From ffe3eb5e5affec95b003d00f8113a17aa9d89e20 Mon Sep 17 00:00:00 2001
From: Ray Speth <speth@mit.edu>
Date: Sat, 15 Nov 2014 00:46:59 +0000
Subject: [PATCH] [Kinetics] Check for undeclared species when using Reaction
 objects

Skip the reaction or raise an exception based on the
'm_skipUndeclaredSpecies' flag
---
 include/cantera/kinetics/Kinetics.h   | 11 +++++++++
 src/kinetics/Kinetics.cpp             | 32 ++++++++++++++++++++++++++-
 test/kinetics/kineticsFromScratch.cpp | 24 ++++++++++++++++++++
 3 files changed, 66 insertions(+), 1 deletion(-)

diff --git a/include/cantera/kinetics/Kinetics.h b/include/cantera/kinetics/Kinetics.h
index b2076f4d6..8844a679b 100644
--- a/include/cantera/kinetics/Kinetics.h
+++ b/include/cantera/kinetics/Kinetics.h
@@ -806,6 +806,14 @@ public:
      */
     virtual void addReaction(shared_ptr<Reaction> r);
 
+    //! Determine behavior when adding a new reaction that contains species not
+    //! defined in any of the phases associated with this kinetics manager. If
+    //! set to true, the reaction will silently be ignored. If false, (the
+    //! default) an exception will be raised.
+    void skipUndeclaredSpecies(bool skip) {
+        m_skipUndeclaredSpecies = skip;
+    }
+
     //! @deprecated To be removed after Cantera 2.2. No longer called as part
     //!     of addReaction.
     virtual void installReagents(const ReactionData& r) {
@@ -1073,6 +1081,9 @@ protected:
     //! Net rate-of-progress for each reaction
     vector_fp m_ropnet;
 
+    //! @see skipUndeclaredSpecies()
+    bool m_skipUndeclaredSpecies;
+
 private:
     std::map<size_t, std::vector<grouplist_t> > m_rgroups;
     std::map<size_t, std::vector<grouplist_t> > m_pgroups;
diff --git a/src/kinetics/Kinetics.cpp b/src/kinetics/Kinetics.cpp
index b56b394ee..b8238c420 100644
--- a/src/kinetics/Kinetics.cpp
+++ b/src/kinetics/Kinetics.cpp
@@ -22,7 +22,8 @@ Kinetics::Kinetics() :
     m_thermo(0),
     m_surfphase(npos),
     m_rxnphase(npos),
-    m_mindim(4)
+    m_mindim(4),
+    m_skipUndeclaredSpecies(false)
 {
 }
 
@@ -75,6 +76,7 @@ Kinetics& Kinetics::operator=(const Kinetics& right)
     m_ropf = right.m_ropf;
     m_ropr = right.m_ropr;
     m_ropnet = right.m_ropnet;
+    m_skipUndeclaredSpecies = right.m_skipUndeclaredSpecies;
 
     return *this;
 }
@@ -648,6 +650,34 @@ void Kinetics::addReaction(ReactionData& r) {
 
 void Kinetics::addReaction(shared_ptr<Reaction> r)
 {
+    // Check for undeclared species
+    for (Composition::const_iterator iter = r->reactants.begin();
+         iter != r->reactants.end();
+         ++iter) {
+        if (kineticsSpeciesIndex(iter->first) == npos) {
+            if (m_skipUndeclaredSpecies) {
+                return;
+            } else {
+                throw CanteraError("Kinetics::addReaction", "Reaction '" +
+                    r->equation() + "' contains the undeclared species '" +
+                    iter->first + "'");
+            }
+        }
+    }
+    for (Composition::const_iterator iter = r->products.begin();
+         iter != r->products.end();
+         ++iter) {
+        if (kineticsSpeciesIndex(iter->first) == npos) {
+            if (m_skipUndeclaredSpecies) {
+                return;
+            } else {
+                throw CanteraError("Kinetics::addReaction", "Reaction '" +
+                    r->equation() + "' contains the undeclared species '" +
+                    iter->first + "'");
+            }
+        }
+    }
+
     checkReactionBalance(*r);
 
     size_t irxn = nReactions();
diff --git a/test/kinetics/kineticsFromScratch.cpp b/test/kinetics/kineticsFromScratch.cpp
index 3c35cd8ae..e24252acd 100644
--- a/test/kinetics/kineticsFromScratch.cpp
+++ b/test/kinetics/kineticsFromScratch.cpp
@@ -161,6 +161,30 @@ TEST_F(KineticsFromScratch, add_chebyshev_reaction)
     check_rates(4);
 }
 
+TEST_F(KineticsFromScratch, undeclared_species)
+{
+    Composition reac = parseCompString("CO:1 OH:1");
+    Composition prod = parseCompString("CO2:1 H:1");
+    Arrhenius rate(3.87e1, 2.7, 6260.0 / GasConst_cal_mol_K);
+    shared_ptr<ElementaryReaction> R(new ElementaryReaction(reac, prod, rate));
+
+    ASSERT_THROW(kin.addReaction(R), CanteraError);
+    ASSERT_EQ(0, kin.nReactions());
+}
+
+TEST_F(KineticsFromScratch, skip_undeclared_species)
+{
+    Composition reac = parseCompString("CO:1 OH:1");
+    Composition prod = parseCompString("CO2:1 H:1");
+    Arrhenius rate(3.87e1, 2.7, 6260.0 / GasConst_cal_mol_K);
+    shared_ptr<ElementaryReaction> R(new ElementaryReaction(reac, prod, rate));
+
+    kin.skipUndeclaredSpecies(true);
+    kin.addReaction(R);
+    ASSERT_EQ(0, kin.nReactions());
+}
+
+
 class InterfaceKineticsFromScratch : public testing::Test
 {
 public: