Gas transport polynomial fits in Python

include/cantera/cython/wrappers.h

@@ -59,11 +59,32 @@ void CxxArray2D_set(Cantera::Array2D& array, size_t i, size_t j, double value)
     void PREFIX ## _ ## FUNC_NAME(Cantera::CLASS_NAME* object, size_t dim, double* data) \
     { object->FUNC_NAME(dim, data); }
 
+// Function which populates a 1D array, extra arguments
+#define ARRAY_FUNC1_1SPEC(PREFIX, CLASS_NAME, FUNC_NAME) \
+    void PREFIX ## _ ## FUNC_NAME(Cantera::CLASS_NAME* object, size_t i, double* data) \
+    { object->FUNC_NAME(i, data); }
+
+#define ARRAY_FUNC1_2SPEC(PREFIX, CLASS_NAME, FUNC_NAME) \
+    void PREFIX ## _ ## FUNC_NAME(Cantera::CLASS_NAME* object, size_t i, size_t j, double* data) \
+    { object->FUNC_NAME(i, j, data); }
+
+#define ARRAY_FUNC3_2SPEC(PREFIX, CLASS_NAME, FUNC_NAME) \
+    void PREFIX ## _ ## FUNC_NAME(Cantera::CLASS_NAME* object, size_t i, size_t j, double* dataA, double* dataB, double* dataC) \
+    { object->FUNC_NAME(i, j, dataA, dataB, dataC); }
+
+#define ARRAY_FUNC3_2SPEC_BOOL(PREFIX, CLASS_NAME, FUNC_NAME) \
+    void PREFIX ## _ ## FUNC_NAME(Cantera::CLASS_NAME* object, size_t i, size_t j, double* dataA, double* dataB, double* dataC, bool flag) \
+    { object->FUNC_NAME(i, j, dataA, dataB, dataC, flag); }
+
 
 #define THERMO_1D(FUNC_NAME) ARRAY_FUNC(thermo, ThermoPhase, FUNC_NAME)
 #define KIN_1D(FUNC_NAME) ARRAY_FUNC(kin, Kinetics, FUNC_NAME)
 #define TRANSPORT_1D(FUNC_NAME) ARRAY_FUNC(tran, Transport, FUNC_NAME)
 #define TRANSPORT_2D(FUNC_NAME) ARRAY_FUNC2(tran, Transport, FUNC_NAME)
+#define TRANSPORT_POLY_1SPECIE(FUNC_NAME) ARRAY_FUNC1_1SPEC(tran, Transport, FUNC_NAME)
+#define TRANSPORT_POLY_2SPECIE(FUNC_NAME) ARRAY_FUNC1_2SPEC(tran, Transport, FUNC_NAME)
+#define TRANSPORT_3POLY_2SPECIE(FUNC_NAME) ARRAY_FUNC3_2SPEC(tran, Transport, FUNC_NAME)
+#define TRANSPORT_3POLY_2SPECIE_BOOL(FUNC_NAME) ARRAY_FUNC3_2SPEC_BOOL(tran, Transport, FUNC_NAME)
 
 THERMO_1D(getMassFractions)
 THERMO_1D(setMassFractions)
@@ -117,3 +138,12 @@ TRANSPORT_1D(getMobilities)
 
 TRANSPORT_2D(getMultiDiffCoeffs)
 TRANSPORT_2D(getBinaryDiffCoeffs)
+
+TRANSPORT_POLY_1SPECIE(getViscosityPolynomials)
+TRANSPORT_POLY_1SPECIE(setViscosityPolynomials)
+TRANSPORT_POLY_1SPECIE(getConductivityPolynomials)
+TRANSPORT_POLY_1SPECIE(setConductivityPolynomials)
+TRANSPORT_POLY_2SPECIE(getBinDiffusivityPolynomials)
+TRANSPORT_POLY_2SPECIE(setBinDiffusivityPolynomials)
+TRANSPORT_3POLY_2SPECIE(getCollisionIntegralPolynomials)
+TRANSPORT_3POLY_2SPECIE_BOOL(setCollisionIntegralPolynomials)

include/cantera/transport/GasTransport.h

@@ -127,7 +127,33 @@ class GasTransport : public Transport
     //! @see fitDiffCoeffs()
     virtual void getBinDiffusivityPolynomials(size_t i, size_t j, double* coeffs) const;
 
