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[Kinetics] Add reactions using Reaction instead of ReactionData

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Deprecate class ReactionData and all related functions.
This commit is contained in:
Ray Speth 2014-11-15 00:47:15 +00:00
parent e3022a8057
commit a2c415aaa5
3 changed files with 32 additions and 567 deletions
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5
include/cantera/kinetics/ReactionData.h
View file

@ -46,7 +46,10 @@ public:
chebPmax(-1.0),
chebDegreeT(0),
chebDegreeP(0)
{}
{
warn_deprecated("class ReactionData",
"To be removed after Cantera 2.2.");
}
virtual ~ReactionData() {}

35
include/cantera/kinetics/importKinetics.h
View file

@ -20,6 +20,7 @@ namespace Cantera
{
//! Rules for parsing and installing reactions
//! @deprecated Unused. To be removed after Cantera 2.2.
struct ReactionRules {
ReactionRules();
bool skipUndeclaredSpecies;
@ -43,6 +44,8 @@ struct ReactionRules {
* stoichiometric coefficients.
*
* @ingroup kineticsmgr
* @deprecated Now handled by Kinetics::checkDuplicateStoich. To be removed
* after Cantera 2.2.
*/
doublereal isDuplicateReaction(std::map<int, doublereal>& r1,
std::map<int, doublereal>& r2);
@ -54,6 +57,8 @@ doublereal isDuplicateReaction(std::map<int, doublereal>& r1,
* @param errorTolerance double containing the error tolerance.
*
* @ingroup kineticsmgr
* @deprecated Now handled by Kinetics::checkReactionBalance. To be removed
* after Cantera 2.2.
*/
void checkRxnElementBalance(Kinetics& kin,
const ReactionData& rdata,
@ -80,36 +85,13 @@ void checkRxnElementBalance(Kinetics& kin,
* a species we simply return false, allowing the calling
* routine to skip this reaction and continue. Otherwise, we
* will throw an error.
* @deprecated Now handled through newReaction() and its support functions. To
* be removed after Cantera 2.2.
*/
bool getReagents(const XML_Node& rxn, Kinetics& kin, int rp, std::string default_phase,
std::vector<size_t>& spnum, vector_fp& stoich,
vector_fp& order, const ReactionRules& rules);
//! Install Butler Volmer Orders into the forward orders array.
/*!
* Install the BV order coefficients into the fullForwardsOrders vector.
*
* @param[in] rxnNode XML node pointing to the reaction element in the xml tree.
* @param[in] kin Reference to the kinetics object to install the information into.
* @param[in] rdata Reaction Data Object containing the information about one reaction
* @param[out] fullForwardsOrders Vectors of the orders of reaction.
*/
void installButlerVolmerOrders(const XML_Node& rxnNode, const Kinetics& kin, const ReactionData& rdata,
std::vector<doublereal>& fullForwardsOrders);
//! Get non-mass-action orders for a reaction
extern bool getOrders(const XML_Node& rxnNode, Kinetics& kin,
std::string default_phase, const ReactionData& rdata,
vector_fp& order, vector_fp& fullForwardsOrders,
const ReactionRules& rules);
extern bool getRxnFormulation(const XML_Node& rxnNode, Kinetics& kin,
std::string default_phase, const ReactionData& rdata,
vector_fp& order, vector_fp& fullForwardsOrders,
doublereal &affinityPower,
doublereal & equilibriumConstantPower,
const ReactionRules& rules);
//! Read the rate coefficient data from the XML file.
/*!
* Extract the rate coefficient for a reaction from the xml node, kf.
@ -124,6 +106,9 @@ extern bool getRxnFormulation(const XML_Node& rxnNode, Kinetics& kin,
*
* Trigger an exception for negative A unless specifically authorized.
*
* @deprecated Now handled through newReaction() and its support functions. To
* be removed after Cantera 2.2.
