SimpleTransport.cpp

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/**
 *  @file SimpleTransport.cpp
 *  Simple mostly constant transport properties
 */
#include "cantera/transport/SimpleTransport.h"
#include "cantera/base/stringUtils.h"

using namespace std;

namespace Cantera
{
SimpleTransport::SimpleTransport(thermo_t* thermo, int ndim) :
    Transport(thermo, ndim),
    tempDepType_(0),
    compositionDepType_(LTI_MODEL_SOLVENT),
    useHydroRadius_(false),
    doMigration_(0),
    m_iStateMF(-1),
    concTot_(0.0),
    meanMolecularWeight_(-1.0),
    dens_(-1.0),
    m_temp(-1.0),
    m_press(-1.0),
    m_lambda(-1.0),
    m_viscmix(-1.0),
    m_visc_mix_ok(false),
    m_visc_temp_ok(false),
    m_diff_mix_ok(false),
    m_diff_temp_ok(false),
    m_cond_temp_ok(false),
    m_cond_mix_ok(false),
    m_nDim(1)
{
}

SimpleTransport::SimpleTransport(const SimpleTransport& right) :
    tempDepType_(0),
    compositionDepType_(LTI_MODEL_SOLVENT),
    useHydroRadius_(false),
    doMigration_(0),
    m_iStateMF(-1),
    concTot_(0.0),
    m_temp(-1.0),
    m_press(-1.0),
    m_lambda(-1.0),
    m_viscmix(-1.0),
    m_visc_mix_ok(false),
    m_visc_temp_ok(false),
    m_diff_mix_ok(false),
    m_diff_temp_ok(false),
    m_cond_temp_ok(false),
    m_cond_mix_ok(false),
    m_nDim(1)
{
    /*
     * Use the assignment operator to do the brunt
     * of the work for the copy constructor.
     */
    *this = right;
}

SimpleTransport& SimpleTransport::operator=(const SimpleTransport& right)
{
    if (&right == this) {
        return *this;
    }
    Transport::operator=(right);

    tempDepType_                          = right.tempDepType_;
    compositionDepType_                   = right.compositionDepType_;
    useHydroRadius_                       = right.useHydroRadius_;
    doMigration_                          = right.doMigration_;
    m_mw                                  = right.m_mw;

    m_coeffVisc_Ns = right.m_coeffVisc_Ns;
    for (size_t k = 0; k <right.m_coeffVisc_Ns.size() ; k++) {
        if (right.m_coeffVisc_Ns[k]) {
            m_coeffVisc_Ns[k] = (right.m_coeffVisc_Ns[k])->duplMyselfAsLTPspecies();
        }
    }

    m_coeffLambda_Ns = right.m_coeffLambda_Ns;
    for (size_t k = 0; k < right.m_coeffLambda_Ns.size(); k++) {
        if (right.m_coeffLambda_Ns[k]) {
            m_coeffLambda_Ns[k] = (right.m_coeffLambda_Ns[k])->duplMyselfAsLTPspecies();
        }
    }

    m_coeffDiff_Ns = right.m_coeffDiff_Ns;
    for (size_t k = 0; k < right.m_coeffDiff_Ns.size(); k++) {
        if (right.m_coeffDiff_Ns[k]) {
            m_coeffDiff_Ns[k] = (right.m_coeffDiff_Ns[k])->duplMyselfAsLTPspecies();
        }
    }

    m_coeffHydroRadius_Ns = right.m_coeffHydroRadius_Ns;
    for (size_t k = 0; k < right.m_coeffHydroRadius_Ns.size(); k++) {
        if (right.m_coeffHydroRadius_Ns[k]) {
            m_coeffHydroRadius_Ns[k] = (right.m_coeffHydroRadius_Ns[k])->duplMyselfAsLTPspecies();
        }
    }

