research/cantera
1
0
Fork 0
Code Issues Pull requests Projects Releases Packages Wiki Activity Actions

Added a new way to specify the kinetics reaction rate coefficient

Browse source 
when dealing with electron transfer surface reactions.
This way specifies an exchange current density reaction rate coefficient
in units of amps / m2.  This is slightly more informative for 
electrode reactions. 

The new also preserves the correct treatment of activity coefficients
for these reactions. 

A memo describing this new capability is in the works.
This commit is contained in:
Harry Moffat 2010-03-01 18:14:07 +00:00
parent 60afcc5d57
commit 263aeb6b35
15 changed files with 781 additions and 295 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

185
Cantera/src/kinetics/InterfaceKinetics.cpp
View file

@ -25,9 +25,8 @@ using namespace std;
namespace Cantera { namespace Cantera {
////////////////////////////////////////////////////////////////// //====================================================================================================================
/*
/**
* Construct an empty InterfaceKinetics reaction mechanism. * Construct an empty InterfaceKinetics reaction mechanism.
* @param thermo This is an optional parameter that may be * @param thermo This is an optional parameter that may be
* used to initialize the inherited Kinetics class with * used to initialize the inherited Kinetics class with
@ -35,8 +34,7 @@ namespace Cantera {
* useful for initialization of homogeneous kinetics * useful for initialization of homogeneous kinetics
* mechanisms. * mechanisms.
*/ */
InterfaceKinetics:: InterfaceKinetics::InterfaceKinetics(thermo_t* thermo) :
InterfaceKinetics(thermo_t* thermo) :
Kinetics(), Kinetics(),
m_kk(0), m_kk(0),
m_redo_rates(false), m_redo_rates(false),
@ -44,27 +42,33 @@ namespace Cantera {
m_nrev(0), m_nrev(0),
m_surf(0), m_surf(0),
m_integrator(0), m_integrator(0),
m_beta(0),
m_ctrxn(0),
m_ctrxn_ecdf(0),
m_logStandardConc(0),
m_deltaG0(0),
m_logProdStanConcReac(0),
m_finalized(false), m_finalized(false),
m_has_coverage_dependence(false), m_has_coverage_dependence(false),
m_has_electrochem_rxns(false), m_has_electrochem_rxns(false),
m_has_exchange_current_density_formulation(false),
m_ioFlag(0) m_ioFlag(0)
{ {
if (thermo != 0) addPhase(*thermo); if (thermo != 0) addPhase(*thermo);
m_kdata = new InterfaceKineticsData; m_kdata = new InterfaceKineticsData;
m_kdata->m_temp = 0.0; m_kdata->m_temp = 0.0;
} }
//====================================================================================================================
/** /*
* Destructor * Destructor
*/ */
InterfaceKinetics:: InterfaceKinetics::~InterfaceKinetics(){
~InterfaceKinetics(){
delete m_kdata; delete m_kdata;
if (m_integrator) { if (m_integrator) {
delete m_integrator; delete m_integrator;
} }
} }
//====================================================================================================================
// Copy Constructor for the %InterfaceKinetics object. // Copy Constructor for the %InterfaceKinetics object.
/* /*
* Currently, this is not fully implemented. If called it will * Currently, this is not fully implemented. If called it will
@ -78,9 +82,16 @@ namespace Cantera {
m_nrev(0), m_nrev(0),
m_surf(0), m_surf(0),
m_integrator(0), m_integrator(0),
m_beta(0),
m_ctrxn(0),
m_ctrxn_ecdf(0),
m_logStandardConc(0),
m_deltaG0(0),
m_logProdStanConcReac(0),
m_finalized(false), m_finalized(false),
m_has_coverage_dependence(false), m_has_coverage_dependence(false),
m_has_electrochem_rxns(false), m_has_electrochem_rxns(false),
m_has_exchange_current_density_formulation(false),
m_ioFlag(0) m_ioFlag(0)
{ {
m_kdata = new InterfaceKineticsData; m_kdata = new InterfaceKineticsData;
@ -90,7 +101,7 @@ namespace Cantera {
*/ */
*this = operator=(right); *this = operator=(right);
} }
//====================================================================================================================
// Assignment operator // Assignment operator
/* /*
* This is NOT a virtual function. * This is NOT a virtual function.
@ -127,19 +138,23 @@ namespace Cantera {
m_E = right.m_E; m_E = right.m_E;
m_surf = right.m_surf; //DANGER - shallow copy m_surf = right.m_surf; //DANGER - shallow copy
m_integrator = right.m_integrator; //DANGER - shallow copy m_integrator = right.m_integrator; //DANGER - shallow copy
m_beta = right.m_beta; m_beta = right.m_beta;
m_ctrxn = right.m_ctrxn; m_ctrxn = right.m_ctrxn;
m_ctrxn_ecdf = right.m_ctrxn_ecdf;
m_logStandardConc = right.m_logStandardConc;
m_deltaG0 = right.m_deltaG0;
m_logProdStanConcReac = right.m_logProdStanConcReac;
m_finalized = right.m_finalized; m_finalized = right.m_finalized;
m_has_coverage_dependence = right.m_has_coverage_dependence; m_has_coverage_dependence = right.m_has_coverage_dependence;
m_has_electrochem_rxns = right.m_has_electrochem_rxns; m_has_electrochem_rxns = right.m_has_electrochem_rxns;
m_has_exchange_current_density_formulation = right.m_has_exchange_current_density_formulation;
m_ioFlag = right.m_ioFlag; m_ioFlag = right.m_ioFlag;
return *this; return *this;
} }
//====================================================================================================================
// Duplication routine for objects which inherit from Kinetics
// Duplication routine for objects which inherit from
// Kinetics
/* /*
* This virtual routine can be used to duplicate %Kinetics objects * This virtual routine can be used to duplicate %Kinetics objects
* inherited from %Kinetics even if the application only has * inherited from %Kinetics even if the application only has
@ -152,14 +167,18 @@ namespace Cantera {
InterfaceKinetics* tp = new InterfaceKinetics(*this); InterfaceKinetics* tp = new InterfaceKinetics(*this);
return dynamic_cast<Kinetics *>(tp); return dynamic_cast<Kinetics *>(tp);
} }
//====================================================================================================================
// Update properties that depend on temperature
/** /*
* Update properties that depend on temperature * This is called to update all of the properties that depend on temperature
* *
*/ * Current objects that this function updates
void InterfaceKinetics:: * m_kdata->m_logtemp
_update_rates_T() { * m_kdata->m_rfn
* m_rates.
* updateKc();
*/
void InterfaceKinetics::_update_rates_T() {
_update_rates_phi(); _update_rates_phi();
if (m_has_coverage_dependence) { if (m_has_coverage_dependence) {
m_surf->getCoverages(DATA_PTR(m_conc)); m_surf->getCoverages(DATA_PTR(m_conc));
@ -167,20 +186,24 @@ namespace Cantera {
m_redo_rates = true; m_redo_rates = true;
} }
doublereal T = thermo(surfacePhaseIndex()).temperature(); doublereal T = thermo(surfacePhaseIndex()).temperature();
m_redo_rates = true;
if (T != m_kdata->m_temp || m_redo_rates) { if (T != m_kdata->m_temp || m_redo_rates) {
m_kdata->m_logtemp = log(T); m_kdata->m_logtemp = log(T);
m_rates.update(T, m_kdata->m_logtemp, DATA_PTR(m_kdata->m_rfn)); m_rates.update(T, m_kdata->m_logtemp, DATA_PTR(m_kdata->m_rfn));
if (m_has_electrochem_rxns) if (m_has_exchange_current_density_formulation) {
applyExchangeCurrentDensityFormulation(DATA_PTR(m_kdata->m_rfn));
}
if (m_has_electrochem_rxns) {
applyButlerVolmerCorrection(DATA_PTR(m_kdata->m_rfn)); applyButlerVolmerCorrection(DATA_PTR(m_kdata->m_rfn));
}
m_kdata->m_temp = T; m_kdata->m_temp = T;
updateKc(); updateKc();
m_kdata->m_ROP_ok = false; m_kdata->m_ROP_ok = false;
m_redo_rates = false; m_redo_rates = false;
} }
} }
//====================================================================================================================
void InterfaceKinetics:: void InterfaceKinetics::_update_rates_phi() {
_update_rates_phi() {
int np = nPhases(); int np = nPhases();
for (int n = 0; n < np; n++) { for (int n = 0; n < np; n++) {
if (thermo(n).electricPotential() != m_phi[n]) { if (thermo(n).electricPotential() != m_phi[n]) {
@ -189,6 +212,7 @@ namespace Cantera {
} }
} }
} }
//====================================================================================================================
/** /**
@ -198,8 +222,7 @@ namespace Cantera {
* representing phases should overload to return the appropriate * representing phases should overload to return the appropriate
* quantities. * quantities.
*/ */
void InterfaceKinetics:: void InterfaceKinetics::_update_rates_C() {
_update_rates_C() {
int n; int n;
int np = nPhases(); int np = nPhases();
@ -263,6 +286,8 @@ namespace Cantera {
} }
} }
} }
