cleaned up and added more comments
This commit is contained in:
Dave Goodwin
parent
d78dff3f1e
commit
af33365205
1 changed files with 124 additions and 93 deletions
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@ -26,7 +26,8 @@ namespace Cantera {
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/**
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* Public interface for kinetics managers. This class serves as a
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* base class to derive 'kinetics managers', which are classes
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* that manage homogeneous chemistry within one phase.
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* that manage homogeneous chemistry within one phase, or
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* heterogeneous chemistry at one interface.
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*/
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class Kinetics {
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@ -51,15 +52,16 @@ namespace Cantera {
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Kinetics(thermo_t* thermo)
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: m_ii(0), m_index(-1), m_surfphase(-1) {
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if (thermo) {
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m_start.push_back(0);
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if (thermo->eosType() == cSurf) m_surfphase = nPhases();
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m_thermo.push_back(thermo);
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m_phaseindex[m_thermo.back()->id()] = nPhases();
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// addPhase(*thermo);
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// m_start.push_back(0);
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// if (thermo->eosType() == cSurf) m_surfphase = nPhases();
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// m_thermo.push_back(thermo);
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// m_phaseindex[m_thermo.back()->id()] = nPhases();
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}
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}
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/// Destructor. Does nothing.
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virtual ~Kinetics() {} // delete m_xml; }
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virtual ~Kinetics() {}
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int index(){ return m_index; }
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void setIndex(int index) { m_index = index; }
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@ -75,6 +77,7 @@ namespace Cantera {
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int nReactions() const {return m_ii;}
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//@}
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/**
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* @name Information/Lookup Functions about Phases and Species
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*/
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@ -102,16 +105,20 @@ namespace Cantera {
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int phaseIndex(string ph) { return m_phaseindex[ph] - 1; }
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/**
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* This returns the integer index of the phase
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* which has ThermoPhase type cSurf.
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* This returns the integer index of the phase which has
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* ThermoPhase type cSurf. For heterogeneous mechanisms, this
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* identifies the one surface phase. For homogeneous
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* mechanisms, this reurns -1.
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*/
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int surfacePhaseIndex() { return m_surfphase; }
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/**
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* This method returns a reference to the nth ThermoPhase
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* defined in this kinetics mechanism.
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* It is typically used so that member functions of the the
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* ThermoPhase may be called.
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* object defined in this kinetics mechanism. It is typically
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* used so that member functions of the ThermoPhase object may
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* be called. For homogeneous mechanisms, there is only one
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* object, and this method can be called without an argument
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* to access it.
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*/
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thermo_t& thermo(int n=0) { return *m_thermo[n]; }
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const thermo_t& thermo(int n=0) const { return *m_thermo[n]; }
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@ -120,14 +127,16 @@ namespace Cantera {
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* This method returns a reference to the nth ThermoPhase
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* defined in this kinetics mechanism.
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* It is typically used so that member functions of the
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* ThermoPhase may be called.
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* ThermoPhase may be called. @deprecated This method is redundant.
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*/
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thermo_t& phase(int n=0) { return *m_thermo[n]; }
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const thermo_t& phase(int n=0) const { return *m_thermo[n]; }
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/**
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* Returns the total number of species in all phases
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* participating in the kinetics mechanism
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* participating in the kinetics mechanism. This is useful to
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* dimension arrays for use in calls to methods that return
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* the species production rates, for example.
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*/
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int nTotalSpecies() const {
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int n=0, np;
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@ -138,7 +147,8 @@ namespace Cantera {
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/**
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* Returns the starting index of the species in the nth phase
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* associated with the reaction mechanism
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* associated with the reaction mechanism. @deprecated. Can be
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* replaced by kineticsSpeciesIndex(0).
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*
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* @param n Return the index of first species in the nth phase
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* associated with the reaction mechanism.
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@ -147,7 +157,7 @@ namespace Cantera {
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/**
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* This method returns the index of a species in the source
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* term vector for this kinetics object.
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* term vector for this kinetics object.
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*
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* @param k species index
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* @param n phase index for the species
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@ -158,11 +168,11 @@ namespace Cantera {
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/**
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* Return the string name of the kth species in the kinetics
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* manager. k can be equal to 0 to the number of species
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* in the kinetics manager, which is the sum of the
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* number of species in all phases participating in the
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* kinetics manager.
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* If k is out of bounds, the string "<unknown>" is returned.
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* manager. k is an integer from 0 to ktot - 1, where ktot is
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* the number of species in the kinetics manager, which is the
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* sum of the number of species in all phases participating in
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* the kinetics manager. If k is out of bounds, the string
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* "<unknown>" is returned.
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*/
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string kineticsSpeciesName(int k) const {
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int np = m_start.size();
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@ -177,14 +187,16 @@ namespace Cantera {
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/**
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* This routine will look up a species number based on
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* the input string nm. The lookup of species will
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* occur for all phases listed in the kinetics obect,
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* occur for all phases listed in the kinetics object,
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* unless the string ph refers to a specific phase of
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* the object.
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*
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* return
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* If a match is found, the position in the species list
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* - If a match is found, the position in the species list
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* is returned.
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* If no match is found, the value -2 is returned.
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* - If a specific phase is specified and no match is found,
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* the value -1 is returned.
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* - If no match is found in any phase, the value -2 is returned.
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*/
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int kineticsSpeciesIndex(string nm, string ph = "<any>") const {
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int np = m_thermo.size();
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@ -232,14 +244,16 @@ namespace Cantera {
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* manager) and returns the species' owning ThermoPhase object.
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*/
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thermo_t& speciesPhase(int k) {
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int np = m_start.size();
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for (int n = np-1; n >= 0; n--) {
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if (k >= m_start[n]) {
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return thermo(n);
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}
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}
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throw CanteraError("speciesPhase",
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"illegal species index: "+int2str(k));
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return thermo(speciesPhaseIndex(k));
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// int np = m_start.size();
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// for (int n = np-1; n >= 0; n--) {
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// if (k >= m_start[n]) {
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// return thermo(n);
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// }
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// }
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// throw CanteraError("speciesPhase",
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// "illegal species index: "+int2str(k));
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}
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/**
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@ -256,30 +270,31 @@ namespace Cantera {
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}
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}
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throw CanteraError("speciesPhaseIndex",
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"illegal species index: "+int2str(k));
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"illegal species index: "+int2str(k));
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}
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//@}
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/**
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* @name Reaction Rates Of Progress
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*/
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//@{
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/**
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* Forward rates of progress.
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* Return the forward rates of progress in array fwdROP, which
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* must be dimensioned at least as large as the total number
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* of reactions.
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* Forward rates of progress. Return the forward rates of
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* progress in array fwdROP, which must be dimensioned at
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* least as large as the total number of reactions.
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*/
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virtual void getFwdRatesOfProgress(doublereal* fwdROP) {
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err("getFwdRatesOfProgress");
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}
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/**
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* Reverse rates of progress.
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* Return the reverse rates of progress in array revROP, which
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* must be dimensioned at least as large as the total number
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* of reactions.
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* Reverse rates of progress. Return the reverse rates of
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* progress in array revROP, which must be dimensioned at
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* least as large as the total number of reactions.
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*/
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virtual void getRevRatesOfProgress(doublereal* revROP) {
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err("getRevRatesOfProgress");
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@ -300,16 +315,15 @@ namespace Cantera {
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* Equilibrium constants. Return the equilibrium constants of
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* the reactions in concentration units in array kc, which
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* must be dimensioned at least as large as the total number
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* of reactions.
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* of reactions.
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*/
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virtual void getEquilibriumConstants(doublereal* kc) {
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err("getEquilibriumConstants");
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}
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/**
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* Return the vector of values for the reaction gibbs free energy
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* change.
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* These values depend upon the concentration
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* Return the vector of values for the reaction gibbs free
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* energy change. These values depend upon the concentration
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* of the solution.
