[Base] implement initialization of C++ Solution from input files

- implement constructor that loads ThermoPhase, Kinetics, and Transport
from input files (wrapping factory class methods)
- logic for selection of transport manager follows Python object
- add convenience methods to type-cast frequently used classes

include/cantera/base/Solution.h

@@ -20,16 +20,38 @@ class Solution : public std::enable_shared_from_this<Solution>
 {
 private:
     Solution();
+    Solution(const std::string& infile, std::string name, std::string transport,
+             std::vector<shared_ptr<Solution> > adjacent);
 
 public:
     ~Solution() {}
     Solution(const Solution&) = delete;
     Solution& operator=(const Solution&) = delete;
 
+    //! Create an empty Solution object
     static shared_ptr<Solution> create() {
         return shared_ptr<Solution>( new Solution );
     }
 
+    //! Create and initialize a Solution object from an input file
+    /*!
+     * This constructor wraps newPhase(), newKinetics() and
+     * newTransportMgr() routines for initialization.
+     *
+     * @param infile name of the input file
+     * @param name   name of the phase in the file.
+     *               If this is blank, the first phase in the file is used.
+     * @param transport name of the transport model.
+     * @param adjacent vector containing adjacent solution objects.
+     * @returns an initialized Solution object.
+     */
+    static shared_ptr<Solution> create(const std::string& infile,
+                                       std::string name="",
+                                       std::string transport="",
+                                       std::vector<shared_ptr<Solution> > adjacent={}) {
+        return shared_ptr<Solution>( new Solution(infile, name, transport, adjacent) );
+    }
+
     //! Return the name of this Solution object
     std::string name() const;
 
@@ -60,11 +82,35 @@ public:
         return *m_transport;
     }
 
+    //! Accessor for the ThermoPhase pointer
+    shared_ptr<ThermoPhase> thermoPtr() {
+        return m_thermo;
+    }
+
+    //! Accessor for the Kinetics pointer
+    shared_ptr<Kinetics> kineticsPtr() {
+        return m_kinetics;
+    }
+
+    //! Accessor for the Transport pointer
+    shared_ptr<Transport> transportPtr() {
+        return m_transport;
+    }
+
 protected:
     shared_ptr<ThermoPhase> m_thermo;  //!< ThermoPhase manager
     shared_ptr<Kinetics> m_kinetics;  //!< Kinetics manager
     shared_ptr<Transport> m_transport;  //!< Transport manager
 };
 
+/**
+ *  Create a new solution manager.
+ */
+inline shared_ptr<Solution> newSolution(const std::string& infile, std::string name="",
+                                        std::string transport="",
+                                        std::vector<shared_ptr<Solution> > adjacent={}) {
+    return Solution::create(infile, name, transport, adjacent);
+}
+
 }
 #endif

include/cantera/kinetics/GasKinetics.h

@@ -119,6 +119,19 @@ protected:
     void updateKc();
 };
 
+/**
+ *  Return a pointer to an GasKinetics object contained in Solution.
+ */
+inline shared_ptr<GasKinetics> getGasKineticsPtr(shared_ptr<Solution> sol) {
+    auto kin = sol->kineticsPtr();
+    if (kin->kineticsType()=="Surf") {
+        return std::dynamic_pointer_cast<GasKinetics>(kin);
+    } else {
+        throw CanteraError("getGasKineticsPtr",
+                           "Incompatible kinetics");
+    }
+}
+
 }
 
 #endif

include/cantera/kinetics/InterfaceKinetics.h

@@ -678,6 +678,20 @@ protected:
     //! EdgeKinetics)
     size_t m_nDim;
 };
+
+/**
+ *  Return a pointer to an InterfaceKinetics object contained in Solution.
+ */
+inline shared_ptr<InterfaceKinetics> getInterfaceKineticsPtr(shared_ptr<Solution> sol) {
+    auto kin = sol->kineticsPtr();
+    if (kin->kineticsType()=="Surf") {
+        return std::dynamic_pointer_cast<InterfaceKinetics>(kin);
+    } else {
+        throw CanteraError("getInterfaceKineticsPtr",
+                           "Incompatible kinetics");
+    }
+}
+
 }
 
