/
Reaction.cpp
667 lines (603 loc) · 21.9 KB
/
Reaction.cpp
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/**
* @file Reaction.cpp
*/
// This file is part of Cantera. See License.txt in the top-level directory or
// at http://www.cantera.org/license.txt for license and copyright information.
#include "cantera/kinetics/Reaction.h"
#include "cantera/kinetics/FalloffFactory.h"
#include "cantera/base/ctml.h"
#include "cantera/base/Array.h"
#include <sstream>
namespace Cantera
{
Reaction::Reaction(int type)
: reaction_type(type)
, reversible(true)
, duplicate(false)
, allow_nonreactant_orders(false)
, allow_negative_orders(false)
{
}
Reaction::Reaction(int type, const Composition& reactants_,
const Composition& products_)
: reaction_type(type)
, reactants(reactants_)
, products(products_)
, reversible(true)
, duplicate(false)
, allow_nonreactant_orders(false)
, allow_negative_orders(false)
{
}
void Reaction::validate()
{
if (!allow_nonreactant_orders) {
for (const auto& order : orders) {
if (reactants.find(order.first) == reactants.end()) {
throw CanteraError("Reaction::validate", "Reaction order "
"specified for non-reactant species '" + order.first + "'");
}
}
}
if (!allow_negative_orders) {
for (const auto& order : orders) {
if (order.second < 0.0) {
throw CanteraError("Reaction::validate", "Negative reaction "
"order specified for species '" + order.first + "'");
}
}
}
}
std::string Reaction::reactantString() const
{
std::ostringstream result;
for (auto iter = reactants.begin(); iter != reactants.end(); ++iter) {
if (iter != reactants.begin()) {
result << " + ";
}
if (iter->second != 1.0) {
result << iter->second << " ";
}
result << iter->first;
}
return result.str();
}
std::string Reaction::productString() const
{
std::ostringstream result;
for (auto iter = products.begin(); iter != products.end(); ++iter) {
if (iter != products.begin()) {
result << " + ";
}
if (iter->second != 1.0) {
result << iter->second << " ";
}
result << iter->first;
}
return result.str();
}
std::string Reaction::equation() const
{
if (reversible) {
return reactantString() + " <=> " + productString();
} else {
return reactantString() + " => " + productString();
}
}
ElementaryReaction::ElementaryReaction(const Composition& reactants_,
const Composition products_,
const Arrhenius& rate_)
: Reaction(ELEMENTARY_RXN, reactants_, products_)
, rate(rate_)
, allow_negative_pre_exponential_factor(false)
{
}
ElementaryReaction::ElementaryReaction()
: Reaction(ELEMENTARY_RXN)
, allow_negative_pre_exponential_factor(false)
{
}
void ElementaryReaction::validate()
{
Reaction::validate();
if (!allow_negative_pre_exponential_factor &&
rate.preExponentialFactor() < 0) {
throw CanteraError("ElementaryReaction::validate",
"Undeclared negative pre-exponential factor found in reaction '"
+ equation() + "'");
}
}
ThirdBody::ThirdBody(double default_eff)
: default_efficiency(default_eff)
{
}
ThreeBodyReaction::ThreeBodyReaction()
{
reaction_type = THREE_BODY_RXN;
}
ThreeBodyReaction::ThreeBodyReaction(const Composition& reactants_,
const Composition& products_,
const Arrhenius& rate_,
const ThirdBody& tbody)
: ElementaryReaction(reactants_, products_, rate_)
, third_body(tbody)
{
reaction_type = THREE_BODY_RXN;
}
std::string ThreeBodyReaction::reactantString() const {
return ElementaryReaction::reactantString() + " + M";
