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15 #include <unordered_set>
21 Kinetics::Kinetics() :
27 m_skipUndeclaredSpecies(false),
28 m_skipUndeclaredThirdBodies(false)
32 Kinetics::~Kinetics() {}
37 throw IndexError(
"Kinetics::checkReactionIndex",
"reactions", i,
67 throw IndexError(
"Kinetics::checkSpeciesIndex",
"species", k,
m_kk-1);
81 std::map<size_t, std::vector<size_t> > participants;
82 std::vector<std::map<int, double> > net_stoich;
83 std::unordered_set<size_t> unmatched_duplicates;
86 unmatched_duplicates.insert(i);
92 unsigned long int key = 0;
94 net_stoich.emplace_back();
95 std::map<int, double>& net = net_stoich.back();
99 net[-1 -k] -= sp.second;
104 net[1+k] += sp.second;
108 vector<size_t>& related = participants[key];
109 for (
size_t m : related) {
113 unmatched_duplicates.erase(i);
114 unmatched_duplicates.erase(m);
128 bool thirdBodyOk =
true;
144 bool thirdBodyOk =
true;
161 "Undeclared duplicate reactions detected:\n"
162 "Reaction {}: {}\nReaction {}: {}\n",
168 participants[key].push_back(i);
170 if (unmatched_duplicates.size()) {
171 size_t i = *unmatched_duplicates.begin();
175 "No duplicate found for declared duplicate reaction number {}"
185 std::map<int, double>& r2)
const
187 std::unordered_set<int> keys;
189 keys.insert(r.first);
192 keys.insert(r.first);
194 int k1 = r1.begin()->first;
196 doublereal ratio = 0.0;
197 if (r1[k1] && r2[k1]) {
198 ratio = r2[k1]/r1[k1];
199 bool different =
false;
201 if ((r1[k] && !r2[k]) ||
203 (r1[k] && fabs(r2[k]/r1[k] - ratio) > 1.e-8)) {
214 if (r1[k1] == 0.0 || r2[-k1] == 0.0) {
217 ratio = r2[-k1]/r1[k1];
219 if ((r1[k] && !r2[-k]) ||
220 (!r1[k] && r2[-k]) ||
221 (r1[k] && fabs(r2[-k]/r1[k] - ratio) > 1.e-8)) {
235 double stoich = sp.second;
236 for (
size_t m = 0; m < ph.
nElements(); m++) {
244 double stoich = sp.second;
245 for (
size_t m = 0; m < ph.
nElements(); m++) {
252 for (
const auto& el : balr) {
253 const string& elem = el.first;
254 double elemsum = balr[elem] + balp[elem];
255 double elemdiff = fabs(balp[elem] - balr[elem]);
256 if (elemsum > 0.0 && elemdiff/elemsum > 1e-4) {
258 msg += fmt::format(
" {} {} {}\n",
259 elem, balr[elem], balp[elem]);
264 "The following reaction is unbalanced: {}\n"
265 " Element Reactants Products\n{}",
271 doublereal* phase_data)
273 for (
size_t n = 0; n <
nPhases(); n++) {
277 data +
m_start[n] + nsp, phase_data);
281 throw CanteraError(
"Kinetics::selectPhase",
"Phase not found.");
286 for (
size_t n =
m_start.size()-1; n !=
npos; n--) {
296 for (
size_t n = 0; n <
m_thermo.size(); n++) {
307 const std::string& ph)
const
313 for (
size_t n = 0; n <
m_thermo.size(); n++) {
328 for (
size_t n = 0; n <
m_thermo.size(); n++) {
334 throw CanteraError(
"Kinetics::speciesPhase",
"unknown species '{}'", nm);
344 throw CanteraError(
"Kinetics::speciesPhase",
"unknown species '{}'", nm);
349 for (
size_t n =
m_start.size()-1; n !=
npos; n--) {
355 "illegal species index: {}", k);
390 fill(deltaProp, deltaProp +
nReactions(), 0.0);
400 fill(deltaProp, deltaProp +
nReactions(), 0.0);
412 fill(cdot, cdot +
m_kk, 0.0);
426 fill(ddot, ddot +
m_kk, 0.0);
437 fill(net, net +
m_kk, 0.0);
469 for (
size_t i = 0; i <
m_thermo.size(); i++) {
488 if (r->reversible && !r->orders.empty()) {
490 "Reaction orders may only be given for irreversible reactions");
494 for (
const auto& sp : r->reactants) {
500 "Reaction '{}' contains the undeclared species '{}'",
501 r->equation(), sp.first);
505 for (
const auto& sp : r->products) {
511 "Reaction '{}' contains the undeclared species '{}'",
512 r->equation(), sp.first);
516 for (
const auto& sp : r->orders) {
522 "Reaction '{}' has a reaction order specified for the "
523 "undeclared species '{}'",
524 r->equation(), sp.first);
533 std::vector<size_t> rk, pk;
539 for (
const auto& sp : r->reactants) {
541 rstoich.push_back(sp.second);
544 for (
const auto& sp : r->products) {
546 pstoich.push_back(sp.second);
553 for (
const auto& sp : r->orders) {
