TransportBase.h

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/**
 * @file TransportBase.h Headers for the Transport object, which is the virtual
 *     base class for all transport property evaluators and also includes the
 *     tranprops group definition (see \ref tranprops and \link
 *     Cantera::Transport Transport \endlink) .
 */

// This file is part of Cantera. See License.txt in the top-level directory or
// at http://www.cantera.org/license.txt for license and copyright information.

/**
 * @defgroup tranprops Transport Properties for Species in Phases
 *
 * @ingroup phases
 *
 * These classes provide transport properties.
 */

#ifndef CT_TRANSPORTBASE_H
#define CT_TRANSPORTBASE_H

#include "cantera/thermo/ThermoPhase.h"

namespace Cantera
{

class LiquidTransportParams;
class SolidTransportData;

/*!
 * \addtogroup tranprops
 */
//!  \cond

const int CK_Mode = 10;

//!   \endcond

//! The diffusion fluxes must be referenced to a particular reference
//! fluid velocity.
/*!
 * Most typical is to reference the diffusion fluxes to the mass averaged
 * velocity, but referencing to the mole averaged velocity is suitable for some
 * liquid flows, and referencing to a single species is suitable for solid phase
 * transport within a lattice.  Currently, the identity of the reference
 * velocity is coded into each transport object as a typedef named
 * VelocityBasis, which is equated to an integer. Negative values of this
 * variable refer to mass or mole-averaged velocities.  Zero or positive
 * quantities refers to the reference velocity being referenced to a particular
 * species. Below are the predefined constants for its value.
 *
 * - VB_MASSAVG    Diffusion velocities are based on the mass averaged velocity
 * - VB_MOLEAVG    Diffusion velocities are based on the mole averaged velocities
 * - VB_SPECIES_0  Diffusion velocities are based on the relative motion wrt species 0
 * - ...
 * - VB_SPECIES_3  Diffusion velocities are based on the relative motion wrt species 3
 *
 * @ingroup tranprops
 */
typedef int VelocityBasis;

/*!
 * \addtogroup tranprops
 */
//@{
//! Diffusion velocities are based on the mass averaged velocity
const VelocityBasis VB_MASSAVG = -1;
//! Diffusion velocities are based on the mole averaged velocities
const VelocityBasis VB_MOLEAVG = -2;
//! Diffusion velocities are based on the relative motion wrt species 0
const VelocityBasis VB_SPECIES_0 = 0;
//! Diffusion velocities are based on the relative motion wrt species 1
const VelocityBasis VB_SPECIES_1 = 1;
//! Diffusion velocities are based on the relative motion wrt species 2
const VelocityBasis VB_SPECIES_2 = 2;
//! Diffusion velocities are based on the relative motion wrt species 3
const VelocityBasis VB_SPECIES_3 = 3;
//@}

