Standardize code

include/cantera/base/AnyMap.h

@@ -476,7 +476,7 @@ class AnyMap : public AnyBase
 
     //! Return an unordered set of keys
     //! @since New in %Cantera 3.0.
-    std::set<std::string> keys() const;
+    set<string> keys() const;
 
     //! Set a metadata value that applies to this AnyMap and its children.
     //! Mainly for internal use in reading or writing from files.

include/cantera/base/ct_defs.h

@@ -158,8 +158,6 @@ const int VT = -100, PH = -101, PS = -102, VP = -103, PT = -104,
 const double SmallNumber = 1.e-300;
 //! largest number to compare to inf.
 const double BigNumber = 1.e300;
-//! largest x such that exp(x) is valid
-const double MaxExp = 690.775527898;
 
 //! Fairly random number to be used to initialize variables against
 //! to see if they are subsequently defined.
@@ -177,6 +175,7 @@ const double Tiny = 1.e-20;
 //! Map connecting a string name with a double.
 /*!
  * This is used mostly to assign concentrations and mole fractions to species.
+ * @deprecated To be removed after %Cantera 3.0
  */
 typedef map<string, double> compositionMap;
 
@@ -190,9 +189,6 @@ typedef vector<double> vector_fp;
 //! Vector of ints
 typedef vector<int> vector_int;
 
-//! A grouplist is a vector of groups of species
-typedef vector<vector<size_t>> grouplist_t;
-
 //! index returned by functions to indicate "no position"
 const size_t npos = static_cast<size_t>(-1);
 

include/cantera/base/stringUtils.h

@@ -58,8 +58,8 @@ std::string stripnonprint(const std::string& s);
  *      empty or unspecified, all values are allowed.
  * @return     map of names to values
  */
-compositionMap parseCompString(const std::string& ss,
-        const std::vector<std::string>& names=std::vector<std::string>());
+Composition parseCompString(const string& ss,
+        const vector<string>& names=vector<string>());
 
 //! Translate a string into one doublereal value
 /*!

include/cantera/equil/MultiPhase.h

@@ -458,11 +458,11 @@ class MultiPhase
 
     //! Set the number of moles of species in the mixture
     /*!
-     * @param xMap  CompositionMap of the species with nonzero mole numbers.
+     * @param xMap  Composition of the species with nonzero mole numbers.
      *              Mole numbers that are less than or equal to zero will be
      *              set to zero. units = kmol.
      */
-    void setMolesByName(const compositionMap& xMap);
+    void setMolesByName(const Composition& xMap);
 
     //! Set the moles via a string containing their names.
     /*!

include/cantera/thermo/LatticeSolidPhase.h

@@ -429,7 +429,7 @@ class LatticeSolidPhase : public ThermoPhase
     void addLattice(shared_ptr<ThermoPhase> lattice);
 
     //! Set the lattice stoichiometric coefficients, @f$ \theta_i @f$
-    void setLatticeStoichiometry(const compositionMap& comp);
+    void setLatticeStoichiometry(const Composition& comp);
 
     virtual void setParameters(const AnyMap& phaseNode,
                                const AnyMap& rootNode=AnyMap());

include/cantera/thermo/MolalityVPSSTP.h

@@ -361,7 +361,7 @@ class MolalityVPSSTP : public VPStandardStateTP
      *
      * @param xMap  Composition Map containing the molalities.
      */
-    void setMolalitiesByName(const compositionMap& xMap);
+    void setMolalitiesByName(const Composition& xMap);
 
     //! Set the molalities of a phase
     /*!
@@ -514,9 +514,9 @@ class MolalityVPSSTP : public VPStandardStateTP
     /*!
      * @param t           Temperature (K)
      * @param p           Pressure (Pa)
-     * @param m           compositionMap containing the molalities
+     * @param m           Composition containing the molalities
      */
-    void setState_TPM(doublereal t, doublereal p, const compositionMap& m);
+    void setState_TPM(doublereal t, doublereal p, const Composition& m);
 