}
std::string ThreeBodyReaction::productString() const {
return ElementaryReaction::productString() + " + M";
}
FalloffReaction::FalloffReaction()
: Reaction(FALLOFF_RXN)
, falloff(new Falloff())
{
}
FalloffReaction::FalloffReaction(
const Composition& reactants_, const Composition& products_,
const Arrhenius& low_rate_, const Arrhenius& high_rate_,
const ThirdBody& tbody)
: Reaction(FALLOFF_RXN, reactants_, products_)
, low_rate(low_rate_)
, high_rate(high_rate_)
, third_body(tbody)
, falloff(new Falloff())
{
}
std::string FalloffReaction::reactantString() const {
if (third_body.default_efficiency == 0 &&
third_body.efficiencies.size() == 1) {
return Reaction::reactantString() + " (+" +
third_body.efficiencies.begin()->first + ")";
} else {
return Reaction::reactantString() + " (+M)";
}
}
std::string FalloffReaction::productString() const {
if (third_body.default_efficiency == 0 &&
third_body.efficiencies.size() == 1) {
return Reaction::productString() + " (+" +
third_body.efficiencies.begin()->first + ")";
} else {
return Reaction::productString() + " (+M)";
}
}
void FalloffReaction::validate() {
Reaction::validate();
if (low_rate.preExponentialFactor() < 0 ||
high_rate.preExponentialFactor() < 0) {
throw CanteraError("FalloffReaction::validate", "Negative "
"pre-exponential factor found for reaction '" + equation() + "'");
}
}
ChemicallyActivatedReaction::ChemicallyActivatedReaction()
{
reaction_type = CHEMACT_RXN;
}
ChemicallyActivatedReaction::ChemicallyActivatedReaction(
const Composition& reactants_, const Composition& products_,
const Arrhenius& low_rate_, const Arrhenius& high_rate_,
const ThirdBody& tbody)
: FalloffReaction(reactants_, products_, low_rate_, high_rate_, tbody)
{
reaction_type = CHEMACT_RXN;
}
PlogReaction::PlogReaction()
: Reaction(PLOG_RXN)
{
}
PlogReaction::PlogReaction(const Composition& reactants_,
const Composition& products_, const Plog& rate_)
: Reaction(PLOG_RXN, reactants_, products_)
, rate(rate_)
{
}
ChebyshevReaction::ChebyshevReaction()
: Reaction(CHEBYSHEV_RXN)
{
}
ChebyshevReaction::ChebyshevReaction(const Composition& reactants_,
const Composition& products_,
const ChebyshevRate& rate_)
: Reaction(CHEBYSHEV_RXN, reactants_, products_)
, rate(rate_)
{
}
InterfaceReaction::InterfaceReaction()
: is_sticking_coefficient(false)
, use_motz_wise_correction(false)
{
reaction_type = INTERFACE_RXN;
}
InterfaceReaction::InterfaceReaction(const Composition& reactants_,
const Composition& products_,
const Arrhenius& rate_,
bool isStick)
: ElementaryReaction(reactants_, products_, rate_)
, is_sticking_coefficient(isStick)
, use_motz_wise_correction(false)
{
reaction_type = INTERFACE_RXN;
}
ElectrochemicalReaction::ElectrochemicalReaction()
: film_resistivity(0.0)
, beta(0.0)
, exchange_current_density_formulation(false)
{
}
ElectrochemicalReaction::ElectrochemicalReaction(const Composition& reactants_,
const Composition& products_,
const Arrhenius& rate_)
: InterfaceReaction(reactants_, products_, rate_)
, film_resistivity(0.0)
, beta(0.0)
, exchange_current_density_formulation(false)
{
}
Arrhenius readArrhenius(const XML_Node& arrhenius_node)
{
return Arrhenius(getFloat(arrhenius_node, "A", "toSI"),
getFloat(arrhenius_node, "b"),
getFloat(arrhenius_node, "E", "actEnergy") / GasConstant);
}
//! Parse falloff parameters, given a rateCoeff node
/*!
