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Reduced complexity of duplicate reaction detection from n^2 to n*log(n)

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This commit is contained in:
Ray Speth 2012-04-04 18:44:56 +00:00
parent d16f70ab44
commit 3d9efad94f
1 changed files with 25 additions and 18 deletions
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43
src/kinetics/importKinetics.cpp
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@ -44,25 +44,28 @@ namespace Cantera
class rxninfo
{
public:
//! rdata
//! Net stoichiometric coefficients for each reaction
std::vector< std::map<int, doublereal> > m_rdata;
//! string name
//! string name (i.e. the reaction equation)
std::vector<std::string> m_eqn;
//! string vector of ints
//! Indicates whether each reaction is marked "duplicate"
std::vector<int> m_dup;
//! string vector of ints
//! Number of reactants in each reaction
std::vector<size_t> m_nr;
//! string vector of ints
//! Indicates "type" of each reaction (see reaction_defs.h)
std::vector<int> m_typ;
//! vector of bools.
//! Indicates whether each reaction is reversible
std::vector<bool> m_rev;
~rxninfo() {
m_eqn.clear();
m_dup.clear();
m_nr.clear();
m_typ.clear();
m_rdata.clear();
}
//! Map of (vector indicating participating species) to reaction numbers
//! Used to speed up duplicate reaction checks.
std::map<std::vector<char>, std::vector<size_t> > m_participants;
bool installReaction(int i, const XML_Node& r, Kinetics* k,
std::string default_phase, int rule,
bool validate_rxn) ;
@ -868,20 +871,23 @@ bool rxninfo::installReaction(int i, const XML_Node& r, Kinetics* k,
* Look for undeclared duplicate reactions.
*/
if (validate_rxn) {
doublereal c = 0.0;
map<int, doublereal> rxnstoich;
rxnstoich.clear();
vector<char> participants(kin.nTotalSpecies(), 0);
for (size_t nn = 0; nn < rdata.reactants.size(); nn++) {
rxnstoich[-1 - int(rdata.reactants[nn])] -= rdata.rstoich[nn];
participants[rdata.reactants[nn]] += 1;
}
for (size_t nn = 0; nn < rdata.products.size(); nn++) {
rxnstoich[int(rdata.products[nn])+1] += rdata.pstoich[nn];
participants[rdata.products[nn]] += 2;
}
for (size_t nn = 0; nn < m_rdata.size(); nn++) {
vector<size_t>& related = m_participants[participants];
for (size_t mm = 0; mm < related.size(); mm++) {
size_t nn = related[mm];
if ((rdata.reactants.size() == m_nr[nn])
&& (rdata.reactionType == m_typ[nn])) {
c = isDuplicateReaction(rxnstoich, m_rdata[nn]);
doublereal c = isDuplicateReaction(rxnstoich, m_rdata[nn]);
if (c > 0.0
|| (c < 0.0 && rdata.reversible)
|| (c < 0.0 && m_rev[nn])) {
@ -900,6 +906,7 @@ bool rxninfo::installReaction(int i, const XML_Node& r, Kinetics* k,
m_nr.push_back(rdata.reactants.size());
m_typ.push_back(rdata.reactionType);
m_rdata.push_back(rxnstoich);
m_participants[participants].push_back(m_rdata.size() - 1);
}
rdata.equation = eqn;