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Doxygen update of some kinetics classes. Have a ways to go

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before these are documented.
This commit is contained in:
Harry Moffat 2007-05-11 23:11:11 +00:00
parent 4178af28fe
commit 6e64d22031
3 changed files with 178 additions and 116 deletions
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8
Cantera/src/kinetics/GasKinetics.h
View file

@ -207,11 +207,15 @@ namespace Cantera {
*/
//@{
/**
* Species net production rates [kmol/m^3]. Return the species
//! Return the species net production rates
/*!
* Species net production rates [kmol/m^3/s]. Return the species
* net production rates (creation - destruction) in array
* wdot, which must be dimensioned at least as large as the
* total number of species.
*
* @param net Vector of species production rates.
* units kmol m-3 s-1
*/
virtual void getNetProductionRates(doublereal* net) {
updateROP();

58
Cantera/src/kinetics/InterfaceKinetics.cpp
View file

@ -274,12 +274,8 @@ namespace Cantera {
// compute the change in electrical potential energy for each
// reaction. This will only be non-zero if a potential
// difference is present.
//fill(m_rwork.begin(), m_rwork.begin() + m_ii, 0.0);
//m_reactantStoich.decrementReactions(m_pot.begin(), m_rwork.begin());
//m_revProductStoich.incrementReactions(m_pot.begin(), m_rwork.begin());
//m_irrevProductStoich.incrementReactions(m_pot.begin(), m_rwork.begin());
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
// non-zero activation energy, and do not decrease the
@ -462,33 +458,35 @@ namespace Cantera {
m_rxnstoich.getReactionDelta(m_ii, DATA_PTR(m_grt), deltaH);
}
/************************************************************************
*
* getDeltaEntropy():
*
* Return the vector of values for the reactions change in
* entropy.
* These values depend upon the concentration
* of the solution.
*
* units = J kmol-1 Kelvin-1
// Return the vector of values for the change in
// entropy due to each reaction
/*
* These values depend upon the concentration
* of the solution.
*
* units = J kmol-1 Kelvin-1
*
* @param deltaS vector of Enthalpy changes
* Length = m_ii, number of reactions
*
*/
void InterfaceKinetics::getDeltaEntropy(doublereal* deltaS) {
/*
* Get the partial molar entropy of all species in all of
* the phases
*/
void InterfaceKinetics::getDeltaEntropy( doublereal* deltaS) {
/*
* Get the partial molar entropy of all species in the
* solid solution.
*/
int np = nPhases();
int n;
for (n = 0; n < np; n++) {
thermo(n).getPartialMolarEntropies(DATA_PTR(m_grt) + m_start[n]);
}
/*
* Use the stoichiometric manager to find deltaS for each
* reaction.
*/
m_rxnstoich.getReactionDelta(m_ii, DATA_PTR(m_grt), deltaS);
int np = nPhases();
int n;
for (n = 0; n < np; n++) {
thermo(n).getPartialMolarEntropies(DATA_PTR(m_grt) + m_start[n]);
}
/*
* Use the stoichiometric manager to find deltaS for each
* reaction.
*/
m_rxnstoich.getReactionDelta(m_ii, DATA_PTR(m_grt), deltaS);
}
/**
*