//! Base class for transport property managers.
/*!
 * All classes that compute transport properties for a single phase derive from
 * this class.  Class Transport is meant to be used as a base class only. It is
 * possible to instantiate it, but its methods throw exceptions if called.
 *
 * ## Relationship of the Transport class to the ThermoPhase Class
 *
 * This section describes how calculations are carried out within the Transport
 * class. The Transport class and derived classes of the the Transport class
 * necessarily use the ThermoPhase class to obtain the list of species and the
 * thermodynamic state of the phase.
 *
 * No state information is stored within Transport classes. Queries to the
 * underlying ThermoPhase object must be made to obtain the state of the system.
 *
 * An exception to this however is the state information concerning the the
 * gradients of variables. This information is not stored within the ThermoPhase
 * objects. It may be collected within the Transport objects. In fact, the
 * meaning of const operations within the Transport class refers to calculations
 * which do not change the state of the system nor the state of the first order
 * gradients of the system.
 *
 * When a const operation is evoked within the Transport class, it is also
 * implicitly assumed that the underlying state within the ThermoPhase object
 * has not changed its values.
 *
 * ## Diffusion Fluxes and their Relationship to Reference Velocities
 *
 * The diffusion fluxes must be referenced to a particular reference fluid
 * velocity. Most typical is to reference the diffusion fluxes to the mass
 * averaged velocity, but referencing to the mole averaged velocity is suitable
 * for some liquid flows, and referencing to a single species is suitable for
 * solid phase transport within a lattice.  Currently, the identity of the
 * reference velocity is coded into each transport object as a typedef named
 * VelocityBasis, which is equated to an integer. Negative values of this
 * variable refer to mass or mole-averaged velocities.  Zero or positive
 * quantities refers to the reference velocity being referenced to a particular
 * species. Below are the predefined constants for its value.
 *
 * - VB_MASSAVG    Diffusion velocities are based on the mass averaged velocity
 * - VB_MOLEAVG    Diffusion velocities are based on the mole averaged velocities
 * - VB_SPECIES_0  Diffusion velocities are based on the relative motion wrt species 0
 * - ...
 * - VB_SPECIES_3  Diffusion velocities are based on the relative motion wrt species 3
 *
 * All transport managers specify a default reference velocity in their default
 * constructors. All gas phase transport managers by default specify the mass-
 * averaged velocity as their reference velocities.
 *
 * @todo Provide a general mechanism to store the gradients of state variables
 *        within the system.
 *
 * @ingroup tranprops
 */
class Transport
{
public:
    //!  Constructor.
    /*!
     * New transport managers should be created using TransportFactory, not by
     * calling the constructor directly.
     *
     * @param thermo   Pointer to the ThermoPhase class representing this phase.
     * @param ndim     Dimension of the flux vector used in the calculation.
     *
     * @see TransportFactory
     */
    Transport(thermo_t* thermo=0, size_t ndim = 1);

    virtual ~Transport() {}

    // Transport objects are not copyable or assignable
    Transport(const Transport&) = delete;
    Transport& operator=(const Transport&) = delete;

    //! Identifies the Transport object type. Each derived class should override
    //! this method to return a meaningful identifier.
    virtual std::string transportType() const {
        return "Transport";
    }

    /*!
     * Phase object. Every transport manager is designed to compute properties
     * for a specific phase of a mixture, which might be a liquid solution, a
     * gas mixture, a surface, etc. This method returns a reference to the
     * object representing the phase itself.
     */
    thermo_t& thermo() {
        return *m_thermo;
    }

    /*!
     * Returns true if the transport manager is ready for use.
     */
    bool ready();

    //! Set the number of dimensions to be expected in flux expressions
    /*!
     *  @param ndim  Number of dimensions in flux expressions
     */
    void setNDim(const int ndim);

    //! Return the number of dimensions in flux expressions
    size_t nDim() const {
        return m_nDim;
    }

    //! Check that the specified species index is in range. Throws an exception
    //! if k is greater than nSpecies()
    void checkSpeciesIndex(size_t k) const;

    //! Check that an array size is at least nSpecies(). Throws an exception if
    //! kk is less than nSpecies(). Used before calls which take an array
    //! pointer.
    void checkSpeciesArraySize(size_t kk) const;

    /**
     * @name Transport Properties
     */
    //@{

    /*!
     * The viscosity in Pa-s.
     */
    virtual doublereal viscosity() {
        throw NotImplementedError("Transport::viscosity");
    }

    //! Returns the pure species viscosities
    /*!
     * The units are Pa-s and the length is the number of species
     *
     * @param visc   Vector of viscosities
     */
    virtual void getSpeciesViscosities(doublereal* const visc) {
        throw NotImplementedError("Transport::getSpeciesViscosities");
    }

    //! The bulk viscosity in Pa-s.
    /*!
     * The bulk viscosity is only non-zero in rare cases. Most transport
     * managers either overload this method to return zero, or do not implement
     * it, in which case an exception is thrown if called.
     */
    virtual doublereal bulkViscosity() {
        throw NotImplementedError("Transport::bulkViscosity");
    }

    //! The ionic conductivity in 1/ohm/m.
    virtual doublereal ionConductivity() {
        throw NotImplementedError("Transport::ionConductivity");
    }