    m_Grad_X                              = right.m_Grad_X;
    m_Grad_T                              = right.m_Grad_T;
    m_Grad_P                              = right.m_Grad_P;
    m_Grad_V                              = right.m_Grad_V;

    m_diffSpecies                         = right.m_diffSpecies;
    m_viscSpecies                         = right.m_viscSpecies;
    m_condSpecies                         = right.m_condSpecies;
    m_iStateMF = -1;
    m_molefracs                           = right.m_molefracs;
    m_concentrations                      = right.m_concentrations;
    concTot_                              = right.concTot_;
    meanMolecularWeight_                  = right.meanMolecularWeight_;
    dens_                                 = right.dens_;
    m_chargeSpecies                       = right.m_chargeSpecies;

    m_temp                                = right.m_temp;
    m_press                               = right.m_press;
    m_lambda                              = right.m_lambda;
    m_viscmix                             = right.m_viscmix;
    m_spwork                              = right.m_spwork;
    m_visc_mix_ok    = false;
    m_visc_temp_ok   = false;
    m_diff_mix_ok    = false;
    m_diff_temp_ok   = false;
    m_cond_temp_ok   = false;
    m_cond_mix_ok    = false;
    m_nDim                                = right.m_nDim;

    return *this;
}

Transport* SimpleTransport::duplMyselfAsTransport() const
{
    return new SimpleTransport(*this);
}

SimpleTransport::~SimpleTransport()
{
    for (size_t k = 0; k < m_coeffVisc_Ns.size() ; k++) {
        delete m_coeffVisc_Ns[k];
    }
    for (size_t k = 0; k < m_coeffLambda_Ns.size(); k++) {
        delete m_coeffLambda_Ns[k];
    }
    for (size_t k = 0; k < m_coeffDiff_Ns.size(); k++) {
        delete m_coeffDiff_Ns[k];
    }
    for (size_t k = 0; k < m_coeffHydroRadius_Ns.size(); k++) {
        delete m_coeffHydroRadius_Ns[k];
    }
}

bool SimpleTransport::initLiquid(LiquidTransportParams& tr)
{
    // constant substance attributes
    m_thermo = tr.thermo;
    m_nsp   = m_thermo->nSpecies();

    /*
     * Read the transport block in the phase XML Node
     * It's not an error if this block doesn't exist. Just use the defaults
     */
    XML_Node& phaseNode = m_thermo->xml();
    if (phaseNode.hasChild("transport")) {
        XML_Node& transportNode = phaseNode.child("transport");
        string transportModel = transportNode.attrib("model");
        if (transportModel == "Simple") {

            compositionDepType_ = tr.compositionDepTypeDefault_;

        } else {
            throw CanteraError("SimpleTransport::initLiquid()",
                               "transport model isn't the correct type: " + transportModel);
        }
    }

    // make a local copy of the molecular weights
    m_mw.resize(m_nsp);
    copy(m_thermo->molecularWeights().begin(), m_thermo->molecularWeights().end(), m_mw.begin());

    /*
     *  Get the input Viscosities
     */
    m_viscSpecies.resize(m_nsp);
    m_coeffVisc_Ns.clear();
    m_coeffVisc_Ns.resize(m_nsp);

    std::string spName = m_thermo->speciesName(0);

    for (size_t k = 0; k < m_nsp; k++) {
        spName = m_thermo->speciesName(k);
        Cantera::LiquidTransportData& ltd = tr.LTData[k];
        m_coeffVisc_Ns[k] = ltd.viscosity;
        ltd.viscosity = 0;
    }

    /*
     *  Get the input thermal conductivities
     */
    m_condSpecies.resize(m_nsp);
    m_coeffLambda_Ns.clear();
    m_coeffLambda_Ns.resize(m_nsp);

    for (size_t k = 0; k < m_nsp; k++) {
        spName = m_thermo->speciesName(k);
        Cantera::LiquidTransportData& ltd = tr.LTData[k];
        m_coeffLambda_Ns[k] = ltd.thermalCond;
        ltd.thermalCond = 0;
    }