//====================================================================================================================
void InterfaceKinetics::checkPartialEquil() { void InterfaceKinetics::checkPartialEquil() {
@ -338,6 +363,36 @@ namespace Cantera {
} }
} }
void InterfaceKinetics::getExchangeCurrentQuantities() {
/*
* First collect vectors of the standard Gibbs free energies of the
* species and the standard concentrations
* - m_mu0
* - m_logStandardConc
*/
int ik = 0;
int np = nPhases();
for (int n = 0; n < np; n++) {
thermo(n).getStandardChemPotentials(DATA_PTR(m_mu0) + m_start[n]);
int nsp = thermo(n).nSpecies();
for (int k = 0; k < nsp; k++) {
m_logStandardConc[ik] = thermo(n).logStandardConc(k);
ik++;
}
}
m_rxnstoich.getReactionDelta(m_ii, DATA_PTR(m_mu0), DATA_PTR(m_deltaG0));
for (int i = 0; i < m_ii; i++) {
m_logProdStanConcReac[i] = 1.0;
}
m_rxnstoich.multiplyReactants(DATA_PTR(m_logStandardConc), DATA_PTR(m_logProdStanConcReac));
}
// Returns the Species creation rates [kmol/m^2/s]. // Returns the Species creation rates [kmol/m^2/s].
/* /*
* Return the species * Return the species
@ -385,12 +440,17 @@ namespace Cantera {
net); net);
} }
/** //====================================================================================================================
// Apply corrections for interfacial charge transfer reactions
/*
* For reactions that transfer charge across a potential difference, * For reactions that transfer charge across a potential difference,
* the activation energies are modified by the potential difference. * the activation energies are modified by the potential difference.
* (see, for example, ...). This method applies this correction. * (see, for example, ...). This method applies this correction.
*
* @param kf Vector of forward reaction rate constants on which to have
* the correction applied
*/ */
void InterfaceKinetics::applyButlerVolmerCorrection(doublereal* kf) { void InterfaceKinetics::applyButlerVolmerCorrection(doublereal* const kf) {
int i; int i;
int n, nsp, k, ik=0; int n, nsp, k, ik=0;
@ -410,8 +470,7 @@ namespace Cantera {
// Compute the change in electrical potential energy for each // Compute the change in electrical potential energy for each
// reaction. This will only be non-zero if a potential // reaction. This will only be non-zero if a potential
// difference is present. // difference is present.
m_rxnstoich.getReactionDelta(m_ii, DATA_PTR(m_pot), m_rxnstoich.getReactionDelta(m_ii, DATA_PTR(m_pot), DATA_PTR(m_rwork));
DATA_PTR(m_rwork));
// Modify the reaction rates. Only modify those with a // Modify the reaction rates. Only modify those with a
// non-zero activation energy. Below we decrease the // non-zero activation energy. Below we decrease the
@ -432,7 +491,8 @@ namespace Cantera {
for (i = 0; i < nct; i++) { for (i = 0; i < nct; i++) {
irxn = m_ctrxn[i]; irxn = m_ctrxn[i];
eamod = m_beta[i]*m_rwork[irxn]; eamod = m_beta[i]*m_rwork[irxn];
if (eamod != 0.0 && m_E[irxn] != 0.0) { // if (eamod != 0.0 && m_E[irxn] != 0.0) {
if (eamod != 0.0) {
#ifdef DEBUG_KIN_MODE #ifdef DEBUG_KIN_MODE
ea = GasConstant * m_E[irxn]; ea = GasConstant * m_E[irxn];
if (eamod + ea < 0.0) { if (eamod + ea < 0.0) {
@ -450,18 +510,31 @@ namespace Cantera {
} }
} }
} }
//====================================================================================================================
void InterfaceKinetics::applyExchangeCurrentDensityFormulation(doublereal* const kfwd) {
getExchangeCurrentQuantities();
int nct = m_ctrxn.size();
doublereal rt = GasConstant*thermo(0).temperature();
doublereal rrt = 1.0/rt;
for (int i = 0; i < nct; i++) {
int irxn = m_ctrxn[i];
int iECDFormulation = m_ctrxn_ecdf[i];
if (iECDFormulation) {
double tmp = exp(- m_beta[i] * m_deltaG0[irxn] * rrt);
tmp *= 1.0 / m_logProdStanConcReac[irxn] / Faraday;
kfwd[irxn] *= tmp;
}
}
}
//====================================================================================================================
/** /**
* Update the rates of progress of the reactions in the reaciton * Update the rates of progress of the reactions in the reaciton
* mechanism. This routine operates on internal data. * mechanism. This routine operates on internal data.
*/ */
void InterfaceKinetics::getFwdRateConstants(doublereal* kfwd) { void InterfaceKinetics::getFwdRateConstants(doublereal* kfwd) {
// _update_rates_T();
// _update_rates_C();
updateROP(); updateROP();
const vector_fp& rf = m_kdata->m_rfn; const vector_fp& rf = m_kdata->m_rfn;
@ -738,7 +811,7 @@ namespace Cantera {
m_rxnstoich.getReactionDelta(m_ii, DATA_PTR(m_grt), deltaS); m_rxnstoich.getReactionDelta(m_ii, DATA_PTR(m_grt), deltaS);
} }
//====================================================================================================================
/** /**
* Add a single reaction to the mechanism. This routine * Add a single reaction to the mechanism. This routine
* must be called after init() and before finalize(). * must be called after init() and before finalize().
@ -752,8 +825,7 @@ namespace Cantera {
* There is no difference between elementary and surface * There is no difference between elementary and surface
* reactions. * reactions.
*/ */
void InterfaceKinetics:: void InterfaceKinetics::addReaction(const ReactionData& r) {
addReaction(const ReactionData& r) {
addElementaryReaction(r); addElementaryReaction(r);
@ -763,10 +835,8 @@ namespace Cantera {
incrementRxnCount(); incrementRxnCount();
m_rxneqn.push_back(r.equation); m_rxneqn.push_back(r.equation);
} }
//====================================================================================================================
void InterfaceKinetics::addElementaryReaction(const ReactionData& r) {
void InterfaceKinetics::
addElementaryReaction(const ReactionData& r) {
int iloc; int iloc;
// install rate coeff calculator // install rate coeff calculator
@ -776,12 +846,11 @@ namespace Cantera {
if (ncov > 3) { if (ncov > 3) {
m_has_coverage_dependence = true; m_has_coverage_dependence = true;
} }
for (int m = 0; m < ncov; m++) rp.push_back(r.cov[m]); for (int m = 0; m < ncov; m++) {
rp.push_back(r.cov[m]);
iloc = m_rates.install( reactionNumber(), }
r.rateCoeffType, rp.size(), // iloc = m_rates.install(reactionNumber(), r.rateCoeffType, rp.size(), DATA_PTR(rp));
DATA_PTR(rp) ); iloc = m_rates.install(reactionNumber(), ARRHENIUS_REACTION_RATECOEFF_TYPE, rp.size(), DATA_PTR(rp));
// store activation energy // store activation energy
m_E.push_back(r.rateCoeffParameters[2]); m_E.push_back(r.rateCoeffParameters[2]);
@ -789,13 +858,19 @@ namespace Cantera {
m_has_electrochem_rxns = true; m_has_electrochem_rxns = true;
m_beta.push_back(r.beta); m_beta.push_back(r.beta);
m_ctrxn.push_back(reactionNumber()); m_ctrxn.push_back(reactionNumber());
if (r.rateCoeffType == EXCHANGE_CURRENT_REACTION_RATECOEFF_TYPE) {
m_has_exchange_current_density_formulation = true;
m_ctrxn_ecdf.push_back(1);
} else {
m_ctrxn_ecdf.push_back(0);
}
} }
// add constant term to rate coeff value vector // add constant term to rate coeff value vector
m_kdata->m_rfn.push_back(r.rateCoeffParameters[0]); m_kdata->m_rfn.push_back(r.rateCoeffParameters[0]);
registerReaction( reactionNumber(), ELEMENTARY_RXN, iloc); registerReaction( reactionNumber(), ELEMENTARY_RXN, iloc);
} }
//====================================================================================================================
void InterfaceKinetics::setIOFlag(int ioFlag) { void InterfaceKinetics::setIOFlag(int ioFlag) {
m_ioFlag = ioFlag; m_ioFlag = ioFlag;
@ -958,6 +1033,7 @@ namespace Cantera {
* since we don't know this number up to now. * since we don't know this number up to now.
*/ */
void InterfaceKinetics::finalize() { void InterfaceKinetics::finalize() {
Kinetics::finalize();
m_rwork.resize(nReactions()); m_rwork.resize(nReactions());
int ks = reactionPhaseIndex(); int ks = reactionPhaseIndex();
if (ks < 0) throw CanteraError("InterfaceKinetics::finalize", if (ks < 0) throw CanteraError("InterfaceKinetics::finalize",
@ -967,6 +1043,13 @@ namespace Cantera {
throw CanteraError("InterfaceKinetics::finalize", throw CanteraError("InterfaceKinetics::finalize",
"expected interface dimension = 2, but got dimension = " "expected interface dimension = 2, but got dimension = "
+int2str(m_surf->nDim())); +int2str(m_surf->nDim()));
m_logStandardConc.resize(m_nTotalSpecies, 0.0);
m_deltaG0.resize(m_ii, 0.0);
m_logProdStanConcReac.resize(m_ii, 0.0);
m_finalized = true; m_finalized = true;
} }