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*
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* units = J kmol-1
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@ -320,9 +334,8 @@ namespace Cantera {
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/**
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* Return the vector of values for the reactions change in
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* enthalpy.
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* These values depend upon the concentration
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* of the solution.
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* enthalpy. These values depend upon the concentration of
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* the solution.
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*
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* units = J kmol-1
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*/
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@ -332,9 +345,8 @@ namespace Cantera {
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/**
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* Return the vector of values for the reactions change in
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* entropy.
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* These values depend upon the concentration
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* of the solution.
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* entropy. These values depend upon the concentration of the
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* solution.
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*
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* units = J kmol-1 Kelvin-1
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*/
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@ -343,10 +355,9 @@ namespace Cantera {
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}
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/**
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* Return the vector of values for the reaction
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* standard state gibbs free energy change.
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* These values don't depend upon the concentration
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* of the solution.
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* Return the vector of values for the reaction standard state
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* gibbs free energy change. These values don't depend upon
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* the concentration of the solution.
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*
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* units = J kmol-1
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*/
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@ -355,10 +366,9 @@ namespace Cantera {
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}
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/**
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* Return the vector of values for the change in the
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* standard state enthalpies of reaction.
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* These values don't depend upon the concentration
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* of the solution.
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* Return the vector of values for the change in the standard
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* state enthalpies of reaction. These values don't depend
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* upon the concentration of the solution.
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*
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* units = J kmol-1
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*/
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@ -367,10 +377,9 @@ namespace Cantera {
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}
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/**
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* Return the vector of values for the change in the
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* standard state entropies for each reaction.
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* These values don't depend upon the concentration
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* of the solution.
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* Return the vector of values for the change in the standard
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* state entropies for each reaction. These values don't
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* depend upon the concentration of the solution.
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*
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* units = J kmol-1 Kelvin-1
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*/
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@ -386,10 +395,10 @@ namespace Cantera {
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//@{
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/**
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* Species creation rates [kmol/m^3]. Return the species
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* creation rates in array cdot, which must be
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* Species creation rates [kmol/m^3 or kmol/m^2]. Return the
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* species creation rates in array cdot, which must be
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* dimensioned at least as large as the total number of
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* species.
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* species. @see nTotalSpecies.
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*
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*/
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virtual void getCreationRates(doublereal* cdot) {
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@ -397,10 +406,10 @@ namespace Cantera {
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}
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/**
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* Species destruction rates [kmol/m^3]. Return the species
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* destruction rates in array ddot, which must be
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* Species destruction rates [kmol/m^3 or kmol/m^2]. Return
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* the species destruction rates in array ddot, which must be
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* dimensioned at least as large as the total number of
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* species.
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* species. @see nTotalSpecies.
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*
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*/
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virtual void getDestructionRates(doublereal* ddot) {
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@ -408,16 +417,18 @@ namespace Cantera {
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}
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/**
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* Species net production rates [kmol/m^3]. Return the species
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* net production rates (creation - destruction) in array
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* wdot, which must be dimensioned at least as large as the
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* total number of species.
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* Species net production rates [kmol/m^3 or kmol/m^2]. Return
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* the species net production rates (creation - destruction)
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* in array wdot, which must be dimensioned at least as large
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* as the total number of species. @see nTotalSpecies.
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*/
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virtual void getNetProductionRates(doublereal* wdot) {
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err("getNetProductionRates");
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}
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//@}
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/**
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* @name Reaction Mechanism Informational Query Routines
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*/
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@ -488,7 +499,8 @@ namespace Cantera {
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* Return the forward rate constants
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*
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* length is the number of reactions. units depends
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* on many issues.
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* on many issues. @todo DGG: recommend changing name to
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* getFwdRateCoefficients.
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*/
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virtual void getFwdRateConstants(doublereal *kfwd) {
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err("getFwdRateConstants");
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@ -500,7 +512,8 @@ namespace Cantera {
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* length is the number of reactions. units depends
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* on many issues. Note, this routine will return rate constants
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* for irreversible reactions if the default for
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* doIrreversible is overridden.
