Deprecate unused methods of class Phase

include/cantera/thermo/Phase.h

@@ -224,6 +224,7 @@ class Phase
     //!     @param  k         species index
     //!     @param atomArray  vector containing the atomic number in the species.
     //!                       Length: m_mm
+    //! @deprecated Unused. To be removed after Cantera 3.0
     void getAtoms(size_t k, double* atomArray) const;
 
     //! Returns the index of a species named 'name' within the Phase object.
@@ -243,6 +244,7 @@ class Phase
     //! This is guaranteed to be unique within a Cantera problem.
     //!     @param k  Species index within the phase
     //!     @return   The "phaseName:speciesName" string
+    //! @deprecated Unused. To be removed after Cantera 3.0
     std::string speciesSPName(int k) const;
 
     //! Return a const reference to the vector of species names
@@ -406,6 +408,7 @@ class Phase
     //!     @param t     Temperature in kelvin
     //!     @param n     molar density (kmol/m^3)
     //!     @param x     vector of species mole fractions, length m_kk
+    //! @deprecated Unused. To be removed after Cantera 3.0
     void setState_TNX(doublereal t, doublereal n, const doublereal* x);
 
     //! Set the internally stored temperature (K) and density (kg/m^3)
@@ -423,21 +426,25 @@ class Phase
     //! Set the internally stored temperature (K) and mole fractions.
     //!     @param t   Temperature in kelvin
     //!     @param x   vector of species mole fractions, length m_kk
+    //! @deprecated Unused. To be removed after Cantera 3.0
     void setState_TX(doublereal t, doublereal* x);
 
     //! Set the internally stored temperature (K) and mass fractions.
     //!     @param t   Temperature in kelvin
     //!     @param y   vector of species mass fractions, length m_kk
+    //! @deprecated Unused. To be removed after Cantera 3.0
     void setState_TY(doublereal t, doublereal* y);
 
     //! Set the density (kg/m^3) and mole fractions.
     //!     @param rho  Density (kg/m^3)
     //!     @param x    vector of species mole fractions, length m_kk
+    //! @deprecated Unused. To be removed after Cantera 3.0
     void setState_RX(doublereal rho, doublereal* x);
 
     //! Set the density (kg/m^3) and mass fractions.
     //!     @param rho  Density (kg/m^3)
     //!     @param y    vector of species mass fractions, length m_kk
+    //! @deprecated Unused. To be removed after Cantera 3.0
     void setState_RY(doublereal rho, doublereal* y);
 
     //! @} end group set thermo state
@@ -449,6 +456,7 @@ class Phase
 
     //! Copy the vector of molecular weights into vector weights.
     //!     @param weights Output vector of molecular weights (kg/kmol)
+    //! @deprecated Unused. To be removed after Cantera 3.0
     void getMolecularWeights(vector_fp& weights) const;
 
     //! Copy the vector of molecular weights into array weights.
@@ -696,6 +704,7 @@ class Phase
 
     //! Set the internally stored molar density (kmol/m^3) of the phase.
     //!     @param[in] molarDensity Input molar density (kmol/m^3).
+    //! @deprecated Unused. To be removed after Cantera 3.0
     virtual void setMolarDensity(const double molarDensity);
 
     //! Set the internally stored pressure (Pa) at constant temperature and

include/cantera/thermo/SurfPhase.h

@@ -211,12 +211,8 @@ class SurfPhase : public ThermoPhase
 
     //! Since interface phases have no volume, setting this to a value other than 0.0
     //! raises an exception.
-    virtual void setMolarDensity(const double vm) {
-        if (vm != 0.0) {
-            throw CanteraError("SurfPhase::setMolarDensity",
-                               "The volume of an interface is zero");
-        }
-    }
+    //! @deprecated Unused. To be removed after Cantera 3.0
+    virtual void setMolarDensity(const double vm);
 
     //! Returns the site density
     /*!

samples/cxx/LiC6_electrode/LiC6_electrode.cpp

@@ -60,7 +60,8 @@ void calc_potentials()
             }
         }
 
-        electrodebulk->setState_TX(Tk, &xv[0]);
+        electrodebulk->setMoleFractions(&xv[0]);
+        electrodebulk->setTemperature(Tk);
         electrodebulk->getChemPotentials(spvals.data());
 
