From 37f71bd9129710b499a0339551519ca5f82bbd5b Mon Sep 17 00:00:00 2001
From: Ray Speth <speth@mit.edu>
Date: Fri, 7 Nov 2014 02:14:50 +0000
Subject: [PATCH] [Kinetics] Deprecate 'reactants' and 'products' methods

These methods are rarely used, and they expose a now-unused internal data
structure that isn't even correct for all reactions.
---
 include/cantera/kinetics/Kinetics.h |  9 +++++++++
 src/kinetics/InterfaceKinetics.cpp  | 10 ++++------
 src/kinetics/ReactionPath.cpp       | 25 +++++++++++++++++++------
 3 files changed, 32 insertions(+), 12 deletions(-)

diff --git a/include/cantera/kinetics/Kinetics.h b/include/cantera/kinetics/Kinetics.h
index b415084b45..45f94a9f89 100644
--- a/include/cantera/kinetics/Kinetics.h
+++ b/include/cantera/kinetics/Kinetics.h
@@ -13,6 +13,7 @@
 #include "cantera/thermo/ThermoPhase.h"
 #include "StoichManager.h"
 #include "cantera/thermo/mix_defs.h"
+#include "cantera/base/global.h"
 
 namespace Cantera
 {
@@ -652,8 +653,11 @@ class Kinetics
      * index numbers for reaction i.
      *
      * @param i  reaction index
+     * @deprecated To be removed after Cantera 2.2.
      */
     virtual const std::vector<size_t>& reactants(size_t i) const {
+        warn_deprecated("Kinetics::reactants",
+                        "To be removed after Cantera 2.2.");
         return m_reactants[i];
     }
 
@@ -662,8 +666,11 @@ class Kinetics
      * index numbers for reaction i.
      *
      * @param i reaction index
+     * @deprecated To be removed after Cantera 2.2.
      */
     virtual const std::vector<size_t>& products(size_t i) const {
+        warn_deprecated("Kinetics::products",
+                        "To be removed after Cantera 2.2.");
         return m_products[i];
     }
 
@@ -912,6 +919,7 @@ class Kinetics
      * stoichiometric coefficient.
      * NOTE: These vectors will be wrong if there are real
      *       stoichiometric coefficients in the expression.
+     * @deprecated To be removed after Cantera 2.2.
      */
     std::vector<std::vector<size_t> > m_reactants;
 
@@ -925,6 +933,7 @@ class Kinetics
      * coefficient.
      * NOTE: These vectors will be wrong if there are real
      *       stoichiometric coefficients in the expression.
+     * @deprecated To be removed after Cantera 2.2.
      */
     std::vector<std::vector<size_t> > m_products;
 
diff --git a/src/kinetics/InterfaceKinetics.cpp b/src/kinetics/InterfaceKinetics.cpp
index b9eeef6b96..b1ef16b54a 100644
--- a/src/kinetics/InterfaceKinetics.cpp
+++ b/src/kinetics/InterfaceKinetics.cpp
@@ -811,15 +811,13 @@ void InterfaceKinetics::addReaction(ReactionData& r)
     m_rxnPhaseIsProduct.push_back(std::vector<bool>(nPhases(), false));
 
     size_t i = m_ii - 1;
-    const std::vector<size_t>& vr = reactants(i);
-    for (size_t ik = 0; ik < vr.size(); ik++) {
-        size_t k = vr[ik];
+    for (size_t ik = 0; ik < r.reactants.size(); ik++) {
+        size_t k = r.reactants[ik];
         size_t p = speciesPhaseIndex(k);
         m_rxnPhaseIsReactant[i][p] = true;
     }
-    const std::vector<size_t>& vp = products(i);
-    for (size_t ik = 0; ik < vp.size(); ik++) {
-        size_t k = vp[ik];
+    for (size_t ik = 0; ik < r.products.size(); ik++) {
+        size_t k = r.products[ik];
         size_t p = speciesPhaseIndex(k);
         m_rxnPhaseIsProduct[i][p] = true;
     }
diff --git a/src/kinetics/ReactionPath.cpp b/src/kinetics/ReactionPath.cpp
index b232d63d2f..a38ad8b406 100644
--- a/src/kinetics/ReactionPath.cpp
+++ b/src/kinetics/ReactionPath.cpp
@@ -439,8 +439,15 @@ int ReactionPathBuilder::findGroups(ostream& logfile, Kinetics& s)
 
         size_t nrnet = m_reac[i].size();
         size_t npnet = m_prod[i].size();
-        const std::vector<size_t>& r = s.reactants(i);
-        const std::vector<size_t>& p = s.products(i);
+        std::vector<size_t> r, p;
+        for (size_t k = 0; k < s.nTotalSpecies(); k++) {
+            if (s.reactantStoichCoeff(k,i)) {
+                r.push_back(k);
+            }
+            if (s.productStoichCoeff(k,i)) {
+                p.push_back(k);
+            }
+        }
 
         size_t nr = r.size();
         size_t np = p.size();
@@ -656,11 +663,17 @@ int ReactionPathBuilder::init(ostream& logfile, Kinetics& kin)
 
     // all reactants / products, even ones appearing on both sides
     // of the reaction
-    vector<vector<size_t> > allProducts;
-    vector<vector<size_t> > allReactants;
+    vector<vector<size_t> > allProducts(m_nr);
+    vector<vector<size_t> > allReactants(m_nr);
     for (size_t i = 0; i < m_nr; i++) {
-        allReactants.push_back(kin.reactants(i));
-        allProducts.push_back(kin.products(i));
+        for (size_t k = 0; k < m_ns; k++) {
+            if (kin.reactantStoichCoeff(k, i)) {
+                allReactants[i].push_back(k);
+            }
+            if (kin.productStoichCoeff(k, i)) {
+                allProducts[i].push_back(k);
+            }
+        }
     }
 
     // m_reac and m_prod exclude indices for species that appear on