    /*
     *  Get the input species diffusivities
     */
    useHydroRadius_ = false;

    m_diffSpecies.resize(m_nsp);
    m_coeffDiff_Ns.clear();
    m_coeffDiff_Ns.resize(m_nsp);

    for (size_t k = 0; k < m_nsp; k++) {
        spName = m_thermo->speciesName(k);
        Cantera::LiquidTransportData& ltd = tr.LTData[k];
        m_coeffDiff_Ns[k] = ltd.speciesDiffusivity;
        ltd.speciesDiffusivity = 0;

        if (!(m_coeffDiff_Ns[k])) {
            if (ltd.hydroRadius) {
                m_coeffHydroRadius_Ns[k] = (ltd.hydroRadius)->duplMyselfAsLTPspecies();
            }
            if (!(m_coeffHydroRadius_Ns[k])) {
                throw CanteraError("SimpleTransport::initLiquid",
                                   "Neither diffusivity nor hydroradius is set for species " + spName);
            }
        }
    }

    m_molefracs.resize(m_nsp);
    m_concentrations.resize(m_nsp);

    m_chargeSpecies.resize(m_nsp);
    for (size_t k = 0; k < m_nsp; k++) {
        m_chargeSpecies[k] = m_thermo->charge(k);
    }
    m_spwork.resize(m_nsp);

    // resize the internal gradient variables
    m_Grad_X.resize(m_nDim * m_nsp, 0.0);
    m_Grad_T.resize(m_nDim, 0.0);
    m_Grad_P.resize(m_nDim, 0.0);
    m_Grad_V.resize(m_nDim, 0.0);

    // set all flags to false
    m_visc_mix_ok   = false;
    m_visc_temp_ok  = false;

    m_cond_temp_ok = false;
    m_cond_mix_ok  = false;

    m_diff_temp_ok   = false;
    m_diff_mix_ok  = false;

    return true;
}

doublereal SimpleTransport::viscosity()
{
    update_T();
    update_C();

    if (m_visc_mix_ok) {
        return m_viscmix;
    }

    // update m_viscSpecies[] if necessary
    if (!m_visc_temp_ok) {
        updateViscosity_T();
    }

    if (compositionDepType_ == LTI_MODEL_SOLVENT) {
        m_viscmix = m_viscSpecies[0];
    } else if (compositionDepType_ == LTI_MODEL_MOLEFRACS) {
        m_viscmix = 0.0;
        for (size_t k = 0; k < m_nsp; k++) {
            m_viscmix += m_viscSpecies[k] * m_molefracs[k];
        }
    } else {
        throw CanteraError("SimpleTransport::viscosity()",
                           "Unknowns compositionDepType");
    }
    m_visc_mix_ok = true;
    return m_viscmix;
}

void SimpleTransport::getSpeciesViscosities(doublereal* const visc)
{
    update_T();
    if (!m_visc_temp_ok) {
        updateViscosity_T();
    }
    copy(m_viscSpecies.begin(), m_viscSpecies.end(), visc);
}

void SimpleTransport::getBinaryDiffCoeffs(size_t ld, doublereal* d)
{
    double bdiff;
    update_T();

    // if necessary, evaluate the species diffusion coefficients
    // from the polynomial fits
    if (!m_diff_temp_ok) {
        updateDiff_T();
    }

    for (size_t i = 0; i < m_nsp; i++) {
        for (size_t j = 0; j < m_nsp; j++) {
            bdiff = 0.5 * (m_diffSpecies[i] + m_diffSpecies[j]);
            d[i*m_nsp+j] = bdiff;
        }
    }
}

void SimpleTransport::getMobilities(doublereal* const mobil)
{
    getMixDiffCoeffs(DATA_PTR(m_spwork));
    doublereal c1 = ElectronCharge / (Boltzmann * m_temp);
    for (size_t k = 0; k < m_nsp; k++) {
        mobil[k] = c1 * m_spwork[k];
    }
}

