Save case sensitive species names

include/cantera/thermo/Phase.h

@@ -4,7 +4,7 @@
  */
 
 // This file is part of Cantera. See License.txt in the top-level directory or
-// at http://www.cantera.org/license.txt for license and copyright information.
+// at https://cantera.org/license.txt for license and copyright information.
 
 #ifndef CT_PHASE_H
 #define CT_PHASE_H
@@ -747,6 +747,17 @@ class Phase
     //! change in state is detected
     virtual void invalidateCache();
 
+    //! Returns `true` if case sensitive species names are enforced
+    bool caseSensitiveSpecies() const {
+        return m_caseSensitiveSpecies;
+    }
+
+    //! Set flag that determines whether case sensitive species are enforced
+    //! in look-up operations, e.g. speciesIndex
+    void setCaseSensitiveSpecies(bool cflag = true) {
+        m_caseSensitiveSpecies = cflag;
+    }
+
 protected:
     //! Cached for saved calculations within each ThermoPhase.
     /*!
@@ -794,7 +805,15 @@ class Phase
     //! Flag determining behavior when adding species with an undefined element
     UndefElement::behavior m_undefinedElementBehavior;
 
+    //! Flag determining whether case sensitive species names are enforced
+    bool m_caseSensitiveSpecies;
+
 private:
+    //! Find lowercase species name in m_speciesIndices when case sensitive
+    //! species names are not enforced and a user specifies a non-canonical
+    //! species name. Raise exception if lowercase name is not unique.
+    size_t findSpeciesLower(const std::string& nameStr) const;
+
     XML_Node* m_xml; //!< XML node containing the XML info for this phase
 
     //! ID of the phase. This is the value of the ID attribute of the XML
@@ -840,6 +859,9 @@ class Phase
     //! Map of species names to indices
     std::map<std::string, size_t> m_speciesIndices;
 
+    //! Map of lower-case species names to indices
+    std::map<std::string, size_t> m_speciesLower;
+
     size_t m_mm; //!< Number of elements.
     vector_fp m_atomicWeights; //!< element atomic weights (kg kmol-1)
     vector_int m_atomicNumbers; //!< element atomic numbers

interfaces/cython/cantera/_cantera.pxd

@@ -171,6 +171,8 @@ cdef extern from "cantera/thermo/ThermoPhase.h" namespace "Cantera":
         string speciesName(size_t) except +translate_exception
         double nAtoms(size_t, size_t) except +translate_exception
         void getAtoms(size_t, double*) except +translate_exception
+        cbool caseSensitiveSpecies()
+        void setCaseSensitiveSpecies(cbool)
 
         double molecularWeight(size_t) except +translate_exception
         double meanMolecularWeight()

interfaces/cython/cantera/test/test_thermo.py

@@ -1253,6 +1253,39 @@ def test_stringify_bad(self):
         with self.assertRaises(AttributeError):
             ct.Solution(3)
 
+    def test_case_sensitive_names(self):
+        gas = ct.Solution('h2o2.xml')
+        self.assertFalse(gas.case_sensitive_species_names)
+        self.assertTrue(gas.species_index('h2') == 0)
+        gas.X = 'h2:.5, o2:.5'
+        self.assertNear(gas.X[0], 0.5)
+        gas.Y = 'h2:.5, o2:.5'
+        self.assertNear(gas.Y[0], 0.5)
+
+        gas.case_sensitive_species_names = True
+        self.assertTrue(gas.case_sensitive_species_names)
+        with self.assertRaises(ValueError):
+            gas.species_index('h2')
+        with self.assertRaisesRegex(ct.CanteraError, 'Unknown species'):
+            gas.X = 'h2:1.0, o2:1.0'
+        with self.assertRaisesRegex(ct.CanteraError, 'Unknown species'):
+            gas.Y = 'h2:1.0, o2:1.0'
+
+        gas_cti = """ideal_gas(
+            name="gas",
+            elements=" S C Cs ",
+            species=" nasa: all ",
+            options=["skip_undeclared_elements"],
+            initial_state=state(temperature=300, pressure=(1, "bar"))
+        )"""
+        ct.suppress_thermo_warnings(True)
+        gas = ct.Solution(source=gas_cti)
+        with self.assertRaisesRegex(ct.CanteraError, 'is not unique'):
+            gas.species_index('cs')
+        gas.case_sensitive_species_names = True
+        with self.assertRaises(ValueError):
+            gas.species_index('cs')
+
 
 class TestElement(utilities.CanteraTest):
     @classmethod

interfaces/cython/cantera/thermo.pyx

@@ -1,5 +1,5 @@
 # This file is part of Cantera. See License.txt in the top-level directory or
-# at http://www.cantera.org/license.txt for license and copyright information.
+# at https://cantera.org/license.txt for license and copyright information.
 
