Doxygen updates -> worked on documenting functions
Changed a few functions from private to protected so that they would be available to derived classes
This commit is contained in:
Harry Moffat
parent
4084343fcf
commit
4b406f06bf
2 changed files with 351 additions and 277 deletions
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@ -248,6 +248,52 @@ namespace Cantera {
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}
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}
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// Returns the Species creation rates [kmol/m^2/s].
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/*
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* Return the species
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* 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 in all phases of the kinetics
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* model
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*
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* @param cdot Vector containing the creation rates.
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* length = m_kk. units = kmol/m^2/s
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*/
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void InterfaceKinetics::getCreationRates(doublereal* cdot) {
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updateROP();
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m_rxnstoich.getCreationRates(m_kk, &m_kdata->m_ropf[0],
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&m_kdata->m_ropr[0], cdot);
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}
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// Return the Species destruction rates [kmol/m^2/s].
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/*
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* Return 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 in all phases of the kinetics model
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*/
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void InterfaceKinetics::getDestructionRates(doublereal* ddot) {
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updateROP();
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m_rxnstoich.getDestructionRates(m_kk, &m_kdata->m_ropf[0],
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&m_kdata->m_ropr[0], ddot);
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}
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// Return the species net production rates
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/*
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* Species net production rates [kmol/m^2/s]. 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 in all phases of the kinetics
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* model
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*
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* @param net Vector of species production rates.
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* units kmol m-d s-1, where d is dimension.
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*/
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void InterfaceKinetics::getNetProductionRates(doublereal* net) {
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updateROP();
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m_rxnstoich.getNetProductionRates(m_kk,
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&m_kdata->m_ropnet[0],
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net);
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}
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/**
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* For reactions that transfer charge across a potential difference,
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@ -661,108 +707,99 @@ namespace Cantera {
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// }
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void InterfaceKinetics::installReagents(const ReactionData& r) {
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void InterfaceKinetics::installReagents(const ReactionData& r) {
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int n, ns, m;
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doublereal nsFlt;
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/*
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* extend temporary storage by one for this rxn.
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*/
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m_kdata->m_ropf.push_back(0.0);
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m_kdata->m_ropr.push_back(0.0);
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m_kdata->m_ropnet.push_back(0.0);
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m_kdata->m_rkcn.push_back(0.0);
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int n, ns, m;
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doublereal nsFlt;
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/*
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* extend temporary storage by one for this rxn.
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*/
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m_kdata->m_ropf.push_back(0.0);
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m_kdata->m_ropr.push_back(0.0);
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m_kdata->m_ropnet.push_back(0.0);
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m_kdata->m_rkcn.push_back(0.0);
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/*
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* Obtain the current reaction index for the reaction that we
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* are adding. The first reaction is labeled 0.
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*/
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int rnum = reactionNumber();
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/*
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* Obtain the current reaction index for the reaction that we
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* are adding. The first reaction is labeled 0.
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*/
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int rnum = reactionNumber();
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// vectors rk and pk are lists of species numbers, with
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// repeated entries for species with stoichiometric
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// coefficients > 1. This allows the reaction to be defined
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// with unity reaction order for each reactant, and so the
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// faster method 'multiply' can be used to compute the rate of
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// progress instead of 'power'.
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// vectors rk and pk are lists of species numbers, with
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// repeated entries for species with stoichiometric
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// coefficients > 1. This allows the reaction to be defined
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// with unity reaction order for each reactant, and so the
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// faster method 'multiply' can be used to compute the rate of
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// progress instead of 'power'.
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vector_int rk;
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int nr = r.reactants.size();
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for (n = 0; n < nr; n++) {
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nsFlt = r.rstoich[n];
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ns = (int) nsFlt;
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if ((doublereal) ns != nsFlt) {
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if (ns < 1) ns = 1;
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}
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/*
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* Add to m_rrxn. m_rrxn is a vector of maps. m_rrxn has a length
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* equal to the total number of species for each species, there
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* exists a map, with the reaction number being the key, and the
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* reactant stoichiometric coefficient being the value.