void  SimpleTransport::getFluidMobilities(doublereal* const mobil_f)
{
    getMixDiffCoeffs(DATA_PTR(m_spwork));
    doublereal c1 = 1.0 / (GasConstant * m_temp);
    for (size_t k = 0; k < m_nsp; k++) {
        mobil_f[k] = c1 * m_spwork[k];
    }
}

void SimpleTransport::set_Grad_V(const doublereal* const grad_V)
{
    doMigration_ = false;
    for (size_t a = 0; a < m_nDim; a++) {
        m_Grad_V[a] = grad_V[a];
        if (fabs(grad_V[a]) > 1.0E-13) {
            doMigration_ = true;
        }
    }
}

void SimpleTransport::set_Grad_T(const doublereal* const grad_T)
{
    for (size_t a = 0; a < m_nDim; a++) {
        m_Grad_T[a] = grad_T[a];
    }
}

void SimpleTransport::set_Grad_X(const doublereal* const grad_X)
{
    size_t itop = m_nDim * m_nsp;
    for (size_t i = 0; i < itop; i++) {
        m_Grad_X[i] = grad_X[i];
    }
}

doublereal SimpleTransport::thermalConductivity()
{
    update_T();
    update_C();
    if (!m_cond_temp_ok) {
        updateCond_T();
    }
    if (!m_cond_mix_ok) {
        if (compositionDepType_ == LTI_MODEL_SOLVENT) {
            m_lambda = m_condSpecies[0];
        } else if (compositionDepType_ == LTI_MODEL_MOLEFRACS) {
            m_lambda = 0.0;
            for (size_t k = 0; k < m_nsp; k++) {
                m_lambda += m_condSpecies[k] * m_molefracs[k];
            }
        } else {
            throw CanteraError("SimpleTransport::thermalConductivity()",
                               "Unknown compositionDepType"); 
        }
        m_cond_mix_ok = true;
    }
    return m_lambda;
}

void SimpleTransport::getThermalDiffCoeffs(doublereal* const dt)
{
    for (size_t k = 0; k < m_nsp; k++) {
        dt[k] = 0.0;
    }
}

void SimpleTransport::getSpeciesVdiff(size_t ndim,
                                      const doublereal* grad_T,
                                      int ldx,
                                      const doublereal* grad_X,
                                      int ldf,
                                      doublereal* Vdiff)
{
    set_Grad_T(grad_T);
    set_Grad_X(grad_X);
    const doublereal* y  = m_thermo->massFractions();
    const doublereal rho = m_thermo->density();

    getSpeciesFluxesExt(m_nsp, DATA_PTR(Vdiff));

    for (size_t n = 0; n < m_nDim; n++) {
        for (size_t k = 0; k < m_nsp; k++) {
            if (y[k] > 1.0E-200) {
                Vdiff[n * m_nsp + k] *=  1.0 / (rho * y[k]);
            } else {
                Vdiff[n * m_nsp + k] = 0.0;
            }
        }
    }
}

void SimpleTransport::getSpeciesVdiffES(size_t ndim, const doublereal* grad_T,
                                        int ldx,  const doublereal* grad_X,
                                        int ldf,  const doublereal* grad_Phi,
                                        doublereal* Vdiff)
{
    set_Grad_T(grad_T);
    set_Grad_X(grad_X);
    set_Grad_V(grad_Phi);
    const doublereal* y  = m_thermo->massFractions();
    const doublereal rho = m_thermo->density();

    getSpeciesFluxesExt(m_nsp, DATA_PTR(Vdiff));

    for (size_t n = 0; n < m_nDim; n++) {
        for (size_t k = 0; k < m_nsp; k++) {
            if (y[k] > 1.0E-200) {
                Vdiff[n * m_nsp + k] *=  1.0 / (rho * y[k]);
            } else {
                Vdiff[n * m_nsp + k] = 0.0;
            }
        }
    }
}