     //! Set the temperature (K), pressure (Pa), and molalities.
     /*!

include/cantera/thermo/Phase.h

@@ -358,7 +358,7 @@ class Phase
     //! Set the species mole fractions by name.
     //! Species not listed by name in \c xMap are set to zero.
     //!     @param xMap map from species names to mole fraction values.
-    void setMoleFractionsByName(const compositionMap& xMap);
+    void setMoleFractionsByName(const Composition& xMap);
 
     //! Set the mole fractions of a group of species by name. Species which
     //! are not listed by name in the composition map are set to zero.
@@ -368,7 +368,7 @@ class Phase
     //! Set the species mass fractions by name.
     //! Species not listed by name in \c yMap are set to zero.
     //!     @param yMap map from species names to mass fraction values.
-    void setMassFractionsByName(const compositionMap& yMap);
+    void setMassFractionsByName(const Composition& yMap);
 
     //! Set the species mass fractions by name.
     //! Species not listed by name in \c x are set to zero.
@@ -391,7 +391,7 @@ class Phase
     //!                  a zero mole fraction.
     //!     @deprecated To be removed after %Cantera 3.0; replaceable by calls to
     //!                 setMoleFractionsByName() and setState_TD().
-    void setState_TRX(doublereal t, doublereal dens, const compositionMap& x);
+    void setState_TRX(doublereal t, doublereal dens, const Composition& x);
 
     //! Set the internally stored temperature (K), density, and mass fractions.
     //!     @param t     Temperature in kelvin
@@ -409,7 +409,7 @@ class Phase
     //!                  a zero mass fraction.
     //!     @deprecated To be removed after %Cantera 3.0; replaceable by calls to
     //!                 setMassFractionsByName() and setState_TD().
-    void setState_TRY(doublereal t, doublereal dens, const compositionMap& y);
+    void setState_TRY(doublereal t, doublereal dens, const Composition& y);
 
     //! Set the internally stored temperature (K), molar density (kmol/m^3), and
     //! mole fractions.
@@ -490,7 +490,7 @@ class Phase
     //!     @param threshold   Exclude species with mole fractions less than or
     //!                        equal to this threshold.
     //!     @return Map of species names to mole fractions
-    compositionMap getMoleFractionsByName(double threshold=0.0) const;
+    Composition getMoleFractionsByName(double threshold=0.0) const;
 
     //! Return the mole fraction of a single species
     //!     @param  k  species index
@@ -506,7 +506,7 @@ class Phase
     //!     @param threshold   Exclude species with mass fractions less than or
     //!                        equal to this threshold.
     //!     @return Map of species names to mass fractions
-    compositionMap getMassFractionsByName(double threshold=0.0) const;
+    Composition getMassFractionsByName(double threshold=0.0) const;
 
     //! Return the mass fraction of a single species
     //!     @param  k species index
@@ -830,9 +830,9 @@ class Phase
     void addSpeciesAlias(const std::string& name, const std::string& alias);
 
     //! Return a vector with isomers names matching a given composition map
-    //!     @param compMap compositionMap of the species.
+    //!     @param compMap Composition of the species.
     //!     @return A vector of species names for matching species.
-    virtual std::vector<std::string> findIsomers(const compositionMap& compMap) const;
+    virtual vector<string> findIsomers(const Composition& compMap) const;
 
     //! Return a vector with isomers names matching a given composition string
     //!     @param comp String containing a composition map
@@ -893,13 +893,13 @@ class Phase
         m_caseSensitiveSpecies = cflag;
     }
 