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*/
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m_rrxn[r.reactants[n]][rnum] = ns;
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for (m = 0; m < ns; m++) {
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rk.push_back(r.reactants[n]);
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}
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}
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/*
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* Now that we have rk[], we add it into the vector<vector_int> m_reactants
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* in the rnum index spot. Thus m_reactants[rnum] yields a vector
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* of reactants for the rnum'th reaction
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*/
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m_reactants.push_back(rk);
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vector_int pk;
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int np = r.products.size();
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for (n = 0; n < np; n++) {
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nsFlt = r.pstoich[n];
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ns = (int) nsFlt;
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if ((doublereal) ns != nsFlt) {
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if (ns < 1) ns = 1;
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}
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/*
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* Add to m_prxn. m_prxn is a vector of maps. m_prxn has a length
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* equal to the total number of species for each species, there
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* exists a map, with the reaction number being the key, and the
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* product stoichiometric coefficient being the value.
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*/
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m_prxn[r.products[n]][rnum] = ns;
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for (m = 0; m < ns; m++) {
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pk.push_back(r.products[n]);
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}
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}
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/*
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* Now that we have pk[], we add it into the vector<vector_int> m_products
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* in the rnum index spot. Thus m_products[rnum] yields a vector
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* of products for the rnum'th reaction
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*/
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m_products.push_back(pk);
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/*
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* Add this reaction to the stoichiometric coefficient manager. This
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* calculates rates of species production from reaction rates of
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* progress.
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*/
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m_rxnstoich.add( reactionNumber(), r);
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/*
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* register reaction in lists of reversible and irreversible rxns.
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*/
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if (r.reversible) {
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m_revindex.push_back(reactionNumber());
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m_nrev++;
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} else {
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m_irrev.push_back( reactionNumber() );
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m_nirrev++;
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}
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vector_int rk;
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int nr = r.reactants.size();
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for (n = 0; n < nr; n++) {
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nsFlt = r.rstoich[n];
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ns = (int) nsFlt;
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if ((doublereal) ns != nsFlt) {
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if (ns < 1) ns = 1;
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}
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/*
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* Add to m_rrxn. m_rrxn is a vector of maps. m_rrxn has a length
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* equal to the total number of species for each species, there
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* exists a map, with the reaction number being the key, and the
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* reactant stoichiometric coefficient being the value.
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*/
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m_rrxn[r.reactants[n]][rnum] = nsFlt;
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for (m = 0; m < ns; m++) {
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rk.push_back(r.reactants[n]);
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}
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}
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//void InterfaceKinetics::installGroups(int irxn,
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// const vector<grouplist_t>& r, const vector<grouplist_t>& p) {
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// if (!r.empty()) {
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// m_rgroups[reactionNumber()] = r;
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// m_pgroups[reactionNumber()] = p;
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// }
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//}
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/*
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* Now that we have rk[], we add it into the vector<vector_int> m_reactants
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* in the rnum index spot. Thus m_reactants[rnum] yields a vector
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* of reactants for the rnum'th reaction
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*/
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m_reactants.push_back(rk);
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vector_int pk;
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int np = r.products.size();
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for (n = 0; n < np; n++) {
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nsFlt = r.pstoich[n];
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ns = (int) nsFlt;
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if ((doublereal) ns != nsFlt) {
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if (ns < 1) ns = 1;
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}
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/*
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* Add to m_prxn. m_prxn is a vector of maps. m_prxn has a length
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* equal to the total number of species for each species, there
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* exists a map, with the reaction number being the key, and the
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* product stoichiometric coefficient being the value.
