Fixed an error where the users data was changed before it was used.

Eliminated some deprecations which were not sanctioned.

Worked on Cantera.mak. There is a problem with scons eliminating $ from strings.

include/cantera/thermo/AdsorbateThermo.h

@@ -67,11 +67,9 @@ class Adsorbate : public SpeciesThermoInterpType
         return (SpeciesThermoInterpType*) np;
     }
 
-    //! @deprecated Not a member of the base class
     virtual void install(const std::string& name, size_t index, int type,
                          const doublereal* c, doublereal minTemp_, doublereal maxTemp_,
                          doublereal refPressure_) {
-        warn_deprecated("Adsorbate::install", "Not a member of the base class.");
         m_be = c[1];
         m_nFreqs = int(c[0]);
         for (size_t n = 0; n < m_nFreqs; n++) {
@@ -98,12 +96,10 @@ class Adsorbate : public SpeciesThermoInterpType
         s_R[m_index] = h_RT[m_index] - _free_energy_RT(temp);
     }
 
-    //! @deprecated
     void reportParameters(size_t& n, int& type,
                           doublereal& tlow, doublereal& thigh,
                           doublereal& pref,
                           doublereal* const coeffs) const {
-        warn_deprecated("AdsorbateThermo::reportParameters");
         n = m_index;
         type = ADSORBATE;
         tlow = m_lowT;

include/cantera/thermo/ConstDensityThermo.h

@@ -289,10 +289,8 @@ class ConstDensityThermo : public ThermoPhase
      *
      * @param n number of parameters
      * @param c array of \a n coefficients
-     * @deprecated Use setDensity()
      */
     virtual void setParameters(int n, doublereal* const c) {
-        warn_deprecated("ConstDensityThermo::setParamters");
         setDensity(c[0]);
     }
 
@@ -303,10 +301,8 @@ class ConstDensityThermo : public ThermoPhase
      *
      * @param n number of parameters
      * @param c array of \a n coefficients
-     * @deprecated Use density()
      */
     virtual void getParameters(int& n, doublereal* const c) const {
-        warn_deprecated("ConstDensityThermo::getParameters");
         double d = density();
         c[0] = d;
         n = 1;

include/cantera/thermo/DebyeHuckel.h

@@ -904,7 +904,6 @@ class DebyeHuckel : public MolalityVPSSTP
      * @param k species index. Defaults to 0.
      * @param sizeUA output int containing the size of the vector.
      *        Currently, this is equal to 6.
-     * @deprecated
      */
     virtual void getUnitsStandardConc(double* uA, int k = 0,
                                       int sizeUA = 6) const;
@@ -1074,7 +1073,6 @@ class DebyeHuckel : public MolalityVPSSTP
      *
      * @param n number of parameters
      * @param c array of \a n coefficients
-     * @deprecated Unimplemented
      */
     virtual void setParameters(int n, doublereal* const c);
 
@@ -1085,7 +1083,6 @@ class DebyeHuckel : public MolalityVPSSTP
      *
      * @param n number of parameters
      * @param c array of \a n coefficients
-     * @deprecated Unimplemented
      */
     virtual void getParameters(int& n, doublereal* const c) const;
 

include/cantera/thermo/Elements.h

@@ -110,8 +110,6 @@ class XML_Node;
  * in a particular instantiation of the class.
  *
  * @ingroup phases
- * @deprecated The functionality of this class was merged into class Phase in
- *     Cantera 2.0. This class will be removed in Cantera 2.2.
  */
 class Elements
 {

include/cantera/thermo/FixedChemPotSSTP.h

@@ -350,7 +350,6 @@ class FixedChemPotSSTP : public SingleSpeciesTP
      * @param k species index. Defaults to 0.
      * @param sizeUA output int containing the size of the vector.
      *        Currently, this is equal to 6.
-     * @deprecated
      */
     virtual void getUnitsStandardConc(doublereal* uA, int k = 0,
                                       int sizeUA = 6) const;
@@ -543,7 +542,6 @@ class FixedChemPotSSTP : public SingleSpeciesTP
      * @param n number of parameters = 1
      * @param c array of \a n coefficients
      *        c[0] = density of phase [ kg/m3 ]
-     * @deprecated Use setChemicalPotential()
      */
     virtual void setParameters(int n, doublereal* const c);
 
@@ -557,7 +555,6 @@ class FixedChemPotSSTP : public SingleSpeciesTP
      *  For this phase:
      *       -  n = 1
      *       -  c[0] = density of phase [ kg/m3 ]
-     * @deprecated Use getChemPotentials()
      */
     virtual void getParameters(int& n, doublereal* const c) const;
 

include/cantera/thermo/GeneralSpeciesThermo.h

@@ -117,7 +117,6 @@ class GeneralSpeciesThermo : public SpeciesThermo
     virtual doublereal refPressure(size_t k=npos) const;
     virtual int reportType(size_t index) const;
 