+    //! Return the polynomial fits to the collision integral of species pair (i, j)
+    //! @see fitCollisionIntegrals()
+    virtual void getCollisionIntegralPolynomials(size_t i, size_t j, double* astar_coeffs, 
+                                                double* bstar_coeffs, double* cstar_coeffs) const;
+
+    //! Modify the polynomial fits to the viscosity of species i
+    //! @see fitProperties()
+    virtual void setViscosityPolynomials(size_t i, double* coeffs);
+
+    //! Modify the temperature fits of the heat conductivity of species i
+    //! @see fitProperties()
+    virtual void setConductivityPolynomials(size_t i, double* coeffs);
+
+    //! Modify the polynomial fits to the binary diffusivity of species pair (i, j)
+    //! @see fitDiffCoeffs()
+    virtual void setBinDiffusivityPolynomials(size_t i, size_t j, double* coeffs);
+
+    //! Modify the polynomial fits to the collision integral of species pair (i, j)
+    //! @see fitCollisionIntegrals()
+    virtual void setCollisionIntegralPolynomials(size_t i, size_t j, double* astar_coeffs, 
+                                                double* bstar_coeffs, double* cstar_coeffs, bool actualT);
+
     virtual void init(ThermoPhase* thermo, int mode=0, int log_level=0);
+
+    bool CKMode() const {
+        return m_mode == CK_Mode;
+    }
 
 protected:
     GasTransport(ThermoPhase* thermo=0);
@@ -386,6 +412,10 @@ class GasTransport : public Transport
      * (i,j).
      */
     std::vector<vector_fp> m_omega22_poly;
+
+    //! Flag to indicate for which (i,j) interaction pairs the 
+    //! actual temperature is used instead of the reduced temperature
+    std::vector<vector_int> m_star_poly_actualT;
 
     //! Fit for astar collision integral
     /*!

include/cantera/transport/TransportBase.h

@@ -585,6 +585,41 @@ class Transport
         throw NotImplementedError("Transport::getMixDiffCoeffsMass");
     }
 
+    //! Get/set the polynomial fits to the transport properties
+    virtual void getViscosityPolynomials(size_t i, double* coeffs) const{
+        throw NotImplementedError("Transport::getViscosityPolynomials");
+    }
+
+    virtual void getConductivityPolynomials(size_t i, double* coeffs) const{
+        throw NotImplementedError("Transport::getConductivityPolynomials");
+    }
+
+    virtual void getBinDiffusivityPolynomials(size_t i, size_t j, double* coeffs) const{
+        throw NotImplementedError("Transport::getBinDiffusivityPolynomials");
+    }
+
+    virtual void getCollisionIntegralPolynomials(size_t i, size_t j, double* astar_coeffs, 
+                                                double* bstar_coeffs, double* cstar_coeffs) const{
+        throw NotImplementedError("Transport::getCollisionIntegralPolynomials");
+    }
+
+    virtual void setViscosityPolynomials(size_t i, double* coeffs){
+        throw NotImplementedError("Transport::setViscosityPolynomials");
+    }
+
+    virtual void setConductivityPolynomials(size_t i, double* coeffs){
+        throw NotImplementedError("Transport::setConductivityPolynomials");
+    }
+
+    virtual void setBinDiffusivityPolynomials(size_t i, size_t j, double* coeffs){
+        throw NotImplementedError("Transport::setBinDiffusivityPolynomials");
+    }
+
+    virtual void setCollisionIntegralPolynomials(size_t i, size_t j, double* astar_coeffs, 
+                                                double* bstar_coeffs, double* cstar_coeffs, bool flag){
+        throw NotImplementedError("Transport::setCollisionIntegralPolynomials");
+    }
+
     //! Set model parameters for derived classes
     /*!
      * This method may be derived in subclasses to set model-specific
@@ -667,6 +702,10 @@ class Transport
 