void SimpleTransport::getSpeciesFluxes(size_t ndim,  const doublereal* const grad_T,
                                       size_t ldx, const doublereal* const grad_X,
                                       size_t ldf, doublereal* const fluxes)
{
    set_Grad_T(grad_T);
    set_Grad_X(grad_X);
    getSpeciesFluxesExt(ldf, fluxes);
}

void SimpleTransport::getSpeciesFluxesExt(size_t ldf, doublereal* fluxes)
{
    AssertThrow(ldf >= m_nsp ,"SimpleTransport::getSpeciesFluxesExt: Stride must be greater than m_nsp");
    update_T();
    update_C();

    getMixDiffCoeffs(DATA_PTR(m_spwork));

    const vector_fp& mw = m_thermo->molecularWeights();
    const doublereal* y  = m_thermo->massFractions();

    doublereal concTotal = m_thermo->molarDensity();

    // Unroll wrt ndim


    if (doMigration_) {
        double FRT =  ElectronCharge / (Boltzmann * m_temp);
        for (size_t n = 0; n < m_nDim; n++) {
            rhoVc[n] = 0.0;
            for (size_t k = 0; k < m_nsp; k++) {
                fluxes[n*ldf + k] = - concTotal * mw[k] * m_spwork[k] *
                                    (m_Grad_X[n*m_nsp + k] + FRT * m_molefracs[k] * m_chargeSpecies[k] * m_Grad_V[n]);
                rhoVc[n] += fluxes[n*ldf + k];
            }
        }
    } else {
        for (size_t n = 0; n < m_nDim; n++) {
            rhoVc[n] = 0.0;
            for (size_t k = 0; k < m_nsp; k++) {
                fluxes[n*ldf + k] = - concTotal * mw[k] * m_spwork[k] * m_Grad_X[n*m_nsp + k];
                rhoVc[n] += fluxes[n*ldf + k];
            }
        }
    }

    if (m_velocityBasis == VB_MASSAVG) {
        for (size_t n = 0; n < m_nDim; n++) {
            rhoVc[n] = 0.0;
            for (size_t k = 0; k < m_nsp; k++) {
                rhoVc[n] += fluxes[n*ldf + k];
            }
        }
        for (size_t n = 0; n < m_nDim; n++) {
            for (size_t k = 0; k < m_nsp; k++) {
                fluxes[n*ldf + k] -= y[k] * rhoVc[n];
            }
        }
    } else if (m_velocityBasis == VB_MOLEAVG) {
        for (size_t n = 0; n < m_nDim; n++) {
            rhoVc[n] = 0.0;
            for (size_t k = 0; k < m_nsp; k++) {
                rhoVc[n] += fluxes[n*ldf + k] / mw[k];
            }
        }
        for (size_t n = 0; n < m_nDim; n++) {
            for (size_t k = 0; k < m_nsp; k++) {
                fluxes[n*ldf + k] -= m_molefracs[k] * rhoVc[n] * mw[k];
            }
        }
    } else if (m_velocityBasis >= 0) {
        for (size_t n = 0; n < m_nDim; n++) {
            rhoVc[n] = - fluxes[n*ldf + m_velocityBasis] / mw[m_velocityBasis];
            for (size_t k = 0; k < m_nsp; k++) {
                rhoVc[n] += fluxes[n*ldf + k] / mw[k];
            }
        }
        for (size_t n = 0; n < m_nDim; n++) {
            for (size_t k = 0; k < m_nsp; k++) {
                fluxes[n*ldf + k] -= m_molefracs[k] * rhoVc[n] * mw[k];
            }
            fluxes[n*ldf + m_velocityBasis] = 0.0;
        }