*
* @ingroup kineticsmgr
*/
void getRateCoefficient(const XML_Node& kf, Kinetics& kin, ReactionData& rdata,

559
src/kinetics/importKinetics.cpp
View file

@ -14,6 +14,7 @@
#include "cantera/kinetics/importKinetics.h"
#include "cantera/thermo/ThermoFactory.h"
#include "cantera/kinetics/ReactionData.h"
#include "cantera/kinetics/Reaction.h"
#include "cantera/base/stringUtils.h"
#include "cantera/base/ctml.h"
@ -32,48 +33,11 @@ ReactionRules::ReactionRules() :
{
}
//! these are all used to check for duplicate reactions
class rxninfo
{
public:
std::vector<ReactionData*> m_rdata;
//! Map of (key indicating participating species) to reaction numbers
//! Used to speed up duplicate reaction checks.
std::map<unsigned long int, std::vector<size_t> > m_participants;
/**
* Install an individual reaction into a kinetics manager. The
* data for the reaction is in the xml_node r. In other words, r
* points directly to a ctml element named "reaction". i refers
* to the number id of the reaction in the kinetics object.
*
* @param i Reaction number.
* @param r XML_Node containing reaction data.
* @param kin Kinetics manager to which reaction will be added.
* @param default_phase Default phase for locating a species
* @param rules Rule for handling reactions with missing species
* (skip or flag as error)
* @param validate_rxn If true, check that this reaction is not a
* duplicate of one already entered, and check that
* the reaction balances.
*
* @ingroup kineticsmgr
*/
bool installReaction(int i, const XML_Node& r, Kinetics& kin,
std::string default_phase, ReactionRules& rules,
bool validate_rxn) ;
~rxninfo() {
for (size_t i = 0; i < m_rdata.size(); i++) {
delete m_rdata[i];
}
}
};
void checkRxnElementBalance(Kinetics& kin,
const ReactionData& rdata, doublereal errorTolerance)
{
warn_deprecated("checkRxnElementBalance", "Now handled by "
"Kinetics::checkReactionBalance. To be removed after Cantera 2.2.");
doublereal kstoich;
map<string, double> bal, balr, balp;
@ -133,6 +97,8 @@ bool getReagents(const XML_Node& rxn, Kinetics& kin, int rp,
vector_fp& stoich, vector_fp& order,
const ReactionRules& rules)
{
warn_deprecated("getReagents", "Now handled through newReaction() and its "
"support functions. To be removed after Cantera 2.2.");
string rptype;
/*
@ -229,255 +195,11 @@ bool getReagents(const XML_Node& rxn, Kinetics& kin, int rp,
return true;
}
// Install the BV order coefficients into the fullForwardsOrders vector.
void installButlerVolmerOrders(const XML_Node& rxnNode, const Kinetics& kin, const ReactionData& rdata,
std::vector<doublereal>& fullForwardsOrders)
{
const std::vector<size_t>& reactants = rdata.reactants;
const std::vector<size_t>& products = rdata.products;
const std::vector<doublereal>& rstoich = rdata.rstoich;
const std::vector<doublereal>& pstoich = rdata.pstoich;
// Gather the number of species in the kinetics object and resize fullForwardsOrders
size_t nsp = kin.nTotalSpecies();
fullForwardsOrders.resize(nsp, 0.0);
// Ok first thing to do is get the electrochemical transfer coefficient
// since the order depend on the value.
// Also, if we don't find one, then it's an error. Zero is an acceptable value.
// Beta below 0 or greater than 1 are probably not good.
double beta = -10.0;
if (rxnNode.hasChild("rateCoeff")) {
XML_Node& rc = rxnNode.child("rateCoeff");
if (rc.hasChild("electrochem")) {
XML_Node& eb = rc.child("electrochem");
string sbeta = eb["beta"];
beta = fpValueCheck(sbeta);
}
}
if (beta == -10.0) {
throw CanteraError("installButlerVolmerOrders()",
"ButlerVolmerOrders model requested but no electrochem beta input");
}
double betar = 1.0 - beta;
for (size_t k = 0; k < nsp; k++) {
fullForwardsOrders[k] = 0.0;
}
for (size_t n = 0; n < reactants.size(); n++) {
size_t k = reactants[n];
double fac = rstoich[n];
fullForwardsOrders[k] += fac * betar;
}
for (size_t n = 0; n < products.size(); n++) {
size_t k = products[n];
double fac = pstoich[n];
fullForwardsOrders[k] += fac * beta;
}
}
// Fill in the fullForwardsOrders array for a specific reaction
/*
* rxnNode XML node for the reaction
*/
bool getOrders(const XML_Node& rxnNode, Kinetics& kin,
std::string default_phase, const ReactionData& rdata,
vector_fp& order, vector_fp& fullForwardsOrders,
const ReactionRules& rules)
{
// Gather the number of species in the kinetics object and resize
// fullForwardsOrders
size_t nsp = kin.nTotalSpecies();
fullForwardsOrders.resize(nsp, 0.0);
const std::vector<size_t>& reactants = rdata.reactants;
//const std::vector<doublereal>& rstoich = rdata.rstoich;
const std::vector<size_t>& products = rdata.products;
const std::vector<doublereal>& pstoich = rdata.pstoich;
// Check to see if reaction orders have been specified.