-    //! @deprecated
     virtual void reportParams(size_t index, int& type,
                               doublereal* const c,
                               doublereal& minTemp,

include/cantera/thermo/GibbsExcessVPSSTP.h

@@ -261,7 +261,6 @@ class GibbsExcessVPSSTP : public VPStandardStateTP
      * @param k species index. Defaults to 0.
      * @param sizeUA output int containing the size of the vector.
      *        Currently, this is equal to 6.
-     * @deprecated
      */
     virtual void getUnitsStandardConc(double* uA, int k = 0,
                                       int sizeUA = 6) const;
@@ -487,7 +486,6 @@ class GibbsExcessVPSSTP : public VPStandardStateTP
     //! utility routine to check mole fraction sum
     /*!
      * @param x   vector of mole fractions.
-     * @deprecated
      */
     double checkMFSum(const doublereal* const x) const;
 
@@ -518,12 +516,12 @@ class GibbsExcessVPSSTP : public VPStandardStateTP
 
     //! Storage for the current derivative values of the
     //! gradients with respect to logarithm of the mole fraction of the
-    //! log of the activity coefficients of the species  @deprecated
+    //! log of the activity coefficients of the species  
     mutable std::vector<doublereal> dlnActCoeffdlnN_diag_;
 
     //! Storage for the current derivative values of the
     //! gradients with respect to logarithm of the mole fraction of the
-    //! log of the activity coefficients of the species  @deprecated
+    //! log of the activity coefficients of the species 
     mutable std::vector<doublereal> dlnActCoeffdlnX_diag_;
 
     //! Storage for the current derivative values of the  gradients with respect to logarithm of the species mole number of the

include/cantera/thermo/HMWSoln.h

@@ -1302,7 +1302,6 @@ class HMWSoln : public MolalityVPSSTP
      *
      * @param testProb Hard -coded test problem to instantiate.
      *                 Current valid values are 1.
-     * @deprecated To be refactored into a standalone test
      */
     HMWSoln(int testProb);
 
@@ -1740,7 +1739,6 @@ class HMWSoln : public MolalityVPSSTP
      * @param k species index. Defaults to 0.
      * @param sizeUA output int containing the size of the vector.
      *        Currently, this is equal to 6.
-     * @deprecated
      */
     virtual void getUnitsStandardConc(double* uA, int k = 0,
                                       int sizeUA = 6) const;
@@ -1904,7 +1902,6 @@ class HMWSoln : public MolalityVPSSTP
      *
      * @param n number of parameters
      * @param c array of \a n coefficients
-     * @deprecated Unimplemented
      */
     virtual void setParameters(int n, doublereal* const c);
 
@@ -1915,7 +1912,6 @@ class HMWSoln : public MolalityVPSSTP
      *
      * @param n number of parameters
      * @param c array of \a n coefficients
-     * @deprecated Unimplemented
      */
     virtual void getParameters(int& n, doublereal* const c) const;
 

include/cantera/thermo/IdealMolalSoln.h

@@ -436,7 +436,6 @@ class IdealMolalSoln : public MolalityVPSSTP
      * @param k species index. Defaults to 0.
      * @param sizeUA output int containing the size of the vector.
      *        Currently, this is equal to 6.
-     * @deprecated
      */
     virtual void getUnitsStandardConc(double* uA, int k = 0,
                                       int sizeUA = 6) const;
@@ -609,7 +608,6 @@ class IdealMolalSoln : public MolalityVPSSTP
      * these depends on the subclass.
      * @param n number of parameters
      * @param c array of <I>n</I> coefficients
-     * @deprecated Unimplemented
      */
     virtual void setParameters(int n, doublereal* const c);
 
@@ -619,7 +617,6 @@ class IdealMolalSoln : public MolalityVPSSTP
      *
      * @param n  number of parameters (output)
      * @param c array of <I>n</I> coefficients
-     * * @deprecated Unimplemented
      */
     virtual void getParameters(int& n, doublereal* const c) const;
 

include/cantera/thermo/IdealSolidSolnPhase.h

@@ -460,7 +460,6 @@ class IdealSolidSolnPhase : public ThermoPhase
      *  kmol/m3 holds for standard concentration units. For
      *  cIdealSolidSolnPhase0 type, the standard concentration is
      *  unitless.
-     * @deprecated
      */
     virtual void getUnitsStandardConc(double* uA, int k = 0,
                                       int sizeUA = 6) const;

