Changed the name of getLNActivityCoefficient to getLnActivityCoefficient
Doxygen updates
This commit is contained in:
Harry Moffat
parent
2af06f0e79
commit
b216c194aa
4 changed files with 99 additions and 41 deletions
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@ -39,7 +39,7 @@ using namespace std;
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namespace Cantera {
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static const double xxSmall = 1.0E-150;
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//====================================================================================================================
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/*
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* Default constructor.
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*
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@ -54,11 +54,14 @@ namespace Cantera {
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numAnionSpecies_(0),
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numPassThroughSpecies_(0),
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neutralMoleculePhase_(0),
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IOwnNThermoPhase_(true)
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IOwnNThermoPhase_(true),
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moleFractionsTmp_(0),
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muNeutralMolecule_(0),
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lnActCoeff_NeutralMolecule_(0)
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{
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}
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//====================================================================================================================
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// Construct and initialize an IonsFromNeutralVPSSTP object
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// directly from an asci input file
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/*
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@ -95,14 +98,17 @@ namespace Cantera {
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numAnionSpecies_(0),
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numPassThroughSpecies_(0),
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neutralMoleculePhase_(neutralPhase),
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IOwnNThermoPhase_(true)
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IOwnNThermoPhase_(true),
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moleFractionsTmp_(0),
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muNeutralMolecule_(0),
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lnActCoeff_NeutralMolecule_(0)
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{
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if (neutralPhase) {
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IOwnNThermoPhase_ = false;
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}
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constructPhaseFile(inputFile, id);
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}
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//====================================================================================================================
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IonsFromNeutralVPSSTP::IonsFromNeutralVPSSTP(XML_Node& phaseRoot, std::string id,
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ThermoPhase *neutralPhase) :
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GibbsExcessVPSSTP(),
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@ -114,7 +120,11 @@ namespace Cantera {
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numAnionSpecies_(0),
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numPassThroughSpecies_(0),
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neutralMoleculePhase_(neutralPhase),
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IOwnNThermoPhase_(true)
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IOwnNThermoPhase_(true),
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moleFractionsTmp_(0),
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muNeutralMolecule_(0),
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lnActCoeff_NeutralMolecule_(0)
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{
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if (neutralPhase) {
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IOwnNThermoPhase_ = false;
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@ -122,7 +132,7 @@ namespace Cantera {
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constructPhaseXML(phaseRoot, id);
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}
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//====================================================================================================================
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/*
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* Copy Constructor:
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@ -140,11 +150,15 @@ namespace Cantera {
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numAnionSpecies_(0),
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numPassThroughSpecies_(0),
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neutralMoleculePhase_(0),
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IOwnNThermoPhase_(true)
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IOwnNThermoPhase_(true),
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moleFractionsTmp_(0),
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muNeutralMolecule_(0),
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lnActCoeff_NeutralMolecule_(0)
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{
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IonsFromNeutralVPSSTP::operator=(b);
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}
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//====================================================================================================================
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/*
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* operator=()
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*
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@ -196,10 +210,12 @@ namespace Cantera {
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IOwnNThermoPhase_ = b.IOwnNThermoPhase_;
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moleFractionsTmp_ = b.moleFractionsTmp_;
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muNeutralMolecule_ = b.muNeutralMolecule_;
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gammaNeutralMolecule_ = b.gammaNeutralMolecule_;
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// gammaNeutralMolecule_ = b.gammaNeutralMolecule_;
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lnActCoeff_NeutralMolecule_ = b.lnActCoeff_NeutralMolecule_;
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dlnActCoeffdT_NeutralMolecule_ = b.dlnActCoeffdT_NeutralMolecule_;
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dlnActCoeffdlnX_diag_NeutralMolecule_ = b.dlnActCoeffdlnX_diag_NeutralMolecule_;
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dlnActCoeffdlnN_diag_NeutralMolecule_ = b.dlnActCoeffdlnN_diag_NeutralMolecule_;
