General cleanup of class ThermoPhase

include/cantera/thermo/ThermoPhase.h

@@ -90,19 +90,15 @@ class XML_Node;
  *   activity concentrations. The dimensions depend on the number
  *   of products and reactants.
  *
- *
  * The kinetics manager requires the calculation of K_c for the
  * calculation of the reverse rate constant
  *
- *
  * @ingroup thermoprops
  * @ingroup phases
  */
 class ThermoPhase : public Phase
 {
-
 public:
-
     //! Constructor. Note that ThermoPhase is meant to be used as
     //! a base class, so this constructor should not be called
     //! explicitly.
@@ -119,15 +115,12 @@ public:
 
     //! Assignment operator
     /*!
-     *  This is NOT a virtual function.
-     *
      * @param right    Reference to %ThermoPhase object to be copied into the
      *                 current one.
      */
     ThermoPhase& operator=(const ThermoPhase& right);
 
-    //! Duplication routine for objects which inherit from
+    //! Duplication routine for objects which inherit from ThermoPhase.
-    //!  ThermoPhase.
     /*!
     *  This virtual routine can be used to duplicate %ThermoPhase objects
     *  inherited from %ThermoPhase even if the application only has
@@ -335,9 +328,8 @@ public:
      * @}
      * @name Electric Potential
      *
-     * The phase may be at some non-zero electrical
+     * The phase may be at some non-zero electrical potential. These methods
-     * potential. These methods set or get the value of the
+     * set or get the value of the electric potential.
-     * electric potential.
      */
     //@{
 
@@ -372,8 +364,7 @@ public:
      * \hat R T \log a_k. \f] The quantity \f$\mu_k^0(T,P)\f$ is
      * the standard chemical potential at unit activity,
      * which depends on  temperature and pressure,
-     * but not on composition. The
+     * but not on composition. The activity is dimensionless.
-     * activity is dimensionless.
      * @{
      */
 
@@ -951,8 +942,7 @@ public:
     /**
      * @name Setting the State
      *
-     * These methods set all or part of the thermodynamic
+     * These methods set all or part of the thermodynamic state.
-     * state.
      * @{
      */
 
@@ -1084,7 +1074,6 @@ public:
     virtual void setState_UV(doublereal u, doublereal v, doublereal tol = 1.e-4);
 
 private:
-
     //! Carry out work in HP and UV calculations.
     /*!
      * @param h     Specific enthalpy or internal energy (J/kg)
@@ -1098,7 +1087,6 @@ private:
                          doublereal tol = 1.e-4, bool doUV = false);
 
 public:
-
     //! Set the specific entropy (J/kg/K) and pressure (Pa).
     /*!
      * This function fixes the internal state of the phase so that
@@ -1152,7 +1140,6 @@ public:
      * @{
      */
 
-
     //!This method is used by the ChemEquil equilibrium solver.
     /*!
      * It sets the state such that the chemical potentials satisfy
@@ -1182,7 +1169,6 @@ public:
      */
     void setElementPotentials(const vector_fp& lambda);
 
-
     //!  Returns the element potentials stored in the ThermoPhase object
     /*!
      * Returns the stored element potentials.
@@ -1209,20 +1195,17 @@ public:
 
     /// Critical temperature (K).
     virtual doublereal critTemperature() const {
-        err("critTemperature");
+        return err("critTemperature");
-        return -1.0;
     }
 
     /// Critical pressure (Pa).
     virtual doublereal critPressure() const {
-        err("critPressure");
+        return err("critPressure");
-        return -1.0;
     }
 
     /// Critical density (kg/m3).
     virtual doublereal critDensity() const {
-        err("critDensity");
+        return err("critDensity");
-        return -1.0;
     }
 
     //@}
@@ -1240,8 +1223,7 @@ public:
      * @param p Pressure (Pa)
      */
     virtual doublereal satTemperature(doublereal p) const {
-        err("satTemperature");
+        return err("satTemperature");
-        return -1.0;
     }
 
     //! Return the saturation pressure given the temperature
@@ -1249,14 +1231,12 @@ public:
      * @param t Temperature (Kelvin)
      */
     virtual doublereal satPressure(doublereal t) {
-        err("satPressure");
+        return err("satPressure");
-        return -1.0;
     }
 
     //! Return the fraction of vapor at the current conditions
     virtual doublereal vaporFraction() const {
-        err("vaprFraction");
+        return err("vaprFraction");
-        return -1.0;
     }
 
     //! Set the state to a saturated system at a particular temperature
@@ -1334,8 +1314,7 @@ public:
 
     /**
      * @internal
-     * Initialization of a ThermoPhase object using an
+     * Initialization of a ThermoPhase object using an ctml file.
-     * ctml file.
      *
      *   This routine is a precursor to initThermoXML(XML_Node*)
      *   routine, which does most of the work.
@@ -1426,7 +1405,6 @@ public:
     virtual void setParameters(int n, doublereal* const c) {
     }
 
-
     //! Get the equation of state parameters in a vector
     /*!
      * @internal
@@ -1438,10 +1416,8 @@ public:
     virtual void getParameters(int& n, doublereal* const c) const {
     }
 