    //! Returns the pure species ionic conductivity
    /*!
     *  The units are 1/ohm/m and the length is the number of species
     *
     * @param ionCond   Vector of ionic conductivities
     */
    virtual void getSpeciesIonConductivity(doublereal* const ionCond) {
        throw NotImplementedError("Transport::getSpeciesIonConductivity");
    }

    //! Returns the pointer to the mobility ratios of the species in the phase
    /*!
     * @param mobRat Returns a matrix of mobility ratios for the current
     *               problem. The mobility ratio mobRat(i,j) is defined as the
     *               ratio of the mobility of species i to species j.
     *
     *         mobRat(i,j) = mu_i / mu_j
     *
     * It is returned in fortran-ordering format. i.e. it is returned as
     * mobRat[k], where
     *
     *        k = j * nsp + i
     *
     * The size of mobRat must be at least equal to nsp*nsp
     */
    virtual void mobilityRatio(double* mobRat) {
        throw NotImplementedError("Transport::mobilityRatio");
    }

    //! Returns the pure species limit of the mobility ratios
    /*!
     * The value is dimensionless and the length is the number of species
     *
     * @param mobRat   Vector of mobility ratios
     */
    virtual void getSpeciesMobilityRatio(double** mobRat) {
        throw NotImplementedError("Transport::getSpeciesMobilityRatio");
    }

    //! Returns the self diffusion coefficients of the species in the phase
    /*!
     * The self diffusion coefficient is the diffusion coefficient of a tracer
     * species at the current temperature and composition of the species.
     * Therefore, the dilute limit of transport is assumed for the tracer
     * species. The effective formula may be calculated from the Stefan-Maxwell
     * formulation by adding another row for the tracer species, assigning all
     * D's to be equal to the respective species D's, and then taking the limit
     * as the tracer species mole fraction goes to zero. The corresponding flux
     * equation for the tracer species k in units of kmol m-2 s-1 is.
     *
     * \f[
     *     J_k = - D^{sd}_k \frac{C_k}{R T}  \nabla \mu_k
     * \f]
     *
     * The derivative is taken at constant T and P.
     *
     * The self diffusion calculation is handled by subclasses of
     * LiquidTranInteraction as specified in the input file. These in turn
     * employ subclasses of LTPspecies to determine the individual species self
     * diffusion coeffs.
     *
     * @param selfDiff Vector of self-diffusion coefficients. Length = number
     *                 of species in phase. units = m**2 s-1.
     */
    virtual void selfDiffusion(doublereal* const selfDiff) {
        throw NotImplementedError("Transport::selfDiffusion");
    }

    //! Returns the pure species self diffusion in solution of each species
    /*!
     * The pure species molar volumes are evaluated using the appropriate
     * subclasses of LTPspecies as specified in the input file.
     *
     * @param selfDiff  array of length "number of species"
     *              to hold returned self diffusion coeffs.
     */
    virtual void getSpeciesSelfDiffusion(double** selfDiff) {
        throw NotImplementedError("Transport::getSpeciesSelfDiffusion");
    }

    //! Returns the mixture thermal conductivity in W/m/K.
    /*!
     * Units are in W / m K  or equivalently kg m / s3 K
     *
     * @returns thermal conductivity in W/m/K.
     */
    virtual doublereal thermalConductivity() {
        throw NotImplementedError("Transport::thermalConductivity");
    }

    //! The electrical conductivity (Siemens/m).
    virtual doublereal electricalConductivity() {
        throw NotImplementedError("Transport::electricalConductivity");
    }

    //! Get the Electrical mobilities (m^2/V/s).
    /*!
     * This function returns the mobilities. In some formulations this is equal
     * to the normal mobility multiplied by Faraday's constant.
     *
     * Frequently, but not always, the mobility is calculated from the diffusion
     * coefficient using the Einstein relation
     *
     * \f[
     *      \mu^e_k = \frac{F D_k}{R T}
     * \f]
     *
     * @param mobil_e  Returns the mobilities of the species in array \c
     *               mobil_e. The array must be dimensioned at least as large as
     *               the number of species.
     */
    virtual void getMobilities(doublereal* const mobil_e) {
        throw NotImplementedError("Transport::getMobilities");
    }

