Improve performance of importing phases

Replace the O(k) implementation of Phase::speciesIndex with one that is
O(log(k)). This function is called frequently as part of Kinetics object
initialization. Optimize for the more common case where the species name is not
qualified with a phase name.

include/cantera/thermo/Phase.h

@@ -894,6 +894,9 @@ private:
     //! Vector of the species names
     std::vector<std::string> m_speciesNames;
 
+    //! Map of species names to indices
+    std::map<std::string, size_t> m_speciesIndices;
+
     size_t m_mm; //!< Number of elements.
     vector_fp m_atomicWeights; //!< element atomic weights (kg kmol-1)
     vector_int m_atomicNumbers; //!< element atomic numbers

src/thermo/Phase.cpp

@@ -256,19 +256,17 @@ void Phase::getAtoms(size_t k, double* atomArray) const
 
 size_t Phase::speciesIndex(const std::string& nameStr) const
 {
-    std::string pn;
-    std::string sn = parseSpeciesName(nameStr, pn);
-    if (pn == "" || pn == m_name || pn == m_id) {
-        vector<string>::const_iterator it = m_speciesNames.begin();
-        for (size_t k = 0; k < m_kk; k++) {
-            if (*it == sn) {
-                return k;
-            }
-            ++it;
+    if (nameStr.find(':') != npos) {
+        std::string pn;
+        std::string sn = parseSpeciesName(nameStr, pn);
+        if (pn == "" || pn == m_name || pn == m_id) {
+            return getValue(m_speciesIndices, sn, npos);
+        } else {
+            return npos;
         }
-        return npos;
+    } else {
+        return getValue(m_speciesIndices, nameStr, npos);
     }
-    return npos;
 }
 
 string Phase::speciesName(size_t k) const
@@ -868,6 +866,7 @@ bool Phase::addSpecies(shared_ptr<Species>& spec) {
     }
 
     m_speciesNames.push_back(spec->name);
+    m_speciesIndices[spec->name] = m_kk;
     m_speciesCharge.push_back(spec->charge);
     m_speciesSize.push_back(spec->size);
     size_t ne = nElements();