140
Cantera/src/kinetics/InterfaceKinetics.h
View file

@ -45,11 +45,15 @@ namespace Cantera {
class InterfaceKineticsData { class InterfaceKineticsData {
public: public:
InterfaceKineticsData() : InterfaceKineticsData() :
m_logp0(0.0),
m_logc0(0.0),
m_ROP_ok(false), m_ROP_ok(false),
m_temp(0.0), m_logtemp(0.0) m_temp(0.0),
m_logtemp(0.0)
{} {}
//! Virtual destructor //! Virtual destructor
virtual ~InterfaceKineticsData(){} virtual ~InterfaceKineticsData() {
}
doublereal m_logp0; doublereal m_logp0;
doublereal m_logc0; doublereal m_logc0;
@ -59,7 +63,9 @@ namespace Cantera {
bool m_ROP_ok; bool m_ROP_ok;
//! Current temperature of the data
doublereal m_temp; doublereal m_temp;
//! Current log of the temperature
doublereal m_logtemp; doublereal m_logtemp;
vector_fp m_rfn; vector_fp m_rfn;
vector_fp m_rkcn; vector_fp m_rkcn;
@ -76,9 +82,9 @@ namespace Cantera {
public: public:
/**
* Constructor //! Constructor
* /*!
* @param thermo The optional parameter may be used to initialize * @param thermo The optional parameter may be used to initialize
* the object with one ThermoPhase object. * the object with one ThermoPhase object.
* HKM Note -> Since the interface kinetics * HKM Note -> Since the interface kinetics
@ -125,9 +131,9 @@ namespace Cantera {
virtual int ID() const { return cInterfaceKinetics; } virtual int ID() const { return cInterfaceKinetics; }
virtual int type() const { return cInterfaceKinetics; } virtual int type() const { return cInterfaceKinetics; }
/**
* Set the electric potential in the nth phase //! Set the electric potential in the nth phase
* /*!
* @param n phase Index in this kinetics object. * @param n phase Index in this kinetics object.
* @param V Electric potential (volts) * @param V Electric potential (volts)
*/ */
@ -172,8 +178,17 @@ namespace Cantera {
std::copy(m_kdata->m_ropnet.begin(), m_kdata->m_ropnet.end(), netROP); std::copy(m_kdata->m_ropnet.begin(), m_kdata->m_ropnet.end(), netROP);
} }
//! Get the equilibrium constants of all reactions, whether
//! the reaction is reversible or not.
/*!
* @param kc Returns the concentration equation constant for the reaction.
* Length is the number of reactions
*/
virtual void getEquilibriumConstants(doublereal* kc); virtual void getEquilibriumConstants(doublereal* kc);
void getExchangeCurrentQuantities();
virtual void getDeltaGibbs( doublereal* deltaG); virtual void getDeltaGibbs( doublereal* deltaG);
@ -394,8 +409,19 @@ namespace Cantera {
void updateROP(); void updateROP();
//! Update properties that depend on temperature
/*!
* This is called to update all of the properties that depend on temperature
*
* Current objects that this function updates
* m_kdata->m_logtemp
* m_kdata->m_rfn
* m_rates.
* updateKc();
*/
void _update_rates_T(); void _update_rates_T();
void _update_rates_phi(); void _update_rates_phi();
void _update_rates_C(); void _update_rates_C();
@ -445,12 +471,50 @@ namespace Cantera {
void setIOFlag(int ioFlag); void setIOFlag(int ioFlag);
void checkPartialEquil(); void checkPartialEquil();
int reactionNumber() const { return m_ii;}
void addElementaryReaction(const ReactionData& r);
void addGlobalReaction(const ReactionData& r);
void installReagents(const ReactionData& r);
void updateKc();
//! Write values into m_index
/*!
* @param rxnNumber reaction number
* @param type reaction type
* @param loc location ??
*/
void registerReaction(int rxnNumber, int type, int loc) {
m_index[rxnNumber] = std::pair<int, int>(type, loc);
}
//! Apply corrections for interfacial charge transfer reactions
/*!
* For reactions that transfer charge across a potential difference,
* the activation energies are modified by the potential difference.
* (see, for example, ...). This method applies this correction.
*
* @param kf Vector of forward reaction rate constants on which to have
* the correction applied
*/
void applyButlerVolmerCorrection(doublereal* const kf);
//! When an electrode reaction rate is optionally specified in terms of its
//! exchange current density, extra vectors need to be precalculated
/*!
*
*/
void applyExchangeCurrentDensityFormulation(doublereal* const kfwd);
protected:
//! Temporary work vector of length m_kk //! Temporary work vector of length m_kk
vector_fp m_grt; vector_fp m_grt;
protected:
//! m_kk is the number of species in all of the phases //! m_kk is the number of species in all of the phases
//! that participate in this kinetics mechanism. //! that participate in this kinetics mechanism.
int m_kk; int m_kk;
@ -489,7 +553,7 @@ namespace Cantera {
* production rates and also handles turning thermo * production rates and also handles turning thermo
* properties into reaction thermo properties. * properties into reaction thermo properties.
*/ */
ReactionStoichMgr m_rxnstoich; ReactionStoichMgr m_rxnstoich;
//! Number of irreversible reactions in the mechanism //! Number of irreversible reactions in the mechanism
int m_nirrev; int m_nirrev;
@ -607,42 +671,58 @@ namespace Cantera {
ImplicitSurfChem* m_integrator; ImplicitSurfChem* m_integrator;
vector_fp m_beta; vector_fp m_beta;
//! Vector of reaction indexes specifying the id of the current transfer reactions
//! in the mechanism
/*!
* Vector of reaction indecices which involve current transfers. This provides
* an index into the m_beta array.
*
* irxn = m_ctrxn[i]
*/
vector_int m_ctrxn; vector_int m_ctrxn;
int reactionNumber(){ return m_ii;} //! Vector of booleans indicating whether the charge transfer reaction may be
//! described by an exchange current density expression
vector_int m_ctrxn_ecdf;
void addElementaryReaction(const ReactionData& r); vector_fp m_logStandardConc;
void addGlobalReaction(const ReactionData& r); vector_fp m_deltaG0;
void installReagents(const ReactionData& r); vector_fp m_logProdStanConcReac;
void updateKc();
//! Write values into m_index
/*!
* @param rxnNumber reaction number
* @param type reaction type
* @param loc location ??
*/
void registerReaction(int rxnNumber, int type, int loc) {
m_index[rxnNumber] = std::pair<int, int>(type, loc);
}
void applyButlerVolmerCorrection(doublereal* kf);
//! boolean indicating whether mechanism has been finalized //! boolean indicating whether mechanism has been finalized
bool m_finalized; bool m_finalized;
//! Boolean flag indicating whether any reaction in the mechanism
//! has a coverage dependent forward reaction rate
/*!
* If this is true, then the coverage dependence is multiplied into
* the forward reaction rates constant
*/
bool m_has_coverage_dependence; bool m_has_coverage_dependence;
//! Boolean flag indicating whether any reaction in the mechanism //! Boolean flag indicating whether any reaction in the mechanism
//! has a beta electrochemical parameter. //! has a beta electrochemical parameter.
/*! /*!
* If this is true, the the Butler-Volmer correction is applied * If this is true, the Butler-Volmer correction is applied
* to the forward reaction rate for those reactions. * to the forward reaction rate for those reactions.
* *
* fac = exp ( - beta * (delta_phi)) * fac = exp ( - beta * (delta_phi))
*/ */
bool m_has_electrochem_rxns; bool m_has_electrochem_rxns;
//! Boolean flag indicating whether any reaction in the mechanism
//! is described by an exchange current density expression
/*!
* If this is true, the standard state gibbs free energy of the reaction and
* the product of the reactant standard concentrations must be precalculated
* in order to calculate the rate constant.
*/
bool m_has_exchange_current_density_formulation;
int m_ioFlag; int m_ioFlag;
private: private:

26
Cantera/src/kinetics/Kinetics.cpp
View file

@ -29,9 +29,16 @@ using namespace std;
namespace Cantera { namespace Cantera {
Kinetics::Kinetics() : m_ii(0), m_thermo(0), Kinetics::Kinetics() :
m_index(-1), m_surfphase(-1), m_rxnphase(-1), m_ii(0),
m_mindim(4) {} m_nTotalSpecies(0),
m_thermo(0),
m_index(-1),
m_surfphase(-1),
m_rxnphase(-1),
m_mindim(4)
{
}
Kinetics::~Kinetics(){} Kinetics::~Kinetics(){}
@ -42,7 +49,8 @@ namespace Cantera {
* throw an exception. * throw an exception.
*/ */
Kinetics::Kinetics(const Kinetics &right) : Kinetics::Kinetics(const Kinetics &right) :
m_ii(0), m_ii(0),
m_nTotalSpecies(0),
m_thermo(0), m_thermo(0),
m_index(-1), m_index(-1),
m_surfphase(-1), m_surfphase(-1),
@ -70,6 +78,7 @@ namespace Cantera {
if (this == &right) return *this; if (this == &right) return *this;
m_ii = right.m_ii; m_ii = right.m_ii;
m_nTotalSpecies = right.m_nTotalSpecies;
m_perturb = right.m_perturb; m_perturb = right.m_perturb;
m_reactants = right.m_reactants; m_reactants = right.m_reactants;
m_products = right.m_products; m_products = right.m_products;
@ -285,6 +294,15 @@ namespace Cantera {
m_phaseindex[m_thermo.back()->id()] = nPhases(); m_phaseindex[m_thermo.back()->id()] = nPhases();
} }
void Kinetics::finalize() {
m_nTotalSpecies = 0;
int np = nPhases();
for (int n = 0; n < np; n++) {
int nsp = m_thermo[n]->nSpecies();
m_nTotalSpecies += nsp;
}
}
//! Private function of the class Kinetics, indicating that a function //! Private function of the class Kinetics, indicating that a function
//! inherited from the base class hasn't had a definition assigned to it //! inherited from the base class hasn't had a definition assigned to it

5
Cantera/src/kinetics/Kinetics.h
View file

@ -811,7 +811,7 @@ namespace Cantera {
* any initialization (allocating arrays, etc.) that must be * any initialization (allocating arrays, etc.) that must be
* done after the reactions are entered. * done after the reactions are entered.
*/ */
virtual void finalize() {} virtual void finalize();
/** /**
* Add a single reaction to the mechanism. This routine * Add a single reaction to the mechanism. This routine
@ -904,6 +904,9 @@ namespace Cantera {
//! Number of reactions in the mechanism //! Number of reactions in the mechanism
int m_ii; int m_ii;
//! Number of species in the species vector for this kinetics operator
int m_nTotalSpecies;
/// Vector of perturbation factors for each reaction's rate of /// Vector of perturbation factors for each reaction's rate of
/// progress vector. It is initialized to one. /// progress vector. It is initialized to one.

14
Cantera/src/kinetics/ReactionData.h
View file

@ -25,7 +25,7 @@ namespace Cantera {
number = 0; number = 0;
rxn_number = 0; rxn_number = 0;
reversible = true; reversible = true;
rateCoeffType = ARRHENIUS; rateCoeffType = ARRHENIUS_REACTION_RATECOEFF_TYPE;
falloffType = NONE; falloffType = NONE;
error = 0; error = 0;
equation = ""; equation = "";
@ -36,7 +36,12 @@ namespace Cantera {
} }
virtual ~ReactionData(){} virtual ~ReactionData(){}
//! type of the reaction
/*!
* The valid types are listed in the file, reaction_defs.h.
*/
int reactionType; int reactionType;
int number; int number;
int rxn_number; int rxn_number;
vector_int reactants; vector_int reactants;
@ -51,7 +56,14 @@ namespace Cantera {
//! True if the current reaction is reversible. False otherwise //! True if the current reaction is reversible. False otherwise
bool reversible; bool reversible;
//! type of the rate coefficient for the forward rate constant
/*!
* The valid types are listed in the file, reaction_defs.h and they
* all end in RATECOEFF_TYPE
*/
int rateCoeffType; int rateCoeffType;
vector_fp rateCoeffParameters; vector_fp rateCoeffParameters;
vector_fp auxRateCoeffParameters; vector_fp auxRateCoeffParameters;
int falloffType; int falloffType;

1
Cantera/src/kinetics/ReactionStoichMgr.h
View file

@ -214,6 +214,7 @@ namespace Cantera {
* \f[ * \f[
* R_i = R_i * \prod_k C_k^{o_{k,i}} * R_i = R_i * \prod_k C_k^{o_{k,i}}
* \f] * \f]
*
* Here \f$ o_{k,i} \f$ is the reaction order of species k in reaction i. * Here \f$ o_{k,i} \f$ is the reaction order of species k in reaction i.
*/ */
virtual void multiplyReactants(const doublereal* C, doublereal* R); virtual void multiplyReactants(const doublereal* C, doublereal* R);