* @verbatim
<falloff type="Troe"> 0.5 73.2 5000. 9999. </falloff>
@endverbatim
*/
void readFalloff(FalloffReaction& R, const XML_Node& rc_node)
{
XML_Node& falloff = rc_node.child("falloff");
std::vector<std::string> p;
vector_fp falloff_parameters;
getStringArray(falloff, p);
size_t np = p.size();
for (size_t n = 0; n < np; n++) {
falloff_parameters.push_back(fpValueCheck(p[n]));
}
int falloff_type = 0;
if (ba::iequals(falloff["type"], "lindemann")) {
falloff_type = SIMPLE_FALLOFF;
if (np != 0) {
throw CanteraError("readFalloff", "Lindemann parameterization "
"takes no parameters, but {} were given", np);
}
} else if (ba::iequals(falloff["type"], "troe")) {
falloff_type = TROE_FALLOFF;
if (np != 3 && np != 4) {
throw CanteraError("readFalloff", "Troe parameterization takes "
"3 or 4 parameters, but {} were given", np);
}
} else if (ba::iequals(falloff["type"], "sri")) {
falloff_type = SRI_FALLOFF;
if (np != 3 && np != 5) {
throw CanteraError("readFalloff", "SRI parameterization takes "
"3 or 5 parameters, but {} were given", np);
}
} else {
throw CanteraError("readFalloff", "Unrecognized falloff type: '{}'",
falloff["type"]);
}
R.falloff = newFalloff(falloff_type, falloff_parameters);
}
void readEfficiencies(ThirdBody& tbody, const XML_Node& rc_node)
{
if (!rc_node.hasChild("efficiencies")) {
tbody.default_efficiency = 1.0;
return;
}
const XML_Node& eff_node = rc_node.child("efficiencies");
tbody.default_efficiency = fpValue(eff_node["default"]);
tbody.efficiencies = parseCompString(eff_node.value());
}
void setupReaction(Reaction& R, const XML_Node& rxn_node)
{
// Reactant and product stoichiometries
R.reactants = parseCompString(rxn_node.child("reactants").value());
R.products = parseCompString(rxn_node.child("products").value());
// Non-stoichiometric reaction orders
std::vector<XML_Node*> orders = rxn_node.getChildren("order");
for (size_t i = 0; i < orders.size(); i++) {
R.orders[orders[i]->attrib("species")] = orders[i]->fp_value();
}
// Flags
R.id = rxn_node.attrib("id");
R.duplicate = rxn_node.hasAttrib("duplicate");
const std::string& rev = rxn_node["reversible"];
R.reversible = (rev == "true" || rev == "yes");
}
void setupElementaryReaction(ElementaryReaction& R, const XML_Node& rxn_node)
{
const XML_Node& rc_node = rxn_node.child("rateCoeff");
if (rc_node.hasChild("Arrhenius")) {
R.rate = readArrhenius(rc_node.child("Arrhenius"));
} else if (rc_node.hasChild("Arrhenius_ExchangeCurrentDensity")) {
R.rate = readArrhenius(rc_node.child("Arrhenius_ExchangeCurrentDensity"));
} else {
throw CanteraError("setupElementaryReaction", "Couldn't find Arrhenius node");
}
if (rxn_node["negative_A"] == "yes") {
R.allow_negative_pre_exponential_factor = true;
}
if (rxn_node["negative_orders"] == "yes") {
R.allow_negative_orders = true;
}
if (rxn_node["nonreactant_orders"] == "yes") {
R.allow_nonreactant_orders = true;
}
setupReaction(R, rxn_node);
}
void setupThreeBodyReaction(ThreeBodyReaction& R, const XML_Node& rxn_node)
{
readEfficiencies(R.third_body, rxn_node.child("rateCoeff"));
setupElementaryReaction(R, rxn_node);
}
void setupFalloffReaction(FalloffReaction& R, const XML_Node& rxn_node)
{
XML_Node& rc_node = rxn_node.child("rateCoeff");
std::vector<XML_Node*> rates = rc_node.getChildren("Arrhenius");
int nLow = 0;
int nHigh = 0;
for (size_t i = 0; i < rates.size(); i++) {
XML_Node& node = *rates[i];
if (node["name"] == "") {
R.high_rate = readArrhenius(node);
nHigh++;
} else if (node["name"] == "k0") {
R.low_rate = readArrhenius(node);
nLow++;
} else {
throw CanteraError("setupFalloffReaction", "Found an Arrhenius XML "
"node with an unexpected type '" + node["name"] + "'");
}
}
if (nLow != 1 || nHigh != 1) {
throw CanteraError("setupFalloffReaction", "Did not find the correct "
"number of Arrhenius rate expressions");
}
readFalloff(R, rc_node);
readEfficiencies(R.third_body, rc_node);
setupReaction(R, rxn_node);
}
void setupChemicallyActivatedReaction(ChemicallyActivatedReaction& R,
const XML_Node& rxn_node)
{