-
     //! Set equation of state parameter values from XML entries.
     /*!
-     *
      * This method is called by function importPhase() in
      * file importCTML.cpp when processing a phase definition in
      * an input file. It should be overloaded in subclasses to set
@@ -1454,7 +1430,6 @@ public:
      */
     virtual void setParametersFromXML(const XML_Node& eosdata) {}
 
-
     //! Set the initial state of the phase to the conditions
     //! specified in the state XML element.
     /*!
@@ -1576,7 +1551,6 @@ public:
     //@}
 
 protected:
-
     //! Fills `names` and `data` with the column names and species thermo
     //! properties to be included in the output of the reportCSV method.
     virtual void getCsvReportData(std::vector<std::string>& names,
@@ -1637,13 +1611,11 @@ protected:
     std::vector<doublereal> xMol_Ref;
 
 private:
-
     //! Error function that gets called for unhandled cases
     /*!
      * @param msg String containing the message.
      */
     doublereal err(const std::string& msg) const;
-
 };
 
 //! typedef for the ThermoPhase class
@@ -1652,4 +1624,3 @@ typedef ThermoPhase thermo_t;
 }
 
 #endif
-

src/thermo/ThermoPhase.cpp

@@ -21,7 +21,6 @@ namespace Cantera
 {
 
 ThermoPhase::ThermoPhase() :
-    Phase(),
     m_spthermo(0), m_speciesData(0),
     m_phi(0.0),
     m_hasElementPotentials(false),
@@ -39,7 +38,6 @@ ThermoPhase::~ThermoPhase()
 }
 
 ThermoPhase::ThermoPhase(const ThermoPhase& right)  :
-    Phase(),
     m_spthermo(0),
     m_speciesData(0),
     m_phi(0.0),
@@ -53,8 +51,7 @@ ThermoPhase::ThermoPhase(const ThermoPhase& right)  :
     *this = operator=(right);
 }
 
-ThermoPhase& ThermoPhase::
+ThermoPhase& ThermoPhase::operator=(const ThermoPhase& right)
-operator=(const ThermoPhase& right)
 {
     /*
      * Check for self assignment.
@@ -153,22 +150,19 @@ void ThermoPhase::setState_TPX(doublereal t, doublereal p, const std::string& x)
     setState_TP(t,p);
 }
 
-void ThermoPhase::setState_TPY(doublereal t, doublereal p,
+void ThermoPhase::setState_TPY(doublereal t, doublereal p, const doublereal* y)
-                               const doublereal* y)
 {
     setMassFractions(y);
     setState_TP(t,p);
 }
 
-void ThermoPhase::setState_TPY(doublereal t, doublereal p,
+void ThermoPhase::setState_TPY(doublereal t, doublereal p, compositionMap& y)
-                               compositionMap& y)
 {
     setMassFractionsByName(y);
     setState_TP(t,p);
 }
 
-void ThermoPhase::setState_TPY(doublereal t, doublereal p,
+void ThermoPhase::setState_TPY(doublereal t, doublereal p, const std::string& y)
-                               const std::string& y)
 {
     compositionMap yy = parseCompString(y, speciesNames());
     setMassFractionsByName(yy);
@@ -199,8 +193,7 @@ void ThermoPhase::setState_HP(doublereal Htarget, doublereal p,
     setState_HPorUV(Htarget, p, dTtol, false);
 }
 
-void ThermoPhase::setState_UV(doublereal u, doublereal v,
+void ThermoPhase::setState_UV(doublereal u, doublereal v, doublereal dTtol)
-                              doublereal dTtol)
 {
     setState_HPorUV(u, v, dTtol, true);
 }
@@ -217,12 +210,11 @@ void ThermoPhase::setState_HPorUV(doublereal Htarget, doublereal p,
                                   doublereal dTtol, bool doUV)
 {
     doublereal dt;
-    doublereal Hmax = 0.0, Hmin = 0.0;
     doublereal v = 0.0;
 