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*/
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m_prxn[r.products[n]][rnum] = nsFlt;
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for (m = 0; m < ns; m++) {
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pk.push_back(r.products[n]);
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}
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}
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/*
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* Now that we have pk[], we add it into the vector<vector_int> m_products
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* in the rnum index spot. Thus m_products[rnum] yields a vector
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* of products for the rnum'th reaction
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*/
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m_products.push_back(pk);
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/*
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* Add this reaction to the stoichiometric coefficient manager. This
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* calculates rates of species production from reaction rates of
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* progress.
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*/
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m_rxnstoich.add( reactionNumber(), r);
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/*
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* register reaction in lists of reversible and irreversible rxns.
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*/
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if (r.reversible) {
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m_revindex.push_back(reactionNumber());
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m_nrev++;
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} else {
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m_irrev.push_back( reactionNumber() );
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m_nirrev++;
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}
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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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@ -826,9 +863,3 @@ namespace Cantera {
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}
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@ -88,43 +88,56 @@ namespace Cantera {
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virtual int ID() { return cInterfaceKinetics; }
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virtual int type() { return cInterfaceKinetics; }
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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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/// @name Reaction Rates Of Progress
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///
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//@{
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//! Return the forward rates of progress for each reaction
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/*!
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* @param fwdROP vector of rates of progress.
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* length = number of reactions, Units are kmol m-2 s-1.
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*/
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virtual void getFwdRatesOfProgress(doublereal* fwdROP) {
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updateROP();
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std::copy(m_kdata->m_ropf.begin(), m_kdata->m_ropf.end(), fwdROP);
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}
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//! Return the reverse rates of progress for each reaction
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/*!
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* @param revROP vector of rates of progress.
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* length = number of reactions, Units are kmol m-2 s-1.
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*/
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virtual void getRevRatesOfProgress(doublereal* revROP) {
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updateROP();
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std::copy(m_kdata->m_ropr.begin(), m_kdata->m_ropr.end(), revROP);
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}
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//! Return the net rates of progress for each reaction
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/*!
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* @param netROP vector of rates of progress.
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* length = number of reactions, Units are kmol m-2 s-1.
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*/
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virtual void getNetRatesOfProgress(doublereal* netROP) {
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updateROP();
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std::copy(m_kdata->m_ropnet.begin(), m_kdata->m_ropnet.end(), netROP);
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}
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virtual void getEquilibriumConstants(doublereal* kc);
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virtual void getFwdRatesOfProgress(doublereal* fwdROP) {
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updateROP();
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std::copy(m_kdata->m_ropf.begin(), m_kdata->m_ropf.end(), fwdROP);
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}
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virtual void getDeltaGibbs( doublereal* deltaG);
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virtual void getRevRatesOfProgress(doublereal* revROP) {
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updateROP();
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std::copy(m_kdata->m_ropr.begin(), m_kdata->m_ropr.end(), revROP);
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}
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virtual void getNetRatesOfProgress(doublereal* netROP) {
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updateROP();
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std::copy(m_kdata->m_ropnet.begin(), m_kdata->m_ropnet.end(), netROP);
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}
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virtual void getEquilibriumConstants(doublereal* kc);
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virtual void getDeltaGibbs( doublereal* deltaG);
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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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*
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* units = J kmol-1
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*/
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virtual void getDeltaEnthalpy( doublereal* deltaH);
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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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*
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* units = J kmol-1
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*/
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virtual void getDeltaEnthalpy( doublereal* deltaH);
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//! Return the vector of values for the change in
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//! entropy due to each reaction
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/*!
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@ -139,72 +152,73 @@ namespace Cantera {
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*/
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virtual void getDeltaEntropy(doublereal* deltaS);
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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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*
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* units = J kmol-1
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*/
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virtual void getDeltaSSGibbs(doublereal* deltaG);
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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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*
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* units = J kmol-1
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*/
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virtual void getDeltaSSEnthalpy(doublereal* deltaH);
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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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/*!
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* These values don't depend upon the concentration
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* of the solution.
