5720d7cf90
Eliminated some deprecations which were not sanctioned. Worked on Cantera.mak. There is a problem with scons eliminating $ from strings.
494 lines
13 KiB
C++
494 lines
13 KiB
C++
/**
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* @file AqueousKinetics.cpp
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*
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* Homogeneous kinetics in an aqueous phase, either condensed
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* or dilute in salts
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*
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*/
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/*
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* Copyright (2006) Sandia Corporation. Under the terms of
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* Contract DE-AC04-94AL85000 with Sandia Corporation, the
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* U.S. Government retains certain rights in this software.
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*/
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#include "cantera/kinetics/AqueousKinetics.h"
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#include "cantera/kinetics/ReactionData.h"
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#include "cantera/kinetics/RateCoeffMgr.h"
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#include "cantera/base/stringUtils.h"
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using namespace std;
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namespace Cantera
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{
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AqueousKinetics::AqueousKinetics(thermo_t* thermo) :
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Kinetics(),
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m_nfall(0),
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m_nirrev(0),
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m_nrev(0),
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m_ROP_ok(false),
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m_temp(0.0),
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m_finalized(false)
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{
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if (thermo != 0) {
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addPhase(*thermo);
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}
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}
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AqueousKinetics::AqueousKinetics(const AqueousKinetics& right) :
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Kinetics(),
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m_nfall(0),
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m_nirrev(0),
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m_nrev(0),
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m_ROP_ok(false),
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m_temp(0.0),
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m_finalized(false)
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{
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*this = right;
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}
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AqueousKinetics& AqueousKinetics::operator=(const AqueousKinetics& right)
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{
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if (this == &right) {
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return *this;
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}
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Kinetics::operator=(right);
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m_nfall = right.m_nfall;
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m_rates = right.m_rates;
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m_index = right.m_index;
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m_irrev = right.m_irrev;
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m_rxnstoich = right.m_rxnstoich;
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m_fwdOrder = right.m_fwdOrder;
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m_nirrev = right.m_nirrev;
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m_nrev = right.m_nrev;
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m_rgroups = right.m_rgroups;
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m_pgroups = right.m_pgroups;
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m_rxntype = right.m_rxntype;
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m_rrxn = right.m_rrxn;
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m_prxn = right.m_prxn;
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m_dn = right.m_dn;
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m_revindex = right.m_revindex;
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m_rxneqn = right.m_rxneqn;
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m_ropf = right.m_ropf;
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m_ropr = right.m_ropr;
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m_ropnet = right.m_ropnet;
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m_ROP_ok = right.m_ROP_ok;
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m_temp = right.m_temp;
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m_rfn = right.m_rfn;
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m_rkcn = right.m_rkcn;
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m_conc = right.m_conc;
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m_grt = right.m_grt;
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m_finalized = right.m_finalized;
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throw CanteraError("GasKinetics::operator=()",
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"Unfinished implementation");
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return *this;
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}
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Kinetics* AqueousKinetics::duplMyselfAsKinetics(const std::vector<thermo_t*> & tpVector) const
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{
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AqueousKinetics* gK = new AqueousKinetics(*this);
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gK->assignShallowPointers(tpVector);
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return gK;
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}
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void AqueousKinetics::
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update_T() {}
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void AqueousKinetics::
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update_C() {}
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void AqueousKinetics::_update_rates_T()
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{
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doublereal T = thermo().temperature();
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doublereal logT = log(T);
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m_rates.update(T, logT, &m_rfn[0]);
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m_temp = T;
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updateKc();
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m_ROP_ok = false;
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}
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void AqueousKinetics::
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_update_rates_C()
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{
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thermo().getActivityConcentrations(&m_conc[0]);
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m_ROP_ok = false;
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}
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void AqueousKinetics::updateKc()
