651 lines
18 KiB
C++
651 lines
18 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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* Copywrite (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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/*
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* $Date$
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* $Revision$
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*/
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#ifdef WIN32
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#pragma warning(disable:4786)
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#pragma warning(disable:4503)
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#endif
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#include "AqueousKinetics.h"
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#include "ReactionData.h"
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#include "RateCoeffMgr.h"
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#include <iostream>
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using namespace std;
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namespace Cantera {
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//====================================================================================================================
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AqueousKineticsData::AqueousKineticsData() :
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m_logp_ref(0.0),
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m_logc_ref(0.0),
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m_ROP_ok(false),
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m_temp(0.0)
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{
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}
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//====================================================================================================================
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AqueousKineticsData::~AqueousKineticsData()
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{
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}
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//====================================================================================================================
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AqueousKineticsData::AqueousKineticsData(const AqueousKineticsData &right) :
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m_logp_ref(0.0),
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m_logc_ref(0.0),
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m_ROP_ok(false),
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m_temp(0.0)
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{
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*this=right;
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}
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//====================================================================================================================
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AqueousKineticsData& AqueousKineticsData::operator=(const AqueousKineticsData &right)
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{
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if (this != &right) {
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m_logp_ref = right.m_logp_ref;
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m_logc_ref = right.m_logc_ref;
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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_rfn_low = right.m_rfn_low;
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m_rfn_high = right.m_rfn_high;
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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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}
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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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* Construct an empty reaction mechanism.
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*/
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AqueousKinetics::AqueousKinetics(thermo_t* thermo) :
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Kinetics(),
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m_kk(0),
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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_finalized(false)
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{
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if (thermo != 0) addPhase(*thermo);
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m_kdata = new AqueousKineticsData;
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m_kdata->m_temp = 0.0;
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m_rxnstoich = new ReactionStoichMgr;
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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_kk(0),
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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_finalized(false)
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{
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*this = right;
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}
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//====================================================================================================================
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AqueousKinetics::~AqueousKinetics() {
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delete m_kdata;
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delete m_rxnstoich;
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}
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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) return *this;
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Kinetics::operator=(right);
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m_kk = right.m_kk;
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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_kdata = *(right.m_kdata);
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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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//====================================================================================================================
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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 dynamic_cast<Kinetics *>(gK);
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}
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//====================================================================================================================
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/**
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* Update temperature-dependent portions of reaction rates and
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* falloff functions.
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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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doublereal T = thermo().temperature();
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// m_kdata->m_logStandConc = log(thermo().standardConcentration());
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doublereal logT = log(T);
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m_rates.update(T, logT, &m_kdata->m_rfn[0]);
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m_kdata->m_temp = T;
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updateKc();
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m_kdata->m_ROP_ok = false;
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};
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/**
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* Update properties that depend on concentrations. Currently only
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* the enhanced collision partner concentrations are updated here.
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*/
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void AqueousKinetics::
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_update_rates_C() {
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thermo().getActivityConcentrations(&m_conc[0]);
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m_kdata->m_ROP_ok = false;
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}
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/**
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* Update the equilibrium constants in molar units.
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*/
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void AqueousKinetics::updateKc() {
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int i, irxn;
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vector_fp& m_rkc = m_kdata->m_rkcn;
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doublereal rt = GasConstant* m_kdata->m_temp;
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thermo().getStandardChemPotentials(&m_grt[0]);
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fill(m_rkc.begin(), m_rkc.end(), 0.0);
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int nsp = thermo().nSpecies();
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for (int k = 0; k < nsp; 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_rkc[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 (i = 0; i < m_nrev; i++) {
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irxn = m_revindex[i];
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m_rkc[irxn] = exp(m_rkc[irxn]*rrt);
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}
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for(i = 0; i != m_nirrev; ++i) {
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m_rkc[ m_irrev[i] ] = 0.0;
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}
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}
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/**
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* Get the equilibrium constants of all reactions, whether
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* reversible or not.
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*/
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void AqueousKinetics::getEquilibriumConstants(doublereal* kc) {
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int i;
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_update_rates_T();
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vector_fp& rkc = m_kdata->m_rkcn;
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thermo().getStandardChemPotentials(&m_grt[0]);
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fill(rkc.begin(), rkc.end(), 0.0);
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doublereal rt = GasConstant * m_kdata->m_temp;
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int nsp = thermo().nSpecies();
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for (int k = 0; k < nsp; 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], &rkc[0]);
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doublereal rrt = 1.0/(GasConstant * thermo().temperature());
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for (i = 0; i < m_ii; i++) {
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kc[i] = exp(-rkc[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_kdata->m_temp = 0.0;
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}
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/**
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*
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* getDeltaGibbs():
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*
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* Return the vector of values for the reaction gibbs free energy
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* change
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* These values depend upon the concentration
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* of the ideal gas.
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*
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* units = J kmol-1
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*/
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void AqueousKinetics::getDeltaGibbs(doublereal* deltaG) {
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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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/**
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*
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* getDeltaEnthalpy():
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*
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* Return the vector of values for the reactions change in
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* enthalpy.
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* These values depend upon the concentration
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* of the solution.
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*
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* units = J kmol-1
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*/
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void AqueousKinetics::getDeltaEnthalpy(doublereal* deltaH) {
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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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/*
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*
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* getDeltaEntropy():
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*
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* Return the vector of values for the reactions change in
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* entropy.
