Organized the functions to list better under doxygen.
Added more comments. Didn't change any of the actual code.
This commit is contained in:
Harry Moffat
parent
0524cc9f71
commit
1fcc324d2c
1 changed files with 169 additions and 142 deletions
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@ -70,23 +70,60 @@ namespace Cantera {
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*/
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virtual int type() { return 0; }
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/// Number of reactions in the reaction mechanism
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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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//@{
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/**
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* Return the number of phases defined within the kinetics
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* object.
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*/
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int nPhases() const { return m_thermo.size(); }
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int nPhases() const { return m_thermo.size(); }
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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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* Return the phase index of a phase in the list of phases
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* defined within the object.
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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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* Input
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* ----------
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* ph = string name of the phase
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*
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* If a -1 is returned, then the phase is not defined in
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* the Kinetics object.
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* (HKM -> unfound object will create another entry in the
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* map, suggest rewriting this function)
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*/
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int start(int n) { return m_start[n]; }
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int phaseIndex(string ph) { return m_phaseindex[ph] - 1; }
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/// Number of reactions in the reaction mechanism
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int nReactions() const {return m_ii;}
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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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*/
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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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*/
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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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/**
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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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*/
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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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@ -99,8 +136,128 @@ namespace Cantera {
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return n;
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}
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int surfacePhaseIndex() { return m_surfphase; }
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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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*
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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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*/
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int start(int n) { return m_start[n]; }
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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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*
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* @param k species index
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* @param n phase index for the species
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*/
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int kineticsSpeciesIndex(int k, int n) const {
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return m_start[n] + k;
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}
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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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*/
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string kineticsSpeciesName(int k) const {
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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).speciesName(k - m_start[n]);
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}
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}
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return "<unknown>";
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}
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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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* 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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* is returned.
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* If no match is found, 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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int k;
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string id;
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for (int n = 0; n < np; n++) {
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id = thermo(n).id();
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if (ph == id) {
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k = thermo(n).speciesIndex(nm);
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if (k < 0) return -1;
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return k + m_start[n];
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}
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else if (ph == "<any>") {
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/*
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* Call the speciesIndex() member function of the
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* ThermoPhase object to find a match.
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*/
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k = thermo(n).speciesIndex(nm);
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if (k >= 0) return k + m_start[n];
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}
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}
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return -2;
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}
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/**
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* This function looks up the string name of a species and
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* returns a reference to the ThermoPhase object of the
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* phase where the species resides.
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* Will throw an error if the species string doesn't match.
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*/
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thermo_t& speciesPhase(string nm) {
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int np = m_thermo.size();
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int k;
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string id;
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for (int n = 0; n < np; n++) {
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k = thermo(n).speciesIndex(nm);
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if (k >= 0) return thermo(n);
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}
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throw CanteraError("speciesPhase", "unknown species "+nm);
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}
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/**
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* This function takes as an argument the kineticsSpecies index
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* (i.e., the list index in the list of species in the kinetics
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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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}
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/**
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* This function takes as an argument the kineticsSpecies index
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* (i.e., the list index in the list of species in the kinetics
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* manager) and returns the index of the phase owning the
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* species.
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*/
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int speciesPhaseIndex(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 n;
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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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}
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//@}
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/**
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@ -357,21 +514,6 @@ namespace Cantera {
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*/
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//@{
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/**
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* Return the phase index of a phase in the list of phases
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* defined within the object.
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*
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* Input
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* ----------
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* ph = string name of the phase
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*
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* If a -1 is returned, then the phase is not defined in
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* the Kinetics object.
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* (HKM -> unfound object will create another entry in the
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* map, suggest rewriting this function)
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*/
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int phaseIndex(string ph) { return m_phaseindex[ph] - 1; }
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/**
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* Add a phase to the kinetics manager object. This must
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* be done before the function init() is called or
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@ -402,122 +544,6 @@ namespace Cantera {
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m_phaseindex[m_thermo.back()->id()] = nPhases();
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}
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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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*/
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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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/**
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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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*/
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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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* 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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*
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* @param k species index
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* @param n phase index for the species
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*/
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int kineticsSpeciesIndex(int k, int n) const {
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return m_start[n] + k;
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}
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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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*/
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string kineticsSpeciesName(int k) const {
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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).speciesName(k - m_start[n]);
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}
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}
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return "<unknown>";
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}
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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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* 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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* is returned.
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* If no match is found, 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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int k;
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string id;
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for (int n = 0; n < np; n++) {
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id = thermo(n).id();
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if (ph == id) {
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k = thermo(n).speciesIndex(nm);
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if (k < 0) return -1;
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return k + m_start[n];
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}
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else if (ph == "<any>") {
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/*
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* Call the speciesIndex() member function of the
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* ThermoPhase object to find a match.
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*/
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k = thermo(n).speciesIndex(nm);
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if (k >= 0) return k + m_start[n];
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}
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}
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return -2;
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}
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thermo_t& speciesPhase(string nm) {
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int np = m_thermo.size();
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int k;
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string id;
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for (int n = 0; n < np; n++) {
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k = thermo(n).speciesIndex(nm);
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if (k >= 0) return thermo(n);
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}
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throw CanteraError("speciesPhase", "unknown species "+nm);
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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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}
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int speciesPhaseIndex(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 n;
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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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}
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/**
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* Prepare the class for the addition of reactions. This function
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* must be called after instantiation of the class, but before
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@ -572,7 +598,8 @@ namespace Cantera {
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void incrementRxnCount() { m_ii++; m_perturb.push_back(1.0); }
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/**
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*
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* Returns true if the kinetics manager has been properly
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* initialized and finalized.
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*/
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virtual bool ready() const {
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return false;
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@ -640,7 +667,7 @@ namespace Cantera {
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int m_index;
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/**
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* ????????
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* Index in the list of phases of the last surface phase entered.
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*/
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int m_surfphase;
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