         // Calculate the open circuit potential

src/thermo/Phase.cpp

@@ -109,6 +109,8 @@ doublereal Phase::nAtoms(size_t k, size_t m) const
 
 void Phase::getAtoms(size_t k, double* atomArray) const
 {
+    warn_deprecated("Phase::getAtoms", "To be removed after Cantera 3.0. "
+                    "Use 'nAtoms(species_index, element_index)' instead.");
     for (size_t m = 0; m < m_mm; m++) {
         atomArray[m] = (double) m_speciesComp[m_mm * k + m];
     }
@@ -173,6 +175,7 @@ void Phase::checkSpeciesArraySize(size_t kk) const
 
 std::string Phase::speciesSPName(int k) const
 {
+    warn_deprecated("Phase::speciesSPName", "To be removed after Cantera 3.0");
     return m_name + ":" + speciesName(k);
 }
 
@@ -384,6 +387,8 @@ void Phase::setState_TRX(doublereal t, doublereal dens, const doublereal* x)
 
 void Phase::setState_TNX(doublereal t, doublereal n, const doublereal* x)
 {
+    warn_deprecated("Phase::setState_TNX", "To be removed after Cantera 3.0. "
+                    "Use 'setMoleFractions' and 'setState_TD' instead.");
     setMoleFractions(x);
     setTemperature(t);
     setMolarDensity(n);
@@ -431,24 +436,32 @@ void Phase::setState_TD(double t, double rho)
 
 void Phase::setState_TX(doublereal t, doublereal* x)
 {
+    warn_deprecated("Phase::setState_TX", "To be removed after Cantera 3.0. "
+                    "Use calls to 'setTemperature' and 'setMoleFractions' instead.");
     setTemperature(t);
     setMoleFractions(x);
 }
 
 void Phase::setState_TY(doublereal t, doublereal* y)
 {
+    warn_deprecated("Phase::setState_TY", "To be removed after Cantera 3.0. "
+                    "Use calls to 'setTemperature' and 'setMassFractions' instead.");
     setTemperature(t);
     setMassFractions(y);
 }
 
 void Phase::setState_RX(doublereal rho, doublereal* x)
 {
+    warn_deprecated("Phase::setState_RX", "To be removed after Cantera 3.0. "
+                    "Use calls to 'setDensity' and 'setMoleFractions' instead.");
     setMoleFractions(x);
     setDensity(rho);
 }
 
 void Phase::setState_RY(doublereal rho, doublereal* y)
 {
+    warn_deprecated("Phase::setState_RY", "To be removed after Cantera 3.0. "
+                    "Use calls to 'setDensity' and 'setMassFractions' instead.");
     setMassFractions(y);
     setDensity(rho);
 }
@@ -461,6 +474,8 @@ doublereal Phase::molecularWeight(size_t k) const
 
 void Phase::getMolecularWeights(vector_fp& weights) const
 {
+    warn_deprecated("Phase::getMolecularWeights(vector_fp&)", "To be removed after "
+        "Cantera 3.0. Use 'getMolecularWeights(vec.data())' instead.");
     weights = molecularWeights();
 }
 
@@ -663,6 +678,8 @@ double Phase::molarDensity() const
 
 void Phase::setMolarDensity(const double molar_density)
 {
+    warn_deprecated("Phase::setMolarDensity", "To be removed after Cantera 3.0. "
+        "Use 'setDensity(molar_density * meanMolecularWeight())' instead.");
     assertCompressible("setMolarDensity");
     m_dens = molar_density*meanMolecularWeight();
 }

src/thermo/SurfPhase.cpp

@@ -201,6 +201,14 @@ bool SurfPhase::addSpecies(shared_ptr<Species> spec)
     return added;
 }
 
+void SurfPhase::setMolarDensity(const double vm) {
+    warn_deprecated("SurfPhase::setMolarDensity", "To be removed after Cantera 3.0");
+    if (vm != 0.0) {
+        throw CanteraError("SurfPhase::setMolarDensity",
+                            "The volume of an interface is zero");
+    }
+}
+
 void SurfPhase::setSiteDensity(doublereal n0)
 {
     if (n0 <= 0.0) {

test_problems/diamondSurf/runDiamond.cpp

@@ -53,7 +53,8 @@ int main(int argc, char** argv)
         x[i0] = 0.1;
         size_t i1 = diamond100->speciesIndex("c6HH");
         x[i1] = 0.9;
-        diamond100->setState_TX(1200., x);
+        diamond100->setMoleFractions(x);
+        diamond100->setTemperature(1200.);
 
         for (i = 0; i < 20; i++) {
             x[i] = 0.0;