include/cantera/thermo/IdealSolnGasVPSS.h

@@ -208,7 +208,6 @@ class IdealSolnGasVPSS : public VPStandardStateTP
      * @param k species index. Defaults to 0.
      * @param sizeUA output int containing the size of the vector.
      *        Currently, this is equal to 6.
-     * @deprecated
      */
     virtual void getUnitsStandardConc(double* uA, int k = 0,
                                       int sizeUA = 6) const;

include/cantera/thermo/LatticePhase.h

@@ -853,7 +853,6 @@ class LatticePhase : public ThermoPhase
      * @param n number of parameters. Must be one
      * @param c array of \a n coefficients
      *           c[0] = The bulk  lattice density (kmol m-3)
-     * @deprecated Use setMolarDensity()
      */
     virtual void setParameters(int n, doublereal* const c);
 
@@ -867,7 +866,6 @@ class LatticePhase : public ThermoPhase
      *  For this phase:
      *       -  n = 1
      *       -  c[0] = molar density of phase [ kmol/m^3 ]
-     * @deprecated Use molarDensity()
      */
     virtual void getParameters(int& n, doublereal* const c) const;
 

include/cantera/thermo/MargulesVPSSTP.h

@@ -300,7 +300,6 @@ class MargulesVPSSTP : public GibbsExcessVPSSTP
      *  @param testProb Hard-coded value. Only the value of 1 is used. It's
      *                  for a LiKCl system test to predict the eutectic and
      *                  liquidus correctly.
-     *  @deprecated To be refactored into a standalone test
      */
     MargulesVPSSTP(int testProb);
 

include/cantera/thermo/MetalSHEelectrons.h

@@ -362,7 +362,6 @@ class MetalSHEelectrons : public SingleSpeciesTP
      * @param k species index. Defaults to 0.
      * @param sizeUA output int containing the size of the vector.
      *        Currently, this is equal to 6.
-     * @deprecated
      */
     virtual void getUnitsStandardConc(doublereal* uA, int k = 0,
                                       int sizeUA = 6) const;
@@ -465,7 +464,6 @@ class MetalSHEelectrons : public SingleSpeciesTP
      * @param n number of parameters
      * @param c array of \a n coefficients
      *        c[0] = density of phase [ kg/m3 ]
-     * @deprecated Use setDensity()
      */
     virtual void setParameters(int n, doublereal* const c);
 
@@ -479,7 +477,6 @@ class MetalSHEelectrons : public SingleSpeciesTP
      *  For this phase:
      *       -  n = 1
      *       -  c[0] = density of phase [ kg/m3 ]
-     * @deprecated Use density()
      */
     virtual void getParameters(int& n, doublereal* const c) const;
 

include/cantera/thermo/MineralEQ3.h

@@ -280,7 +280,6 @@ class MineralEQ3 : public StoichSubstanceSSTP
      * @param k species index. Defaults to 0.
      * @param sizeUA output int containing the size of the vector.
      *        Currently, this is equal to 6.
-     * @deprecated
      */
     virtual void getUnitsStandardConc(doublereal* uA, int k = 0,
                                       int sizeUA = 6) const;
@@ -397,7 +396,6 @@ class MineralEQ3 : public StoichSubstanceSSTP
      * @param n number of parameters
      * @param c array of \a n coefficients
      *        c[0] = density of phase [ kg/m3 ]
-     * @deprecated Use setDensity()
      */
     virtual void setParameters(int n, doublereal* const c);
 
@@ -411,7 +409,6 @@ class MineralEQ3 : public StoichSubstanceSSTP
      *  For this phase:
      *       -  n = 1
      *       -  c[0] = density of phase [ kg/m3 ]
-     * @deprecated use density()
      */
     virtual void getParameters(int& n, doublereal* const c) const;
 

include/cantera/thermo/MixedSolventElectrolyte.h

@@ -295,7 +295,6 @@ class MixedSolventElectrolyte : public MolarityIonicVPSSTP
      *  @param testProb Hard-coded value. Only the value of 1 is used. It's
      *                  for a LiKCl system -> test to predict the eutectic and
      *                  liquidus correctly.
-     *  @deprecated To be refactored into a standalone test
      */
     MixedSolventElectrolyte(int testProb);
 

include/cantera/thermo/MolalityVPSSTP.h

@@ -460,7 +460,6 @@ class MolalityVPSSTP : public VPStandardStateTP
      * @param k species index. Defaults to 0.
      * @param sizeUA output int containing the size of the vector.
      *        Currently, this is equal to 6.
-     * @deprecated
      */
     virtual void getUnitsStandardConc(double* uA, int k = 0,
                                       int sizeUA = 6) const;

