)
             f.restore(os.path.join(data_directory, file_name),
                       name='solution', loglevel=0)
 
@@ -187,7 +185,7 @@
     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)
+    file_name = 'extinction_{0:04d}.yaml'.format(n_last_burning)
     f.restore(os.path.join(data_directory, file_name),
               name='solution', loglevel=0)
 print('----------------------------------------------------------------------')

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

@@ -63,7 +63,7 @@
     f.write_hdf('flame_fixed_T.h5', group='mix', mode='w',
                 description='solution with mixture-averaged transport')
 except ImportError:
-    f.save('flame_fixed_T.xml','mixav',
+    f.save('flame_fixed_T.yaml','mixav',
            'solution with mixture-averaged transport')
 
 print('\n\n switching to multicomponent transport...\n\n')
@@ -75,7 +75,7 @@
     f.write_hdf('flame_fixed_T.h5', group='multi',
                 description='solution with multicomponent transport')
 except ImportError:
-    f.save('flame_fixed_T.xml','multi',
+    f.save('flame_fixed_T.yaml','multi',
            'solution with  multicomponent transport')
 
 # write the velocity, temperature, density, and mole fractions to a CSV file

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

@@ -29,6 +29,6 @@
     f.write_hdf('ion_burner_flame.h5', group='ion', mode='w',
                 description='solution with ionized gas transport')
 except ImportError:
-    f.save('ion_burner_flame.xml', 'mix', 'solution with mixture-averaged transport')
+    f.save('ion_burner_flame.yaml', 'mix', 'solution with mixture-averaged transport')
 
 f.write_csv('ion_burner_flame.csv', quiet=False)

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

@@ -34,7 +34,7 @@
     f.write_hdf('ion_free_flame.h5', group='ion', mode='w',
                 description='solution with ionized gas transport')
 except ImportError:
-    f.save('ion_free_flame.xml', 'ion', 'solution with ionized gas transport')
+    f.save('ion_free_flame.yaml', 'ion', 'solution with ionized gas transport')
 
 f.show_solution()
 print('mixture-averaged flamespeed = {0:7f} m/s'.format(f.velocity[0]))

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

@@ -76,7 +76,7 @@
 if hdf_output:
     outfile = 'stagnation_flame.h5'
 else:
-    outfile = 'stagnation_flame.xml'
+    outfile = 'stagnation_flame.yaml'
 if os.path.exists(outfile):
     os.remove(outfile)
 

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

@@ -111,13 +111,13 @@
 # show the solution
 sim.show_solution()
 
-# save the solution in XML format. The 'restore' method can be used to restart
+# save the full solution. The 'restore' method can be used to restart
 # a simulation from a solution stored in this form.
 try:
     sim.write_hdf('catalytic_combustion.h5', group='soln1', mode='w',
                   description='catalytic combustion example')
 except ImportError:
-    sim.save("catalytic_combustion.xml", "soln1")
+    sim.save("catalytic_combustion.yaml", "soln1")
 
 # save selected solution components in a CSV file for plotting in
 # Excel or MATLAB.