 #endif

include/cantera/kinetics/Kinetics.h

@@ -19,8 +19,6 @@
 namespace Cantera
 {
 
-class Solution;
-
 /**
  * @defgroup chemkinetics Chemical Kinetics
  */

include/cantera/thermo/IdealGasPhase.h

@@ -631,6 +631,20 @@ private:
      */
     void _updateThermo() const;
 };
+
+/**
+ *  Return a pointer to an IdealGasPhase object contained in Solution.
+ */
+inline shared_ptr<IdealGasPhase> getIdealGasPhasePtr(shared_ptr<Solution> sol) {
+    auto ph = sol->thermoPtr();
+    if (ph->type()=="IdealGas") {
+        return std::dynamic_pointer_cast<IdealGasPhase>(ph);
+    } else {
+        throw CanteraError("getIdealGasPhasePtr",
+                           "Incompatible phase");
+    }
+}
+
 }
 
 #endif

include/cantera/thermo/Phase.h

@@ -10,6 +10,7 @@
 #define CT_PHASE_H
 
 #include "cantera/base/ctexceptions.h"
+#include "cantera/base/Solution.h"
 #include "cantera/thermo/Elements.h"
 #include "cantera/thermo/Species.h"
 #include "cantera/base/ValueCache.h"
@@ -29,8 +30,6 @@ namespace Cantera
  * support thermodynamic calculations (see \ref thermoprops).
  */
 
-class Solution;
-
 //! Class Phase is the base class for phases of matter, managing the species and
 //! elements in a phase, as well as the independent variables of temperature,
 //! mass density, species mass/mole fraction, and other generalized forces and

include/cantera/thermo/SurfPhase.h

@@ -447,6 +447,20 @@ private:
      */
     void _updateThermo(bool force=false) const;
 };
+
+/**
+ *  Return a pointer to an SurfPhase object contained in Solution.
+ */
+  inline shared_ptr<SurfPhase> getSurfPhasePtr(shared_ptr<Solution> sol) {
+    auto ph = sol->thermoPtr();
+    if (ph->type()=="Surf") {
+        return std::dynamic_pointer_cast<SurfPhase>(ph);
+    } else {
+        throw CanteraError("getSurfPhasePtr",
+                           "Incompatible phase");
+    }
+}
+
 }
 
 #endif

include/cantera/transport/TransportBase.h

@@ -74,8 +74,6 @@ const VelocityBasis VB_SPECIES_2 = 2;
 const VelocityBasis VB_SPECIES_3 = 3;
 //@}
 
-class Solution;
-
 //! Base class for transport property managers.
 /*!
  * All classes that compute transport properties for a single phase derive from

include/cantera/zeroD/Reactor.h

@@ -64,6 +64,11 @@ public:
         setKineticsMgr(contents);
     }
 
+    void insert(shared_ptr<Solution> sol) {
+        setThermoMgr(sol->thermo());
+        setKineticsMgr(sol->kinetics());
+    }
+
     virtual void setKineticsMgr(Kinetics& kin);
 
     virtual void setChemistry(bool cflag = true) {

include/cantera/zeroD/Reservoir.h

@@ -35,6 +35,10 @@ public:
     void insert(ThermoPhase& contents) {
         setThermoMgr(contents);
     }
+
+    void insert(shared_ptr<Solution> sol) {
+        setThermoMgr(sol->thermo());
+    }
 };
 
 }

src/base/Solution.cpp

@@ -8,14 +8,39 @@
 
 #include "cantera/base/Solution.h"
 #include "cantera/thermo/ThermoPhase.h"
+#include "cantera/thermo/ThermoFactory.h"
 #include "cantera/kinetics/Kinetics.h"
+#include "cantera/kinetics/KineticsFactory.h"
 #include "cantera/transport/TransportBase.h"
+#include "cantera/transport/TransportFactory.h"
 
 namespace Cantera
 {
 
 Solution::Solution() {}
 
+  Solution::Solution(const std::string& infile, std::string name, std::string transport,
+                     std::vector<shared_ptr<Solution> > adjacent) {
+
+    // thermo phase
+    m_thermo = shared_ptr<ThermoPhase>(newPhase(infile, name));
+
+    // kinetics
+    std::vector<ThermoPhase*> phases;
+    for (auto & adj : adjacent) {
+        phases.push_back(adj->thermoPtr().get());
+    }
+    phases.push_back(m_thermo.get());
+    m_kinetics = std::move(newKinetics(phases, infile, name));
+
+    // transport
+    if (transport=="") {
+        m_transport = shared_ptr<Transport>(newDefaultTransportMgr(m_thermo.get()));
+    } else if (transport!="None") {
+        m_transport = shared_ptr<Transport>(newTransportMgr(transport, m_thermo.get()));
+    }
+}
+
 std::string Solution::name() const {
     if (m_thermo) {
         return m_thermo->name();

test/kinetics/kineticsFromYaml.cpp

@@ -1,6 +1,6 @@
 #include "gtest/gtest.h"
 #include "cantera/base/Units.h"
-#include "cantera/IdealGasMix.h"
+#include "cantera/kinetics/GasKinetics.h"
 #include "cantera/thermo/SurfPhase.h"
 #include "cantera/kinetics/KineticsFactory.h"
 #include "cantera/thermo/ThermoFactory.h"
@@ -9,15 +9,13 @@ using namespace Cantera;
 