    //! Get the fluid mobilities (s kmol/kg).
    /*!
     * This function returns the fluid mobilities. Usually, you have to multiply
     * Faraday's constant into the resulting expression to general a species
     * flux expression.
     *
     * Frequently, but not always, the mobility is calculated from the diffusion
     * coefficient using the Einstein relation
     *
     * \f[
     *      \mu^f_k = \frac{D_k}{R T}
     * \f]
     *
     * @param mobil_f  Returns the mobilities of the species in array \c mobil.
     *               The array must be dimensioned at least as large as the
     *               number of species.
     */
    virtual void getFluidMobilities(doublereal* const mobil_f) {
        throw NotImplementedError("Transport::getFluidMobilities");
    }

    //@}

    //! Compute the mixture electrical conductivity (S m-1) at the current
    //! conditions of the phase (Siemens m-1)
    /*!
     * The electrical conductivity, \f$ \sigma \f$, relates the electric current
     * density, J, to the electric field, E.
     *
     * \f[
     *        \vec{J} = \sigma \vec{E}
     * \f]
     *
     * We assume here that the mixture electrical conductivity is an isotropic
     * quantity, at this stage. Tensors may be included at a later time.
     *
     * The conductivity is the reciprocal of the resistivity.
     *
     * The units are Siemens m-1, where 1 S = 1 A / volt = 1 s^3 A^2 /kg /m^2
     */
    virtual doublereal getElectricConduct() {
        throw NotImplementedError("Transport::getElectricConduct");
    }

    //! Compute the electric current density in A/m^2
    /*!
     * Calculates the electric current density as a vector, given the gradients
     * of the field variables.
     *
     * @param ndim    The number of spatial dimensions (1, 2, or 3).
     * @param grad_T  The temperature gradient (ignored in this model).
     * @param ldx     Leading dimension of the grad_X array.
     * @param grad_X  The gradient of the mole fraction
     * @param ldf     Leading dimension of the grad_V and current vectors.
     * @param grad_V  The electrostatic potential gradient.
     * @param current The electric current in A/m^2. This is a vector of length ndim
     */
    virtual void getElectricCurrent(int ndim,
                                    const doublereal* grad_T,
                                    int ldx,
                                    const doublereal* grad_X,
                                    int ldf,
                                    const doublereal* grad_V,
                                    doublereal* current) {
        throw NotImplementedError("Transport::getElectricCurrent");
    }

    //! Get the species diffusive mass fluxes wrt to the specified solution
    //! averaged velocity, given the gradients in mole fraction and temperature
    /*!
     * Units for the returned fluxes are kg m-2 s-1.
     *
     * Usually the specified solution average velocity is the mass averaged
     * velocity. This is changed in some subclasses, however.
     *
     * @param ndim       Number of dimensions in the flux expressions
     * @param grad_T     Gradient of the temperature (length = ndim)
     * @param ldx        Leading dimension of the grad_X array (usually equal to
     *                   m_nsp but not always)
     * @param grad_X     Gradients of the mole fraction Flat vector with the
     *                   m_nsp in the inner loop. length = ldx * ndim
     * @param ldf        Leading dimension of the fluxes array (usually equal to
     *                   m_nsp but not always)
     * @param fluxes     Output of the diffusive mass fluxes. Flat vector with
     *                   the m_nsp in the inner loop. length = ldx * ndim
     */
    virtual void getSpeciesFluxes(size_t ndim, const doublereal* const grad_T,
                                  size_t ldx, const doublereal* const grad_X,
                                  size_t ldf, doublereal* const fluxes);