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*
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* @param deltaG vector of rxn SS free energy changes
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* units = J kmol-1
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*/
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virtual void getDeltaSSGibbs(doublereal* deltaG);
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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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/*!
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* These values don't depend upon the concentration
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* of the solution.
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*
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* @param deltaH vector of rxn SS enthalpy changes
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* units = J kmol-1
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*/
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virtual void getDeltaSSEnthalpy(doublereal* deltaH);
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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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/*!
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* These values don't depend upon the concentration
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* of the solution.
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*
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* @param deltaS vector of rxn SS entropy changes
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* units = J kmol-1 Kelvin-1
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*/
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virtual void getDeltaSSEntropy(doublereal* deltaS);
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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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*
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* units = J kmol-1 Kelvin-1
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*/
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virtual void getDeltaSSEntropy(doublereal* deltaS);
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//@}
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/**
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* @name Species Production Rates
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*/
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//@{
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/**
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* Species creation rates [kmol/m^2/s]. Return the species
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* 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 in all phases of the kinetics
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* model
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*
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*/
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virtual void getCreationRates(doublereal* cdot) {
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updateROP();
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m_rxnstoich.getCreationRates(m_kk, &m_kdata->m_ropf[0],
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&m_kdata->m_ropr[0], cdot);
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}
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/**
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* Species destruction rates [kmol/m^2/s]. Return the species
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* 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 in all phases of the kinetics
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* model
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*
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*/
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virtual void getDestructionRates(doublereal* ddot) {
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updateROP();
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m_rxnstoich.getDestructionRates(m_kk, &m_kdata->m_ropf[0],
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&m_kdata->m_ropr[0], ddot);
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}
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//! Return the species net production rates
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//@}
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/**
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* @name Species Production Rates
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*/
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//@{
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//! Returns the Species creation rates [kmol/m^2/s].
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/*!
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* Return the species
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* 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 in all phases of the kinetics
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* model
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*
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* @param cdot Vector containing creation rates.
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* length = m_kk. units = kmol/m^2/s
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*/
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virtual void getCreationRates(doublereal* cdot);
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//! Return the Species destruction rates [kmol/m^2/s].
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/*!
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* Return 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 in all phases of the kinetics model
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*
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* @param ddot Vector containing destruction rates.
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* length = m_kk. units = kmol/m^2/s
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*/
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virtual void getDestructionRates(doublereal* ddot);
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|
||||
//! Return the species net production rates [kmol/m^2/s].
|
||||
/*!
|
||||
* Species net production rates [kmol/m^2/s]. Return the species
|
||||
* net production rates (creation - destruction) in array
|
||||
|
|
@ -215,18 +229,13 @@ namespace Cantera {
|
|||
* @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);
|
||||
}
|
||||
virtual void getNetProductionRates(doublereal* net);
|
||||
|
||||
//@}
|
||||
/**
|
||||
* @name Reaction Mechanism Informational Query Routines
|
||||
*/
|
||||
//@{
|
||||
//@}
|
||||
/**
|
||||
* @name Reaction Mechanism Informational Query Routines
|
||||
*/
|
||||
//@{
|
||||
|
||||
/**
|
||||
* Stoichiometric coefficient of species k as a reactant in
|
||||
|
|
@ -279,26 +288,29 @@ namespace Cantera {
|
|||
|
||||
virtual void getActivationEnergies(doublereal *E);
|
||||
|
||||
//@}
|
||||
/**
|
||||
* @name Reaction Mechanism Construction
|
||||
*/
|
||||
//@{
|
||||
//@}
|
||||
/**
|
||||
* @name Reaction Mechanism Construction
|
||||
*/
|
||||
//@{
|
||||
|
||||
|
||||
//! Prepare the class for the addition of reactions.
|
||||
/*!
|
||||
* This function must be called after instantiation of the class, but before
|
||||
* any reactions are actually added to the mechanism.
|
||||
* This function calculates m_kk the number of species in all
|
||||
* phases participating in the reaction mechanism. We don't know
|
||||
* m_kk previously, before all phases have been added.