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dlnActCoeffdlnN_NeutralMolecule_ = b.dlnActCoeffdlnN_NeutralMolecule_;
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return *this;
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}
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@ -472,7 +488,8 @@ namespace Cantera {
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neutralMoleculePhase_->getChemPotentials(mu);
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break;
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case cIonSolnType_SINGLEANION:
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neutralMoleculePhase_->getActivityCoefficients(DATA_PTR(gammaNeutralMolecule_));
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// neutralMoleculePhase_->getActivityCoefficients(DATA_PTR(gammaNeutralMolecule_));
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neutralMoleculePhase_->getLnActivityCoefficients(DATA_PTR(lnActCoeff_NeutralMolecule_));
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fact2 = 2.0 * RT_ * log(2.0);
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@ -482,7 +499,7 @@ namespace Cantera {
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icat = cationList_[k];
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jNeut = fm_invert_ionForNeutral[icat];
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xx = fmaxx(SmallNumber, moleFractions_[icat]);
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mu[icat] = muNeutralMolecule_[jNeut] + fact2 + RT_ * log(gammaNeutralMolecule_[jNeut] * xx);
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mu[icat] = muNeutralMolecule_[jNeut] + fact2 + RT_ * (lnActCoeff_NeutralMolecule_[jNeut] + log(xx));
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}
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// Do the anion list
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@ -496,7 +513,7 @@ namespace Cantera {
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icat = passThroughList_[k];
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jNeut = fm_invert_ionForNeutral[icat];
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xx = fmaxx(SmallNumber, moleFractions_[icat]);
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mu[icat] = muNeutralMolecule_[jNeut] + RT_ * log( gammaNeutralMolecule_[jNeut] * xx);
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mu[icat] = muNeutralMolecule_[jNeut] + RT_ * (lnActCoeff_NeutralMolecule_[jNeut] + log(xx));
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}
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break;
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@ -1156,7 +1173,7 @@ namespace Cantera {
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}
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//====================================================================================================================
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/*
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* @internal Initialize. This method is provided to allow
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* subclasses to perform any initialization required after all
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@ -1174,7 +1191,7 @@ namespace Cantera {
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initLengths();
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GibbsExcessVPSSTP::initThermo();
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}
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//====================================================================================================================
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// Initialize lengths of local variables after all species have
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// been identified.
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@ -1190,7 +1207,7 @@ namespace Cantera {
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passThroughList_.resize(m_kk);
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moleFractionsTmp_.resize(m_kk);
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muNeutralMolecule_.resize(numNeutralMoleculeSpecies_);
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gammaNeutralMolecule_.resize(numNeutralMoleculeSpecies_);
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lnActCoeff_NeutralMolecule_.resize(numNeutralMoleculeSpecies_);
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dlnActCoeffdT_NeutralMolecule_.resize(numNeutralMoleculeSpecies_);
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dlnActCoeffdlnX_diag_NeutralMolecule_.resize(numNeutralMoleculeSpecies_);
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dlnActCoeffdlnN_diag_NeutralMolecule_.resize(numNeutralMoleculeSpecies_);
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@ -1399,7 +1416,7 @@ namespace Cantera {
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/*
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* Get the activity coefficiens of the neutral molecules
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*/
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neutralMoleculePhase_->getActivityCoefficients(DATA_PTR(gammaNeutralMolecule_));
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neutralMoleculePhase_->getLnActivityCoefficients(DATA_PTR(lnActCoeff_NeutralMolecule_));
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switch (ionSolnType_) {
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case cIonSolnType_PASSTHROUGH:
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@ -1412,7 +1429,7 @@ namespace Cantera {
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icat = cationList_[k];
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jNeut = fm_invert_ionForNeutral[icat];
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fmij = fm_neutralMolec_ions_[icat + jNeut * m_kk];
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lnActCoeff_Scaled_[icat] = log(gammaNeutralMolecule_[jNeut])/fmij;
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lnActCoeff_Scaled_[icat] = lnActCoeff_NeutralMolecule_[jNeut] / fmij;
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}
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// Do the anion list
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@ -1424,7 +1441,7 @@ namespace Cantera {
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for (k = 0; k < numPassThroughSpecies_; k++) {
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icat = passThroughList_[k];
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jNeut = fm_invert_ionForNeutral[icat];
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lnActCoeff_Scaled_[icat] = log(gammaNeutralMolecule_[jNeut]);
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lnActCoeff_Scaled_[icat] = lnActCoeff_NeutralMolecule_[jNeut];
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}
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break;
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@ -892,9 +892,36 @@ namespace Cantera {
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//! Temporary mole fraction vector
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mutable std::vector<doublereal> moleFractionsTmp_;
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//! Storage vector for the neutral molecule chemical potentials
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/*!