    } else {
        throw CanteraError("SimpleTransport::getSpeciesFluxesExt()",
                           "unknown velocity basis");
    }
}

void SimpleTransport::getMixDiffCoeffs(doublereal* const d)
{
    update_T();
    update_C();
    // update the binary diffusion coefficients if necessary
    if (!m_diff_temp_ok) {
        updateDiff_T();
    }
    for (size_t k = 0; k < m_nsp; k++) {
        d[k] = m_diffSpecies[k];
    }
}

bool SimpleTransport::update_C()
{
    // If the pressure has changed then the concentrations
    // have changed.
    doublereal pres = m_thermo->pressure();
    bool qReturn = true;
    if (pres != m_press) {
        qReturn = false;
        m_press = pres;
    }
    int iStateNew = m_thermo->stateMFNumber();
    if (iStateNew != m_iStateMF) {
        qReturn = false;
        m_thermo->getMoleFractions(DATA_PTR(m_molefracs));
        m_thermo->getConcentrations(DATA_PTR(m_concentrations));
        concTot_ = 0.0;
        for (size_t k = 0; k < m_nsp; k++) {
            m_molefracs[k] = std::max(0.0, m_molefracs[k]);
            concTot_ += m_concentrations[k];
        }
        dens_ = m_thermo->density();
        meanMolecularWeight_ =  m_thermo->meanMolecularWeight();
    }
    if (qReturn) {
        return false;
    }


    // Mixture stuff needs to be evaluated
    m_visc_mix_ok = false;
    m_diff_mix_ok = false;
    m_cond_mix_ok = false;

    return true;
}

void SimpleTransport::updateCond_T()
{
    if (compositionDepType_ == LTI_MODEL_SOLVENT) {
        m_condSpecies[0] = m_coeffLambda_Ns[0]->getSpeciesTransProp();
    } else {
        for (size_t k = 0; k < m_nsp; k++) {
            m_condSpecies[k] = m_coeffLambda_Ns[k]->getSpeciesTransProp();
        }
    }
    m_cond_temp_ok = true;
    m_cond_mix_ok = false;
}

void SimpleTransport::updateDiff_T()
{
    if (useHydroRadius_) {
        double visc = viscosity();
        double RT = GasConstant * m_temp;
        for (size_t k = 0; k < m_nsp; k++) {
            double rad = m_coeffHydroRadius_Ns[k]->getSpeciesTransProp() ;
            m_diffSpecies[k] = RT / (6.0 * Pi * visc * rad);
        }
    } else {
        for (size_t k = 0; k < m_nsp; k++) {
            m_diffSpecies[k] = m_coeffDiff_Ns[k]->getSpeciesTransProp();
        }
    }
    m_diff_temp_ok = true;
    m_diff_mix_ok = false;
}

void SimpleTransport::updateViscosities_C()
{
}

void SimpleTransport::updateViscosity_T()
{
    if (compositionDepType_ == LTI_MODEL_SOLVENT) {
        m_viscSpecies[0] = m_coeffVisc_Ns[0]->getSpeciesTransProp();
    } else {
        for (size_t k = 0; k < m_nsp; k++) {
            m_viscSpecies[k] = m_coeffVisc_Ns[k]->getSpeciesTransProp();
        }
    }
    m_visc_temp_ok = true;
    m_visc_mix_ok = false;
}

bool SimpleTransport::update_T()
{
    doublereal t = m_thermo->temperature();
    if (t == m_temp) {
        return false;
    }
    if (t < 0.0) {
        throw CanteraError("SimpleTransport::update_T",
                           "negative temperature "+fp2str(t));
    }

    // Compute various functions of temperature
    m_temp = t;

    // temperature has changed, so polynomial temperature
    // interpolations will need to be reevaluated.
    // Set all of these flags to false
    m_visc_mix_ok = false;
    m_visc_temp_ok  = false;

    m_cond_temp_ok = false;
    m_cond_mix_ok = false;

    m_diff_mix_ok = false;
    m_diff_temp_ok = false;

    return true;
}

}