From 1660167bd7dadec072a3d163ae2daff635bfae6c Mon Sep 17 00:00:00 2001
From: Ray Speth <speth@mit.edu>
Date: Thu, 8 Sep 2016 22:24:38 -0400
Subject: [PATCH] Allow adding species / reactions from Python

This enables the base functionality, but does not protect against any erroneous
usage.
---
 interfaces/cython/cantera/kinetics.pyx        |  4 +++
 .../cython/cantera/test/test_kinetics.py      | 28 +++++++++++++++++++
 interfaces/cython/cantera/test/test_thermo.py | 18 ++++++++++++
 interfaces/cython/cantera/thermo.pyx          | 11 ++++++++
 4 files changed, 61 insertions(+)

diff --git a/interfaces/cython/cantera/kinetics.pyx b/interfaces/cython/cantera/kinetics.pyx
index a849ce1da5..a98eb29974 100644
--- a/interfaces/cython/cantera/kinetics.pyx
+++ b/interfaces/cython/cantera/kinetics.pyx
@@ -97,6 +97,10 @@ cdef class Kinetics(_SolutionBase):
         """
         self.kinetics.modifyReaction(irxn, rxn._reaction)
 
+    def add_reaction(self, Reaction rxn):
+        """ Add a new reaction to this phase. """
+        self.kinetics.addReaction(rxn._reaction)
+
     def is_reversible(self, int i_reaction):
         """True if reaction `i_reaction` is reversible."""
         self._check_reaction_index(i_reaction)
diff --git a/interfaces/cython/cantera/test/test_kinetics.py b/interfaces/cython/cantera/test/test_kinetics.py
index 81974570bc..99eb336351 100644
--- a/interfaces/cython/cantera/test/test_kinetics.py
+++ b/interfaces/cython/cantera/test/test_kinetics.py
@@ -223,6 +223,34 @@ def test_surface(self):
             k2 = surf2.kinetics_species_index(k)
             self.assertNear(rop1[k1], rop2[k2])
 
+    def test_add_reaction(self):
+        gas1 = ct.Solution('h2o2.xml')
+
+        S = ct.Species.listFromFile('h2o2.xml')
+        R = ct.Reaction.listFromFile('h2o2.xml')
+        gas2 = ct.Solution(thermo='IdealGas', kinetics='GasKinetics',
+                           species=S, reactions=R[:5])
+
+        gas1.TPY = 800, 2*ct.one_atm, 'H2:0.3, O2:0.7, OH:2e-4, O:1e-3, H:5e-5'
+        gas2.TPY = gas1.TPY
+
+        for r in R[5:]:
+            gas2.add_reaction(r)
+
+        self.assertEqual(gas1.n_reactions, gas2.n_reactions)
+
+        self.assertTrue((gas1.reactant_stoich_coeffs() ==
+                         gas2.reactant_stoich_coeffs()).all())
+        self.assertTrue((gas1.product_stoich_coeffs() ==
+                         gas2.product_stoich_coeffs()).all())
+
+        self.assertArrayNear(gas1.delta_gibbs,
+                             gas2.delta_gibbs)
+        self.assertArrayNear(gas1.reverse_rate_constants,
+                             gas2.reverse_rate_constants)
+        self.assertArrayNear(gas1.net_production_rates,
+                             gas2.net_production_rates)
+
 
 class KineticsRepeatability(utilities.CanteraTest):
     """
diff --git a/interfaces/cython/cantera/test/test_thermo.py b/interfaces/cython/cantera/test/test_thermo.py
index fdc57435ec..a9a5b04299 100644
--- a/interfaces/cython/cantera/test/test_thermo.py
+++ b/interfaces/cython/cantera/test/test_thermo.py
@@ -578,6 +578,24 @@ def test_uncopyable(self):
         with self.assertRaises(NotImplementedError):
             copy.copy(self.phase)
 
+    def test_add_species(self):
+        ref = ct.Solution('gri30.xml')
+        n_orig = self.phase.n_species
+        self.phase.add_species(ref.species('CO2'))
+        self.phase.add_species(ref.species('CO'))
+
+        self.assertEqual(self.phase.n_species, n_orig + 2)
+        self.assertIn('CO2', self.phase.species_names)
+        self.assertIn('CO', self.phase.species_names)
+
+        state = 400, 2e5, 'H2:0.7, CO2:0.2, CO:0.1'
+        ref.TPY = state
+        self.phase.TPY = state
+        self.assertNear(self.phase.enthalpy_mass, ref.enthalpy_mass)
+        self.assertNear(self.phase.entropy_mole, ref.entropy_mole)
+        self.assertArrayNear(ref[self.phase.species_names].partial_molar_cp,
+                             self.phase.partial_molar_cp)
+
 
 class TestThermo(utilities.CanteraTest):
     def setUp(self):
diff --git a/interfaces/cython/cantera/thermo.pyx b/interfaces/cython/cantera/thermo.pyx
index 179133b638..45eff40e1b 100644
--- a/interfaces/cython/cantera/thermo.pyx
+++ b/interfaces/cython/cantera/thermo.pyx
@@ -450,6 +450,17 @@ cdef class ThermoPhase(_SolutionBase):
         if self.kinetics:
             self.kinetics.invalidateCache()
 
+    def add_species(self, Species species):
+        """
+        Add a new species to this phase. Missing elements will be added
+        automatically.
+        """
+        self.thermo.addUndefinedElements()
+        self.thermo.addSpecies(species._species)
+        self.thermo.initThermo()
+        if self.kinetics:
+            self.kinetics.invalidateCache()
+
     def n_atoms(self, species, element):
         """
         Number of atoms of element *element* in species *species*. The element