include/cantera/thermo/Mu0Poly.h

@@ -140,7 +140,6 @@ class Mu0Poly: public SpeciesThermoInterpType
                                       doublereal* cp_R,
                                       doublereal* h_RT,
                                       doublereal* s_R) const ;
-    //! @deprecated
     virtual void reportParameters(size_t& n, int& type,
                                   doublereal& tlow, doublereal& thigh,
                                   doublereal& pref,

include/cantera/thermo/Nasa9Poly1.h

@@ -169,7 +169,6 @@ class Nasa9Poly1 : public SpeciesThermoInterpType
      *      coeffs[1] is min temperature
      *      coeffs[2] is max temperature
      *      coeffs[3+i] from i =0,9 are the coefficients themselves
-     * @deprecated
      */
     virtual void reportParameters(size_t& n, int& type,
                                   doublereal& tlow, doublereal& thigh,
@@ -180,7 +179,6 @@ class Nasa9Poly1 : public SpeciesThermoInterpType
     /*!
      * @param coeffs   Vector of coefficients used to set the
      *                 parameters for the standard state.
-     * @deprecated
      */
     virtual void modifyParameters(doublereal* coeffs);
 

include/cantera/thermo/NasaPoly1.h

@@ -162,12 +162,10 @@ class NasaPoly1 : public SpeciesThermoInterpType
         updateProperties(tPoly, cp_R, h_RT, s_R);
     }
 
-    //! @deprecated
     virtual void reportParameters(size_t& n, int& type,
                                   doublereal& tlow, doublereal& thigh,
                                   doublereal& pref,
                                   doublereal* const coeffs) const {
-        warn_deprecated("NasaPoly1::reportParameters");
         n = m_index;
         type = NASA1;
         tlow = m_lowT;
@@ -184,10 +182,8 @@ class NasaPoly1 : public SpeciesThermoInterpType
     /*!
      * @param coeffs   Vector of coefficients used to set the
      *                 parameters for the standard state.
-     * @deprecated
      */
     virtual void modifyParameters(doublereal* coeffs) {
-        warn_deprecated("NasaPoly1::modifyParameters");
         m_coeff[0] = coeffs[5];
         m_coeff[1] = coeffs[6];
         for (int i = 0; i < 5; i++) {

include/cantera/thermo/PDSS.h

@@ -532,7 +532,6 @@ class PDSS
      * @param minTemp   output - Minimum temperature
      * @param maxTemp   output - Maximum temperature
      * @param refPressure output - reference pressure (Pa).
-     * @deprecated
      */
     virtual void reportParams(size_t& kindex, int& type, doublereal* const c,
                               doublereal& minTemp, doublereal& maxTemp,

include/cantera/thermo/PDSS_HKFT.h

@@ -109,7 +109,6 @@ class PDSS_HKFT : public PDSS
      *  Note this is just an extra routine to check the arithmetic
      *
      * @return returns the species standard state enthalpy in  J kmol-1
-     * @deprecated
      */
     doublereal enthalpy_mole2() const;
 #endif
@@ -229,7 +228,6 @@ class PDSS_HKFT : public PDSS
      * @param minTemp   output - Minimum temperature
      * @param maxTemp   output - Maximum temperature
      * @param refPressure output - reference pressure (Pa).
-     * @deprecated
      */
     virtual void reportParams(size_t& kindex, int& type, doublereal* const c,
                               doublereal& minTemp, doublereal& maxTemp,
@@ -258,7 +256,6 @@ class PDSS_HKFT : public PDSS
     //! between the reference state at Tr, Pr and T,P
     /*!
      *  This is an extra routine that was added to check the arithmetic
-     *  @deprecated
      */
     doublereal deltaH() const;
 #endif

include/cantera/thermo/PhaseCombo_Interaction.h

@@ -368,7 +368,6 @@ class PhaseCombo_Interaction : public GibbsExcessVPSSTP
      *  @param testProb Hard-coded value. Only the value of 1 is used. It's
      *                  for a LiKCl system -> test to predict the eutectic and
      *                  liquidus correctly.
-     *  @deprecated unimplemented
      */
     PhaseCombo_Interaction(int testProb);
 

include/cantera/thermo/RedlichKisterVPSSTP.h

@@ -292,7 +292,6 @@ class RedlichKisterVPSSTP : public GibbsExcessVPSSTP
      *  @param testProb Hard-coded value. Only the value of 1 is used. It's
      *                  for a LiKCl system -> test to predict the eutectic and
      *                  liquidus correctly.
-     *  @deprecated To be refactored into a standalone test
      */
     RedlichKisterVPSSTP(int testProb);