    //! Get the species diffusive mass fluxes wrt to the mass averaged velocity,
    //! given the gradients in mole fraction, temperature and electrostatic
    //! potential.
    /*!
     * Units for the returned fluxes are kg m-2 s-1.
     *
     * @param[in] ndim Number of dimensions in the flux expressions
     * @param[in] grad_T Gradient of the temperature. (length = ndim)
     * @param[in] ldx  Leading dimension of the grad_X array (usually equal to
     *              m_nsp but not always)
     * @param[in] grad_X Gradients of the mole fraction. Flat vector with the
     *             m_nsp in the inner loop. length = ldx * ndim.
     * @param[in] ldf  Leading dimension of the fluxes array (usually equal to
     *              m_nsp but not always).
     * @param[in] grad_Phi Gradients of the electrostatic potential (length = ndim)
     * @param[out] fluxes  The diffusive mass fluxes. Flat vector with the m_nsp
     *             in the inner loop. length = ldx * ndim.
     */
    virtual void getSpeciesFluxesES(size_t ndim,
                                    const doublereal* grad_T,
                                    size_t ldx,
                                    const doublereal* grad_X,
                                    size_t ldf,
                                    const doublereal* grad_Phi,
                                    doublereal* fluxes) {
        getSpeciesFluxes(ndim, grad_T, ldx, grad_X, ldf, fluxes);
    }

    //! Get the species diffusive velocities wrt to the mass averaged velocity,
    //! given the gradients in mole fraction and temperature
    /*!
     * @param[in] ndim Number of dimensions in the flux expressions
     * @param[in] grad_T Gradient of the temperature (length = ndim)
     * @param[in] ldx  Leading dimension of the grad_X array (usually equal to
     *              m_nsp but not always)
     * @param[in] grad_X Gradients of the mole fraction. Flat vector with the
     *             m_nsp in the inner loop. length = ldx * ndim
     * @param[in] ldf  Leading dimension of the fluxes array (usually equal to
     *              m_nsp but not always)
     * @param[out] Vdiff  Diffusive velocities wrt the mass- averaged velocity.
     *               Flat vector with the m_nsp in the inner loop.
     *               length = ldx * ndim. units are m / s.
     */
    virtual void getSpeciesVdiff(size_t ndim,
                                 const doublereal* grad_T,
                                 int ldx,
                                 const doublereal* grad_X,
                                 int ldf,
                                 doublereal* Vdiff) {
        throw NotImplementedError("Transport::getSpeciesVdiff");
    }

    //! Get the species diffusive velocities wrt to the mass averaged velocity,
    //! given the gradients in mole fraction, temperature, and electrostatic
    //! potential.
    /*!
     * @param[in] ndim Number of dimensions in the flux expressions
     * @param[in] grad_T Gradient of the temperature (length = ndim)
     * @param[in] ldx  Leading dimension of the grad_X array (usually equal to
     *              m_nsp but not always)
     * @param[in] grad_X Gradients of the mole fraction. Flat vector with the
     *             m_nsp in the inner loop. length = ldx * ndim.
     * @param[in] ldf  Leading dimension of the fluxes array (usually equal to
     *              m_nsp but not always)
     * @param[in] grad_Phi Gradients of the electrostatic potential
     *                 (length = ndim)
     * @param[out] Vdiff  Diffusive velocities wrt the mass-averaged velocity.
     *               Flat vector with the m_nsp in the inner loop. length = ldx
     *               * ndim. units are m / s.
     */
    virtual void getSpeciesVdiffES(size_t ndim,
                                   const doublereal* grad_T,
                                   int ldx,
                                   const doublereal* grad_X,
                                   int ldf,
                                   const doublereal* grad_Phi,
                                   doublereal* Vdiff) {
        getSpeciesVdiff(ndim, grad_T, ldx, grad_X, ldf, Vdiff);
    }