397
Cantera/src/kinetics/RxnRates.h
View file

@ -19,93 +19,100 @@
namespace Cantera { namespace Cantera {
/** //! Arrhenius reaction rate type depends only on temperature
* A rate coefficient of the form /**
* \f[ * A reaction rate coefficient of the following form.
* A T^b \exp (-E/RT) *
* \f] * \f[
* k_f = A T^b \exp (-E/RT)
* \f]
*
*/
class Arrhenius {
public:
//! return the rate coefficient type.
static int type() {
return ARRHENIUS_REACTION_RATECOEFF_TYPE;
}
//! Default constructor.
Arrhenius() :
m_logA(-1.0E300),
m_b (0.0),
m_E (0.0),
m_A(0.0) {}
//! Constructor with Arrhenius parameters specified with an array.
Arrhenius(int csize, const doublereal* c) :
m_b (c[1]),
m_E (c[2]),
m_A (c[0])
{
if (m_A <= 0.0) {
m_logA = -1.0E300;
} else {
m_logA = log(m_A);
}
}
/// Constructor.
/// @param A pre-exponential. The unit system is
/// (kmol, m, s). The actual units depend on the reaction
/// order and the dimensionality (surface or bulk).
/// @param b Temperature exponent. Non-dimensional.
/// @param E Activation energy in temperature units. Kelvin.
Arrhenius(doublereal A, doublereal b, doublereal E) :
m_b (b),
m_E (E),
m_A (A)
{
if (m_A <= 0.0) {
m_logA = -1.0E300;
} else {
m_logA = log(m_A);
}
}
//! Update concentration-dependent parts of the rate coefficient.
/*!
* For this class, there are no
* concentration-dependent parts, so this method does nothing.
*/ */
class Arrhenius { void update_C(const doublereal* c) {
}
public:
/// return the rate coefficient type. /**
static int type(){ return ARRHENIUS; } * Update the value of the logarithm of the rate constant.
*
/// Default constructor. * Note, this function should never be called for negative A values.
Arrhenius() : * If it does then it will produce a negative overflow result, and
m_logA(-1.0E300), * a zero net forwards reaction rate, instead of a negative reaction
m_b (0.0), * rate constant that is the expected result.
m_E (0.0), */
m_A(0.0) {} doublereal update(doublereal logT, doublereal recipT) const {
return m_logA + m_b*logT - m_E*recipT;
/// Constructor with Arrhenius parameters specified with an array. }
Arrhenius(int csize, const doublereal* c) :
m_b (c[1]),
m_E (c[2]),
m_A (c[0])
{
if (m_A <= 0.0) {
m_logA = -1.0E300;
} else {
m_logA = log(m_A);
}
}
/// Constructor.
/// @param A pre-exponential. The unit system is
/// (kmol, m, s). The actual units depend on the reaction
/// order and the dimensionality (surface or bulk).
/// @param b Temperature exponent. Non-dimensional.
/// @param E Activation energy in temperature units. Kelvin.
Arrhenius(doublereal A, doublereal b, doublereal E) :
m_b (b),
m_E (E),
m_A (A)
{
if (m_A <= 0.0) {
m_logA = -1.0E300;
} else {
m_logA = log(m_A);
}
}
/// Update concentration-dependent parts of the rate
/// coefficient. For this class, there are no
/// concentration-dependent parts, so this method does
/// nothing.
void update_C(const doublereal* c) {}
/** /**
* Update the value of the logarithm of the rate constant. * Update the value the rate constant.
* *
* Note, this function should never be called for negative A values. * This function returns the actual value of the rate constant.
* If it does then it will produce a negative overflow result, and * It can be safely called for negative values of the pre-exponential
* a zero net forwards reaction rate, instead of a negative reaction * factor.
* rate constant that is the expected result. */
*/ doublereal updateRC(doublereal logT, doublereal recipT) const {
doublereal update(doublereal logT, doublereal recipT) const { return m_A * exp(m_b*logT - m_E*recipT);
return m_logA + m_b*logT - m_E*recipT; }
}
/**
* Update the value the rate constant.
*
* This function returns the actual value of the rate constant.
* It can be safely called for negative values of the pre-exponential
* factor.
*/
doublereal updateRC(doublereal logT, doublereal recipT) const {
return m_A * exp(m_b*logT - m_E*recipT);
}
void writeUpdateRHS(std::ostream& s) const { void writeUpdateRHS(std::ostream& s) const {
s << " exp(" << m_logA; s << " exp(" << m_logA;
if (m_b != 0.0) s << " + " << m_b << " * tlog"; if (m_b != 0.0) s << " + " << m_b << " * tlog";
if (m_E != 0.0) s << " - " << m_E << " * rt"; if (m_E != 0.0) s << " - " << m_E << " * rt";
s << ");" << std::endl; s << ");" << std::endl;
} }
doublereal activationEnergy_R() const { doublereal activationEnergy_R() const {
return m_E; return m_E;
@ -121,19 +128,22 @@ namespace Cantera {
class ArrheniusSum { class ArrheniusSum {
public: public:
static int type(){ return ARRHENIUS_SUM; } static int type() {
return ARRHENIUS_SUM_REACTION_RATECOEFF_TYPE;
}
ArrheniusSum() : m_nterms(0) {} ArrheniusSum() : m_nterms(0) {}
void addArrheniusTerm(doublereal A, doublereal b, doublereal E) { void addArrheniusTerm(doublereal A, doublereal b, doublereal E) {
if (A > 0.0) { if (A > 0.0) {
m_terms.push_back(Arrhenius(A, b, E)); m_terms.push_back(Arrhenius(A, b, E));
m_sign.push_back(1); m_sign.push_back(1);
} }
else if (A < 0.0) { else if (A < 0.0) {
m_terms.push_back(Arrhenius(-A, b, E)); m_terms.push_back(Arrhenius(-A, b, E));
m_sign.push_back(-1); m_sign.push_back(-1);
} }
m_nterms++; m_nterms++;
} }
void update_C(const doublereal* c) {} void update_C(const doublereal* c) {}
@ -169,38 +179,41 @@ namespace Cantera {
return fsum; return fsum;
} }
void writeUpdateRHS(std::ostream& s) const { void writeUpdateRHS(std::ostream& s) const {
; ;
} }
static bool alwaysComputeRate() { return false;} static bool alwaysComputeRate() { return false;}
protected: protected:
std::vector<Arrhenius> m_terms; std::vector<Arrhenius> m_terms;
vector_int m_sign; vector_int m_sign;
int m_nterms; int m_nterms;
}; };
/** /**
* An Arrhenius rate with coverage-dependent terms. * An Arrhenius rate with coverage-dependent terms.
*/ */
class SurfaceArrhenius { class SurfaceArrhenius {
public: public:
static int type(){ return ARRHENIUS; } static int type() {
SurfaceArrhenius() : return ARRHENIUS_REACTION_RATECOEFF_TYPE;
m_logA(-1.0E300), }
m_b (0.0),
m_E (0.0), SurfaceArrhenius() :
m_A(0.0), m_logA(-1.0E300),
m_acov(0.0), m_b (0.0),
m_ecov(0.0), m_E (0.0),
m_mcov(0.0), m_A(0.0),
m_ncov(0), m_acov(0.0),
m_nmcov(0) m_ecov(0.0),
{ m_mcov(0.0),
} m_ncov(0),
m_nmcov(0)
{
}
SurfaceArrhenius( int csize, const doublereal* c ) : SurfaceArrhenius( int csize, const doublereal* c ) :
m_b (c[1]), m_b (c[1]),
@ -325,7 +338,7 @@ namespace Cantera {
return exp(lres); return exp(lres);
} }
void writeUpdateRHS(std::ostream& s) const {} void writeUpdateRHS(std::ostream& s) const {}
protected: protected:
doublereal delta_s0, delta_e0; doublereal delta_s0, delta_e0;
@ -335,37 +348,143 @@ namespace Cantera {
#endif #endif
}
// class LandauTeller { //! Arrhenius reaction rate type depends only on temperature
/**
* A reaction rate coefficient of the following form.
*
* \f[
* k_f = A T^b \exp (-E/RT)
* \f]
*
*/
class ExchangeCurrent {
// public: public:
// static int type(){ return LANDAUTELLER; }
// LandauTeller(){}
// LandauTeller( const vector_fp& c ) : m_c(c) { m_c[0] = log(c[0]); }
// doublereal update(doublereal logT, doublereal recipT) const { //! return the rate coefficient type.
// return m_c[0] + m_c[1]*tt[1] - m_c[2]*tt[2] static int type() {
// + m_c[3]*tt[3] + m_c[4]*tt[4]; return EXCHANGE_CURRENT_REACTION_RATECOEFF_TYPE;
// } }
// //void writeUpdateRHS(ostream& s) const {
// // s << exp(m_logA);
// // s << " * exp(";
// // if (m_b != 0.0) s << m_b << " * tlog";
// // if (m_E != 0.0) s << " - " << m_E << " * rt";
// // if (m_E != 0.0) s << " - " << m_E << " * rt";
// // s << ");" << endl;
// // }
// //}
// protected: //! Default constructor.
// doublereal m_logA, m_b, m_E; ExchangeCurrent() :
// }; m_logA(-1.0E300),
m_b (0.0),
m_E (0.0),
m_A(0.0) {}
//! Constructor with Arrhenius parameters specified with an array.
ExchangeCurrent(int csize, const doublereal* c) :
m_b (c[1]),
m_E (c[2]),
m_A (c[0])
{
if (m_A <= 0.0) {
m_logA = -1.0E300;
} else {
m_logA = log(m_A);
}
}
/// Constructor.
/// @param A pre-exponential. The unit system is
/// (kmol, m, s). The actual units depend on the reaction
/// order and the dimensionality (surface or bulk).
/// @param b Temperature exponent. Non-dimensional.
/// @param E Activation energy in temperature units. Kelvin.
ExchangeCurrent(doublereal A, doublereal b, doublereal E) :
m_b (b),
m_E (E),
m_A (A)
{
if (m_A <= 0.0) {
m_logA = -1.0E300;
} else {
m_logA = log(m_A);
}
}
//! Update concentration-dependent parts of the rate coefficient.
/*!
* For this class, there are no
* concentration-dependent parts, so this method does nothing.
*/
void update_C(const doublereal* c) {
}
/**
* Update the value of the logarithm of the rate constant.
*
* Note, this function should never be called for negative A values.
* If it does then it will produce a negative overflow result, and
* a zero net forwards reaction rate, instead of a negative reaction
* rate constant that is the expected result.
*/
doublereal update(doublereal logT, doublereal recipT) const {
return m_logA + m_b*logT - m_E*recipT;
}
/**
* Update the value the rate constant.
*
* This function returns the actual value of the rate constant.
* It can be safely called for negative values of the pre-exponential
* factor.
*/
doublereal updateRC(doublereal logT, doublereal recipT) const {
return m_A * exp(m_b*logT - m_E*recipT);
}
void writeUpdateRHS(std::ostream& s) const {
s << " exp(" << m_logA;
if (m_b != 0.0) s << " + " << m_b << " * tlog";
if (m_E != 0.0) s << " - " << m_E << " * rt";
s << ");" << std::endl;
}
doublereal activationEnergy_R() const {
return m_E;
}
static bool alwaysComputeRate() { return false;}
protected:
doublereal m_logA, m_b, m_E, m_A;
};
// class LandauTeller {
// public:
// static int type(){ return LANDAUTELLER; }
// LandauTeller(){}
// LandauTeller( const vector_fp& c ) : m_c(c) { m_c[0] = log(c[0]); }
// doublereal update(doublereal logT, doublereal recipT) const {
// return m_c[0] + m_c[1]*tt[1] - m_c[2]*tt[2]
// + m_c[3]*tt[3] + m_c[4]*tt[4];
// }
// //void writeUpdateRHS(ostream& s) const {
// // s << exp(m_logA);
// // s << " * exp(";
// // if (m_b != 0.0) s << m_b << " * tlog";
// // if (m_E != 0.0) s << " - " << m_E << " * rt";
// // if (m_E != 0.0) s << " - " << m_E << " * rt";
// // s << ");" << endl;
// // }
// //}
// protected:
// doublereal m_logA, m_b, m_E;
// };
//} //}
}
#endif #endif