-    //! Converts a compositionMap to a vector with entries for each species
+    //! Converts a Composition to a vector with entries for each species
     //! Species that are not specified are set to zero in the vector
     /*!
-     * @param[in] comp compositionMap containing the mixture composition
+     * @param[in] comp Composition containing the mixture composition
      * @return vector with length m_kk
      */
-    vector_fp getCompositionFromMap(const compositionMap& comp) const;
+    vector_fp getCompositionFromMap(const Composition& comp) const;
 
     //! Converts a mixture composition from mole fractions to mass fractions
     //!     @param[in] Y mixture composition in mass fractions (length m_kk)

include/cantera/thermo/Species.h

@@ -27,7 +27,7 @@ class Species
     Species() = default;
 
     //! Constructor
-    Species(const std::string& name, const compositionMap& comp,
+    Species(const string& name, const Composition& comp,
             double charge=0.0, double size=1.0);
 
     //! Species objects are not copyable or assignable
@@ -42,7 +42,7 @@ class Species
 
     //! The elemental composition of the species. Keys are element names; values
     //! are the corresponding atomicities.
-    compositionMap composition;
+    Composition composition;
 
     //! The electrical charge on the species, in units of the elementary charge.
     double charge = 0.0;

include/cantera/thermo/SurfPhase.h

@@ -292,7 +292,7 @@ class SurfPhase : public ThermoPhase
     void setCoveragesByName(const std::string& cov);
 
     //! Set the coverages from a map of name:value pairs
-    void setCoveragesByName(const compositionMap& cov);
+    void setCoveragesByName(const Composition& cov);
 
     //! Return a vector of surface coverages
     /*!

include/cantera/thermo/ThermoPhase.h

@@ -816,7 +816,7 @@ class ThermoPhase : public Phase
      * @param x    Composition map of mole fractions. Species not in
      *             the composition map are assumed to have zero mole fraction
      */
-    virtual void setState_TPX(doublereal t, doublereal p, const compositionMap& x);
+    virtual void setState_TPX(doublereal t, doublereal p, const Composition& x);
 
     //! Set the temperature (K), pressure (Pa), and mole fractions.
     /*!
@@ -855,7 +855,7 @@ class ThermoPhase : public Phase
      * @param y    Composition map of mass fractions. Species not in
      *             the composition map are assumed to have zero mass fraction
      */
-    virtual void setState_TPY(doublereal t, doublereal p, const compositionMap& y);
+    virtual void setState_TPY(doublereal t, doublereal p, const Composition& y);
 
     //! Set the internally stored temperature (K), pressure (Pa), and mass
     //! fractions of the phase
@@ -1130,7 +1130,7 @@ class ThermoPhase : public Phase
      * @deprecated To be removed after %Cantera 3.0; replaceable by calls to
      *              setMoleFractionsByName() and setState_DP().
      */
-    virtual void setState_RPX(doublereal rho, doublereal p, const compositionMap& x);
+    virtual void setState_RPX(doublereal rho, doublereal p, const Composition& x);
 
     //! Set the density (kg/m**3), pressure (Pa) and mole fractions
     /*!
@@ -1176,7 +1176,7 @@ class ThermoPhase : public Phase
      * @deprecated To be removed after %Cantera 3.0; replaceable by calls to
      *              setMassFractionsByName() and setState_DP().
      */
-    virtual void setState_RPY(doublereal rho, doublereal p, const compositionMap& y);
+    virtual void setState_RPY(doublereal rho, doublereal p, const Composition& y);
 