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* doIrreversible is overridden. @todo DGG: recommend changing name to
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* getRevRateCoefficients.
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*/
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virtual void getRevRateConstants(doublereal *krev,
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bool doIrreversible = false) {
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@ -531,15 +544,26 @@ namespace Cantera {
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* index of the phase within the kinetics
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* manager object as the value.
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*/
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void addPhase(thermo_t& thermo) {
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void addPhase(thermo_t& thermo) {
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// if not the first thermo object, set the start position
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// to that of the last object added + the number of its species
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if (m_thermo.size() > 0) {
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m_start.push_back(m_start.back()
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+ m_thermo.back()->nSpecies());
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}
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// otherwise start at 0
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else {
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m_start.push_back(0);
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}
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if (thermo.eosType() == cSurf) m_surfphase = nPhases();
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// there should only be one surface phase
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if (thermo.eosType() == cSurf) {
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if (m_surfphase >= 0) {
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throw CanteraError("Kinetics::addPhase",
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"cannot add more than one surface phase");
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}
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m_surfphase = nPhases();
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}
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m_thermo.push_back(&thermo);
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m_phaseindex[m_thermo.back()->id()] = nPhases();
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}
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@ -592,8 +616,10 @@ namespace Cantera {
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void setMultiplier(int i, doublereal f) {m_perturb[i] = f;}
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//@}
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/**
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* Increment the number of reactions in the mechanism by one.
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* @todo Should be protected?
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*/
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void incrementRxnCount() { m_ii++; m_perturb.push_back(1.0); }
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@ -605,6 +631,7 @@ namespace Cantera {
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return false;
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}
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protected:
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/**
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@ -619,22 +646,24 @@ namespace Cantera {
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vector_fp m_perturb;
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/**
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* This is a vector of vectors containing the reactants for each
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* reaction. The outer vector is over the number of reactions, m_ii.
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* The inner vector is a list of species indecises. If the stoichiometric
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* coefficient for a reactant is greater than one, then the
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* reactant is listed contiguously in the vector a number of
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* times equal to its stoichiometric coefficient.
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* This is a vector of vectors containing the reactants for
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* each reaction. The outer vector is over the number of
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* reactions, m_ii. The inner vector is a list of species
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* indicises. If the stoichiometric coefficient for a reactant
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* is greater than one, then the reactant is listed
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* contiguously in the vector a number of times equal to its
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* stoichiometric coefficient.
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*/
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vector<vector_int> m_reactants;
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/**
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* This is a vector of vectors containing the products for each
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* reaction. The outer vector is over the number of reactions, m_ii.
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* The inner vector is a list of species indecises. If the stoichiometric
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* coefficient for a product is greater than one, then the
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* reactant is listed contiguously in the vector a number of
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* times equal to its stoichiometric coefficient.
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* This is a vector of vectors containing the products for
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* each reaction. The outer vector is over the number of
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* reactions, m_ii. The inner vector is a list of species
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* indecises. If the stoichiometric coefficient for a product
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* is greater than one, then the reactant is listed
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* contiguously in the vector a number of times equal to its
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* stoichiometric coefficient.
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*/
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vector<vector_int> m_products;
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@ -658,16 +687,18 @@ namespace Cantera {
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vector_int m_start;
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/**
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* Mapping of the phase id, i.e., the id attribute in the xml phase
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* element to the position of the phase within the kinetics object.
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* Positions start with the value of 1. The member function, phaseIndex()
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* decrements by one before returning the index value.
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* Mapping of the phase id, i.e., the id attribute in the xml
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* phase element to the position of the phase within the
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* kinetics object. Positions start with the value of 1. The
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* member function, phaseIndex() decrements by one before
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* returning the index value, so that missing phases return
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* -1.
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*/
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map<string, int> m_phaseindex;
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int m_index;
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/**
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* Index in the list of phases of the last surface phase entered.
|
||||
* Index in the list of phases of the one surface phase.
|
||||
*/
|
||||
int m_surfphase;
|
||||
|
||||
|
|
|
|||
Loading…
Add table
Reference in a new issue