if (rxnNode.hasChild("order")) {
std::vector<XML_Node*> ord = rxnNode.getChildren("order");
doublereal forder;
for (size_t nn = 0; nn < ord.size(); nn++) {
const XML_Node& oo = *ord[nn];
forder = oo.fp_value();
std::string spName = oo["species"];
size_t k = kin.kineticsSpeciesIndex(spName);
if (k == npos) {
throw CanteraError("getOrders()",
"Species not in kinetics species list: " + spName);
}
for (size_t n = 0; n < reactants.size(); n++) {
if (reactants[n] == k) {
order[n] = forder;
}
}
}
}
if (rxnNode.hasChild("orders")) {
std::vector<XML_Node*> orders = rxnNode.getChildren("orders");
// Doesn't really make sense to have more than one of these blocks
if (orders.size() != 1) {
throw CanteraError("getOrders()", " More than one XML orders block");
}
XML_Node& osNode = *orders[0];
// read the model attribute and figure out how to initialize the full
// orders vector.
string baseHndling = osNode["model"];
string ss = lowercase(baseHndling);
if (ss == "zeroorders") {
for (size_t k = 0; k < nsp; k++) {
fullForwardsOrders[k] = 0.0;
}
} else if (ss == "reactantorders") {
for (size_t k = 0; k < nsp; k++) {
fullForwardsOrders[k] = 0.0;
}
for (size_t n = 0; n < order.size(); n++) {
size_t k = reactants[n];
double fac = order[n];
fullForwardsOrders[k] = fac;
}
} else if (ss == "butlervolmerorders") {
// ok first thing to do is get the electrochemical transfer
// coefficient since the order depend on the value.
// Also, if we don't find one, then it's an error
double beta = -10.0;
if (rxnNode.hasChild("rateCoeff")) {
XML_Node& rc = rxnNode.child("rateCoeff");
if (rc.hasChild("electrochem")) {
XML_Node& eb = rc.child("electrochem");
string sbeta = eb["beta"];
beta = fpValueCheck(sbeta);
}
}
if (beta == -10.0) {
throw CanteraError("getOrders()",
"ButlerVolmerOrders model requested but no electrochem beta input");
}
double betar = 1.0 - beta;
for (size_t k = 0; k < nsp; k++) {
fullForwardsOrders[k] = 0.0;
}
for (size_t n = 0; n < reactants.size(); n++) {
size_t k = reactants[n];
double fac = order[n];
fullForwardsOrders[k] += fac * betar;
}
for (size_t n = 0; n < products.size(); n++) {
size_t k = products[n];
double fac = pstoich[n];
fullForwardsOrders[k] += fac * beta;
}
} else {
throw CanteraError("getOrders()", "unknown model for orders XML_Node: " + baseHndling);
}
std::vector<string> key, val;
int numFound = ctml::getPairs(osNode, key, val);
// Fill in the fullForwardsOrders array
for (size_t n = 0; n < (size_t) numFound; n++) {
double fac = fpValueCheck(val[n]);
string ss = key[n];
size_t k = kin.kineticsSpeciesIndex(ss);
fullForwardsOrders[k] = fac;
}
}
return true;
}
bool getRxnFormulation(const XML_Node& rxnNode, Kinetics& kin,
std::string default_phase, const ReactionData& rdata,
vector_fp& order, vector_fp& fullForwardsOrders,
doublereal &affinityPower,doublereal & equilibriumConstantPower,
const ReactionRules& rules)
{
// Gather the number of species in the kinetics object and resize
// fullForwardsOrders
size_t nsp = kin.nTotalSpecies();
fullForwardsOrders.resize(nsp, 0.0);
const std::vector<size_t>& reactants = rdata.reactants;
//const std::vector<doublereal>& rstoich = rdata.rstoich;
const std::vector<size_t>& products = rdata.products;
const std::vector<doublereal>& pstoich = rdata.pstoich;
if (rxnNode.hasChild("reactionOrderFormulation")) {
XML_Node& rfNode = rxnNode.child("reactionOrderFormulation");
// read the model attribute and figure out how to initialize the full
// orders vector.