    //! Get the molar fluxes [kmol/m^2/s], given the thermodynamic state at two
    //! nearby points.
    /*!
     * @param[in] state1 Array of temperature, density, and mass fractions for
     *               state 1.
     * @param[in] state2 Array of temperature, density, and mass fractions for
     *               state 2.
     * @param[in] delta  Distance from state 1 to state 2 (m).
     * @param[out] cfluxes Output array containing the diffusive molar fluxes of
     *               species from state1 to state2. This is a flat vector with
     *               m_nsp in the inner loop. length = ldx * ndim. Units are
     *               [kmol/m^2/s].
     */
    virtual void getMolarFluxes(const doublereal* const state1,
                                const doublereal* const state2, const doublereal delta,
                                doublereal* const cfluxes) {
        throw NotImplementedError("Transport::getMolarFluxes");
    }

    //! Get the mass fluxes [kg/m^2/s], given the thermodynamic state at two
    //! nearby points.
    /*!
     * @param[in] state1 Array of temperature, density, and mass
     *               fractions for state 1.
     * @param[in] state2 Array of temperature, density, and mass fractions for
     *               state 2.
     * @param[in] delta Distance from state 1 to state 2 (m).
     * @param[out] mfluxes Output array containing the diffusive mass fluxes of
     *               species from state1 to state2. This is a flat vector with
     *               m_nsp in the inner loop. length = ldx * ndim. Units are
     *               [kg/m^2/s].
     */
    virtual void getMassFluxes(const doublereal* state1,
                               const doublereal* state2, doublereal delta,
                               doublereal* mfluxes) {
        throw NotImplementedError("Transport::getMassFluxes");
    }

    //! Return a vector of Thermal diffusion coefficients [kg/m/sec].
    /*!
     * The thermal diffusion coefficient \f$ D^T_k \f$ is defined so that the
     * diffusive mass flux of species *k* induced by the local temperature
     * gradient is given by the following formula:
     *
     * \f[
     *     M_k J_k = -D^T_k \nabla \ln T.
     * \f]
     *
     * The thermal diffusion coefficient can be either positive or negative.
     *
     * @param dt On return, dt will contain the species thermal diffusion
     *           coefficients.  Dimension dt at least as large as the number of
     *           species. Units are kg/m/s.
     */
    virtual void getThermalDiffCoeffs(doublereal* const dt) {
        throw NotImplementedError("Transport::getThermalDiffCoeffs");
    }

    //! Returns the matrix of binary diffusion coefficients [m^2/s].
    /*!
     * @param[in] ld   Inner stride for writing the two dimension diffusion
     *                 coefficients into a one dimensional vector
     * @param[out] d   Diffusion coefficient matrix (must be at least m_k * m_k
     *                 in length.
     */
    virtual void getBinaryDiffCoeffs(const size_t ld, doublereal* const d) {
        throw NotImplementedError("Transport::getBinaryDiffCoeffs");
    }

    //! Return the Multicomponent diffusion coefficients. Units: [m^2/s].
    /*!
     * If the transport manager implements a multicomponent diffusion
     * model, then this method returns the array of multicomponent
     * diffusion coefficients. Otherwise it throws an exception.
     *
     * @param[in] ld  The dimension of the inner loop of d (usually equal to m_nsp)
     * @param[out] d  flat vector of diffusion coefficients, fortran ordering.
     *            d[ld*j+i] is the D_ij diffusion coefficient (the diffusion
     *            coefficient for species i due to species j).
     */
    virtual void getMultiDiffCoeffs(const size_t ld, doublereal* const d) {
        throw NotImplementedError("Transport::getMultiDiffCoeffs");
    }

    //! Returns a vector of mixture averaged diffusion coefficients
    /**
     * Mixture-averaged diffusion coefficients [m^2/s].  If the transport
     * manager implements a mixture-averaged diffusion model, then this method
     * returns the array of mixture-averaged diffusion coefficients. Otherwise
     * it throws an exception.
     *
     * @param d  Return vector of mixture averaged diffusion coefficients
     *           Units = m2/s. Length = n_sp
     */
    virtual void getMixDiffCoeffs(doublereal* const d) {
        throw NotImplementedError("Transport::getMixDiffCoeffs");
    }

    //! Returns a vector of mixture averaged diffusion coefficients
    virtual void getMixDiffCoeffsMole(doublereal* const d) {
        throw NotImplementedError("Transport::getMixDiffCoeffsMole");
    }

