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[Kinetics] Detection and serialization of Reaction edge cases
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@ischoegl @speth
ischoegl authored and speth committed Jul 24, 2022
1 parent 55b7b0f commit 451dd75
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Showing 2 changed files with 78 additions and 26 deletions.
9 changes: 7 additions & 2 deletions include/cantera/kinetics/Reaction.h
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Original file line number Diff line number Diff line change
Expand Up @@ -195,7 +195,10 @@ class Reaction
bool m_valid = true;

//! Flag indicating that serialization uses explicit type
bool m_explicit_rate = false;
bool m_explicit_type = false;

//! Flag indicating that third body collider is ambiguous
bool m_explicit_3rd = false;

//! Flag indicating that object was instantiated from reactant/product compositions
bool m_from_composition = false;
Expand Down Expand Up @@ -239,8 +242,10 @@ class ThirdBody
void setParameters(const AnyMap& node);

//! Get third-body efficiencies from AnyMap *node*
//! @param node AnyMap receiving serialized parameters
//! @param explicit_3rd Flag triggering explicit third body efficiency output
//! @since New in Cantera 3.0
void getParameters(AnyMap& node) const;
void getParameters(AnyMap& node, bool explicit_3rd=false) const;

//! Get the third-body efficiency for species *k*
double efficiency(const std::string& k) const;
Expand Down
95 changes: 71 additions & 24 deletions src/kinetics/Reaction.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -37,18 +37,19 @@ Reaction::Reaction(const Composition& reactants_,
, m_third_body(tbody_)
{
setRate(rate_);
if (tbody_ && tbody_->name() != "M") {
// ensure safe serialization
size_t count = 0;
for (const auto& reac : reactants) {
if (products.count(reac.first)) {
count++;
}

// ensure safe serialization
size_t count = 0;
for (const auto& reac : reactants) {
if (products.count(reac.first)) {
count++;
}
if (count) {
throw CanteraError("Reaction::Reaction",
"Not implemented: reaction '{}'\n"
"contains multiple explicit third body colliders", equation());
}
if (count) {
if (tbody_ && tbody_->name() != "M") {
m_explicit_3rd = true;
} else if (!tbody_) {
m_explicit_type = true;
}
}
}
Expand Down Expand Up @@ -185,7 +186,7 @@ void Reaction::getParameters(AnyMap& reactionNode) const
std::string rtype = reactionNode["type"].asString();
if (rtype == "pressure-dependent-Arrhenius") {
// skip
} else if (m_explicit_rate && ba::ends_with(rtype, "Arrhenius")) {
} else if (m_explicit_type && ba::ends_with(rtype, "Arrhenius")) {
// retain type information
if (m_third_body) {
reactionNode["type"] = "three-body";
Expand All @@ -194,14 +195,14 @@ void Reaction::getParameters(AnyMap& reactionNode) const
}
} else if (ba::ends_with(rtype, "Arrhenius")) {
reactionNode.erase("type");
} else if (m_explicit_rate) {
} else if (m_explicit_type) {
reactionNode["type"] = type();
} else if (ba::ends_with(rtype, "Blowers-Masel")) {
reactionNode["type"] = "Blowers-Masel";
}

if (m_third_body) {
m_third_body->getParameters(reactionNode);
m_third_body->getParameters(reactionNode, m_explicit_3rd);
}
}

Expand Down Expand Up @@ -232,7 +233,11 @@ void Reaction::setParameters(const AnyMap& node, const Kinetics& kin)
allow_nonreactant_orders = node.getBool("nonreactant-orders", false);