string baseHndling = rfNode["model"];
string ss = lowercase(baseHndling);
if (ss == "zeroorders") {
for (size_t k = 0; k < nsp; k++) {
fullForwardsOrders[k] = 0.0;
}
} else if (ss == "reactantorders") {
for (size_t k = 0; k < nsp; k++) {
fullForwardsOrders[k] = 0.0;
}
for (size_t n = 0; n < order.size(); n++) {
size_t k = reactants[n];
double fac = order[n];
fullForwardsOrders[k] = fac;
}
} else if (ss == "butlervolmerorders") {
// ok first thing to do is get the electrochemical transfer
// coefficient since the order depend on the value.
// Also, if we don't find one, then it's an error
double beta = -10.0;
if (rxnNode.hasChild("rateCoeff")) {
XML_Node& rc = rxnNode.child("rateCoeff");
if (rc.hasChild("electrochem")) {
XML_Node& eb = rc.child("electrochem");
string sbeta = eb["beta"];
beta = fpValueCheck(sbeta);
}
}
if (beta == -10.0) {
throw CanteraError("getRxnFormulation()",
"ButlerVolmerOrders model requested but no electrochem beta input");
}
double betar = 1.0 - beta;
for (size_t k = 0; k < nsp; k++) {
fullForwardsOrders[k] = 0.0;
}
for (size_t n = 0; n < reactants.size(); n++) {
size_t k = reactants[n];
double fac = order[n];
fullForwardsOrders[k] += fac * betar;
}
for (size_t n = 0; n < products.size(); n++) {
size_t k = products[n];
double fac = pstoich[n];
fullForwardsOrders[k] += fac * beta;
}
} else {
throw CanteraError("getRxnFormulation()", "unknown model for reactionOrders XML_Node: " + baseHndling);
}
if (rfNode.hasChild("affinityPower")) {
XML_Node& fNode = rxnNode.child("affinityPower");
affinityPower = fNode.fp_value();
}
if (rfNode.hasChild("equilibriumConstantPower")) {
XML_Node& eNode = rxnNode.child("equilibriumConstantPower");
equilibriumConstantPower = eNode.fp_value();
}
}
return true;
}
/**
* getArrhenius() parses the xml element called Arrhenius.
* The Arrhenius expression is
* \f[ k = A T^(b) exp (-E_a / RT). \f]
* @deprecated to be removed after Cantera 2.2.
*/
static void getArrhenius(const XML_Node& node, int& labeled,
doublereal& A, doublereal& b, doublereal& E)
@ -514,6 +236,7 @@ static void getArrhenius(const XML_Node& node, int& labeled,
* reactants in the normal manner.
* n - unitless
* E - Units 1/Kelvin
* @deprecated to be removed after Cantera 2.2.
*/
static void getStick(const XML_Node& node, Kinetics& kin,
ReactionData& r, doublereal& A, doublereal& b, doublereal& E)
@ -601,6 +324,7 @@ static void getStick(const XML_Node& node, Kinetics& kin,
<actEnergy> 0.0 </actEnergy>
</coverage>
@endverbatim
* @deprecated to be removed after Cantera 2.2.
*/
static void getCoverageDependence(const XML_Node& node,
thermo_t& surfphase, ReactionData& rdata)
@ -631,6 +355,7 @@ static void getCoverageDependence(const XML_Node& node,
* @verbatim
<falloff type="Troe"> 0.5 73.2 5000. 9999. </falloff>
@endverbatim
* @deprecated to be removed after Cantera 2.2.
*/
static void getFalloff(const XML_Node& f, ReactionData& rdata)
{
@ -664,6 +389,7 @@ static void getFalloff(const XML_Node& f, ReactionData& rdata)
* Get the enhanced collision efficiencies. It is assumed that the
* reaction mechanism is homogeneous, so that all species belong
* to phase(0) of 'kin'.
