Folded InterfaceKineticsData into InterfaceKinetics
This commit is contained in:
Ray Speth
parent
346605abc4
commit
cde96e5191
2 changed files with 89 additions and 169 deletions
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@ -25,51 +25,11 @@ namespace Cantera
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{
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// forward references
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class ReactionData;
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class InterfaceKineticsData;
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class ThermoPhase;
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class SurfPhase;
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class ImplicitSurfChem;
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//! This class holds mechanism-specific data.
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/*!
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*
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*/
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class InterfaceKineticsData
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{
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public:
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InterfaceKineticsData();
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InterfaceKineticsData(const InterfaceKineticsData& right);
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InterfaceKineticsData& operator=(const InterfaceKineticsData& right);
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//! Virtual destructor
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/*!
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* todo - why is this virtual
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*/
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virtual ~InterfaceKineticsData();
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doublereal m_logp0;
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doublereal m_logc0;
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vector_fp m_ropf;
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vector_fp m_ropr;
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vector_fp m_ropnet;
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bool m_ROP_ok;
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//! Current temperature of the data
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doublereal m_temp;
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//! Current log of the temperature
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doublereal m_logtemp;
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vector_fp m_rfn;
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vector_fp m_rkcn;
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};
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//! A kinetics manager for heterogeneous reaction mechanisms. The
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//! reactions are assumed to occur at a 2D interface between two 3D phases.
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/*!
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@ -175,7 +135,7 @@ public:
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*/
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virtual void getFwdRatesOfProgress(doublereal* fwdROP) {
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updateROP();
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std::copy(m_kdata->m_ropf.begin(), m_kdata->m_ropf.end(), fwdROP);
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std::copy(m_ropf.begin(), m_ropf.end(), fwdROP);
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}
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//! Return the reverse rates of progress for each reaction
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@ -185,7 +145,7 @@ public:
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*/
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virtual void getRevRatesOfProgress(doublereal* revROP) {
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updateROP();
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std::copy(m_kdata->m_ropr.begin(), m_kdata->m_ropr.end(), revROP);
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std::copy(m_ropr.begin(), m_ropr.end(), revROP);
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}
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//! Return the net rates of progress for each reaction
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@ -195,7 +155,7 @@ public:
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*/
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virtual void getNetRatesOfProgress(doublereal* netROP) {
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updateROP();
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std::copy(m_kdata->m_ropnet.begin(), m_kdata->m_ropnet.end(), netROP);
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std::copy(m_ropnet.begin(), m_ropnet.end(), netROP);
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}
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@ -723,12 +683,6 @@ protected:
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*/
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std::vector<std::string> m_rxneqn;
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/**
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* Temporary data storage used in calculating the rates of
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* of reactions.
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*/
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InterfaceKineticsData* m_kdata;
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//! an array of generalized concentrations for each species
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/*!
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* An array of generalized concentrations
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@ -819,7 +773,20 @@ protected:
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vector_fp m_deltaG0;
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vector_fp m_ProdStanConcReac;
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doublereal m_logp0;
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doublereal m_logc0;
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vector_fp m_ropf;
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vector_fp m_ropr;
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vector_fp m_ropnet;
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bool m_ROP_ok;
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//! Current temperature of the data
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doublereal m_temp;
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//! Current log of the temperature
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doublereal m_logtemp;
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vector_fp m_rfn;
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vector_fp m_rkcn;
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//! boolean indicating whether mechanism has been finalized
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bool m_finalized;
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@ -18,47 +18,7 @@ using namespace std;
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namespace Cantera
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{
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//====================================================================================================================
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InterfaceKineticsData::InterfaceKineticsData() :
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m_logp0(0.0),
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m_logc0(0.0),
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m_ROP_ok(false),
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m_temp(0.0),
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m_logtemp(0.0)
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{
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}
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//====================================================================================================================
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InterfaceKineticsData:: InterfaceKineticsData(const InterfaceKineticsData& right) :
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m_logp0(0.0),
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m_logc0(0.0),
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m_ROP_ok(false),
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m_temp(0.0),
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m_logtemp(0.0)
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{
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*this = right;
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}
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//====================================================================================================================
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InterfaceKineticsData::~InterfaceKineticsData()
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{
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}
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//====================================================================================================================
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InterfaceKineticsData& InterfaceKineticsData::operator=(const InterfaceKineticsData& 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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m_logp0 = right.m_logp0;
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m_logc0 = right.m_logc0;
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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_logtemp = right.m_logtemp;
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m_rfn = right.m_rfn;
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m_rkcn = right.m_rkcn;
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return *this;
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}
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//====================================================================================================================
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/*
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* Construct an empty InterfaceKinetics reaction mechanism.