     //! Set the density (kg/m**3), pressure (Pa) and mass fractions
     /*!
@@ -1244,8 +1244,8 @@ class ThermoPhase : public Phase
     void setMixtureFraction(double mixFrac, const std::string& fuelComp,
             const std::string& oxComp, ThermoBasis basis=ThermoBasis::molar);
     //! @copydoc ThermoPhase::setMixtureFraction
-    void setMixtureFraction(double mixFrac, const compositionMap& fuelComp,
-            const compositionMap& oxComp, ThermoBasis basis=ThermoBasis::molar);
+    void setMixtureFraction(double mixFrac, const Composition& fuelComp,
+            const Composition& oxComp, ThermoBasis basis=ThermoBasis::molar);
     //! @}
     //! @name Compute Mixture Fraction
     //! @{
@@ -1290,7 +1290,7 @@ class ThermoPhase : public Phase
                            ThermoBasis basis=ThermoBasis::molar,
                            const std::string& element="Bilger") const;
     //! @copydoc ThermoPhase::mixtureFraction
-    double mixtureFraction(const compositionMap& fuelComp, const compositionMap& oxComp,
+    double mixtureFraction(const Composition& fuelComp, const Composition& oxComp,
                            ThermoBasis basis=ThermoBasis::molar,
                            const std::string& element="Bilger") const;
     //! @}
@@ -1317,8 +1317,8 @@ class ThermoPhase : public Phase
     void setEquivalenceRatio(double phi, const std::string& fuelComp,
             const std::string& oxComp, ThermoBasis basis=ThermoBasis::molar);
     //! @copydoc ThermoPhase::setEquivalenceRatio
-    void setEquivalenceRatio(double phi, const compositionMap& fuelComp,
-            const compositionMap& oxComp, ThermoBasis basis=ThermoBasis::molar);
+    void setEquivalenceRatio(double phi, const Composition& fuelComp,
+            const Composition& oxComp, ThermoBasis basis=ThermoBasis::molar);
     //! @}
 
     //! @name Compute Equivalence Ratio
@@ -1354,8 +1354,8 @@ class ThermoPhase : public Phase
     double equivalenceRatio(const std::string& fuelComp, const std::string& oxComp,
                             ThermoBasis basis=ThermoBasis::molar) const;
     //! @copydoc ThermoPhase::equivalenceRatio
-    double equivalenceRatio(const compositionMap& fuelComp,
-            const compositionMap& oxComp, ThermoBasis basis=ThermoBasis::molar) const;
+    double equivalenceRatio(const Composition& fuelComp,
+            const Composition& oxComp, ThermoBasis basis=ThermoBasis::molar) const;
     //! @}
 
     //! Compute the equivalence ratio for the current mixture
@@ -1409,8 +1409,8 @@ class ThermoPhase : public Phase
     double stoichAirFuelRatio(const std::string& fuelComp, const std::string& oxComp,
                               ThermoBasis basis=ThermoBasis::molar) const;
     //! @copydoc ThermoPhase::stoichAirFuelRatio
-    double stoichAirFuelRatio(const compositionMap& fuelComp,
-            const compositionMap& oxComp, ThermoBasis basis=ThermoBasis::molar) const;
+    double stoichAirFuelRatio(const Composition& fuelComp,
+            const Composition& oxComp, ThermoBasis basis=ThermoBasis::molar) const;
     //! @}
 
 private:

interfaces/cython/cantera/ctml2yaml.py

@@ -250,8 +250,7 @@ def split_species_value_string(node: etree.Element) -> Dict[str, float]:
     values are the number associated with each species. This is useful for things like
     elemental composition, mole fraction mappings, coverage mappings, etc.
 
-    The algorithm is reimplemented from ``compositionMap::parseCompString`` in
-    ``base/stringUtils.cpp``.
+    The algorithm is reimplemented from :ct:`parseCompString`.
     """
     text = clean_node_text(node)
     pairs = FlowMap({})

src/base/AnyMap.cpp

@@ -1461,9 +1461,9 @@ std::string AnyMap::keys_str() const
     return to_string(b);
 }
 
-std::set<std::string> AnyMap::keys() const
+set<string> AnyMap::keys() const
 {
-    std::set<std::string> out;
+    set<string> out;
     auto iter = this->begin();
     while (iter != this->end()) {
         out.insert(iter->first);

src/base/YamlWriter.cpp

@@ -73,7 +73,7 @@ std::string YamlWriter::toYamlString() const
     output["date"].setLoc(-2, 0);
 