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* This vector is used as a temporary storage area when calculating the ion chemical
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* potentials.
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*
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* Units = Joules/kmol
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* Length = numNeutralMoleculeSpecies_
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*/
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mutable std::vector<doublereal> muNeutralMolecule_;
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mutable std::vector<doublereal> gammaNeutralMolecule_;
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mutable std::vector<doublereal> dlnActCoeff_NeutralMolecule_;
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//! Storage vector for the neutral molecule activity coefficients
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/*!
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* This vector is used as a temporary storage area when calculating the ion chemical
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* potentials and activity coefficients
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*
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* Units = none
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* Length = numNeutralMoleculeSpecies_
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*/
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// mutable std::vector<doublereal> gammaNeutralMolecule_;
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//! Storage vector for the neutral molecule ln activity coefficients
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/*!
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* This vector is used as a temporary storage area when calculating the ion chemical
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* potentials and activity coefficients
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*
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* Units = none
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* Length = numNeutralMoleculeSpecies_
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*/
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mutable std::vector<doublereal> lnActCoeff_NeutralMolecule_;
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mutable std::vector<doublereal> dlnActCoeffdT_NeutralMolecule_;
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mutable std::vector<doublereal> dlnActCoeffdlnX_diag_NeutralMolecule_;
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mutable std::vector<doublereal> dlnActCoeffdlnN_diag_NeutralMolecule_;
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@ -135,7 +135,7 @@ namespace Cantera {
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m_ssConvention = right.m_ssConvention;
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return *this;
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}
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//====================================================================================================================
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//====================================================================================================================
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/*
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* Duplication routine for objects which inherit from
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* ThermoPhase.
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@ -151,45 +151,42 @@ namespace Cantera {
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ThermoPhase* tp = new ThermoPhase(*this);
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return tp;
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}
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//====================================================================================================================
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//====================================================================================================================
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int ThermoPhase::activityConvention() const {
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return cAC_CONVENTION_MOLAR;
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}
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//=================================================================================================================
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int ThermoPhase::standardStateConvention() const {
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return m_ssConvention;
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}
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//=================================================================================================================
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doublereal ThermoPhase::logStandardConc(int k) const {
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return log(standardConcentration(k));
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}
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//=================================================================================================================
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void ThermoPhase::getActivities(doublereal* a) const {
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getActivityConcentrations(a);
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int nsp = nSpecies();
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int k;
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for (k = 0; k < nsp; k++) a[k] /= standardConcentration(k);
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}
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void ThermoPhase::getLNActivityCoefficients(doublereal *const lnac) const {
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//=================================================================================================================
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void ThermoPhase::getLnActivityCoefficients(doublereal *const lnac) const {
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getActivityCoefficients(lnac);
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for (int k = 0; k < m_kk; k++) {
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lnac[k] = std::log(lnac[k]);
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}
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}
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void ThermoPhase::setState_TPX(doublereal t, doublereal p,
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const doublereal* x) {
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//=================================================================================================================
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void ThermoPhase::setState_TPX(doublereal t, doublereal p, const doublereal* x) {
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setMoleFractions(x); setTemperature(t); setPressure(p);
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}
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void ThermoPhase::setState_TPX(doublereal t, doublereal p,
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compositionMap& x) {
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//=================================================================================================================
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void ThermoPhase::setState_TPX(doublereal t, doublereal p, compositionMap& x) {
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setMoleFractionsByName(x); setTemperature(t); setPressure(p);
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}
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void ThermoPhase::setState_TPX(doublereal t, doublereal p,
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const std::string& x) {
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//=================================================================================================================
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void ThermoPhase::setState_TPX(doublereal t, doublereal p, const std::string& x) {
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compositionMap xx;
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int kk = nSpecies();
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for (int k = 0; k < kk; k++) xx[speciesName(k)] = -1.0;
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@ -202,17 +199,17 @@ namespace Cantera {
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}
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setMoleFractionsByName(xx); setTemperature(t); setPressure(p);
