From e4362d37e7cf2d527a14c6202868b5ffd76f2436 Mon Sep 17 00:00:00 2001
From: Ray Speth <speth@mit.edu>
Date: Mon, 27 Aug 2018 21:22:52 -0400
Subject: [PATCH] [Kinetics] Check for non-existent species in reaction orders

When the nonreactant_orders option was enabled, specifying reactant orders for
species which were not present in the phase previously resulted in out-of-bounds
memory access.
---
 interfaces/cython/cantera/test/test_convert.py |  1 +
 src/kinetics/Kinetics.cpp                      | 11 +++++++++++
 test/data/reaction-orders.cti                  |  6 ++++++
 3 files changed, 18 insertions(+)

diff --git a/interfaces/cython/cantera/test/test_convert.py b/interfaces/cython/cantera/test/test_convert.py
index e994a7fb3..2ddca7cb4 100644
--- a/interfaces/cython/cantera/test/test_convert.py
+++ b/interfaces/cython/cantera/test/test_convert.py
@@ -500,6 +500,7 @@ class CtmlConverterTest(utilities.CanteraTest):
 
     def test_reaction_orders(self):
         gas = ct.Solution('reaction-orders.cti')
+        self.assertEqual(gas.n_reactions, 1)
         R = gas.reaction(0)
         self.assertTrue(R.allow_nonreactant_orders)
         self.assertNear(R.orders.get('OH'), 0.15)
diff --git a/src/kinetics/Kinetics.cpp b/src/kinetics/Kinetics.cpp
index 88643f29e..0675277f6 100644
--- a/src/kinetics/Kinetics.cpp
+++ b/src/kinetics/Kinetics.cpp
@@ -498,6 +498,17 @@ bool Kinetics::addReaction(shared_ptr<Reaction> r)
             }
         }
     }
+    for (const auto& sp : r->orders) {
+        if (kineticsSpeciesIndex(sp.first) == npos) {
+            if (m_skipUndeclaredSpecies) {
+                return false;
+            } else {
+                throw CanteraError("Kinetics::addReaction", "Reaction '{}' has "
+                    "a reaction order specified for the undeclared species '{}'",
+                    r->equation(), sp.first);
+            }
+        }
+    }
 
     checkReactionBalance(*r);
     size_t irxn = nReactions(); // index of the new reaction
diff --git a/test/data/reaction-orders.cti b/test/data/reaction-orders.cti
index 58a3831f7..4fbfa2842 100644
--- a/test/data/reaction-orders.cti
+++ b/test/data/reaction-orders.cti
@@ -6,6 +6,7 @@ ideal_gas(name = "gas",
       elements = " O H ",
       species = """gri30: H2  O2  H2O OH """,
       reactions = "all",
+      options=['skip_undeclared_species'],
       initial_state = state(temperature = 300.0,
                         pressure = OneAtm)    )
 
@@ -13,6 +14,11 @@ ideal_gas(name = "gas",
 #  Reactions data
 #-------------------------------------------------------------------------------
 
+# This reaction should be skipped due to the non-existent species 'HO2'
+reaction("H2 + O2 => 2 OH", [1e13, 0.0, 0.0],
+         order="HO2:-0.25",
+         options=['negative_orders', 'nonreactant_orders'])
+
 #test negative orders and non-reactant orders
 reaction("2 H2 + O2 => 2 H2O", [1e13, 0.0, 0.0],
          order="H2:-0.25 OH:0.15",