     // Add remaining header information, ignoring obsolete information
-    std::set<std::string> exclude = {
+    set<string> exclude = {
         "description", "generator", "cantera-version", "git-commit", "date"};
     for (const auto& [key, value] : m_header) {
         if (!exclude.count(key)) {

src/base/application.h

@@ -437,9 +437,8 @@ class Application
     //! Versions of Python to consider when attempting to load user extensions
     vector<string> m_pythonSearchVersions = {"3.11", "3.10", "3.9", "3.8"};
 
-    //! Vector of deprecation warnings that have been emitted (to suppress
-    //! duplicates)
-    std::set<std::string> warnings;
+    //! Set of deprecation warnings that have been emitted (to suppress duplicates)
+    set<string> warnings;
 
     bool m_suppress_deprecation_warnings = false;
     bool m_fatal_deprecation_warnings = false;
@@ -448,7 +447,7 @@ class Application
     bool m_fatal_warnings = false;
     bool m_use_legacy_rate_constants = false;
 
-    std::set<std::pair<std::string, std::string>> m_loaded_extensions;
+    set<pair<string, string>> m_loaded_extensions;
 
     ThreadMessages pMessenger;
 

src/base/stringUtils.cpp

@@ -56,10 +56,9 @@ std::string stripnonprint(const std::string& s)
     return ss;
 }
 
-compositionMap parseCompString(const std::string& ss,
-                               const std::vector<std::string>& names)
+Composition parseCompString(const string& ss, const vector<string>& names)
 {
-    compositionMap x;
+    Composition x;
     for (size_t k = 0; k < names.size(); k++) {
         x[names[k]] = 0.0;
     }

src/equil/MultiPhase.cpp

@@ -340,7 +340,7 @@ void MultiPhase::setPhaseMoleFractions(const size_t n, const doublereal* const x
     }
 }
 
-void MultiPhase::setMolesByName(const compositionMap& xMap)
+void MultiPhase::setMolesByName(const Composition& xMap)
 {
     size_t kk = nSpecies();
     vector_fp moles(kk, 0.0);
@@ -353,7 +353,7 @@ void MultiPhase::setMolesByName(const compositionMap& xMap)
 void MultiPhase::setMolesByName(const std::string& x)
 {
     // build the composition map from the string, and then set the moles.
-    compositionMap xx = parseCompString(x, m_snames);
+    Composition xx = parseCompString(x, m_snames);
     setMolesByName(xx);
 }
 

src/oneD/Domain1D.cpp

@@ -112,7 +112,7 @@ AnyMap Domain1D::getMeta() const
     auto wrap_tols = [this](const vector_fp& tols) {
         // If all tolerances are the same, just store the scalar value.
         // Otherwise, store them by component name
-        std::set<double> unique_tols(tols.begin(), tols.end());
+        set<double> unique_tols(tols.begin(), tols.end());
         if (unique_tols.size() == 1) {
             return AnyValue(tols[0]);
         } else {

src/oneD/StFlow.cpp

@@ -751,7 +751,7 @@ AnyMap StFlow::getMeta() const
         state["emissivity-right"] = m_epsilon_right;
     }
 
-    std::set<bool> energy_flags(m_do_energy.begin(), m_do_energy.end());
+    set<bool> energy_flags(m_do_energy.begin(), m_do_energy.end());
     if (energy_flags.size() == 1) {
         state["energy-enabled"] = m_do_energy[0];
     } else {
@@ -760,7 +760,7 @@ AnyMap StFlow::getMeta() const
 
     state["Soret-enabled"] = m_do_soret;
 
-    std::set<bool> species_flags(m_do_species.begin(), m_do_species.end());
+    set<bool> species_flags(m_do_species.begin(), m_do_species.end());
     if (species_flags.size() == 1) {
         state["species-enabled"] = m_do_species[0];
     } else {