     //! Set root Solution holding all phase information
     virtual void setRoot(std::shared_ptr<Solution> root);
+
+    virtual bool CKMode() const {
+        throw NotImplementedError("Transport::CK_Mode");
+    }
 
 protected:
     //! Enable the transport object for use.

interfaces/cython/cantera/_cantera.pxd

@@ -581,6 +581,7 @@ cdef extern from "cantera/transport/TransportBase.h" namespace "Cantera":
     cdef cppclass CxxTransport "Cantera::Transport":
         CxxTransport(CxxThermoPhase*)
         string transportType()
+        cbool CKMode()
         double viscosity() except +translate_exception
         double thermalConductivity() except +translate_exception
         double electricalConductivity() except +translate_exception
@@ -1096,6 +1097,16 @@ cdef extern from "cantera/cython/wrappers.h":
     cdef void tran_getMultiDiffCoeffs(CxxTransport*, size_t, double*) except +translate_exception
     cdef void tran_getBinaryDiffCoeffs(CxxTransport*, size_t, double*) except +translate_exception
 
+    cdef void tran_getViscosityPolynomials(CxxTransport*, size_t, double*) except +translate_exception
+    cdef void tran_getConductivityPolynomials(CxxTransport*, size_t, double*) except +translate_exception
+    cdef void tran_getBinDiffusivityPolynomials(CxxTransport*, size_t, size_t, double*) except +translate_exception
+    cdef void tran_getCollisionIntegralPolynomials(CxxTransport*, size_t, size_t, double*, double*, double*) except +translate_exception
+
+    cdef void tran_setViscosityPolynomials(CxxTransport*, size_t, double*) except +translate_exception
+    cdef void tran_setConductivityPolynomials(CxxTransport*, size_t, double*) except +translate_exception
+    cdef void tran_setBinDiffusivityPolynomials(CxxTransport*, size_t, size_t, double*) except +translate_exception
+    cdef void tran_setCollisionIntegralPolynomials(CxxTransport*, size_t, size_t, double*, double*, double*, bool) except +translate_exception
+
 # typedefs
 ctypedef void (*thermoMethod1d)(CxxThermoPhase*, double*) except +translate_exception
 ctypedef void (*transportMethod1d)(CxxTransport*, double*) except +translate_exception