24
Cantera/src/kinetics/importKinetics.cpp
View file

@ -521,9 +521,24 @@ namespace Cantera {
* kf should point to a XML element named "rateCoeff". * kf should point to a XML element named "rateCoeff".
* rdata is the partially filled ReactionData object for the reaction. * rdata is the partially filled ReactionData object for the reaction.
* This function will fill in more fields in the ReactionData object. * This function will fill in more fields in the ReactionData object.
*
* @param kf Reference to the XML Node named rateCoeff
*/ */
void getRateCoefficient(const node_t& kf, kinetics_t& kin, void getRateCoefficient(const node_t& kf, kinetics_t& kin,
ReactionData& rdata, int negA) { ReactionData& rdata, int negA) {
string type = kf.attrib("type");
if (type == "") {
type = "Arrhenius";
rdata.rateCoeffType = ARRHENIUS_REACTION_RATECOEFF_TYPE;
}
if (type == "ExchangeCurrentDensity") {
rdata.rateCoeffType = EXCHANGE_CURRENT_REACTION_RATECOEFF_TYPE;
} else if (type == "Arrhenius") {
} else {
throw CanteraError("getRateCoefficient",
"Unknown type: " + type);
}
int nc = kf.nChildren(); int nc = kf.nChildren();
nodeset_t& kf_children = kf.children(); nodeset_t& kf_children = kf.children();
@ -557,6 +572,12 @@ namespace Cantera {
"negative or zero A coefficient for reaction "+int2str(rdata.number)); "negative or zero A coefficient for reaction "+int2str(rdata.number));
} }
} }
else if (nm == "Arrhenius_ExchangeCurrentDensity") {
vector_fp coeff(3);
getArrhenius(c, highlow, coeff[0], coeff[1], coeff[2]);
chigh = coeff;
rdata.rateCoeffType = EXCHANGE_CURRENT_REACTION_RATECOEFF_TYPE;
}
else if (nm == "falloff") { else if (nm == "falloff") {
getFalloff(c, rdata); getFalloff(c, rdata);
} }
@ -580,6 +601,9 @@ namespace Cantera {
rdata.auxRateCoeffParameters = clow; rdata.auxRateCoeffParameters = clow;
else if (rdata.reactionType == CHEMACT_RXN) else if (rdata.reactionType == CHEMACT_RXN)
rdata.auxRateCoeffParameters = chigh; rdata.auxRateCoeffParameters = chigh;
} }

11
Cantera/src/kinetics/reaction_defs.h
View file

@ -81,11 +81,12 @@ namespace Cantera {
*/ */
//@{ //@{
const int ARRHENIUS = 1; const int ARRHENIUS_REACTION_RATECOEFF_TYPE = 1;
const int LANDAUTELLER = 2; const int LANDAUTELLER_REACTION_RATECOEFF_TYPE = 2;
const int TSTRATE = 3; const int TSTRATE_REACTION_RATECOEFF_TYPE = 3;
const int SURF_ARRHENIUS = 4; const int SURF_ARRHENIUS_REACTION_RATECOEFF_TYPE = 4;
const int ARRHENIUS_SUM = 5; const int ARRHENIUS_SUM_REACTION_RATECOEFF_TYPE = 5;
const int EXCHANGE_CURRENT_REACTION_RATECOEFF_TYPE = 6;
//@} //@}

27
Cantera/src/thermo/GibbsExcessVPSSTP.cpp
View file

@ -72,7 +72,7 @@ namespace Cantera {
return *this; return *this;
} }
/** /*
* *
* ~GibbsExcessVPSSTP(): (virtual) * ~GibbsExcessVPSSTP(): (virtual)
* *
@ -313,7 +313,6 @@ namespace Cantera {
void GibbsExcessVPSSTP::initThermo() { void GibbsExcessVPSSTP::initThermo() {
initLengths(); initLengths();
VPStandardStateTP::initThermo(); VPStandardStateTP::initThermo();
} }
@ -328,34 +327,12 @@ namespace Cantera {
dlnActCoeffdlnN_Scaled_.resize(m_kk); dlnActCoeffdlnN_Scaled_.resize(m_kk);
m_pp.resize(m_kk); m_pp.resize(m_kk);
} }
/*
* initThermoXML() (virtual from ThermoPhase)
* Import and initialize a ThermoPhase object
*
* @param phaseNode This object must be the phase node of a
* complete XML tree
* description of the phase, including all of the
* species data. In other words while "phase" must
* point to an XML phase object, it must have
* sibling nodes "speciesData" that describe
* the species in the phase.
* @param id ID of the phase. If nonnull, a check is done
* to see if phaseNode is pointing to the phase
* with the correct id.
*/
void GibbsExcessVPSSTP::initThermoXML(XML_Node& phaseNode, std::string id) {
VPStandardStateTP::initThermoXML(phaseNode, id);
}
/** /*
* Format a summary of the mixture state for output. * Format a summary of the mixture state for output.
*/ */
std::string GibbsExcessVPSSTP::report(bool show_thermo) const { std::string GibbsExcessVPSSTP::report(bool show_thermo) const {
char p[800]; char p[800];
string s = ""; string s = "";
try { try {