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@ -81,6 +41,11 @@ InterfaceKinetics::InterfaceKinetics(thermo_t* thermo) :
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m_StandardConc(0),
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m_deltaG0(0),
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m_ProdStanConcReac(0),
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m_logp0(0.0),
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m_logc0(0.0),
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m_ROP_ok(false),
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m_temp(0.0),
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m_logtemp(0.0),
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m_finalized(false),
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m_has_coverage_dependence(false),
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m_has_electrochem_rxns(false),
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@ -95,8 +60,6 @@ InterfaceKinetics::InterfaceKinetics(thermo_t* thermo) :
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if (thermo != 0) {
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addPhase(*thermo);
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}
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m_kdata = new InterfaceKineticsData;
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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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@ -104,7 +67,6 @@ InterfaceKinetics::InterfaceKinetics(thermo_t* thermo) :
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*/
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InterfaceKinetics::~InterfaceKinetics()
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{
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delete m_kdata;
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if (m_integrator) {
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delete m_integrator;
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}
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@ -128,6 +90,11 @@ InterfaceKinetics::InterfaceKinetics(const InterfaceKinetics& right) :
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m_StandardConc(0),
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m_deltaG0(0),
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m_ProdStanConcReac(0),
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m_logp0(0.0),
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m_logc0(0.0),
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m_ROP_ok(false),
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m_temp(0.0),
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m_logtemp(0.0),
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m_finalized(false),
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m_has_coverage_dependence(false),
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m_has_electrochem_rxns(false),
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@ -139,8 +106,6 @@ InterfaceKinetics::InterfaceKinetics(const InterfaceKinetics& right) :
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m_rxnPhaseIsProduct(0),
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m_ioFlag(0)
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{
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m_kdata = new InterfaceKineticsData;
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m_kdata->m_temp = 0.0;
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/*
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* Call the assignment operator
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*/
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@ -178,7 +143,6 @@ operator=(const InterfaceKinetics& right)
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m_rrxn = right.m_rrxn;
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m_prxn = right.m_prxn;
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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_mu0 = right.m_mu0;
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m_phi = right.m_phi;
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@ -193,6 +157,16 @@ operator=(const InterfaceKinetics& right)
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m_StandardConc = right.m_StandardConc;
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m_deltaG0 = right.m_deltaG0;
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m_ProdStanConcReac = right.m_ProdStanConcReac;
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m_logp0 = right.m_logp0;
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m_logc0 = right.m_logc0;
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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_logtemp = right.m_logtemp;
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m_rfn = right.m_rfn;
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m_rkcn = right.m_rkcn;
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m_finalized = right.m_finalized;
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m_has_coverage_dependence = right.m_has_coverage_dependence;
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m_has_electrochem_rxns = right.m_has_electrochem_rxns;
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@ -247,8 +221,8 @@ void InterfaceKinetics::setElectricPotential(int n, doublereal V)
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* This is called to update all of the properties that depend on temperature
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*
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* Current objects that this function updates
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* m_kdata->m_logtemp
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* m_kdata->m_rfn
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* m_logtemp
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* m_rfn
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* m_rates.