    //! Returns a vector of mixture averaged diffusion coefficients
    virtual void getMixDiffCoeffsMass(doublereal* const d) {
        throw NotImplementedError("Transport::getMixDiffCoeffsMass");
    }

    //! Set model parameters for derived classes
    /*!
     * This method may be derived in subclasses to set model-specific
     * parameters. The primary use of this class is to set parameters while in
     * the middle of a calculation without actually having to dynamically cast
     * the base Transport pointer.
     *
     * @param type    Specifies the type of parameters to set
     *                 0 : Diffusion coefficient
     *                 1 : Thermal Conductivity
     *                 The rest are currently unused.
     * @param k       Species index to set the parameters on
     * @param p       Vector of parameters. The length of the vector varies with
     *                 the parameterization
     */
    virtual void setParameters(const int type, const int k, const doublereal* const p);

    //! Sets the velocity basis
    /*!
     * What the transport object does with this parameter is up to the
     * individual operator. Currently, this is not functional for most transport
     * operators including all of the gas-phase operators.
     *
     * @param ivb   Species the velocity basis
     */
    void setVelocityBasis(VelocityBasis ivb) {
        m_velocityBasis = ivb;
    }

    //! Gets the velocity basis
    /*!
     * What the transport object does with this parameter is up to the
     * individual operator. Currently, this is not functional for most transport
     * operators including all of the gas-phase operators.
     *
     * @returns the velocity basis
     */
    VelocityBasis getVelocityBasis() const {
        return m_velocityBasis;
    }

    /**
     * @name Transport manager construction
     * These methods are used during construction.
     * @{
     */

    //! Initialize a transport manager
    /*!
     * This routine sets up a transport manager. It calculates the collision
     * integrals and populates species-dependent data structures.
     *
     * @param thermo  Pointer to the ThermoPhase object
     * @param mode    Chemkin compatible mode or not. This alters the
     *                 specification of the collision integrals. defaults to no.
     * @param log_level Defaults to zero, no logging
     */
    virtual void init(thermo_t* thermo, int mode=0, int log_level=0) {}

    //! Called by TransportFactory to set parameters.
    /*!
     * This is called by classes that use the liquid phase parameter list to
     * initialize themselves.
     *
     * @param tr Reference to the parameter list that will be used to initialize
     *           the class
     */
    virtual bool initLiquid(LiquidTransportParams& tr) {
        throw NotImplementedError("Transport::initLiquid");
    }

    //! Called by TransportFactory to set parameters.
    /*!
     * This is called by classes that use the solid phase parameter list to
     * initialize themselves.
     *
     * @param tr Reference to the parameter list that will be used to initialize
     *           the class
     */
    virtual bool initSolid(SolidTransportData& tr) {
        throw NotImplementedError("Transport::initSolid");
    }

    //! Specifies the ThermoPhase object.
    /*!
     * We have relaxed this operation so that it will succeed when the
     * underlying old and new ThermoPhase objects have the same number of
     * species and the same names of the species in the same order. The idea
     * here is to allow copy constructors and duplicators to work. In order for
     * them to work, we need a method to switch the internal pointer within the
     * Transport object after the duplication takes place.  Also, different
     * thermodynamic instantiations of the same species should also work.
     *
     * @param   thermo  Reference to the ThermoPhase object that the transport
     *                  object will use
     */
    virtual void setThermo(thermo_t& thermo);

protected:
    //! Enable the transport object for use.
    /*!
     * Once finalize() has been called, the transport manager should be ready to
     * compute any supported transport property, and no further modifications to
     * the model parameters should be made.
     */
    void finalize();

    //@}

    //! pointer to the object representing the phase
    thermo_t* m_thermo;

    //! true if finalize has been called
    bool m_ready;

    //! Number of species
    size_t m_nsp;

    //! Number of dimensions used in flux expressions
    size_t m_nDim;

    //! Velocity basis from which diffusion velocities are computed.
    //! Defaults to the mass averaged basis = -2
    int m_velocityBasis;
};

}

#endif