 import warnings
 import weakref
@@ -470,6 +470,13 @@ cdef class ThermoPhase(_SolutionBase):
 
         return index
 
+    property case_sensitive_species_names:
+        """Enforce case-sensitivity for look up of species names"""
+        def __get__(self):
+            return self.thermo.caseSensitiveSpecies()
+        def __set__(self, val):
+            self.thermo.setCaseSensitiveSpecies(bool(val))
+
     def species(self, k=None):
         """
         Return the `Species` object for species *k*, where *k* is either the

src/thermo/Phase.cpp

@@ -4,7 +4,7 @@
  */
 
 // This file is part of Cantera. See License.txt in the top-level directory or
-// at http://www.cantera.org/license.txt for license and copyright information.
+// at https://cantera.org/license.txt for license and copyright information.
 
 #include "cantera/thermo/Phase.h"
 #include "cantera/base/utilities.h"
@@ -21,6 +21,7 @@ Phase::Phase() :
     m_kk(0),
     m_ndim(3),
     m_undefinedElementBehavior(UndefElement::add),
+    m_caseSensitiveSpecies(false),
     m_xml(new XML_Node("phase")),
     m_id("<phase>"),
     m_temp(0.001),
@@ -172,20 +173,48 @@ void Phase::getAtoms(size_t k, double* atomArray) const
     }
 }
 
+size_t Phase::findSpeciesLower(const std::string& name) const
+{
+    std::string nLower = toLowerCopy(name);
+    size_t loc = npos;
+    auto it = m_speciesLower.find(nLower);
+    if (it == m_speciesLower.end()) {
+        return npos;
+    } else {
+        loc = it->second;
+        if (loc == npos) {
+            throw CanteraError("Phase::findSpeciesLower",
+                               "Lowercase species name '{}' is not unique. "
+                               "Set Phase::caseSensitiveSpecies to true to "
+                               "enforce case sensitive species names", nLower);
+        }
+    }
+    return loc;
+}
+
 size_t Phase::speciesIndex(const std::string& nameStr) const
 {
-    size_t loc = getValue(m_speciesIndices, toLowerCopy(nameStr), npos);
+    size_t loc = npos;
+
+    auto it = m_speciesIndices.find(nameStr);
+    if (it != m_speciesIndices.end()) {
+        return it->second;
+    } else if (!m_caseSensitiveSpecies) {
+        loc = findSpeciesLower(nameStr);
+    }
     if (loc == npos && nameStr.find(':') != npos) {
         std::string pn;
-        std::string sn = toLowerCopy(parseSpeciesName(nameStr, pn));
+        std::string sn = parseSpeciesName(nameStr, pn);
         if (pn == "" || pn == m_name || pn == m_id) {
-            return getValue(m_speciesIndices, sn, npos);
-        } else {
-            return npos;
+            it = m_speciesIndices.find(nameStr);
+            if (it != m_speciesIndices.end()) {
+                return it->second;
+            } else if (!m_caseSensitiveSpecies) {
+                return findSpeciesLower(sn);
+            }
         }
-    } else {
-        return loc;
     }
+    return loc;
 }
 
 string Phase::speciesName(size_t k) const
@@ -292,10 +321,12 @@ void Phase::setMoleFractions_NoNorm(const doublereal* const x)
 void Phase::setMoleFractionsByName(const compositionMap& xMap)
 {
     vector_fp mf(m_kk, 0.0);
+
     for (const auto& sp : xMap) {
-        try {
-            mf[m_speciesIndices.at(toLowerCopy(sp.first))] = sp.second;
-        } catch (std::out_of_range&) {
+        size_t loc = speciesIndex(sp.first);
+        if (loc != npos) {
+            mf[loc] = sp.second;
+        } else {
             throw CanteraError("Phase::setMoleFractionsByName",
                                "Unknown species '{}'", sp.first);
         }
@@ -337,9 +368,10 @@ void Phase::setMassFractionsByName(const compositionMap& yMap)
 {
     vector_fp mf(m_kk, 0.0);
     for (const auto& sp : yMap) {
-        try {
-            mf[m_speciesIndices.at(toLowerCopy(sp.first))] = sp.second;
-        } catch (std::out_of_range&) {
+        size_t loc = speciesIndex(sp.first);
+        if (loc != npos) {
+            mf[loc] = sp.second;
+        } else {
             throw CanteraError("Phase::setMassFractionsByName",
                                "Unknown species '{}'", sp.first);
         }
@@ -699,7 +731,7 @@ size_t Phase::addElement(const std::string& symbol, doublereal weight,
 }
 