XML_Node& rc_node = rxn_node.child("rateCoeff");
std::vector<XML_Node*> rates = rc_node.getChildren("Arrhenius");
int nLow = 0;
int nHigh = 0;
for (size_t i = 0; i < rates.size(); i++) {
XML_Node& node = *rates[i];
if (node["name"] == "kHigh") {
R.high_rate = readArrhenius(node);
nHigh++;
} else if (node["name"] == "") {
R.low_rate = readArrhenius(node);
nLow++;
} else {
throw CanteraError("setupChemicallyActivatedReaction", "Found an "
"Arrhenius XML node with an unexpected type '" + node["name"] + "'");
}
}
if (nLow != 1 || nHigh != 1) {
throw CanteraError("setupChemicallyActivatedReaction", "Did not find "
"the correct number of Arrhenius rate expressions");
}
readFalloff(R, rc_node);
readEfficiencies(R.third_body, rc_node);
setupReaction(R, rxn_node);
}
void setupPlogReaction(PlogReaction& R, const XML_Node& rxn_node)
{
XML_Node& rc = rxn_node.child("rateCoeff");
std::multimap<double, Arrhenius> rates;
for (size_t m = 0; m < rc.nChildren(); m++) {
const XML_Node& node = rc.child(m);
rates.insert({getFloat(node, "P", "toSI"), readArrhenius(node)});
}
R.rate = Plog(rates);
setupReaction(R, rxn_node);
}
void PlogReaction::validate()
{
Reaction::validate();
rate.validate(equation());
}
void setupChebyshevReaction(ChebyshevReaction& R, const XML_Node& rxn_node)
{
XML_Node& rc = rxn_node.child("rateCoeff");
const XML_Node& coeff_node = rc.child("floatArray");
size_t nP = atoi(coeff_node["degreeP"].c_str());
size_t nT = atoi(coeff_node["degreeT"].c_str());
vector_fp coeffs_flat;
getFloatArray(rc, coeffs_flat, false);
Array2D coeffs(nT, nP);
for (size_t t = 0; t < nT; t++) {
for (size_t p = 0; p < nP; p++) {
coeffs(t,p) = coeffs_flat[nP*t + p];
}
}
R.rate = ChebyshevRate(getFloat(rc, "Tmin", "toSI"),
getFloat(rc, "Tmax", "toSI"),
getFloat(rc, "Pmin", "toSI"),
getFloat(rc, "Pmax", "toSI"),
coeffs);
setupReaction(R, rxn_node);
}
void setupInterfaceReaction(InterfaceReaction& R, const XML_Node& rxn_node)
{
if (ba::iequals(rxn_node["type"], "global")) {
R.reaction_type = GLOBAL_RXN;
}
XML_Node& arr = rxn_node.child("rateCoeff").child("Arrhenius");
if (ba::iequals(arr["type"], "stick")) {
R.is_sticking_coefficient = true;
R.sticking_species = arr["species"];
if (ba::iequals(arr["motz_wise"], "true")) {
R.use_motz_wise_correction = true;
} else if (ba::iequals(arr["motz_wise"], "false")) {
R.use_motz_wise_correction = false;
} else {
// Default value for all reactions
XML_Node* parent = rxn_node.parent();
if (parent && parent->name() == "reactionData"
&& ba::iequals((*parent)["motz_wise"], "true")) {
R.use_motz_wise_correction = true;
}
}
}
std::vector<XML_Node*> cov = arr.getChildren("coverage");
for (const auto& node : cov) {
CoverageDependency& cdep = R.coverage_deps[node->attrib("species")];
cdep.a = getFloat(*node, "a", "toSI");
cdep.m = getFloat(*node, "m");
cdep.E = getFloat(*node, "e", "actEnergy") / GasConstant;
}
setupElementaryReaction(R, rxn_node);
}
void setupElectrochemicalReaction(ElectrochemicalReaction& R,
const XML_Node& rxn_node)
{
// Fix reaction_type for some specialized reaction types
std::string type = ba::to_lower_copy(rxn_node["type"]);
if (type == "butlervolmer") {
R.reaction_type = BUTLERVOLMER_RXN;
} else if (type == "butlervolmer_noactivitycoeffs") {
R.reaction_type = BUTLERVOLMER_NOACTIVITYCOEFFS_RXN;
} else if (type == "surfaceaffinity") {
R.reaction_type = SURFACEAFFINITY_RXN;
} else if (type == "global") {
R.reaction_type = GLOBAL_RXN;
}
XML_Node& rc = rxn_node.child("rateCoeff");
std::string rc_type = ba::to_lower_copy(rc["type"]);
if (rc_type == "exchangecurrentdensity") {
R.exchange_current_density_formulation = true;
} else if (rc_type != "" && rc_type != "arrhenius") {
throw CanteraError("setupElectrochemicalReaction",
"Unknown rate coefficient type: '" + rc_type + "'");
}
if (rc.hasChild("Arrhenius_ExchangeCurrentDensity")) {
R.exchange_current_density_formulation = true;
}
if (rc.hasChild("electrochem") && rc.child("electrochem").hasAttrib("beta")) {
R.beta = fpValueCheck(rc.child("electrochem")["beta"]);
}