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* updateKc();
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*/
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@ -262,18 +236,18 @@ void InterfaceKinetics::_update_rates_T()
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}
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doublereal T = thermo(surfacePhaseIndex()).temperature();
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m_redo_rates = true;
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if (T != m_kdata->m_temp || m_redo_rates) {
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m_kdata->m_logtemp = log(T);
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m_rates.update(T, m_kdata->m_logtemp, DATA_PTR(m_kdata->m_rfn));
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if (T != m_temp || m_redo_rates) {
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m_logtemp = log(T);
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m_rates.update(T, m_logtemp, DATA_PTR(m_rfn));
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if (m_has_exchange_current_density_formulation) {
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applyExchangeCurrentDensityFormulation(DATA_PTR(m_kdata->m_rfn));
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applyExchangeCurrentDensityFormulation(DATA_PTR(m_rfn));
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}
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if (m_has_electrochem_rxns) {
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applyButlerVolmerCorrection(DATA_PTR(m_kdata->m_rfn));
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applyButlerVolmerCorrection(DATA_PTR(m_rfn));
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}
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m_kdata->m_temp = T;
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m_temp = T;
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updateKc();
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m_kdata->m_ROP_ok = false;
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m_ROP_ok = false;
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m_redo_rates = false;
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}
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}
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@ -310,7 +284,7 @@ void InterfaceKinetics::_update_rates_C()
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*/
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thermo(n).getActivityConcentrations(DATA_PTR(m_conc) + m_start[n]);
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}
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m_kdata->m_ROP_ok = false;
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m_ROP_ok = false;
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}
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@ -333,8 +307,7 @@ void InterfaceKinetics::getActivityConcentrations(doublereal* const conc)
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*/
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void InterfaceKinetics::updateKc()
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{
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vector_fp& m_rkc = m_kdata->m_rkcn;
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fill(m_rkc.begin(), m_rkc.end(), 0.0);
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fill(m_rkcn.begin(), m_rkcn.end(), 0.0);
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//static vector_fp mu(nTotalSpecies());
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if (m_nrev > 0) {
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@ -355,7 +328,7 @@ void InterfaceKinetics::updateKc()
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// compute Delta mu^0 for all reversible reactions
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m_rxnstoich.getRevReactionDelta(m_ii, DATA_PTR(m_mu0),
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DATA_PTR(m_rkc));
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DATA_PTR(m_rkcn));
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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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@ -363,10 +336,10 @@ void InterfaceKinetics::updateKc()
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throw CanteraError("InterfaceKinetics",
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"illegal value: irxn = "+int2str(irxn));
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}
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m_rkc[irxn] = exp(m_rkc[irxn]*rrt);
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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_rkc[ m_irrev[i] ] = 0.0;
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m_rkcn[ m_irrev[i] ] = 0.0;
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}
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}
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}
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@ -487,8 +460,7 @@ void InterfaceKinetics::getExchangeCurrentQuantities()
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void InterfaceKinetics::getCreationRates(doublereal* cdot)
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{
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updateROP();
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m_rxnstoich.getCreationRates(m_kk, &m_kdata->m_ropf[0],
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&m_kdata->m_ropr[0], cdot);
