Make species names case-preserving instead of case-sensitive

This improves interoperability when working with mechanisms which use differing
conventions for naming species using uppercase or lowercase.

interfaces/cython/cantera/test/test_thermo.py

@@ -122,7 +122,7 @@ def test_setComposition_singleton(self):
         self.assertEqual(list(X[0,:,0]), list(Y))
 
     def test_setCompositionString(self):
-        self.phase.X = 'H2:1.0, O2:1.0'
+        self.phase.X = 'h2:1.0, o2:1.0'
         X = self.phase.X
         self.assertNear(X[0], 0.5)
         self.assertNear(X[3], 0.5)
@@ -162,7 +162,7 @@ def test_setCompositionDict(self):
         self.assertNear(Y[3], 0.75)
 
     def test_getCompositionDict(self):
-        self.phase.X = 'OH:1e-9, O2:0.4, AR:0.6'
+        self.phase.X = 'oh:1e-9, O2:0.4, AR:0.6'
         self.assertEqual(len(self.phase.mole_fraction_dict(1e-7)), 2)
         self.assertEqual(len(self.phase.mole_fraction_dict()), 3)
 
@@ -203,7 +203,7 @@ def test_setCompositionDict_bad2(self):
             self.phase.Y = {'H2':1.0, 'O2':'xx'}
 
     def test_setCompositionSlice(self):
-        self.phase['H2', 'O2'].X = 0.1, 0.9
+        self.phase['h2', 'o2'].X = 0.1, 0.9
         X = self.phase.X
         self.assertNear(X[0], 0.1)
         self.assertNear(X[3], 0.9)

src/oneD/StFlow.cpp

@@ -89,10 +89,8 @@ StFlow::StFlow(IdealGasPhase* ph, size_t nsp, size_t points) :
 
     // Find indices for radiating species
     m_kRadiating.resize(2, npos);
-    size_t kr = m_thermo->speciesIndex("CO2");
-    m_kRadiating[0] = (kr != npos) ? kr : m_thermo->speciesIndex("co2");
-    kr = m_thermo->speciesIndex("H2O");
-    m_kRadiating[1] = (kr != npos) ? kr : m_thermo->speciesIndex("h2o");
+    m_kRadiating[0] = m_thermo->speciesIndex("CO2");
+    m_kRadiating[1] = m_thermo->speciesIndex("H2O");
 }
 
 void StFlow::resize(size_t ncomponents, size_t points)

src/thermo/Phase.cpp

@@ -252,14 +252,14 @@ size_t Phase::speciesIndex(const std::string& nameStr) const
 {
     if (nameStr.find(':') != npos) {
         std::string pn;
-        std::string sn = parseSpeciesName(nameStr, pn);
+        std::string sn = lowercase(parseSpeciesName(nameStr, pn));
         if (pn == "" || pn == m_name || pn == m_id) {
             return getValue(m_speciesIndices, sn, npos);
         } else {
             return npos;
         }
     } else {
-        return getValue(m_speciesIndices, nameStr, npos);
+        return getValue(m_speciesIndices, lowercase(nameStr), npos);
     }
 }
 
@@ -369,7 +369,7 @@ void Phase::setMoleFractionsByName(const compositionMap& xMap)
     vector_fp mf(m_kk, 0.0);
     for (const auto& sp : xMap) {
         try {
-            mf[m_speciesIndices.at(sp.first)] = sp.second;
+            mf[m_speciesIndices.at(lowercase(sp.first))] = sp.second;
         } catch (std::out_of_range&) {
             throw CanteraError("Phase::setMoleFractionsByName",
                                "Unknown species '{}'", sp.first);
@@ -413,7 +413,7 @@ void Phase::setMassFractionsByName(const compositionMap& yMap)
     vector_fp mf(m_kk, 0.0);
     for (const auto& sp : yMap) {
         try {
-            mf[m_speciesIndices.at(sp.first)] = sp.second;
+            mf[m_speciesIndices.at(lowercase(sp.first))] = sp.second;
         } catch (std::out_of_range&) {
             throw CanteraError("Phase::setMassFractionsByName",
                                "Unknown species '{}'", sp.first);
@@ -758,12 +758,11 @@ size_t Phase::addElement(const std::string& symbol, doublereal weight,
 }
 
 bool Phase::addSpecies(shared_ptr<Species> spec) {
-    if (m_species.find(spec->name) != m_species.end()) {
+    if (m_species.find(lowercase(spec->name)) != m_species.end()) {
         throw CanteraError("Phase::addSpecies",
             "Phase '{}' already contains a species named '{}'.",
             m_name, spec->name);
     }
-    m_species[spec->name] = spec;
     vector_fp comp(nElements());
     for (const auto& elem : spec->composition) {
         size_t m = elementIndex(elem.first);
@@ -789,7 +788,8 @@ bool Phase::addSpecies(shared_ptr<Species> spec) {
     }
 
     m_speciesNames.push_back(spec->name);
-    m_speciesIndices[spec->name] = m_kk;
+    m_species[lowercase(spec->name)] = spec;
+    m_speciesIndices[lowercase(spec->name)] = m_kk;
     m_speciesCharge.push_back(spec->charge);
     m_speciesSize.push_back(spec->size);
     size_t ne = nElements();
@@ -854,19 +854,19 @@ void Phase::modifySpecies(size_t k, shared_ptr<Species> spec)
             "New species name '{}' does not match existing name '{}'",
                            spec->name, speciesName(k));
     }
-    const shared_ptr<Species>& old = m_species[spec->name];
+    const shared_ptr<Species>& old = m_species[lowercase(spec->name)];
     if (spec->composition != old->composition) {
         throw CanteraError("Phase::modifySpecies",
             "New composition for '{}' does not match existing composition",
             spec->name);
     }
-    m_species[spec->name] = spec;
+    m_species[lowercase(spec->name)] = spec;
     invalidateCache();
 }
 
 shared_ptr<Species> Phase::species(const std::string& name) const
 {
-    return m_species.at(name);
+    return m_species.at(lowercase(name));
 }
 
 shared_ptr<Species> Phase::species(size_t k) const

test/thermo/ThermoPhase_Test.cpp

@@ -63,7 +63,7 @@ TEST_F(TestThermoMethods, getMoleFractionsByName)
     EXPECT_DOUBLE_EQ(X["H2"], 0.3);
     EXPECT_DOUBLE_EQ(X["AR"], 0.5);
 
-    thermo->setMoleFractionsByName("OH:1e-9, O2:0.2, H2:0.3, AR:0.5");
+    thermo->setMoleFractionsByName("OH:1e-9, O2:0.2, h2:0.3, AR:0.5");
     X = thermo->getMoleFractionsByName();
     EXPECT_EQ(X.size(), (size_t) 4);
 

test/thermo/phaseConstructors.cpp

@@ -179,7 +179,7 @@ TEST_F(ConstructFromScratch, addUndefinedElements)
     ASSERT_EQ((size_t) 4, p.nSpecies());
     ASSERT_EQ((size_t) 3, p.nElements());
     ASSERT_EQ((size_t) 1, p.nAtoms(p.speciesIndex("CO2"), p.elementIndex("C")));
-    ASSERT_EQ((size_t) 2, p.nAtoms(p.speciesIndex("CO2"), p.elementIndex("O")));
+    ASSERT_EQ((size_t) 2, p.nAtoms(p.speciesIndex("co2"), p.elementIndex("O")));
     p.setMassFractionsByName("H2:0.5, CO2:0.5");
     ASSERT_DOUBLE_EQ(0.5, p.massFraction("CO2"));
 }