interfaces/cython/cantera/test/test_transport.py

@@ -155,7 +155,53 @@ def test_species_visosities(self):
             self.phase.TP = 800, 5*ct.one_atm
             self.assertNear(self.phase[species_name].species_viscosities[0],
                             visc)
-
+
+    def test_transport_polynomial_fits_viscosity(self):
+        visc1_h2o = self.phase['H2O'].species_viscosities[0]
+        mu_poly_h2o = self.phase.viscosity_polynomial(self.phase.species_index('H2O'))        
+        visc1_h2 = self.phase['H2'].species_viscosities[0]
+        mu_poly_h2 = self.phase.viscosity_polynomial(self.phase.species_index('H2'))
+        self.phase.modify_viscosity_polynomial(self.phase.species_index('H2'), mu_poly_h2o)
+        visc2_h2 = self.phase['H2'].species_viscosities[0]
+        self.phase.modify_viscosity_polynomial(self.phase.species_index('H2'), mu_poly_h2)
+        visc3_h2 = self.phase['H2'].species_viscosities[0]
+        self.assertTrue(visc1_h2o != visc1_h2)
+        self.assertEqual(visc1_h2o, visc2_h2)
+        self.assertEqual(visc1_h2, visc3_h2)
+
+    def test_transport_polynomial_fits_conductivity(self):
+        self.phase.X = {'O2': 1}
+        cond1_o2 = self.phase.thermal_conductivity
+        lambda_poly_o2 = self.phase.thermal_conductivity_polynomial(self.phase.species_index('O2'))  
+        self.phase.X = {'H2': 1}      
+        cond1_h2 = self.phase.thermal_conductivity
+        lambda_poly_h2 = self.phase.thermal_conductivity_polynomial(self.phase.species_index('H2'))
+        self.phase.modify_thermal_conductivity_polynomial(self.phase.species_index('H2'), lambda_poly_o2)
+        cond2_h2 = self.phase.thermal_conductivity
+        self.phase.modify_thermal_conductivity_polynomial(self.phase.species_index('H2'), lambda_poly_h2)
+        cond3_h2 = self.phase.thermal_conductivity
+        self.assertTrue(cond1_o2 != cond1_h2)
+        self.assertEqual(cond1_o2, cond2_h2)
+        self.assertEqual(cond1_h2, cond3_h2)
+
+    def test_transport_polynomial_fits_diffusion(self):
+        D12 = self.phase.binary_diff_coeffs[1, 2]
+        D23 = self.phase.binary_diff_coeffs[2, 3]
+        bd_poly_12 = self.phase.binary_diff_coeffs_polynomial(1, 2)
+        bd_poly_23 = self.phase.binary_diff_coeffs_polynomial(2, 3)
+        self.phase.modify_binary_diff_coeffs_polynomial(1, 2, bd_poly_23)
+        self.phase.modify_binary_diff_coeffs_polynomial(2, 3, bd_poly_12)
+        D12mod = self.phase.binary_diff_coeffs[1, 2]
+        D23mod = self.phase.binary_diff_coeffs[2, 3]
+        self.phase.modify_binary_diff_coeffs_polynomial(1, 2, bd_poly_12)
+        self.phase.modify_binary_diff_coeffs_polynomial(2, 3, bd_poly_23)
+        D12new = self.phase.binary_diff_coeffs[1, 2]
+        D23new = self.phase.binary_diff_coeffs[2, 3]
+        self.assertTrue(D12 != D23)
+        self.assertEqual(D12, D23mod)
+        self.assertEqual(D23, D12mod)
+        self.assertEqual(D12, D12new)
+        self.assertEqual(D23, D23new)
 
 class TestIonTransport(utilities.CanteraTest):
     def setUp(self):

interfaces/cython/cantera/transport.pyx

@@ -18,7 +18,6 @@ cdef np.ndarray get_transport_2d(Transport tran, transportMethod2d method):
     method(tran.transport, kk, &data[0,0])
     return data
 
-
 cdef class GasTransportData:
     """
     Transport data for a single gas-phase species which can be used in
@@ -182,6 +181,11 @@ cdef class Transport(_SolutionBase):
             self.transport = newTransportMgr(stringify(model), self.thermo)
             self._transport.reset(self.transport)
 
+    property CK_mode:
+        """Boolean to indicate if the chemkin interpretation is used."""
+        def __get__(self):
+            return self.transport.CKMode()
+
     property viscosity:
         """Viscosity [Pa-s]."""
         def __get__(self):
@@ -256,6 +260,79 @@ cdef class Transport(_SolutionBase):
         def __get__(self):
             return get_transport_1d(self, tran_getMobilities)
 