|
||||
*/
|
||||
virtual void init();
|
||||
|
||||
/**
|
||||
* Prepare the class for the addition of reactions. This function
|
||||
* must be called after instantiation of the class, but before
|
||||
* any reactions are actually added to the mechanism.
|
||||
* This function calculates m_kk the number of species in all
|
||||
* phases participating in the reaction mechanism. We don't know
|
||||
* m_kk previously, before all phases have been added.
|
||||
*/
|
||||
virtual void init();
|
||||
|
||||
/**
|
||||
* Add a single reaction to the mechanism.
|
||||
*/
|
||||
virtual void addReaction(const ReactionData& r);
|
||||
//! Add a single reaction to the mechanism.
|
||||
/*!
|
||||
* @param r Reference to a ReactionData object containing all of
|
||||
* the info needed to describe the reaction.
|
||||
*/
|
||||
virtual void addReaction(const ReactionData& r);
|
||||
|
||||
|
||||
//! Finish adding reactions and prepare for use.
|
||||
|
|
@ -309,16 +321,12 @@ namespace Cantera {
|
|||
*/
|
||||
virtual void finalize();
|
||||
|
||||
virtual bool ready() const;
|
||||
virtual bool ready() const;
|
||||
|
||||
|
||||
void updateROP();
|
||||
void updateROP();
|
||||
|
||||
|
||||
//const std::vector<grouplist_t>& reactantGroups(int i)
|
||||
// { return m_rgroups[i]; }
|
||||
//const std::vector<grouplist_t>& productGroups(int i)
|
||||
// { return m_pgroups[i]; }
|
||||
|
||||
void _update_rates_T();
|
||||
void _update_rates_phi();
|
||||
|
|
@ -326,12 +334,14 @@ namespace Cantera {
|
|||
|
||||
void advanceCoverages(doublereal tstep);
|
||||
void checkPartialEquil();
|
||||
vector_fp m_grt;
|
||||
|
||||
//! Temporary work vector of length m_kk
|
||||
vector_fp m_grt;
|
||||
|
||||
protected:
|
||||
|
||||
//! m_kk here is the number of species in all of the phases
|
||||
//! that participate in the kinetics mechanism.
|
||||
//! m_kk is the number of species in all of the phases
|
||||
//! that participate in this kinetics mechanism.
|
||||
int m_kk;
|
||||
|
||||
//! List of reactions numbers which are reversible reactions
|
||||
|
|
@ -354,41 +364,61 @@ namespace Cantera {
|
|||
*/
|
||||
mutable std::map<int, std::pair<int, int> > m_index;
|
||||
|
||||
std::vector<int> m_irrev;
|
||||
//! Vector of irreversible reaction numbers
|
||||
/*!
|
||||
* vector containing the reaction numbers of irreversible
|
||||
* reactions.
|
||||
*/
|
||||
std::vector<int> m_irrev;
|
||||
|
||||
ReactionStoichMgr m_rxnstoich;
|
||||
//! Stoichiometric manager for the reaction mechanism
|
||||
/*!
|
||||
* This is the manager for the kinetics mechanism that
|
||||
* handles turning reaction extents into species
|
||||
* production rates and also handles turning thermo
|
||||
* properties into reaction thermo properties.
|
||||
*/
|
||||
ReactionStoichMgr m_rxnstoich;
|
||||
|
||||
int m_nirrev;
|
||||
//! Number of irreversible reactions in the mechanism
|
||||
int m_nirrev;
|
||||
|
||||
/**
|
||||
* Number of reversible reactions in the mechanism
|
||||
*/
|
||||
int m_nrev;
|
||||
//! Number of reversible reactions in the mechanism
|
||||
int m_nrev;
|
||||
|
||||
std::vector<int> m_rxntype;
|
||||
|
||||
//! m_rrxn is a vector of maps, containing the reactant
|
||||
//! stochiometric coefficient information
|
||||
/*!