if (m_third_body) {
m_third_body->setParameters(node);
try {
m_third_body->setParameters(node);
} catch (CanteraError& err) {
throw InputFileError("Reaction::setParameters", input, err.getMessage());
}
} else if (node.hasKey("default-efficiency") || node.hasKey("efficiencies")) {
throw InputFileError("Reaction::setParameters", input,
"Reaction '{}' specifies efficiency parameters\n"
Expand Down Expand Up @@ -334,10 +339,10 @@ void Reaction::setEquation(const std::string& equation, const Kinetics* kin)
std::string rate_type = input.getString("type", "");
if (ba::starts_with(rate_type, "three-body")) {
// state type when serializing
m_explicit_rate = true;
m_explicit_type = true;
} else if (rate_type == "elementary") {
// user override
m_explicit_rate = true;
m_explicit_type = true;
return;
} else if (kin && kin->thermo(kin->reactionPhaseIndex()).nDim() != 3) {
// interface reactions
Expand Down Expand Up @@ -378,15 +383,44 @@ void Reaction::setEquation(const std::string& equation, const Kinetics* kin)
// equations with more than one explicit third-body collider are handled as a
// regular elementary reaction unless the equation contains a generic third body
if (countM) {
// skip
third_body = "M";
} else if (m_third_body) {
// third body is defined as explicit object
auto& effs = m_third_body->efficiencies;
if (effs.size() != 1
|| reactants.find(effs.begin()->first) == reactants.end())
{
throw InputFileError("Reaction::setEquation", input,
"Detected ambiguous third body colliders in reaction '{}'\n"
"ThirdBody definition is not valid", equation);
}
third_body = effs.begin()->first;
m_explicit_3rd = true;
} else if (input.hasKey("efficiencies") && input.hasKey("default-efficiency")) {
// third body is implicity defined by efficiency
auto effs = input["efficiencies"].asMap<double>();
if (effs.size() != 1
|| reactants.find(effs.begin()->first) == reactants.end())
{
throw InputFileError("Reaction::setEquation", input,
"Detected ambigous third body colliders in reaction '{}'\n"
"Invalid ThirdBody definition", equation);
}
third_body = effs.begin()->first;
m_explicit_3rd = true;
} else if (ba::starts_with(rate_type, "three-body")) {
// no disambiguation of third bodies
throw InputFileError("Reaction::setEquation", input,
"Detected ambigous third body colliders in reaction '{}'\n"
"A valid ThirdBody definition is required", equation);
} else if (input.hasKey("efficiencies") || input.hasKey("default-efficiency")) {
// insufficient disambiguation of third bodies
throw InputFileError("Reaction::setEquation", input,
"Not implemented: reaction '{}'\n"
"contains multiple explicit third body colliders", equation);
"Detected ambigous third body colliders in reaction '{}'\n"
"A complete ThirdBody definition is required", equation);
} else {
return;
}
third_body = "M";

} else if (third_body != "M" && !ba::starts_with(rate_type, "three-body")
&& !ba::starts_with(third_body, "(+"))
Expand Down Expand Up @@ -420,7 +454,14 @@ void Reaction::setEquation(const std::string& equation, const Kinetics* kin)
}

if (m_third_body) {
m_third_body->setName(third_body);
std::string tName = m_third_body->name();
if (tName == "M") {
m_third_body->setName(third_body);
} else if (tName != third_body) {
throw InputFileError("Reaction::setEquation", input,
"Detected incompatible third body colliders in reaction '{}'\n"
"ThirdBody definition does not match equation", equation);
}
} else {
m_third_body.reset(new ThirdBody(third_body));
}
Expand Down Expand Up @@ -719,11 +760,17 @@ void ThirdBody::setParameters(const AnyMap& node)
if (node.hasKey("efficiencies")) {
efficiencies = node["efficiencies"].asMap<double>();
}
if (m_name != "M"
&& (efficiencies.size() != 1 || efficiencies.begin()->first != m_name))
{
throw CanteraError("Reaction::setEquation",
"Detected incompatible third body colliders definitions");
}
}

void ThirdBody::getParameters(AnyMap& node) const
void ThirdBody::getParameters(AnyMap& node, bool explicit_3rd) const
{
if (m_name == "M") {
if (m_name == "M" || explicit_3rd) {
if (efficiencies.size()) {
node["efficiencies"] = efficiencies;
node["efficiencies"].setFlowStyle();
Expand Down

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