39
Cantera/src/thermo/GibbsExcessVPSSTP.h
View file

@ -71,13 +71,14 @@ namespace Cantera {
* \f$k\f$. * \f$k\f$.
* *
* GibbsExcessVPSSTP contains an internal vector with the current mole * GibbsExcessVPSSTP contains an internal vector with the current mole
* fraction vector. That's one of its primary usages. * fraction vector. That's one of its primary usages. In order to keep the mole fraction
* vector constant, all of the setState functions are redesigned at this layer.
* *
* <H3> SetState Strategy </H3> * <H3> SetState Strategy </H3>
* *
* The gibbsExcessVPSSTP object does not have a setState strategy. * All setState functions that set the internal state of the ThermoPhase object are
* It's strictly an interfacial layer that writes the current mole fractions to the * overloaded at this level, so that a current mole fraction vector is maintained within
* State object. * the object.
* *
* *
*/ */
@ -172,6 +173,7 @@ namespace Cantera {
virtual void setPressure(doublereal p); virtual void setPressure(doublereal p);
protected: protected:
/** /**
* Calculate the density of the mixture using the partial * Calculate the density of the mixture using the partial
* molar volumes and mole fractions as input * molar volumes and mole fractions as input
@ -531,24 +533,6 @@ namespace Cantera {
* @see importCTML.cpp * @see importCTML.cpp
*/ */
virtual void initThermo(); virtual void initThermo();
/**
* Import and initialize a ThermoPhase object
*
* @param phaseNode This object must be the phase node of a
* complete XML tree
* description of the phase, including all of the
* species data. In other words while "phase" must
* point to an XML phase object, it must have
* sibling nodes "speciesData" that describe
* the species in the phase.
* @param id ID of the phase. If nonnull, a check is done
* to see if phaseNode is pointing to the phase
* with the correct id.
*/
void initThermoXML(XML_Node& phaseNode, std::string id);
//! returns a summary of the state of the phase as a string //! returns a summary of the state of the phase as a string
/*! /*!
@ -560,14 +544,10 @@ namespace Cantera {
private: private:
//! Initialize lengths of local variables after all species have //! Initialize lengths of local variables after all species have
//! been identified. //! been identified.
void initLengths(); void initLengths();
private:
//! Error function //! Error function
/*! /*!
* Print an error string and exit * Print an error string and exit
@ -587,6 +567,13 @@ namespace Cantera {
protected: protected:
//! Storage for the current values of the mole fractions of the species //! Storage for the current values of the mole fractions of the species
/*!
* This vector is kept up-to-date when the setState functions are called.
* Therefore, it may be considered to be an independent variable.
*
* Note in order to do this, the setState functions are redefined to always
* keep this vector current.
*/
mutable std::vector<doublereal> moleFractions_; mutable std::vector<doublereal> moleFractions_;
//! Storage for the current values of the activity coefficients of the //! Storage for the current values of the activity coefficients of the

165
configure vendored
View file

@ -9740,6 +9740,154 @@ if test "$BUILD_WITH_F2C"="n"; then
fi fi
#
# Check to see if we have a -lm line
#
echo "$as_me:$LINENO: checking for printf in -lm" >&5
echo $ECHO_N "checking for printf in -lm... $ECHO_C" >&6
if test "${ac_cv_lib_m_printf+set}" = set; then
echo $ECHO_N "(cached) $ECHO_C" >&6
else
ac_check_lib_save_LIBS=$LIBS
LIBS="-lm $LIBS"
cat >conftest.$ac_ext <<_ACEOF
/* confdefs.h. */
_ACEOF
cat confdefs.h >>conftest.$ac_ext
cat >>conftest.$ac_ext <<_ACEOF
/* end confdefs.h. */
/* Override any gcc2 internal prototype to avoid an error. */
#ifdef __cplusplus
extern "C"
#endif
/* We use char because int might match the return type of a gcc2
builtin and then its argument prototype would still apply. */
char printf ();
int
main ()
{
printf ();
;
return 0;
}
_ACEOF
rm -f conftest.$ac_objext conftest$ac_exeext
if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5
(eval $ac_link) 2>conftest.er1
ac_status=$?
grep -v '^ *+' conftest.er1 >conftest.err
rm -f conftest.er1
cat conftest.err >&5
echo "$as_me:$LINENO: \$? = $ac_status" >&5
(exit $ac_status); } &&
{ ac_try='test -z "$ac_cxx_werror_flag"
|| test ! -s conftest.err'
{ (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5
(eval $ac_try) 2>&5
ac_status=$?
echo "$as_me:$LINENO: \$? = $ac_status" >&5
(exit $ac_status); }; } &&
{ ac_try='test -s conftest$ac_exeext'
{ (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5
(eval $ac_try) 2>&5
ac_status=$?
echo "$as_me:$LINENO: \$? = $ac_status" >&5
(exit $ac_status); }; }; then
ac_cv_lib_m_printf=yes
else
echo "$as_me: failed program was:" >&5
sed 's/^/| /' conftest.$ac_ext >&5
ac_cv_lib_m_printf=no
fi
rm -f conftest.err conftest.$ac_objext \
conftest$ac_exeext conftest.$ac_ext
LIBS=$ac_check_lib_save_LIBS
fi
echo "$as_me:$LINENO: result: $ac_cv_lib_m_printf" >&5
echo "${ECHO_T}$ac_cv_lib_m_printf" >&6
if test $ac_cv_lib_m_printf = yes; then
add_stm=1
else
add_stm=0
fi
#
# Check to see if we have a -lstdc++ line
#
echo "$as_me:$LINENO: checking for printf in -lstdc++" >&5
echo $ECHO_N "checking for printf in -lstdc++... $ECHO_C" >&6
if test "${ac_cv_lib_stdcpp_printf+set}" = set; then
echo $ECHO_N "(cached) $ECHO_C" >&6
else
ac_check_lib_save_LIBS=$LIBS
LIBS="-lstdc++ $LIBS"
cat >conftest.$ac_ext <<_ACEOF
/* confdefs.h. */
_ACEOF
cat confdefs.h >>conftest.$ac_ext
cat >>conftest.$ac_ext <<_ACEOF
/* end confdefs.h. */
/* Override any gcc2 internal prototype to avoid an error. */
#ifdef __cplusplus
extern "C"
#endif
/* We use char because int might match the return type of a gcc2
builtin and then its argument prototype would still apply. */
char printf ();
int
main ()
{
printf ();
;
return 0;
}
_ACEOF
rm -f conftest.$ac_objext conftest$ac_exeext
if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5
(eval $ac_link) 2>conftest.er1
ac_status=$?
grep -v '^ *+' conftest.er1 >conftest.err
rm -f conftest.er1
cat conftest.err >&5
echo "$as_me:$LINENO: \$? = $ac_status" >&5
(exit $ac_status); } &&
{ ac_try='test -z "$ac_cxx_werror_flag"
|| test ! -s conftest.err'
{ (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5
(eval $ac_try) 2>&5
ac_status=$?
echo "$as_me:$LINENO: \$? = $ac_status" >&5
(exit $ac_status); }; } &&
{ ac_try='test -s conftest$ac_exeext'
{ (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5
(eval $ac_try) 2>&5
ac_status=$?
echo "$as_me:$LINENO: \$? = $ac_status" >&5
(exit $ac_status); }; }; then
ac_cv_lib_stdcpp_printf=yes
else
echo "$as_me: failed program was:" >&5
sed 's/^/| /' conftest.$ac_ext >&5
ac_cv_lib_stdcpp_printf=no
fi
rm -f conftest.err conftest.$ac_objext \
conftest$ac_exeext conftest.$ac_ext
LIBS=$ac_check_lib_save_LIBS
fi
echo "$as_me:$LINENO: result: $ac_cv_lib_stdcpp_printf" >&5
echo "${ECHO_T}$ac_cv_lib_stdcpp_printf" >&6
if test $ac_cv_lib_stdcpp_printf = yes; then
add_stdc=1
else
add_stdc=0
fi
# #
# Ending Libs for compiling static applications and # Ending Libs for compiling static applications and
# dynamically loaded libraries # dynamically loaded libraries
@ -9755,6 +9903,17 @@ case $ac_sys_system in
LCXX_END_LIBS="$LCXX_END_LIBS"" -lCrun -lCstd -lfsu" ;; LCXX_END_LIBS="$LCXX_END_LIBS"" -lCrun -lCstd -lfsu" ;;
esac ;; esac ;;
esac esac
if test $add_stm = 1 ; then
echo 'Adding -lm to the end of the LCXX_END_LIBS variable'
LCXX_END_LIBS="$LCXX_END_LIBS"" -lm"
echo 'LCXX_END_LIBS = ' $LCXX_END_LIBS
fi
if test $add_stdc = 1 ; then
echo 'Adding -lstdc++ to the end of the LCXX_END_LIBS variable'
LCXX_END_LIBS="$LCXX_END_LIBS"" -lstdc++ "
echo 'LCXX_END_LIBS = ' $LCXX_END_LIBS
fi
@ -9888,7 +10047,7 @@ fi
# Provide some information about the compiler. # Provide some information about the compiler.
echo "$as_me:9891:" \ echo "$as_me:10050:" \
"checking for Fortran 77 compiler version" >&5 "checking for Fortran 77 compiler version" >&5
ac_compiler=`set X $ac_compile; echo $2` ac_compiler=`set X $ac_compile; echo $2`
{ (eval echo "$as_me:$LINENO: \"$ac_compiler --version </dev/null >&5\"") >&5 { (eval echo "$as_me:$LINENO: \"$ac_compiler --version </dev/null >&5\"") >&5
@ -10095,7 +10254,7 @@ _ACEOF
# flags. # flags.
ac_save_FFLAGS=$FFLAGS ac_save_FFLAGS=$FFLAGS
FFLAGS="$FFLAGS $ac_verb" FFLAGS="$FFLAGS $ac_verb"
(eval echo $as_me:10098: \"$ac_link\") >&5 (eval echo $as_me:10257: \"$ac_link\") >&5
ac_f77_v_output=`eval $ac_link 5>&1 2>&1 | grep -v 'Driving:'` ac_f77_v_output=`eval $ac_link 5>&1 2>&1 | grep -v 'Driving:'`
echo "$ac_f77_v_output" >&5 echo "$ac_f77_v_output" >&5
FFLAGS=$ac_save_FFLAGS FFLAGS=$ac_save_FFLAGS
@ -10173,7 +10332,7 @@ _ACEOF
# flags. # flags.
ac_save_FFLAGS=$FFLAGS ac_save_FFLAGS=$FFLAGS
FFLAGS="$FFLAGS $ac_cv_prog_f77_v" FFLAGS="$FFLAGS $ac_cv_prog_f77_v"
(eval echo $as_me:10176: \"$ac_link\") >&5 (eval echo $as_me:10335: \"$ac_link\") >&5
ac_f77_v_output=`eval $ac_link 5>&1 2>&1 | grep -v 'Driving:'` ac_f77_v_output=`eval $ac_link 5>&1 2>&1 | grep -v 'Driving:'`
echo "$ac_f77_v_output" >&5 echo "$ac_f77_v_output" >&5
FFLAGS=$ac_save_FFLAGS FFLAGS=$ac_save_FFLAGS