 TEST(Reaction, ElementaryFromYaml)
 {
-    // @TODO: Use of XML input files in these tests of the YAML format needs to
-    // be eliminated before we can deprecate the XML format.
-    IdealGasMix gas("gri30.xml");
+    auto sol = newSolution("gri30.yaml");
     AnyMap rxn = AnyMap::fromYamlString(
         "{equation: N + NO <=> N2 + O,"
         " rate-constant: [-2.70000E+13 cm^3/mol/s, 0, 355 cal/mol],"
         " negative-A: true}");
 
-    auto R = newReaction(rxn, gas);
+    auto R = newReaction(rxn, sol->kinetics());
     EXPECT_EQ(R->reactants.at("NO"), 1);
     EXPECT_EQ(R->products.at("N2"), 1);
     EXPECT_EQ(R->reaction_type, ELEMENTARY_RXN);
@@ -31,14 +29,14 @@ TEST(Reaction, ElementaryFromYaml)
 
 TEST(Reaction, ThreeBodyFromYaml1)
 {
-    IdealGasMix gas("gri30.xml");
+    auto sol = newSolution("gri30.yaml");
     AnyMap rxn = AnyMap::fromYamlString(
         "{equation: 2 O + M = O2 + M,"
         " type: three-body,"
         " rate-constant: [1.20000E+17 cm^6/mol^2/s, -1, 0],"
         " efficiencies: {AR: 0.83, H2O: 5}}");
 
-    auto R = newReaction(rxn, gas);
+    auto R = newReaction(rxn, sol->kinetics());
     EXPECT_EQ(R->reactants.count("M"), (size_t) 0);
 
     auto TBR = dynamic_cast<ThreeBodyReaction&>(*R);
@@ -49,18 +47,18 @@ TEST(Reaction, ThreeBodyFromYaml1)
 
 TEST(Reaction, ThreeBodyFromYaml2)
 {
-    IdealGasMix gas("gri30.xml");
+    auto sol = newSolution("gri30.yaml");
     AnyMap rxn = AnyMap::fromYamlString(
         "{equation: 2 O <=> O2," // Missing "M" on each side of the equation
         " type: three-body,"
         " rate-constant: [1.20000E+17, -1, 0]}");
 
-    EXPECT_THROW(newReaction(rxn, gas), CanteraError);
+    EXPECT_THROW(newReaction(rxn, sol->kinetics()), CanteraError);
 }
 
 TEST(Reaction, FalloffFromYaml1)
 {
-    IdealGasMix gas("gri30.xml");
+    auto sol = newSolution("gri30.yaml");
     AnyMap rxn = AnyMap::fromYamlString(
         "{equation: N2O (+M) = N2 + O (+ M),"
         " type: falloff,"
@@ -69,7 +67,7 @@ TEST(Reaction, FalloffFromYaml1)
         " SRI: {A: 1.1, B: 700.0, C: 1234.0, D: 56.0, E: 0.7},"
         " efficiencies: {AR: 0.625}}");
 
-    auto R = newReaction(rxn, gas);
+    auto R = newReaction(rxn, sol->kinetics());
     auto FR = dynamic_cast<FalloffReaction&>(*R);
     EXPECT_DOUBLE_EQ(FR.third_body.efficiency("AR"), 0.625);
     EXPECT_DOUBLE_EQ(FR.third_body.efficiency("N2"), 1.0);
@@ -77,7 +75,7 @@ TEST(Reaction, FalloffFromYaml1)
 
 TEST(Reaction, FalloffFromYaml2)
 {
-    IdealGasMix gas("gri30.xml");
+    auto sol = newSolution("gri30.yaml");
     AnyMap rxn = AnyMap::fromYamlString(
         "{equation: H + CH2 (+ N2) <=> CH3 (+N2),"
         " type: falloff,"
@@ -86,7 +84,7 @@ TEST(Reaction, FalloffFromYaml2)
         " Troe: {A: 0.562, T3: 91, T1: 5836},"
         " source: somewhere}");
 