 bool Phase::addSpecies(shared_ptr<Species> spec) {
-    if (m_species.find(toLowerCopy(spec->name)) != m_species.end()) {
+    if (m_species.find(spec->name) != m_species.end()) {
         throw CanteraError("Phase::addSpecies",
             "Phase '{}' already contains a species named '{}'.",
             m_name, spec->name);
@@ -729,11 +761,18 @@ bool Phase::addSpecies(shared_ptr<Species> spec) {
     }
 
     m_speciesNames.push_back(spec->name);
-    m_species[toLowerCopy(spec->name)] = spec;
-    m_speciesIndices[toLowerCopy(spec->name)] = m_kk;
+    m_species[spec->name] = spec;
+    m_speciesIndices[spec->name] = m_kk;
     m_speciesCharge.push_back(spec->charge);
     size_t ne = nElements();
 
+    std::string nLower = toLowerCopy(spec->name);
+    if (m_speciesLower.find(nLower) == m_speciesLower.end()) {
+        m_speciesLower[nLower] = m_kk;
+    } else {
+        m_speciesLower[nLower] = npos;
+    }
+
     double wt = 0.0;
     const vector_fp& aw = atomicWeights();
     if (spec->charge != 0.0) {
@@ -794,24 +833,30 @@ 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[toLowerCopy(spec->name)];
+    const shared_ptr<Species>& old = m_species[spec->name];
     if (spec->composition != old->composition) {
         throw CanteraError("Phase::modifySpecies",
             "New composition for '{}' does not match existing composition",
             spec->name);
     }
-    m_species[toLowerCopy(spec->name)] = spec;
+    m_species[spec->name] = spec;
     invalidateCache();
 }
 
 shared_ptr<Species> Phase::species(const std::string& name) const
 {
-    return m_species.at(toLowerCopy(name));
+    size_t k = speciesIndex(name);
+    if (k != npos) {
+        return m_species.at(speciesName(k));
+    } else {
+        throw CanteraError("Phase::setMassFractionsByName",
+                           "Unknown species '{}'", name);
+    }
 }
 
 shared_ptr<Species> Phase::species(size_t k) const
 {
-    return species(m_speciesNames[k]);
+    return m_species.at(m_speciesNames[k]);
 }
 
 void Phase::ignoreUndefinedElements() {

src/thermo/RedlichKwongMFTP.cpp

@@ -1,7 +1,7 @@
 //! @file RedlichKwongMFTP.cpp
 
 // This file is part of Cantera. See License.txt in the top-level directory or
-// at http://www.cantera.org/license.txt for license and copyright information.
+// at https://cantera.org/license.txt for license and copyright information.
 
 #include "cantera/thermo/RedlichKwongMFTP.h"
 #include "cantera/thermo/ThermoFactory.h"
@@ -718,7 +718,8 @@ vector<double> RedlichKwongMFTP::getCoeff(const std::string& iName)
         if (iNameLower == dbName) {
             // Read from database and calculate a and b coefficients
             double vParams;
-            double T_crit, P_crit;
+            double T_crit=0.;
+            double P_crit=0.;
 
             if (acNodeDoc.hasChild("Tc")) {
                 vParams = 0.0;
@@ -734,6 +735,9 @@ vector<double> RedlichKwongMFTP::getCoeff(const std::string& iName)
                                        "Critical Temperature must be positive ");
                 }
                 T_crit = vParams;
+            } else {
+                throw CanteraError("RedlichKwongMFTP::GetCoeff",
+                                   "Critical Temperature not in database ");
             }
             if (acNodeDoc.hasChild("Pc")) {
                 vParams = 0.0;
@@ -749,6 +753,9 @@ vector<double> RedlichKwongMFTP::getCoeff(const std::string& iName)
                                        "Critical Pressure must be positive ");
                 }
                 P_crit = vParams;
+            } else {
+                throw CanteraError("RedlichKwongMFTP::GetCoeff",
+                                   "Critical Pressure not in database ");
             }
 
             //Assuming no temperature dependence

src/transport/GasTransport.cpp

@@ -395,7 +395,7 @@ void GasTransport::setupCollisionIntegral()
 void GasTransport::getTransportData()
 {
     for (size_t k = 0; k < m_thermo->nSpecies(); k++) {
-        shared_ptr<Species> s = m_thermo->species(m_thermo->speciesName(k));
+        shared_ptr<Species> s = m_thermo->species(k);
         const GasTransportData* sptran =
             dynamic_cast<GasTransportData*>(s->transport.get());
         if (!sptran) {