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{
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doublereal rt = GasConstant * m_temp;
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thermo().getStandardChemPotentials(&m_grt[0]);
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fill(m_rkcn.begin(), m_rkcn.end(), 0.0);
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for (size_t k = 0; k < thermo().nSpecies(); k++) {
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doublereal logStandConc_k = thermo().logStandardConc(k);
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m_grt[k] -= rt * logStandConc_k;
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}
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// compute Delta G^0 for all reversible reactions
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m_rxnstoich.getRevReactionDelta(m_ii, &m_grt[0], &m_rkcn[0]);
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//doublereal logStandConc = m_kdata->m_logStandConc;
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doublereal rrt = 1.0/(GasConstant * thermo().temperature());
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for (size_t i = 0; i < m_nrev; i++) {
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size_t irxn = m_revindex[i];
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m_rkcn[irxn] = exp(m_rkcn[irxn]*rrt);
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}
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for (size_t i = 0; i != m_nirrev; ++i) {
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m_rkcn[ m_irrev[i] ] = 0.0;
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}
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}
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void AqueousKinetics::getEquilibriumConstants(doublereal* kc)
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{
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_update_rates_T();
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thermo().getStandardChemPotentials(&m_grt[0]);
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fill(m_rkcn.begin(), m_rkcn.end(), 0.0);
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doublereal rt = GasConstant * m_temp;
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for (size_t k = 0; k < thermo().nSpecies(); k++) {
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doublereal logStandConc_k = thermo().logStandardConc(k);
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m_grt[k] -= rt * logStandConc_k;
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}
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// compute Delta G^0 for all reactions
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m_rxnstoich.getReactionDelta(m_ii, &m_grt[0], &m_rkcn[0]);
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doublereal rrt = 1.0/(GasConstant * thermo().temperature());
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for (size_t i = 0; i < m_ii; i++) {
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kc[i] = exp(-m_rkcn[i]*rrt);
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}
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// force an update of T-dependent properties, so that m_rkcn will
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// be updated before it is used next.
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m_temp = 0.0;
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}
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void AqueousKinetics::getDeltaGibbs(doublereal* deltaG)
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{
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/*
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* Get the chemical potentials of the species in the
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* ideal gas solution.
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*/
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thermo().getChemPotentials(&m_grt[0]);
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/*
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* Use the stoichiometric manager to find deltaG for each
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* reaction.
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*/
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m_rxnstoich.getReactionDelta(m_ii, &m_grt[0], deltaG);
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}
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void AqueousKinetics::getDeltaEnthalpy(doublereal* deltaH)
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{
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/*
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* Get the partial molar enthalpy of all species in the
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* ideal gas.
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*/
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thermo().getPartialMolarEnthalpies(&m_grt[0]);
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/*
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* Use the stoichiometric manager to find deltaG for each
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* reaction.
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*/
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m_rxnstoich.getReactionDelta(m_ii, &m_grt[0], deltaH);
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}
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void AqueousKinetics::getDeltaEntropy(doublereal* deltaS)
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{
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/*
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* Get the partial molar entropy of all species in the
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* solid solution.
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*/
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thermo().getPartialMolarEntropies(&m_grt[0]);
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/*
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* Use the stoichiometric manager to find deltaS for each
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* reaction.
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*/
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m_rxnstoich.getReactionDelta(m_ii, &m_grt[0], deltaS);
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}
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void AqueousKinetics::getDeltaSSGibbs(doublereal* deltaG)
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{
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/*
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* Get the standard state chemical potentials of the species.
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* This is the array of chemical potentials at unit activity
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* We define these here as the chemical potentials of the pure
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* species at the temperature and pressure of the solution.
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*/
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thermo().getStandardChemPotentials(&m_grt[0]);
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/*
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* Use the stoichiometric manager to find deltaG for each
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* reaction.
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*/
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m_rxnstoich.getReactionDelta(m_ii, &m_grt[0], deltaG);
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}
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void AqueousKinetics::getDeltaSSEnthalpy(doublereal* deltaH)
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{
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/*
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* Get the standard state enthalpies of the species.