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* These values depend upon the concentration
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* of the solution.
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*
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* units = J kmol-1 Kelvin-1
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*/
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void AqueousKinetics::getDeltaEntropy( doublereal* deltaS) {
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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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/**
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*
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* getDeltaSSGibbs():
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*
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* Return the vector of values for the reaction
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* standard state gibbs free energy change.
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* These values don't depend upon the concentration
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* of the solution.
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*
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* units = J kmol-1
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*/
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void AqueousKinetics::getDeltaSSGibbs(doublereal* deltaG) {
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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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/**
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*
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* getDeltaSSEnthalpy():
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*
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* Return the vector of values for the change in the
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* standard state enthalpies of reaction.
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* These values don't depend upon the concentration
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* of the solution.
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*
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* units = J kmol-1
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*/
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void AqueousKinetics::getDeltaSSEnthalpy(doublereal* deltaH) {
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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 (int 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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/*
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*
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* getDeltaSSEntropy():
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*
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* Return the vector of values for the change in the
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* standard state entropies for each reaction.
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* These values don't depend upon the concentration
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* of the solution.
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*
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* units = J kmol-1 Kelvin-1
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*/
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void AqueousKinetics::getDeltaSSEntropy(doublereal* deltaS) {
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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 (int 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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_update_rates_T();
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_update_rates_C();
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if (m_kdata->m_ROP_ok) return;
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const vector_fp& rf = m_kdata->m_rfn;
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const vector_fp& m_rkc = m_kdata->m_rkcn;
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array_fp& ropf = m_kdata->m_ropf;
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array_fp& ropr = m_kdata->m_ropr;
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array_fp& ropnet = m_kdata->m_ropnet;
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// copy rate coefficients into ropf
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copy(rf.begin(), rf.end(), ropf.begin());
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// multiply by perturbation factor
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multiply_each(ropf.begin(), ropf.end(), m_perturb.begin());
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// copy the forward rates to the reverse rates
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copy(ropf.begin(), ropf.end(), 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(ropr.begin(), ropr.end(), m_rkc.begin());
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// multiply ropf by concentration products
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m_rxnstoich->multiplyReactants(&m_conc[0], &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], &ropr[0]);
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//m_revProductStoich.multiply(m_conc.begin(), ropr.begin());
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for (int j = 0; j != m_ii; ++j) {
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ropnet[j] = ropf[j] - ropr[j];
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}
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m_kdata->m_ROP_ok = true;
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}
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/**
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*
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* getFwdRateConstants():
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*
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* Update the rate of progress for the reactions.
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* This key routine makes sure that the rate of progress vectors
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* located in the solid kinetics data class are up to date.
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*/
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void AqueousKinetics::
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getFwdRateConstants(doublereal *kfwd) {
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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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const vector_fp& rf = m_kdata->m_rfn;
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array_fp& ropf = m_kdata->m_ropf;
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copy(rf.begin(), rf.end(), ropf.begin());
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// multiply by perturbation factor
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multiply_each(ropf.begin(), ropf.end(), m_perturb.begin());
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for (int i = 0; i < m_ii; i++) {
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kfwd[i] = ropf[i];
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}
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}
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/**
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*
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* getRevRateConstants():
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*
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* Return a vector of the reverse reaction rate constants
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*
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* Length is the number of reactions. units depends
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* on many issues. Note, this routine will return rate constants
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* for irreversible reactions if the default for
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* doIrreversible is overridden.
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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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* 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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doublereal *tmpKc = &m_kdata->m_ropnet[0];
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getEquilibriumConstants(tmpKc);
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for (int i = 0; i < m_ii; i++) {
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krev[i] /= tmpKc[i];
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}
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} else {
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/*
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* m_rkc[] is zero for irreversibly reactions
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*/
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const vector_fp& m_rkc = m_kdata->m_rkcn;
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for (int i = 0; i < m_ii; i++) {
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krev[i] *= m_rkc[i];
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}
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}
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}
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void AqueousKinetics::addReaction(const ReactionData& r) {
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if (r.reactionType == ELEMENTARY_RXN) addElementaryReaction(r);
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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(const ReactionData& r) {
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int iloc;
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// install rate coeff calculator
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iloc = m_rates.install( reactionNumber(),
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r.rateCoeffType, r.rateCoeffParameters.size(),
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DATA_PTR(r.rateCoeffParameters) );
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// add constant term to rate coeff value vector
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m_kdata->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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m_kdata->m_ropf.push_back(0.0); // extend by one for new rxn
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m_kdata->m_ropr.push_back(0.0);
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m_kdata->m_ropnet.push_back(0.0);
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int 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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int rnum = reactionNumber();
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vector_int rk;
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int 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 = (int) 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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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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vector_int pk;
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int 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 = (int) 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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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_kdata->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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}
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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(int irxn,
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const vector<grouplist_t>& r,
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const vector<grouplist_t>& p) {
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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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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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m_kdata->m_logp_ref = log(thermo().refPressure()) - log(GasConstant);
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}
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void AqueousKinetics::finalize() {
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if (!m_finalized) {
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m_finalized = true;
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}
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}
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bool AqueousKinetics::ready() const {
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return (m_finalized);
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}
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}
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