556 auto rloc = std::find(rk.begin(), rk.end(), k);
557 if (rloc != rk.end()) {
558 rorder[rloc - rk.begin()] = sp.second;
565 rstoich.push_back(0.0);
566 rorder.push_back(sp.second);
579 m_rfn.push_back(0.0);
592 if (rNew->reaction_type != rOld->reaction_type) {
594 "Reaction types are different: {} != {}.",
595 rOld->reaction_type, rNew->reaction_type);
598 if (rNew->reactants != rOld->reactants) {
600 "Reactants are different: '{}' != '{}'.",
601 rOld->reactantString(), rNew->reactantString());
604 if (rNew->products != rOld->products) {
606 "Products are different: '{}' != '{}'.",
607 rOld->productString(), rNew->productString());
vector_fp m_perturb
Vector of perturbation factors for each reaction's rate of progress vector.
size_t kineticsSpeciesIndex(size_t k, size_t n) const
The location of species k of phase n in species arrays.
void selectPhase(const doublereal *data, const thermo_t *phase, doublereal *phase_data)
virtual double productStoichCoeff(size_t k, size_t i) const
Stoichiometric coefficient of species k as a product in reaction i.
virtual void getNetProductionRates(doublereal *wdot)
Species net production rates [kmol/m^3/s or kmol/m^2/s].
std::vector< thermo_t * > m_thermo
m_thermo is a vector of pointers to ThermoPhase objects that are involved with this kinetics operator
void checkReactionArraySize(size_t ii) const
Check that an array size is at least nReactions() Throws an exception if ii is less than nReactions()...
virtual void getRevRatesOfProgress(doublereal *revROP)
Return the Reverse rates of progress of the reactions.
std::vector< shared_ptr< Reaction > > m_reactions
Vector of Reaction objects represented by this Kinetics manager.
virtual void modifyReaction(size_t i, shared_ptr< Reaction > rNew)
Modify the rate expression associated with a reaction.
vector_fp m_ropf
Forward rate-of-progress for each reaction.
size_t m_rxnphase
Phase Index where reactions are assumed to be taking place.
virtual void addPhase(thermo_t &thermo)
Add a phase to the kinetics manager object.
AnyMap input
Input data used for specific models.
thermo_t & speciesPhase(const std::string &nm)
This function looks up the name of a species and returns a reference to the ThermoPhase object of the...
StoichManagerN m_reactantStoich
Stoichiometry manager for the reactants for each reaction.
size_t nPhases() const
The number of phases participating in the reaction mechanism.
A class for managing third-body efficiencies, including default values.
void checkPhaseArraySize(size_t mm) const
Check that an array size is at least nPhases() Throws an exception if mm is less than nPhases().
std::string kineticsSpeciesName(size_t k) const
Return the name of the kth species in the kinetics manager.
double efficiency(const std::string &k) const
Get the third-body efficiency for species k
StoichManagerN m_revProductStoich
Stoichiometry manager for the products of reversible reactions.
virtual void getCreationRates(doublereal *cdot)
Species creation rates [kmol/m^3/s or kmol/m^2/s].
size_t nDim() const
Returns the number of spatial dimensions (1, 2, or 3)
std::map< std::string, size_t > m_phaseindex
Mapping of the phase name to the position of the phase within the kinetics object.
Composition reactants
Reactant species and stoichiometric coefficients.
std::string equation() const
The chemical equation for this reaction.
void checkSpeciesIndex(size_t k) const
Check that the specified species index is in range Throws an exception if k is greater than nSpecies(...
std::vector< double > vector_fp
Turn on the use of stl vectors for the basic array type within cantera Vector of doubles.
bool reversible
True if the current reaction is reversible. False otherwise.
virtual void getReactionDelta(const doublereal *property, doublereal *deltaProperty)
Change in species properties.
std::string name() const
Return the name of the phase.
virtual std::string type() const
String indicating the thermodynamic model implemented.
const int CHEMACT_RXN
A chemical activation reaction.