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* This is the array of chemical potentials at unit activity
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* We define these here as the enthalpies of the pure
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* species at the temperature and pressure of the solution.
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*/
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thermo().getEnthalpy_RT(&m_grt[0]);
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doublereal RT = thermo().temperature() * GasConstant;
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for (size_t k = 0; k < m_kk; k++) {
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m_grt[k] *= RT;
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}
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/*
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* Use the stoichiometric manager to find deltaG for each
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* reaction.
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*/
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m_rxnstoich.getReactionDelta(m_ii, &m_grt[0], deltaH);
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}
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void AqueousKinetics::getDeltaSSEntropy(doublereal* deltaS)
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{
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/*
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* Get the standard state entropy of the species.
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* We define these here as the entropies of the pure
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* species at the temperature and pressure of the solution.
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*/
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thermo().getEntropy_R(&m_grt[0]);
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doublereal R = GasConstant;
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for (size_t k = 0; k < m_kk; k++) {
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m_grt[k] *= R;
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}
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/*
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* Use the stoichiometric manager to find deltaS for each
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* reaction.
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*/
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m_rxnstoich.getReactionDelta(m_ii, &m_grt[0], deltaS);
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}
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void AqueousKinetics::updateROP()
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{
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_update_rates_T();
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_update_rates_C();
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if (m_ROP_ok) {
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return;
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}
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// copy rate coefficients into ropf
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copy(m_rfn.begin(), m_rfn.end(), m_ropf.begin());
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// multiply by perturbation factor
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multiply_each(m_ropf.begin(), m_ropf.end(), m_perturb.begin());
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// copy the forward rates to the reverse rates
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copy(m_ropf.begin(), m_ropf.end(), m_ropr.begin());
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// for reverse rates computed from thermochemistry, multiply
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// the forward rates copied into m_ropr by the reciprocals of
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// the equilibrium constants
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multiply_each(m_ropr.begin(), m_ropr.end(), m_rkcn.begin());
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// multiply ropf by concentration products
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m_rxnstoich.multiplyReactants(&m_conc[0], &m_ropf[0]);
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//m_reactantStoich.multiply(m_conc.begin(), ropf.begin());
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// for reversible reactions, multiply ropr by concentration
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// products
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m_rxnstoich.multiplyRevProducts(&m_conc[0], &m_ropr[0]);
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//m_revProductStoich.multiply(m_conc.begin(), ropr.begin());
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for (size_t j = 0; j != m_ii; ++j) {
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m_ropnet[j] = m_ropf[j] - m_ropr[j];
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}
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m_ROP_ok = true;
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}
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void AqueousKinetics::
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getFwdRateConstants(doublereal* kfwd)
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{
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_update_rates_T();
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_update_rates_C();
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// copy rate coefficients into ropf
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copy(m_rfn.begin(), m_rfn.end(), m_ropf.begin());
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// multiply by perturbation factor
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multiply_each(m_ropf.begin(), m_ropf.end(), m_perturb.begin());
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for (size_t i = 0; i < m_ii; i++) {
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kfwd[i] = m_ropf[i];
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}
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}
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void AqueousKinetics::
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getRevRateConstants(doublereal* krev, bool doIrreversible)
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{
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/*
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* go get the forward rate constants. -> note, we don't
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* really care about speed or redundancy in these
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* informational routines.