+    def viscosity_polynomial(self, i):
+        """Get the polynomial fit to the logarithm of temperature for 
+        the viscosity of species i."""
+        cdef np.ndarray[np.double_t, ndim=1] data = np.empty(4 if self.transport.CKMode() else 5)
+        tran_getViscosityPolynomials(self.transport, i, &data[0])
+        return data
+
+    def thermal_conductivity_polynomial(self, i):
+        """Get the polynomial fit to the logarithm of temperature for 
+        the thermal conductivity of species i."""
+        cdef np.ndarray[np.double_t, ndim=1] data = np.empty(4 if self.transport.CKMode() else 5)
+        tran_getConductivityPolynomials(self.transport, i, &data[0])
+        return data
+
+    def binary_diff_coeffs_polynomial(self, i, j):
+        """Get the polynomial fit to the logarithm of temperature for 
+        the binary diffusion coefficient of species i and j."""
+        cdef np.ndarray[np.double_t, ndim=1] data = np.empty(4 if self.transport.CKMode() else 5)
+        tran_getBinDiffusivityPolynomials(self.transport, i, j, &data[0])
+        return data
+
+    def collision_integral_polynomials(self, i, j):
+        """Get the polynomial fit to the logarithm of temperature for 
+        the collision integral of species i and j."""
+        cdef np.ndarray[np.double_t, ndim=1] adata = np.empty(7 if self.transport.CKMode() else 9)
+        cdef np.ndarray[np.double_t, ndim=1] bdata = np.empty(7 if self.transport.CKMode() else 9)
+        cdef np.ndarray[np.double_t, ndim=1] cdata = np.empty(7 if self.transport.CKMode() else 9)
+        tran_getCollisionIntegralPolynomials(self.transport, i, j, &adata[0], &bdata[0], &cdata[0])
+        return adata, bdata, cdata
+
+    def modify_viscosity_polynomial(self, i, values):
+        """Set the polynomial fit to the logarithm of temperature for 
+        the viscosity of species i."""
+        if len(values) != (4 if self.transport.CKMode() else 5):
+            msg = "Got {}. Expected {}".format(len(values), (4 if self.transport.CKMode() else 5))
+            raise ValueError('Array has incorrect length. ' + msg + '.')
+        cdef np.ndarray[np.double_t, ndim=1] data = np.ascontiguousarray(values, dtype=np.double)
+        tran_setViscosityPolynomials(self.transport, i, &data[0])
+
+    def modify_thermal_conductivity_polynomial(self, i, values):
+        """Set the polynomial fit to the logarithm of temperature for 
+        the thermal conductivity of species i."""
+        if len(values) != (4 if self.transport.CKMode() else 5):
+            msg = "Got {}. Expected {}".format(len(values), (4 if self.transport.CKMode() else 5))
+            raise ValueError('Array has incorrect length. ' + msg + '.')
+        cdef np.ndarray[np.double_t, ndim=1] data = np.ascontiguousarray(values, dtype=np.double)
+        tran_setConductivityPolynomials(self.transport, i, &data[0])
+
+    def modify_binary_diff_coeffs_polynomial(self, i, j, values):
+        """Set the polynomial fit to the logarithm of temperature for 
+        the binary diffusion coefficient of species i and j."""
+        if len(values) != (4 if self.transport.CKMode() else 5):
+            msg = "Got {}. Expected {}".format(len(values), (4 if self.transport.CKMode() else 5))
+            raise ValueError('Array has incorrect length. ' + msg + '.')
+        cdef np.ndarray[np.double_t, ndim=1] data = np.ascontiguousarray(values, dtype=np.double)
+        tran_setBinDiffusivityPolynomials(self.transport, i, j, &data[0])
+
+    def modify_collision_integral_polynomials(self, i, j, avalues, bvalues, cvalues, actualT=True):
+        """Get the polynomial fit to the logarithm of temperature for 
+        the collision integral of species i and j."""
+        if len(avalues) != (7 if self.transport.CKMode() else 9):
+            msg = "Got {}. Expected {}".format(len(avalues), (7 if self.transport.CKMode() else 9))
+            raise ValueError('Array has incorrect length. ' + msg + '.')
+        if len(bvalues) != (7 if self.transport.CKMode() else 9):
+            msg = "Got {}. Expected {}".format(len(bvalues), (7 if self.transport.CKMode() else 9))
+            raise ValueError('Array has incorrect length. ' + msg + '.')
+        if len(cvalues) != (7 if self.transport.CKMode() else 9):
+            msg = "Got {}. Expected {}".format(len(cvalues), (7 if self.transport.CKMode() else 9))
+            raise ValueError('Array has incorrect length. ' + msg + '.')
+        cdef np.ndarray[np.double_t, ndim=1] adata = np.ascontiguousarray(avalues, dtype=np.double)
+        cdef np.ndarray[np.double_t, ndim=1] bdata = np.ascontiguousarray(bvalues, dtype=np.double)
+        cdef np.ndarray[np.double_t, ndim=1] cdata = np.ascontiguousarray(cvalues, dtype=np.double)
+        tran_setCollisionIntegralPolynomials(self.transport, i, j, &adata[0], &bdata[0], &cdata[0], actualT)
 
 cdef class DustyGasTransport(Transport):
     """