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m_rxnstoich.getCreationRates(m_kk, &m_ropf[0], &m_ropr[0], cdot);
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}
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// Return the Species destruction rates [kmol/m^2/s].
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@ -500,8 +472,7 @@ void InterfaceKinetics::getCreationRates(doublereal* cdot)
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void InterfaceKinetics::getDestructionRates(doublereal* ddot)
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{
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updateROP();
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m_rxnstoich.getDestructionRates(m_kk, &m_kdata->m_ropf[0],
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&m_kdata->m_ropr[0], ddot);
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m_rxnstoich.getDestructionRates(m_kk, &m_ropf[0], &m_ropr[0], ddot);
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}
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// Return the species net production rates
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@ -518,9 +489,7 @@ void InterfaceKinetics::getDestructionRates(doublereal* ddot)
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void InterfaceKinetics::getNetProductionRates(doublereal* net)
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{
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updateROP();
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m_rxnstoich.getNetProductionRates(m_kk,
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&m_kdata->m_ropnet[0],
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net);
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m_rxnstoich.getNetProductionRates(m_kk, &m_ropnet[0], net);
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}
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//====================================================================================================================
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@ -617,10 +586,8 @@ void InterfaceKinetics::getFwdRateConstants(doublereal* kfwd)
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updateROP();
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const vector_fp& rf = m_kdata->m_rfn;
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// copy rate coefficients into kfwd
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copy(rf.begin(), rf.end(), kfwd);
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copy(m_rfn.begin(), m_rfn.end(), kfwd);
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// multiply by perturbation factor
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multiply_each(kfwd, kfwd + nReactions(), m_perturb.begin());
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@ -636,14 +603,12 @@ void InterfaceKinetics::getRevRateConstants(doublereal* krev, bool doIrreversibl
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{
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getFwdRateConstants(krev);
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if (doIrreversible) {
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doublereal* tmpKc = DATA_PTR(m_kdata->m_ropnet);
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getEquilibriumConstants(tmpKc);
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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] /= tmpKc[i];
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krev[i] /= m_ropnet[i];
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}
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} else {
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const vector_fp& rkc = m_kdata->m_rkcn;
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multiply_each(krev, krev + nReactions(), rkc.begin());
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multiply_each(krev, krev + nReactions(), m_rkcn.begin());
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}
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}
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//====================================================================================================================
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@ -659,52 +624,44 @@ void InterfaceKinetics::getActivationEnergies(doublereal* E)
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*/
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void InterfaceKinetics::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_kdata->m_ROP_ok) {
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if (m_ROP_ok) {
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return;
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}
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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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vector_fp& ropf = m_kdata->m_ropf;
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vector_fp& ropr = m_kdata->m_ropr;
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vector_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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copy(m_rfn.begin(), m_rfn.end(), m_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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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(ropf.begin(), ropf.end(), ropr.begin());
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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(ropr.begin(), ropr.end(), m_rkc.begin());