* @deprecated to be removed after Cantera 2.2.
*/
static void getEfficiencies(const XML_Node& eff, Kinetics& kin,
ReactionData& rdata, const ReactionRules& rules)
@ -691,6 +417,8 @@ static void getEfficiencies(const XML_Node& eff, Kinetics& kin,
void getRateCoefficient(const XML_Node& kf, Kinetics& kin,
ReactionData& rdata, const ReactionRules& rules)
{
warn_deprecated("getRateCoefficent", "Now handled through newReaction() "
"and its support functions. To be removed after Cantera 2.2.");
if (rdata.reactionType == PLOG_RXN) {
rdata.rateCoeffType = PLOG_REACTION_RATECOEFF_TYPE;
for (size_t m = 0; m < kf.nChildren(); m++) {
@ -792,6 +520,8 @@ void getRateCoefficient(const XML_Node& kf, Kinetics& kin,
doublereal isDuplicateReaction(std::map<int, doublereal>& r1,
std::map<int, doublereal>& r2)
{
warn_deprecated("isDuplicateReaction", "Now handled by "
"Kinetics::checkDuplicateStoich. To be removed after Cantera 2.2.");
map<int, doublereal>::const_iterator b = r1.begin(), e = r1.end();
int k1 = b->first;
// check for duplicate written in the same direction
@ -829,255 +559,9 @@ doublereal isDuplicateReaction(std::map<int, doublereal>& r1,
return ratio;
}
bool rxninfo::installReaction(int iRxn, const XML_Node& rxnNode, Kinetics& kin,
string default_phase, ReactionRules& rules,
bool validate_rxn)
{
// Check to see that we are in fact at a reaction node in the XML tree
if (rxnNode.name() != "reaction") {
throw CanteraError("rxninfo::installReaction()",
"Expected xml node reaction, got " + rxnNode.name());
}
// We use the ReactionData object to store initial values read in from the
// xml data. Then, when we have collected everything, we add the reaction to
// the kinetics object, kin, at the end of the routine.
ReactionData& rdata = **m_rdata.insert(m_rdata.end(), new ReactionData());
rdata.validate = validate_rxn;
/*
* Search the reaction element for the attribute "type".
* If found, then branch on the type, to fill in appropriate
* fields in rdata.
*/
rdata.reactionType = ELEMENTARY_RXN;
string typ = rxnNode["type"];
string ltype = lowercase(typ);
if (typ == "falloff") {
rdata.reactionType = FALLOFF_RXN;
rdata.falloffType = SIMPLE_FALLOFF;
} else if (typ == "chemAct") {
rdata.reactionType = CHEMACT_RXN;
rdata.falloffType = SIMPLE_FALLOFF;
} else if (typ == "threeBody") {
rdata.reactionType = THREE_BODY_RXN;
} else if (typ == "plog") {
rdata.reactionType = PLOG_RXN;
} else if (typ == "chebyshev") {
rdata.reactionType = CHEBYSHEV_RXN;
} else if (typ == "surface") {
rdata.reactionType = SURFACE_RXN;
} else if (typ == "edge") {
rdata.reactionType = EDGE_RXN;
} else if (ltype == "butlervolmer_noactivitycoeffs") {
rdata.reactionType = BUTLERVOLMER_NOACTIVITYCOEFFS_RXN;
} else if (ltype == "butlervolmer") {
rdata.reactionType = BUTLERVOLMER_RXN;
} else if (ltype == "surfaceaffinity") {
rdata.reactionType = SURFACEAFFINITY_RXN;
} else if (ltype == "global") {
rdata.reactionType = GLOBAL_RXN;
} else if (typ != "") {
throw CanteraError("installReaction()", "Unknown reaction type: " + typ);
}
// Check to see if the reaction is specified to be a duplicate of another
// reaction. It's an error if the reaction is a duplicate and this is not
// set.
rdata.duplicate = (rxnNode.hasAttrib("duplicate")) ? 1 : 0;
// Check to see if the reaction rate constant can be negative. It's an
// error if a negative rate constant is found and this is not set.
rules.allowNegativeA = (rxnNode.hasAttrib("negative_A")) ? 1 : 0;
// Use the contents of the "equation" child element as the reaction's
// string representation. Post-process to convert "[" and "]" characters
// back into "<" and ">" which cannot easily be stored in an XML file. This
// reaction string is used only for display purposes. It is not parsed for
// the identities of reactants or products.