|
||||
* m_rrxn has a length
|
||||
* equal to the total number of species in the kinetics
|
||||
* object. For each species, there exists a map, with the
|
||||
* reaction number being the key, and the
|
||||
* reactant stoichiometric coefficient for the species being the value.
|
||||
* HKM -> mutable because search sometimes creates extra
|
||||
* entries. To be fixed in future...
|
||||
*/
|
||||
mutable std::vector<std::map<int, doublereal> > m_rrxn;
|
||||
|
||||
//! m_prxn is a vector of maps, containing the reactant
|
||||
//! stochiometric coefficient information
|
||||
/**
|
||||
* m_prxn is a vector of maps. m_prxn has a length
|
||||
* equal to the total number of species in the kinetics
|
||||
* object. For each species, there exists a map, with the
|
||||
* reaction number being the key, and the
|
||||
* product stoichiometric coefficient for the species being the value.
|
||||
*/
|
||||
mutable std::vector<std::map<int, doublereal> > m_prxn;
|
||||
|
||||
/**
|
||||
* m_rrxn is a vector of maps. m_rrxn has a length
|
||||
* equal to the total number of species in the kinetics
|
||||
* object. For each species, there exists a map, with the
|
||||
* reaction number being the key, and the
|
||||
* reactant stoichiometric coefficient being the value.
|
||||
* HKM -> mutable because search sometimes creates extra
|
||||
* entries. To be fixed in future...
|
||||
*/
|
||||
mutable std::vector<std::map<int, doublereal> > m_rrxn;
|
||||
|
||||
/**
|
||||
* m_rrxn is a vector of maps. m_rrxn has a length
|
||||
* equal to the total number of species in the kinetics
|
||||
* object. For each species, there exists a map, with the
|
||||
* reaction number being the key, and the
|
||||
* product stoichiometric coefficient being the value.
|
||||
*/
|
||||
mutable std::vector<std::map<int, doublereal> > m_prxn;
|
||||
|
||||
|
||||
std::vector<std::string> m_rxneqn;
|
||||
//! String expression for each rxn
|
||||
/*!
|
||||
* Vector of strings of length m_ii, the number of
|
||||
* reactions, containing the
|
||||
* string expressions for each reaction
|
||||
* (e.g., reactants <=> product1 + product2)
|
||||
*/
|
||||
std::vector<std::string> m_rxneqn;
|
||||
|
||||
/**
|
||||
* Temporary data storage used in calculating the rates of
|
||||
|
|
@ -453,23 +483,36 @@ namespace Cantera {
|
|||
*/
|
||||
vector_fp m_E;
|
||||
|
||||
SurfPhase* m_surf;
|
||||
ImplicitSurfChem* m_integrator;
|
||||
//! Pointer to the surface phase
|
||||
SurfPhase* m_surf;
|
||||
|
||||
private:
|
||||
//! Pointer to the surface solver
|
||||
ImplicitSurfChem* m_integrator;
|
||||
|
||||
public:
|
||||
|
||||
int reactionNumber(){ return m_ii;}
|
||||
protected:
|
||||
void addElementaryReaction(const ReactionData& r);
|
||||
void addGlobalReaction(const ReactionData& r);
|
||||
void installReagents(const ReactionData& r);
|
||||
|
||||
private:
|
||||
void updateKc();
|
||||
|
||||
void registerReaction(int rxnNumber, int type, int loc) {
|
||||
m_index[rxnNumber] = std::pair<int, int>(type, loc);
|
||||
}
|
||||
void applyButlerVolmerCorrection(doublereal* kf);
|
||||
//! 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);
|
||||
|
||||
protected:
|
||||
//! boolean indicating whether mechanism has been finalized
|
||||
bool m_finalized;
|
||||
bool m_has_coverage_dependence;
|
||||
|
|
|
|||
Loading…
Add table
Reference in a new issue