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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(DATA_PTR(m_conc), DATA_PTR(ropf));
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m_rxnstoich.multiplyReactants(DATA_PTR(m_conc), DATA_PTR(m_ropf));
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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(DATA_PTR(m_conc),
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DATA_PTR(ropr));
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DATA_PTR(m_ropr));
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//m_revProductStoich.multiply(m_conc.begin(), ropr.begin());
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// do global reactions
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//m_globalReactantStoich.power(m_conc.begin(), ropf.begin());
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for (size_t j = 0; j != m_ii; ++j) {
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ropnet[j] = ropf[j] - ropr[j];
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m_ropnet[j] = m_ropf[j] - m_ropr[j];
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}
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/*
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* For reactions involving multiple phases, we must check that the phase
|
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* being consumed actually exists. This is particularly important for
|
||||
|
|
@ -712,18 +669,18 @@ void InterfaceKinetics::updateROP()
|
|||
*/
|
||||
if (m_phaseExistsCheck) {
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for (size_t j = 0; j != m_ii; ++j) {
|
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if ((ropr[j] > ropf[j]) && (ropr[j] > 0.0)) {
|
||||
if ((m_ropr[j] > m_ropf[j]) && (m_ropr[j] > 0.0)) {
|
||||
for (size_t p = 0; p < nPhases(); p++) {
|
||||
if (m_rxnPhaseIsProduct[j][p]) {
|
||||
if (! m_phaseExists[p]) {
|
||||
ropnet[j] = 0.0;
|
||||
ropr[j] = ropf[j];
|
||||
if (ropf[j] > 0.0) {
|
||||
m_ropnet[j] = 0.0;
|
||||
m_ropr[j] = m_ropf[j];
|
||||
if (m_ropf[j] > 0.0) {
|
||||
for (size_t rp = 0; rp < nPhases(); rp++) {
|
||||
if (m_rxnPhaseIsReactant[j][rp]) {
|
||||
if (! m_phaseExists[rp]) {
|
||||
ropnet[j] = 0.0;
|
||||
ropr[j] = ropf[j] = 0.0;
|
||||
m_ropnet[j] = 0.0;
|
||||
m_ropr[j] = m_ropr[j] = 0.0;
|
||||
}
|
||||
}
|
||||
}
|
||||
|
|
@ -732,23 +689,23 @@ void InterfaceKinetics::updateROP()
|
|||
}
|
||||
if (m_rxnPhaseIsReactant[j][p]) {
|
||||
if (! m_phaseIsStable[p]) {
|
||||
ropnet[j] = 0.0;
|
||||
ropr[j] = ropf[j];
|
||||
m_ropnet[j] = 0.0;
|
||||
m_ropr[j] = m_ropf[j];
|
||||
}
|
||||
}
|
||||
}
|
||||
} else if ((ropf[j] > ropr[j]) && (ropf[j] > 0.0)) {
|
||||
} else if ((m_ropf[j] > m_ropr[j]) && (m_ropf[j] > 0.0)) {
|
||||
for (size_t p = 0; p < nPhases(); p++) {
|
||||
if (m_rxnPhaseIsReactant[j][p]) {
|
||||
if (! m_phaseExists[p]) {
|
||||
ropnet[j] = 0.0;
|
||||
ropf[j] = ropr[j];
|
||||
if (ropf[j] > 0.0) {
|
||||
m_ropnet[j] = 0.0;
|
||||
m_ropf[j] = m_ropr[j];
|
||||
if (m_ropf[j] > 0.0) {
|
||||
for (size_t rp = 0; rp < nPhases(); rp++) {
|
||||
if (m_rxnPhaseIsProduct[j][rp]) {
|
||||
if (! m_phaseExists[rp]) {
|
||||
ropnet[j] = 0.0;
|
||||
ropf[j] = ropr[j] = 0.0;
|
||||
m_ropnet[j] = 0.0;
|
||||
m_ropf[j] = m_ropr[j] = 0.0;
|
||||
}
|
||||
}
|
||||
}
|
||||
|
|
@ -757,8 +714,8 @@ void InterfaceKinetics::updateROP()
|
|||
}
|
||||
if (m_rxnPhaseIsProduct[j][p]) {
|
||||
if (! m_phaseIsStable[p]) {
|
||||
ropnet[j] = 0.0;
|
||||
ropf[j] = ropr[j];
|
||||
m_ropnet[j] = 0.0;
|
||||
m_ropf[j] = m_ropr[j];
|
||||
}
|
||||
}
|
||||
}
|
||||
|
|
@ -766,7 +723,7 @@ void InterfaceKinetics::updateROP()
|
|||
}
|
||||
}
|
||||
|
||||
m_kdata->m_ROP_ok = true;
|
||||
m_ROP_ok = true;
|
||||
}
|
||||
|
||||
#ifdef KINETICS_WITH_INTERMEDIATE_ZEROED_PHASES
|
||||
|
|
@ -775,10 +732,6 @@ InterfaceKinetics::adjustRatesForIntermediatePhases()
|
|||
{
|
||||
doublereal sFac = 1.0;
|
||||
|
||||
vector_fp& ropf = m_kdata->m_ropf;
|
||||
vector_fp& ropr = m_kdata->m_ropr;
|
||||
vector_fp& ropnet = m_kdata->m_ropnet;
|
||||
|
||||
getCreatingRates(DATA_PTR(m_speciestmpP));
|
||||
getDestructionRates(DATA_PTR(m_speciestmpD));
|
||||
|
||||
|
|
@ -1117,7 +1070,7 @@ void InterfaceKinetics::addElementaryReaction(ReactionData& r)
|
|||
}
|
||||
|
||||
// add constant term to rate coeff value vector
|
||||
m_kdata->m_rfn.push_back(r.rateCoeffParameters[0]);
|
||||
m_rfn.push_back(r.rateCoeffParameters[0]);
|
||||
registerReaction(reactionNumber(), ELEMENTARY_RXN, iloc);
|
||||
}
|
||||
//====================================================================================================================
|
||||
|
|
@ -1144,7 +1097,7 @@ void InterfaceKinetics::setIOFlag(int ioFlag)
|
|||
// // store activation energy
|
||||
// m_E.push_back(r.rateCoeffParameters[2]);
|
||||
// // add constant term to rate coeff value vector
|
||||
// m_kdata->m_rfn.push_back(r.rateCoeffParameters[0]);
|
||||
// m_rfn.push_back(r.rateCoeffParameters[0]);
|
||||
|
||||
// int nr = r.order.size();
|
||||
// vector_fp ordr(nr);
|
||||
|
|
@ -1166,10 +1119,10 @@ void InterfaceKinetics::installReagents(const ReactionData& r)
|
|||
/*
|
||||
* extend temporary storage by one for this rxn.
|
||||
*/
|
||||
m_kdata->m_ropf.push_back(0.0);
|
||||
m_kdata->m_ropr.push_back(0.0);
|
||||
m_kdata->m_ropnet.push_back(0.0);
|
||||
m_kdata->m_rkcn.push_back(0.0);
|
||||
m_ropf.push_back(0.0);
|
||||
m_ropr.push_back(0.0);
|
||||
m_ropnet.push_back(0.0);
|
||||
m_rkcn.push_back(0.0);
|
||||
|
||||
/*
|
||||
* Obtain the current reaction index for the reaction that we
|
||||
|
|
|
|||
Loading…
Add table
Reference in a new issue