rdata.equation = (rxnNode.hasChild("equation")) ? rxnNode("equation") : "<no equation>";
static const char* delimiters[] = {" [=] ", " =] ", " = ", "[=]", "=]", "="};
static const char* replacements[] = {" <=> ", " => ", " = ", "<=>", "=>", "="};
for (size_t i = 0; i < 6; i++) {
size_t n = rdata.equation.find(delimiters[i]);
if (n != npos) {
size_t w = strlen(delimiters[i]);
rdata.reactantString = stripws(rdata.equation.substr(0, n));
rdata.productString = stripws(rdata.equation.substr(n+w, npos));
rdata.equation.replace(n, w, replacements[i]);
break;
}
}
// Get the reactant and their stoichiometries
bool ok = getReagents(rxnNode, kin, 1, default_phase, rdata.reactants,
rdata.rstoich, rdata.rorder, rules);
// Get the products. We store the id of products in rdata.products
ok = ok && getReagents(rxnNode, kin, -1, default_phase, rdata.products,
rdata.pstoich, rdata.porder, rules);
// if there was a problem getting either the reactants or the products,
// then abort.
if (!ok) {
return false;
}
// check whether the reaction is specified to be
// reversible. Default is irreversible.
string isrev = rxnNode["reversible"];
rdata.reversible = (isrev == "yes" || isrev == "true");
// HKM this will be removed shortly
// If reaction orders are specified, then this reaction does not follow
// mass-action kinetics, and is not an elementary reaction. So check that
// it is not reversible, since computing the reverse rate from
// thermochemistry only works for elementary reactions. Set the type to
// global, so that kinetics managers will know to process the reaction
// orders.
if (rxnNode.hasChild("order")) {
if (rdata.reversible == true) {
throw CanteraError("installReaction",
"reaction orders may only be given for "
"irreversible reactions");
}
rdata.global = true;
}
// For Butler Volmer reactions, we'll install the orders for the exchange current into the
// forwardFullOrders array. It may be altered by the getOrders function below.
if (rdata.reactionType == BUTLERVOLMER_NOACTIVITYCOEFFS_RXN || rdata.reactionType == BUTLERVOLMER_RXN) {
if (! rdata.reversible) {
throw CanteraError("installReaction()", "a Butler-Volmer rxn must be reversible");
}
installButlerVolmerOrders(rxnNode, kin, rdata, rdata.forwardFullOrder_);
// For Butler Volmer reactions, a common addition to the formulation is to add an electrical resistance
// to the formulation. The resistance modifies the electrical current flow in both directions
if (rxnNode.hasChild("filmResistivity")) {
XML_Node& fNode = rxnNode.child("filmResistivity");
rdata.filmResistivity = fNode.fp_value();
}
}
// Fill in the global reaction formulation terms (Affinity reactions)
if (rxnNode.hasChild("reactionOrderFormulation")) {
ok = getRxnFormulation(rxnNode, kin, default_phase, rdata,
rdata.rorder, rdata.forwardFullOrder_, rdata.affinityPower,
rdata.equilibriumConstantPower, rules);
}
// Fill in the forwardFullOrder_ array
if (rxnNode.hasChild("orders")) {
ok = getOrders(rxnNode, kin, default_phase, rdata,
rdata.rorder, rdata.forwardFullOrder_, rules);
}
// Some reactions can be elementary reactions but have fractional
// stoichiometries wrt to some products and reactants. An example of these
// are solid reactions involving phase transformations. Species with
// fractional stoichiometries must be from single-species phases with
// unity activities. For these reactions set the bool isReversibleWithFrac
// to true.
if (rdata.reversible == true) {
for (size_t i = 0; i < rdata.products.size(); i++) {
doublereal po = rdata.porder[i];
AssertTrace(po == rdata.pstoich[i]);
doublereal chk = po - 1.0 * int(po);
if (chk != 0.0) {
size_t k = rdata.products[i];
// Special case when k is a single species phase.