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}
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//=================================================================================================================
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void ThermoPhase::setState_TPY(doublereal t, doublereal p,
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const doublereal* y) {
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setMassFractions(y); setTemperature(t); setPressure(p);
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}
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//=================================================================================================================
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void ThermoPhase::setState_TPY(doublereal t, doublereal p,
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compositionMap& y) {
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setMassFractionsByName(y); setTemperature(t); setPressure(p);
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}
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//=================================================================================================================
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void ThermoPhase::setState_TPY(doublereal t, doublereal p,
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const std::string& y) {
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compositionMap yy;
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@ -227,28 +224,34 @@ namespace Cantera {
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}
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setMassFractionsByName(yy); setTemperature(t); setPressure(p);
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}
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//=================================================================================================================
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void ThermoPhase::setState_TP(doublereal t, doublereal p) {
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setTemperature(t); setPressure(p);
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}
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//=================================================================================================================
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void ThermoPhase::setState_PX(doublereal p, doublereal* x) {
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setMoleFractions(x); setPressure(p);
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}
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//=================================================================================================================
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void ThermoPhase::setState_PY(doublereal p, doublereal* y) {
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setMassFractions(y); setPressure(p);
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}
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//=================================================================================================================
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void ThermoPhase::setState_HP(doublereal Htarget, doublereal p,
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doublereal dTtol) {
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setState_HPorUV(Htarget, p, dTtol, false);
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}
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//=================================================================================================================
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void ThermoPhase::setState_UV(doublereal u, doublereal v,
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doublereal dTtol) {
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setState_HPorUV(u, v, dTtol, true);
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}
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//=================================================================================================================
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// Do the convergence work
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/*
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@ -513,16 +516,19 @@ namespace Cantera {
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throw CanteraError("setState_HPorUV (HP)", ErrString);
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}
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}
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//=================================================================================================================
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void ThermoPhase::setState_SP(doublereal Starget, doublereal p,
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doublereal dTtol) {
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setState_SPorSV(Starget, p, dTtol, false);
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}
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//=================================================================================================================
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void ThermoPhase::setState_SV(doublereal Starget, doublereal v,
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doublereal dTtol) {
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setState_SPorSV(Starget, v, dTtol, true);
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}
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//=================================================================================================================
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// Do the convergence work for fixed entropy situations
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/*
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@ -772,6 +778,7 @@ namespace Cantera {
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throw CanteraError("setState_SPorSV (SP)", ErrString);
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}
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}
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//=================================================================================================================
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doublereal ThermoPhase::err(std::string msg) const {
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throw CanteraError("ThermoPhase","Base class method "
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@ -816,6 +823,7 @@ namespace Cantera {
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if (i == 5) uA[5] = 0.0;
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}
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}
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//=================================================================================================================
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/*
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* initThermoFile():
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@ -861,6 +869,7 @@ namespace Cantera {
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initThermoXML(*fxml_phase, id);
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delete fxml;
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}
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//=================================================================================================================
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/*
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* Import and initialize a ThermoPhase object
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@ -1153,7 +1153,12 @@ namespace Cantera {
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}
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}
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virtual void getLNActivityCoefficients(doublereal * const lnac) const;
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//! Get the array of non-dimensional molar-based ln activity coefficients at
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//! the current solution temperature, pressure, and solution concentration.
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/*!
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* @param ac Output vector of ln activity coefficients. Length: m_kk.
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*/
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virtual void getLnActivityCoefficients(doublereal * const lnac) const;
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//@}
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/// @name Partial Molar Properties of the Solution
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