228
Cantera/src/kinetics/InterfaceKinetics.h
View file

@ -28,33 +28,36 @@ namespace Cantera {
// forward references
class ReactionData;
class InterfaceKineticsData;
class ThermoPhase;
class SurfPhase;
class ImplicitSurfChem;
class ReactionData;
class InterfaceKineticsData;
class ThermoPhase;
class SurfPhase;
class ImplicitSurfChem;
/**
* Holds mechanism-specific data.
*/
class InterfaceKineticsData {
public:
InterfaceKineticsData() :
m_ROP_ok(false),
m_temp(0.0), m_logtemp(0.0)
{}
virtual ~InterfaceKineticsData(){}
/**
* Holds mechanism-specific data.
*/
class InterfaceKineticsData {
public:
InterfaceKineticsData() :
m_ROP_ok(false),
m_temp(0.0), m_logtemp(0.0)
{}
virtual ~InterfaceKineticsData(){}
doublereal m_logp0, m_logc0;
array_fp m_ropf, m_ropr, m_ropnet;
//array_fp m_rfn_low, m_rfn_high;
bool m_ROP_ok;
doublereal m_logp0, m_logc0;
array_fp m_ropf;
array_fp m_ropr;
array_fp m_ropnet;
bool m_ROP_ok;
doublereal m_temp, m_logtemp;
vector_fp m_rfn;
vector_fp m_rkcn;
};
doublereal m_temp;
doublereal m_logtemp;
vector_fp m_rfn;
vector_fp m_rkcn;
};
///
@ -121,15 +124,20 @@ namespace Cantera {
*/
virtual void getDeltaEnthalpy( doublereal* deltaH);
/**
* Return the vector of values for the reactions change in
* entropy.
* These values depend upon the concentration
* of the solution.
*
* units = J kmol-1 Kelvin-1
*/
virtual void getDeltaEntropy(doublereal* deltaS);
//! Return the vector of values for the change in
//! entropy due to each reaction
/*!
* These values depend upon the concentration
* of the solution.
*
* units = J kmol-1 Kelvin-1
*
* @param deltaS vector of Enthalpy changes
* Length = m_ii, number of reactions
*
*/
virtual void getDeltaEntropy(doublereal* deltaS);
/**
* Return the vector of values for the reaction
@ -196,20 +204,24 @@ namespace Cantera {
&m_kdata->m_ropr[0], ddot);
}
/**
* Species net production rates [kmol/m^2/s]. Return the species
* net production rates (creation - destruction) in array
* wdot, which must be dimensioned at least as large as the
* total number of species in all phases of the kinetics
* model
*/
virtual void getNetProductionRates(doublereal* net) {
updateROP();
m_rxnstoich.getNetProductionRates(m_kk,
&m_kdata->m_ropnet[0],
net);
}
//! Return the species net production rates
/*!
* Species net production rates [kmol/m^2/s]. Return the species
* net production rates (creation - destruction) in array
* wdot, which must be dimensioned at least as large as the
* total number of species in all phases of the kinetics
* model
*
* @param net Vector of species production rates.
* units kmol m-d s-1, where d is dimension.
*/
virtual void getNetProductionRates(doublereal* net) {
updateROP();
m_rxnstoich.getNetProductionRates(m_kk,
&m_kdata->m_ropnet[0],
net);
}
//@}
/**
* @name Reaction Mechanism Informational Query Routines
@ -263,6 +275,8 @@ namespace Cantera {
virtual void getFwdRateConstants(doublereal* kfwd);
virtual void getRevRateConstants(doublereal* krev,
bool doIrreversible = false);
virtual void getActivationEnergies(doublereal *E);
//@}
@ -286,12 +300,15 @@ namespace Cantera {
*/
virtual void addReaction(const ReactionData& r);
/**
* Finish adding reactions and prepare for use. This function
* must be called after all reactions are entered into the mechanism
* and before the mechanism is used to calculate reaction rates.
*/
virtual void finalize();
//! Finish adding reactions and prepare for use.
/*!
* This function
* must be called after all reactions are entered into the mechanism
* and before the mechanism is used to calculate reaction rates.
*/
virtual void finalize();
virtual bool ready() const;
@ -313,12 +330,17 @@ namespace Cantera {
protected:
/**
* m_kk here is the number of species in all of the phases
* that participate in the kinetics mechanism.
*/
int m_kk;
vector_int m_revindex;
//! m_kk here is the number of species in all of the phases
//! that participate in the kinetics mechanism.
int m_kk;
//! List of reactions numbers which are reversible reactions
/*!
* This is a vector of reaction numbers. Each reaction
* in the list is reversible.
* Length = number of reversible reactions
*/
vector_int m_revindex;
Rate1<SurfaceArrhenius> m_rates;
bool m_redo_rates;
@ -368,32 +390,68 @@ namespace Cantera {
std::vector<std::string> m_rxneqn;
/**
* Temporary data storage used in calculating the rates of
* of reactions.
*/
InterfaceKineticsData* m_kdata;
/**
* Temporary data storage used in calculating the rates of
* of reactions.
*/
InterfaceKineticsData* m_kdata;
/**
* An array of generalized concentrations
* \f$ C_k \f$ that are defined such that \f$ a_k = C_k /
* C^0_k, \f$ where \f$ C^0_k \f$ is a standard concentration/
* These generalized concentrations are used
* by this kinetics manager class to compute the forward and
* reverse rates of elementary reactions. The "units" for the
* concentrations of each phase depend upon the implementation
* of kinetics within that phase.
* The order of the species within the vector is based on
* the order of listed ThermoPhase objects in the class, and the
* order of the species within each ThermoPhase class.
*/
vector_fp m_conc;
//! an array of generalized concentrations for each species
/*!
* An array of generalized concentrations
* \f$ C_k \f$ that are defined such that \f$ a_k = C_k /
* C^0_k, \f$ where \f$ C^0_k \f$ is a standard concentration/
* These generalized concentrations are used
* by this kinetics manager class to compute the forward and
* reverse rates of elementary reactions. The "units" for the
* concentrations of each phase depend upon the implementation
* of kinetics within that phase.
* The order of the species within the vector is based on
* the order of listed ThermoPhase objects in the class, and the
* order of the species within each ThermoPhase class.
*/
vector_fp m_conc;
vector_fp m_mu0;
vector_fp m_phi;
vector_fp m_pot;
vector_fp m_rwork;
vector_fp m_E;
//! Vector of standard state chemical potentials
/*!
* This vector contains a temporary vector of
* standard state chemical potentials
* for all of the species in the kinetics object
*
* Length = m_k
* units = J/kmol
*/
vector_fp m_mu0;
//! Vector of phase potentials
/*!
* Temporary vector containing the potential of each phase
* in the kinetics object
*
* length = number of phases
* units = Volts
*/
vector_fp m_phi;
//! Vector of potential energies due to Voltages
/*!
* Length is the number of species in kinetics mech. It's
* used to store the potential energy due to the voltage.
*/
vector_fp m_pot;
//! Vector temporary
/*!
* Length is number of reactions. it's used to store the
* voltage contribution to the activation energy.
*/
vector_fp m_rwork;
//! Vector of raw activation energies for the reactions
/*!
* units are in Kelvin
*/
vector_fp m_E;
SurfPhase* m_surf;
ImplicitSurfChem* m_integrator;
@ -411,8 +469,10 @@ namespace Cantera {
m_index[rxnNumber] = std::pair<int, int>(type, loc);
}
void applyButlerVolmerCorrection(doublereal* kf);
bool m_finalized;
bool m_has_coverage_dependence;
//! boolean indicating whether mechanism has been finalized
bool m_finalized;
bool m_has_coverage_dependence;
};
}