21
configure.in
View file

@ -1463,6 +1463,16 @@ if test "$BUILD_WITH_F2C"="n"; then
fi fi
AC_SUBST(LCXX_FLAGS) AC_SUBST(LCXX_FLAGS)
#
# Check to see if we have a -lm line
#
AC_CHECK_LIB(m, printf, [add_stm=1], [add_stm=0], [ ])
#
# Check to see if we have a -lstdc++ line
#
AC_CHECK_LIB(stdc++, printf, [add_stdc=1], [add_stdc=0], [])
# #
# Ending Libs for compiling static applications and # Ending Libs for compiling static applications and
# dynamically loaded libraries # dynamically loaded libraries
@ -1478,6 +1488,17 @@ case $ac_sys_system in
LCXX_END_LIBS="$LCXX_END_LIBS"" -lCrun -lCstd -lfsu" ;; LCXX_END_LIBS="$LCXX_END_LIBS"" -lCrun -lCstd -lfsu" ;;
esac ;; esac ;;
esac esac
if test $add_stm = 1 ; then
echo 'Adding -lm to the end of the LCXX_END_LIBS variable'
LCXX_END_LIBS="$LCXX_END_LIBS"" -lm"
echo 'LCXX_END_LIBS = ' $LCXX_END_LIBS
fi
if test $add_stdc = 1 ; then
echo 'Adding -lstdc++ to the end of the LCXX_END_LIBS variable'
LCXX_END_LIBS="$LCXX_END_LIBS"" -lstdc++ "
echo 'LCXX_END_LIBS = ' $LCXX_END_LIBS
fi
AC_SUBST(LCXX_END_LIBS) AC_SUBST(LCXX_END_LIBS)

4
data/thermo/nasathermo.dat
View file

@ -1849,7 +1849,7 @@ LiO J 3/64LI 1.O 1. 0. 0.G 300.000 5000.000 22.94040 1
LiO- J12/67LI 1.O 1.E 1. 0.G 300.000 5000.000 22.94095 1 LiO- J12/67LI 1.O 1.E 1. 0.G 300.000 5000.000 22.94095 1
4.18102170E+00 4.17850000E-04-1.50248450E-07 2.83977320E-11-1.97891810E-15 2 4.18102170E+00 4.17850000E-04-1.50248450E-07 2.83977320E-11-1.97891810E-15 2
-9.38497020E+03-1.42392337E-01 2.85158660E+00 5.01698800E-03-5.95474750E-06 3 -9.38497020E+03-1.42392337E-01 2.85158660E+00 5.01698800E-03-5.95474750E-06 3
3.03994510E-09-4.78729690E-13-9.07780760E+03 6.45947067E+00-8.05144594E+03 4 03994510E-09-4.78729690E-13-9.07780760E+03 6.45947067E+00-8.05144594E+03 4
LiOH J 6/71LI 1.O 1.H 1. 0.G 300.000 5000.000 23.94834 1 LiOH J 6/71LI 1.O 1.H 1. 0.G 300.000 5000.000 23.94834 1
5.50969570E+00 1.36854640E-03-3.94414690E-07 5.23321950E-11-2.59586760E-15 2 5.50969570E+00 1.36854640E-03-3.94414690E-07 5.23321950E-11-2.59586760E-15 2
-2.98992310E+04-6.50701600E+00 3.34623000E+00 1.17872530E-02-1.82526570E-05 3 -2.98992310E+04-6.50701600E+00 3.34623000E+00 1.17872530E-02-1.82526570E-05 3
@ -4558,4 +4558,4 @@ ZrO2(L) J12/65ZR 1.O 2. 0. 0.C 2950.000 5000.000 123.22280 1
1.05676750E+01 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 2 1.05676750E+01 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 2
-1.28427450E+05-5.45922640E+01 1.05676750E+01 0.00000000E+00 0.00000000E+00 3 -1.28427450E+05-5.45922640E+01 1.05676750E+01 0.00000000E+00 0.00000000E+00 3
0.00000000E+00 0.00000000E+00-1.28427450E+05-5.45922640E+01 0.00000000E+00 4 0.00000000E+00 0.00000000E+00-1.28427450E+05-5.45922640E+01 0.00000000E+00 4
END END

17
tools/src/cti2ctml.cpp
View file

@ -1,8 +1,12 @@
/** /**
* @file example2.cpp * @file cti2ctml.cpp
* *
*/ */
/*
* $Id$
*/
// Example // Example
// //
// Read a mechanism and a thermodynamics file for the // Read a mechanism and a thermodynamics file for the
@ -21,9 +25,6 @@
using namespace Cantera; using namespace Cantera;
using namespace std; using namespace std;
#ifdef DEBUG_HKM
int iDebug_HKM = 0;
#endif
/*****************************************************************/ /*****************************************************************/
/*****************************************************************/ /*****************************************************************/
@ -38,14 +39,14 @@ static void printUsage()
/*****************************************************************/
int main(int argc, char** argv) { int main(int argc, char** argv) {
string infile; std::string infile;
// look for command-line options // look for command-line options
if (argc > 1) { if (argc > 1) {
string tok; std::string tok;
for (int j = 1; j < argc; j++) { for (int j = 1; j < argc; j++) {
tok = string(argv[j]); tok = string(argv[j]);
if (tok[0] == '-') { if (tok[0] == '-') {
@ -75,7 +76,7 @@ int main(int argc, char** argv) {
try { try {
XML_Node *xc = new XML_Node(); XML_Node *xc = new XML_Node();
string path = findInputFile(infile); std::string path = findInputFile(infile);
ctml::get_CTML_Tree(xc, path, 0); ctml::get_CTML_Tree(xc, path, 0);
//XML_Node *xd = new XML_Node(); //XML_Node *xd = new XML_Node();
//xc->copy(xd); //xc->copy(xd);