getOptionalFloat(rxn_node, "filmResistivity", R.film_resistivity);
setupInterfaceReaction(R, rxn_node);
// For Butler Volmer reactions, install the orders for the exchange current
if (R.reaction_type == BUTLERVOLMER_NOACTIVITYCOEFFS_RXN ||
R.reaction_type == BUTLERVOLMER_RXN) {
if (!R.reversible) {
throw CanteraError("setupElectrochemicalReaction",
"A Butler-Volmer reaction must be reversible");
}
R.orders.clear();
// Reaction orders based on species stoichiometric coefficients
R.allow_nonreactant_orders = true;
for (const auto& sp : R.reactants) {
R.orders[sp.first] += sp.second * (1.0 - R.beta);
}
for (const auto& sp : R.products) {
R.orders[sp.first] += sp.second * R.beta;
}
}
// For affinity reactions, fill in the global reaction formulation terms
if (rxn_node.hasChild("reactionOrderFormulation")) {
Composition initial_orders = R.orders;
R.orders.clear();
R.allow_nonreactant_orders = true;
const XML_Node& rof_node = rxn_node.child("reactionOrderFormulation");
if (ba::iequals(rof_node["model"], "reactantorders")) {
R.orders = initial_orders;
} else if (ba::iequals(rof_node["model"], "zeroorders")) {
for (const auto& sp : R.reactants) {
R.orders[sp.first] = 0.0;
}
} else if (ba::iequals(rof_node["model"], "butlervolmerorders")) {
// Reaction orders based on provided reaction orders
for (const auto& sp : R.reactants) {
double c = getValue(initial_orders, sp.first, sp.second);
R.orders[sp.first] += c * (1.0 - R.beta);
}
for (const auto& sp : R.products) {
double c = getValue(initial_orders, sp.first, sp.second);
R.orders[sp.first] += c * R.beta;
}
} else {
throw CanteraError("setupElectrochemicalReaction", "unknown model "
"for reactionOrderFormulation XML_Node: '" +
rof_node["model"] + "'");
}
}
// Override orders based on the <orders> node
if (rxn_node.hasChild("orders")) {
Composition orders = parseCompString(rxn_node.child("orders").value());
for (const auto& order : orders) {
R.orders[order.first] = order.second;
}
}
}
shared_ptr<Reaction> newReaction(const XML_Node& rxn_node)
{
std::string type = ba::to_lower_copy(rxn_node["type"]);
// Modify the reaction type for interface reactions which contain
// electrochemical reaction data
if (rxn_node.child("rateCoeff").hasChild("electrochem")
&& (type == "edge" || type == "surface")) {
type = "electrochemical";
}
// Create a new Reaction object of the appropriate type
if (type == "elementary" || type == "arrhenius" || type == "") {
auto R = make_shared<ElementaryReaction>();
setupElementaryReaction(*R, rxn_node);
return R;
} else if (type == "threebody" || type == "three_body") {
auto R = make_shared<ThreeBodyReaction>();
setupThreeBodyReaction(*R, rxn_node);
return R;
} else if (type == "falloff") {
auto R = make_shared<FalloffReaction>();
setupFalloffReaction(*R, rxn_node);
return R;
} else if (type == "chemact" || type == "chemically_activated") {
auto R = make_shared<ChemicallyActivatedReaction>();
setupChemicallyActivatedReaction(*R, rxn_node);
return R;
} else if (type == "plog" || type == "pdep_arrhenius") {
auto R = make_shared<PlogReaction>();
setupPlogReaction(*R, rxn_node);
return R;
} else if (type == "chebyshev") {
auto R = make_shared<ChebyshevReaction>();
setupChebyshevReaction(*R, rxn_node);
return R;
} else if (type == "interface" || type == "surface" || type == "edge" ||
type == "global") {
auto R = make_shared<InterfaceReaction>();
setupInterfaceReaction(*R, rxn_node);
return R;
} else if (type == "electrochemical" ||
type == "butlervolmer_noactivitycoeffs" ||
type == "butlervolmer" ||
type == "surfaceaffinity") {
auto R = make_shared<ElectrochemicalReaction>();
setupElectrochemicalReaction(*R, rxn_node);
return R;
} else {
throw CanteraError("newReaction",
"Unknown reaction type '" + rxn_node["type"] + "'");
}
}
std::vector<shared_ptr<Reaction> > getReactions(const XML_Node& node)
{
std::vector<shared_ptr<Reaction> > all_reactions;
for (const auto& rxnnode : node.child("reactionData").getChildren("reaction")) {
all_reactions.push_back(newReaction(*rxnnode));
}
return all_reactions;
}
}