-    auto R = newReaction(rxn, gas);
+    auto R = newReaction(rxn, sol->kinetics());
     auto FR = dynamic_cast<FalloffReaction&>(*R);
     EXPECT_DOUBLE_EQ(FR.third_body.efficiency("N2"), 1.0);
     EXPECT_DOUBLE_EQ(FR.third_body.efficiency("H2O"), 0.0);
@@ -103,7 +101,7 @@ TEST(Reaction, FalloffFromYaml2)
 
 TEST(Reaction, ChemicallyActivatedFromYaml)
 {
-    IdealGasMix gas("gri30.xml");
+    auto sol = newSolution("gri30.yaml");
     AnyMap rxn = AnyMap::fromYamlString(
         "{equation: CH3 + OH (+M) <=> CH2O + H2 (+M),"
         " units: {length: cm, quantity: mol},"
@@ -111,7 +109,7 @@ TEST(Reaction, ChemicallyActivatedFromYaml)
         " high-P-rate-constant: [5.88E-14, 6.721, -3022.227],"
         " low-P-rate-constant: [282320.078, 1.46878, -3270.56495]}");
 
-    auto R = newReaction(rxn, gas);
+    auto R = newReaction(rxn, sol->kinetics());
     auto CAR = dynamic_cast<ChemicallyActivatedReaction&>(*R);
     EXPECT_DOUBLE_EQ(CAR.high_rate.preExponentialFactor(), 5.88e-14);
     EXPECT_DOUBLE_EQ(CAR.low_rate.preExponentialFactor(), 2.82320078e2);
@@ -120,7 +118,7 @@ TEST(Reaction, ChemicallyActivatedFromYaml)
 
 TEST(Reaction, PlogFromYaml)
 {
-    IdealGasMix gas("gri30.xml");
+    auto sol = newSolution("gri30.yaml");
     AnyMap rxn = AnyMap::fromYamlString(
         "equation: 'H + CH4 <=> H2 + CH3'\n"
         "units: {pressure: atm}\n"
@@ -131,7 +129,7 @@ TEST(Reaction, PlogFromYaml)
         "- {P: 1.0 atm, A: 1.230000e+04, b: 2.68, Ea: 6335.0}\n"
         "- {P: 1.01325 MPa, A: 1.680000e+16, b: -0.6, Ea: 14754.0}");
 
-    auto R = newReaction(rxn, gas);
+    auto R = newReaction(rxn, sol->kinetics());
     auto PR = dynamic_cast<PlogReaction&>(*R);
     const auto& rates = PR.rate.rates();
     EXPECT_EQ(rates.size(), (size_t) 4);
@@ -145,7 +143,7 @@ TEST(Reaction, PlogFromYaml)
 
 TEST(Reaction, ChebyshevFromYaml)
 {
-    IdealGasMix gas("gri30.xml");
+    auto sol = newSolution("gri30.yaml");
     AnyMap rxn = AnyMap::fromYamlString(
         "equation: 'CH4 <=> CH3 + H'\n"
         "type: Chebyshev\n"
@@ -158,7 +156,7 @@ TEST(Reaction, ChebyshevFromYaml)
         "       [-2.26210e-01,  1.69190e-01,  4.85810e-03, -2.38030e-03],\n"
         "       [-1.43220e-01,  7.71110e-02,  1.27080e-02, -6.41540e-04]]\n");
 
-    auto R = newReaction(rxn, gas);
+    auto R = newReaction(rxn, sol->kinetics());
     EXPECT_EQ(R->reactants.size(), (size_t) 1);
     auto CR = dynamic_cast<ChebyshevReaction&>(*R);
     double logP = std::log10(2e6);

test/thermo/nasapoly.cpp

@@ -1,6 +1,6 @@
 #include "gtest/gtest.h"
 #include "cantera/thermo/NasaPoly1.h"
-#include "cantera/IdealGasMix.h"
+#include "cantera/thermo/IdealGasPhase.h"
 
 namespace Cantera
 {
@@ -94,7 +94,7 @@ TEST_F(NasaPoly1Test, updatePropertiesTemp)
 
 
 TEST(Nasa9Test, Nasa9Thermo) {
-    IdealGasMix g("../data/gasNASA9.xml", "nasa9");
+    IdealGasPhase g("gasNASA9.xml", "nasa9");
     size_t nsp = g.nSpecies();
     double pres = 1.0E5;
     vector_fp Xset(nsp, 0.0);