     // Assign the specific volume or pressure and make sure it's positive
     if (doUV) {
-        v = p;
+        doublereal v = p;
         if (v < 1.0E-300) {
             throw CanteraError("setState_HPorUV (UV)",
                                "Input specific volume is too small or negative. v = " + fp2str(v));
@@ -301,7 +293,7 @@ void ThermoPhase::setState_HPorUV(doublereal Htarget, doublereal p,
         // Check Max and Min values
         if (Tnew > Tmax && !ignoreBounds) {
             setState_conditional_TP(Tmax, p, !doUV);
-            Hmax = (doUV) ? intEnergy_mass() : enthalpy_mass();
+            double Hmax = (doUV) ? intEnergy_mass() : enthalpy_mass();
             if (Hmax >= Htarget) {
                 if (Htop < Htarget) {
                     Ttop = Tmax;
@@ -314,7 +306,7 @@ void ThermoPhase::setState_HPorUV(doublereal Htarget, doublereal p,
         }
         if (Tnew < Tmin && !ignoreBounds) {
             setState_conditional_TP(Tmin, p, !doUV);
-            Hmin = (doUV) ? intEnergy_mass() : enthalpy_mass();
+            double Hmin = (doUV) ? intEnergy_mass() : enthalpy_mass();
             if (Hmin <= Htarget) {
                 if (Hbot > Htarget) {
                     Tbot = Tmin;
@@ -644,7 +636,6 @@ SpeciesThermo& ThermoPhase::speciesThermo(int k)
 void ThermoPhase::initThermoFile(const std::string& inputFile,
                                  const std::string& id)
 {
-
     if (inputFile.size() == 0) {
         throw CanteraError("ThermoPhase::initThermoFile",
                            "input file is null");
@@ -659,7 +650,6 @@ void ThermoPhase::initThermoFile(const std::string& inputFile,
      * The phase object automatically constructs an XML object.
      * Use this object to store information.
      */
-    //XML_Node& phaseNode_XML = xml();
     XML_Node* fxml = new XML_Node();
     fxml->build(fin);
     XML_Node* fxml_phase = findXMLPhase(fxml, id);
@@ -668,8 +658,6 @@ void ThermoPhase::initThermoFile(const std::string& inputFile,
                            "ERROR: Can not find phase named " +
                            id + " in file named " + inputFile);
     }
-    //fxml_phase->copy(&phaseNode_XML);
-    //initThermoXML(*fxml_phase, id);
     bool m_ok = importPhase(*fxml_phase, this);
     if (!m_ok) {
         throw CanteraError("ThermoPhase::initThermoFile","importPhase failed ");
@@ -679,10 +667,6 @@ void ThermoPhase::initThermoFile(const std::string& inputFile,
 
 void ThermoPhase::initThermoXML(XML_Node& phaseNode, const std::string& id)
 {
-
-    /*
-     * and sets the state
-     */
     if (phaseNode.hasChild("state")) {
         XML_Node& stateNode = phaseNode.child("state");
         setStateFromXML(stateNode);
@@ -694,28 +678,20 @@ void ThermoPhase::setReferenceComposition(const doublereal* const x)
 {
     xMol_Ref.resize(m_kk);
     if (x) {
-        for (size_t k = 0; k < m_kk; k++) {
+        copy(x, x + m_kk, xMol_Ref.begin());
-            xMol_Ref[k] = x[k];
-        }
     } else {
-        getMoleFractions(DATA_PTR(xMol_Ref));
+        getMoleFractions(&xMol_Ref[0]);
-    }
-    double sum = -1.0;
-    for (size_t k = 0; k < m_kk; k++) {
-        sum += xMol_Ref[k];
     }
+    double sum = accumulate(xMol_Ref.begin(), xMol_Ref.end(), -1.0);
     if (fabs(sum) > 1.0E-11) {
         throw CanteraError("ThermoPhase::setReferenceComposition",
                            "input mole fractions don't sum to 1.0");
     }
-
 }
 
 void ThermoPhase::getReferenceComposition(doublereal* const x) const
 {
-    for (size_t k = 0; k < m_kk; k++) {
+    copy(xMol_Ref.begin(), xMol_Ref.end(), x);
-        x[k] = xMol_Ref[k];
-    }
 }
 
 void ThermoPhase::initThermo()
@@ -775,7 +751,6 @@ void ThermoPhase::setStateFromXML(const XML_Node& state)
 
 void ThermoPhase::setElementPotentials(const vector_fp& lambda)
 {
-    doublereal rrt = 1.0/(GasConstant* temperature());
     size_t mm = nElements();
     if (lambda.size() < mm) {
         throw CanteraError("setElementPotentials", "lambda too small");
@@ -783,19 +758,14 @@ void ThermoPhase::setElementPotentials(const vector_fp& lambda)
     if (!m_hasElementPotentials) {
         m_lambdaRRT.resize(mm);
     }
-    for (size_t m = 0; m < mm; m++) {
+    scale(m_lambdaRRT, 1.0/(GasConstant* temperature()));
-        m_lambdaRRT[m] = lambda[m] * rrt;
-    }
     m_hasElementPotentials = true;
 }
 
 bool ThermoPhase::getElementPotentials(doublereal* lambda) const
 {
-    doublereal rt = GasConstant* temperature();
     if (m_hasElementPotentials) {
-        for (size_t m = 0; m < nElements(); m++) {
+        scale(lambda, lambda + nElements(), lambda, GasConstant* temperature());
-            lambda[m] =  m_lambdaRRT[m] * rt;
-        }
     }
     return m_hasElementPotentials;
 }
@@ -946,7 +916,6 @@ std::string ThermoPhase::report(bool show_thermo) const
         getMassFractions(&y[0]);
         getChemPotentials(&mu[0]);
         doublereal rt = GasConstant * temperature();
-        //if (th.nSpecies() > 1) {
 
         if (show_thermo) {
             sprintf(p, " \n                           X     "
@@ -979,7 +948,6 @@ std::string ThermoPhase::report(bool show_thermo) const
             }
         }
     }
-    //}
     catch (CanteraError& err) {
         err.save();
     }