Composition products
Product species and stoichiometric coefficients.
int reaction_type
Type of the reaction.
size_t m_surfphase
Index in the list of phases of the one surface phase.
virtual void getFwdRatesOfProgress(doublereal *fwdROP)
Return the forward rates of progress of the reactions.
double checkDuplicateStoich(std::map< int, double > &r1, std::map< int, double > &r2) const
Check whether r1 and r2 represent duplicate stoichiometries This function returns a ratio if two reac...
std::string elementName(size_t m) const
Name of the element with index m.
virtual std::string kineticsType() const
Identifies the Kinetics manager type.
const int FALLOFF_RXN
The general form for a gas-phase association or dissociation reaction, with a pressure-dependent rate...
doublereal nAtoms(size_t k, size_t m) const
Number of atoms of element m in species k.
const U & getValue(const std::map< T, U > &m, const T &key, const U &default_val)
Const accessor for a value in a std::map.
virtual void getDestructionRates(doublereal *ddot)
Species destruction rates [kmol/m^3/s or kmol/m^2/s].
bool m_skipUndeclaredSpecies
vector_fp m_rkcn
Reciprocal of the equilibrium constant in concentration units.
size_t speciesIndex(const std::string &name) const
Returns the index of a species named 'name' within the Phase object.
std::vector< size_t > m_start
m_start is a vector of integers specifying the beginning position for the species vector for the n'th...
size_t nElements() const
Number of elements.
virtual std::pair< size_t, size_t > checkDuplicates(bool throw_err=true) const
Check for unmarked duplicate reactions and unmatched marked duplicates.
Base class for a phase with thermodynamic properties.
virtual bool addReaction(shared_ptr< Reaction > r)
Add a single reaction to the mechanism.
size_t nTotalSpecies() const
The total number of species in all phases participating in the kinetics mechanism.
size_t m_kk
The number of species in all of the phases that participate in this kinetics mechanism.
vector_fp m_rfn
Forward rate constant for each reaction.
void checkReactionIndex(size_t m) const
Check that the specified reaction index is in range Throws an exception if i is greater than nReactio...
std::map< std::string, double > Composition
Map from string names to doubles.
size_t nSpecies() const
Returns the number of species in the phase.
virtual void getRevReactionDelta(const doublereal *g, doublereal *dg)
Given an array of species properties 'g', return in array 'dg' the change in this quantity in the rev...
const int THREE_BODY_RXN
A gas-phase reaction that requires a third-body collision partner.
StoichManagerN m_irrevProductStoich
Stoichiometry manager for the products of irreversible reactions.
vector_fp m_ropr
Reverse rate-of-progress for each reaction.
size_t speciesPhaseIndex(size_t k) const
This function takes as an argument the kineticsSpecies index (i.e., the list index in the list of spe...
vector_fp m_ropnet
Net rate-of-progress for each reaction.
thermo_t & thermo(size_t n=0)
This method returns a reference to the nth ThermoPhase object defined in this kinetics mechanism.
virtual void getNetRatesOfProgress(doublereal *netROP)
Net rates of progress.
void checkPhaseIndex(size_t m) const
Check that the specified phase index is in range Throws an exception if m is greater than nPhases()
Base class for exceptions thrown by Cantera classes.
shared_ptr< Reaction > reaction(size_t i)
Return the Reaction object for reaction i.
size_t nReactions() const
Number of reactions in the reaction mechanism.
virtual void resizeSpecies()
Resize arrays with sizes that depend on the total number of species.
const size_t npos
index returned by functions to indicate "no position"
Intermediate class which stores data about a reaction and its rate parameterization so that it can be...
An array index is out of range.
void checkReactionBalance(const Reaction &R)
Check that the specified reaction is balanced (same number of atoms for each element in the reactants...
Namespace for the Cantera kernel.
A reaction with a non-reacting third body "M" that acts to add or remove energy from the reacting spe...
void checkSpeciesArraySize(size_t mm) const
Check that an array size is at least nSpecies() Throws an exception if kk is less than nSpecies().
std::string speciesName(size_t k) const
Name of the species with index k.
size_t m_mindim
number of spatial dimensions of lowest-dimensional phase.
A reaction that is first-order in [M] at low pressure, like a third-body reaction,...
virtual double reactantStoichCoeff(size_t k, size_t i) const
Stoichiometric coefficient of species k as a reactant in reaction i.
bool duplicate
True if the current reaction is marked as duplicate.
virtual void init()
Prepare the class for the addition of reactions, after all phases have been added.