if (kin.speciesPhase(k).nSpecies() == 1) {
rdata.porder[i] = 0.0;
}
rdata.isReversibleWithFrac = true;
}
}
for (size_t i = 0; i < rdata.reactants.size(); i++) {
doublereal ro = rdata.rorder[i];
AssertTrace(ro == rdata.rstoich[i]);
doublereal chk = ro - 1.0 * int(ro);
if (chk != 0.0) {
size_t k = rdata.reactants[i];
// Special case when k is a single species phase.
if (kin.speciesPhase(k).nSpecies() == 1) {
rdata.rorder[i] = 0.0;
}
rdata.isReversibleWithFrac = true;
}
}
}
rdata.number = iRxn;
rdata.rxn_number = iRxn;
// Read the rate coefficient data from the XML file. Trigger an
// exception for negative A unless specifically authorized.
getRateCoefficient(rxnNode.child("rateCoeff"), kin, rdata, rules);
if (validate_rxn) {
// Look for undeclared duplicate reactions.
unsigned long int participants = 0;
for (size_t nn = 0; nn < rdata.reactants.size(); nn++) {
rdata.net_stoich[-1 - int(rdata.reactants[nn])] -= rdata.rstoich[nn];
participants += static_cast<unsigned long int>(rdata.reactants[nn]);
}
for (size_t nn = 0; nn < rdata.products.size(); nn++) {
rdata.net_stoich[int(rdata.products[nn])+1] += rdata.pstoich[nn];
participants += static_cast<unsigned long int>(rdata.products[nn]);
}
vector<size_t>& related = m_participants[participants];
for (size_t mm = 0; mm < related.size(); mm++) {
ReactionData& other = *m_rdata[related[mm]];
if (rdata.reactionType != other.reactionType) {
continue; // different reaction types
} else if (rdata.duplicate && other.duplicate) {
continue; // marked duplicates
}
doublereal c = isDuplicateReaction(rdata.net_stoich, other.net_stoich);
if (c == 0) {
continue; // stoichiometries differ (not by a multiple)
} else if (c < 0.0 && !rdata.reversible && !other.reversible) {
continue; // irreversible reactions in opposite directions
} else if (rdata.reactionType == FALLOFF_RXN ||
rdata.reactionType == THREE_BODY_RXN ||
rdata.reactionType == CHEMACT_RXN) {
bool thirdBodyOk = true;
for (size_t k = 0; k < kin.nTotalSpecies(); k++) {
if (rdata.efficiency(k) * other.efficiency(k) != 0.0) {
thirdBodyOk = false;
}
}
if (thirdBodyOk) {
continue; // No overlap in third body efficiencies
}
}
string msg = string("Undeclared duplicate reactions detected: \n")
+"Reaction "+int2str(other.number+1)+": "+other.equation
+"\nReaction "+int2str(iRxn+1)+": "+rdata.equation+"\n";
throw CanteraError("installReaction", msg);
}
m_participants[participants].push_back(m_rdata.size() - 1);
// Check to see that the elements balance in the reaction.
// Throw an error if they don't
checkRxnElementBalance(kin, rdata);
}
// Ok we have read everything in about the reaction. Add it to the
// kinetics object by calling the Kinetics member function addReaction()
kin.addReaction(rdata);
return true;
}
bool installReactionArrays(const XML_Node& p, Kinetics& kin,
std::string default_phase, bool check_for_duplicates)
{
rxninfo _rxns;
int itot = 0;
/*
* Search the children of the phase element for the
@ -1140,13 +624,8 @@ bool installReactionArrays(const XML_Node& p, Kinetics& kin,
// if no 'include' directive, then include all reactions
if (incl.empty()) {
for (size_t i = 0; i < allrxns.size(); i++) {
const XML_Node* r = allrxns[i];
if (r) {
if (_rxns.installReaction(itot, *r, kin,
default_phase, rxnrule, check_for_duplicates)) {
++itot;
}
}
kin.addReaction(newReaction(*allrxns[i]));
++itot;
}
} else {
for (size_t nii = 0; nii < incl.size(); nii++) {
@ -1177,10 +656,8 @@ bool installReactionArrays(const XML_Node& p, Kinetics& kin,
* sometimes has surprising results.
*/
if ((rxid >= imin) && (rxid <= imax)) {
if (_rxns.installReaction(itot, *r, kin,
default_phase, rxnrule, check_for_duplicates)) {
++itot;
}
kin.addReaction(newReaction(*r));
++itot;
}
}
}