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*/
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getFwdRateConstants(krev);
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if (doIrreversible) {
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getEquilibriumConstants(&m_ropnet[0]);
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for (size_t i = 0; i < m_ii; i++) {
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krev[i] /= m_ropnet[i];
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}
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} else {
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/*
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* m_rkcn[] is zero for irreversible reactions
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*/
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for (size_t i = 0; i < m_ii; i++) {
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krev[i] *= m_rkcn[i];
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}
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}
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}
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void AqueousKinetics::addReaction(ReactionData& r)
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{
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if (r.reactionType == ELEMENTARY_RXN) {
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addElementaryReaction(r);
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}
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// operations common to all reaction types
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installReagents(r);
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installGroups(reactionNumber(), r.rgroups, r.pgroups);
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incrementRxnCount();
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m_rxneqn.push_back(r.equation);
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}
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void AqueousKinetics::addElementaryReaction(ReactionData& r)
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{
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size_t iloc;
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// install rate coeff calculator
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iloc = m_rates.install(reactionNumber(), r);
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// add constant term to rate coeff value vector
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m_rfn.push_back(r.rateCoeffParameters[0]);
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// forward rxn order equals number of reactants
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m_fwdOrder.push_back(r.reactants.size());
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registerReaction(reactionNumber(), ELEMENTARY_RXN, iloc);
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}
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void AqueousKinetics::installReagents(const ReactionData& r)
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{
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m_ropf.push_back(0.0); // extend by one for new rxn
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m_ropr.push_back(0.0);
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m_ropnet.push_back(0.0);
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size_t n, ns, m;
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doublereal nsFlt;
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doublereal reactantGlobalOrder = 0.0;
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doublereal productGlobalOrder = 0.0;
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size_t rnum = reactionNumber();
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std::vector<size_t> rk;
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size_t nr = r.reactants.size();
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for (n = 0; n < nr; n++) {
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nsFlt = r.rstoich[n];
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reactantGlobalOrder += nsFlt;
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ns = (size_t) nsFlt;
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if ((doublereal) ns != nsFlt) {
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if (ns < 1) {
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ns = 1;
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}
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}
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if (r.rstoich[n] != 0.0) {
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m_rrxn[r.reactants[n]][rnum] += r.rstoich[n];
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}
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for (m = 0; m < ns; m++) {
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rk.push_back(r.reactants[n]);
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}
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}
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m_reactants.push_back(rk);
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std::vector<size_t> pk;
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size_t np = r.products.size();
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for (n = 0; n < np; n++) {
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nsFlt = r.pstoich[n];
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productGlobalOrder += nsFlt;
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ns = (size_t) nsFlt;
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if ((double) ns != nsFlt) {
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if (ns < 1) {
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ns = 1;
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}
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}
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if (r.pstoich[n] != 0.0) {
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m_prxn[r.products[n]][rnum] += r.pstoich[n];
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}
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for (m = 0; m < ns; m++) {
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pk.push_back(r.products[n]);
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}
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}
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m_products.push_back(pk);
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m_rkcn.push_back(0.0);
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m_rxnstoich.add(reactionNumber(), r);
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if (r.reversible) {
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m_dn.push_back(productGlobalOrder - reactantGlobalOrder);
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m_revindex.push_back(reactionNumber());
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m_nrev++;
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} else {
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m_dn.push_back(productGlobalOrder - reactantGlobalOrder);
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m_irrev.push_back(reactionNumber());
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m_nirrev++;
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}
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}
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void AqueousKinetics::installGroups(size_t irxn,
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const vector<grouplist_t>& r,
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const vector<grouplist_t>& p)
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{
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if (!r.empty()) {
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writelog("installing groups for reaction "+int2str(reactionNumber()));
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m_rgroups[reactionNumber()] = r;
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m_pgroups[reactionNumber()] = p;
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}
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}
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void AqueousKinetics::init()
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{
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m_kk = thermo().nSpecies();
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m_rrxn.resize(m_kk);
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m_prxn.resize(m_kk);
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m_conc.resize(m_kk);
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m_grt.resize(m_kk);
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}
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void AqueousKinetics::finalize()
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{
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if (!m_finalized) {
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m_finalized = true;
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// Guarantee that these arrays can be converted to double* even in the
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// special case where there are no reactions defined.
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if (!m_ii) {
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m_perturb.resize(1, 1.0);
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m_ropf.resize(1, 0.0);
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m_ropr.resize(1, 0.0);
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m_ropnet.resize(1, 0.0);
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m_rkcn.resize(1, 0.0);
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}
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}
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}
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bool AqueousKinetics::ready() const
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{
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return m_finalized;
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}
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}
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