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reaction.cpp
Go to the documentation of this file.
#include "gridfire/reaction/reaction.h"
#include<string_view>
#include<string>
#include<vector>
#include<unordered_set>
#include<algorithm>
#include <ranges>
#include "quill/LogMacros.h"
#include "fourdst/composition/atomicSpecies.h"
#include "xxhash64.h"
namespace gridfire::reaction {
using namespace fourdst::atomic;
Reaction::Reaction(
const std::string_view id,
const std::string_view peName,
const int chapter,
const std::vector<Species>& reactants,
const std::vector<Species>& products,
const double qValue,
const std::string_view label,
const RateCoefficientSet& sets,
const bool reverse) :
m_id(id),
m_peName(peName),
m_chapter(chapter),
m_qValue(qValue),
m_reactants(reactants),
m_products(products),
m_sourceLabel(label),
m_rateCoefficients(sets),
m_reverse(reverse) {}
double Reaction::calculate_rate(const double T9) const {
return calculate_rate<double>(T9);
}
CppAD::AD<double> Reaction::calculate_rate(const CppAD::AD<double> T9) const {
return calculate_rate<CppAD::AD<double>>(T9);
}
double Reaction::calculate_forward_rate_log_derivative(const double T9) const {
constexpr double r_p13 = 1.0 / 3.0;
constexpr double r_p53 = 5.0 / 3.0;
constexpr double r_p23 = 2.0 / 3.0;
constexpr double r_p43 = 4.0 / 3.0;
const double T9_m1 = 1.0 / T9;
const double T9_m23 = std::pow(T9, -r_p23);
const double T9_m43 = std::pow(T9, -r_p43);
const double d_log_k_fwd_dT9 =
-m_rateCoefficients.a1 * T9_m1 * T9_m1
- r_p13 * m_rateCoefficients.a2 * T9_m43
+ r_p13 * m_rateCoefficients.a3 * T9_m23
+ m_rateCoefficients.a4
+ r_p53 * m_rateCoefficients.a5 * std::pow(T9, r_p23)
+ m_rateCoefficients.a6 * T9_m1;
return d_log_k_fwd_dT9; // Return the derivative of the log rate with respect to T9
}
bool Reaction::contains(const Species &species) const {
return contains_reactant(species) || contains_product(species);
}
bool Reaction::contains_reactant(const Species& species) const {
for (const auto& reactant : m_reactants) {
if (reactant == species) {
return true;
}
}
return false;
}
bool Reaction::contains_product(const Species& species) const {
for (const auto& product : m_products) {
if (product == species) {
return true;
}
}
return false;
}
std::unordered_set<Species> Reaction::all_species() const {
auto rs = reactant_species();
auto ps = product_species();
rs.insert(ps.begin(), ps.end());
return rs;
}
std::unordered_set<Species> Reaction::reactant_species() const {
std::unordered_set<Species> reactantsSet;
for (const auto& reactant : m_reactants) {
reactantsSet.insert(reactant);
}
return reactantsSet;
}
std::unordered_set<Species> Reaction::product_species() const {
std::unordered_set<Species> productsSet;
for (const auto& product : m_products) {
productsSet.insert(product);
}
return productsSet;
}
int Reaction::stoichiometry(const Species& species) const {
int s = 0;
for (const auto& reactant : m_reactants) {
if (reactant == species) {
s--;
}
}
for (const auto& product : m_products) {
if (product == species) {
s++;
}
}
return s;
}
size_t Reaction::num_species() const {
return all_species().size();
}
std::unordered_map<Species, int> Reaction::stoichiometry() const {
std::unordered_map<Species, int> stoichiometryMap;
for (const auto& reactant : m_reactants) {
stoichiometryMap[reactant]--;
}
for (const auto& product : m_products) {
stoichiometryMap[product]++;
}
return stoichiometryMap;
}
double Reaction::excess_energy() const {
double reactantMass = 0.0;
double productMass = 0.0;
constexpr double AMU2MeV = 931.494893; // Conversion factor from atomic mass unit to MeV
for (const auto& reactant : m_reactants) {
reactantMass += reactant.mass();
}
for (const auto& product : m_products) {
productMass += product.mass();
}
return (reactantMass - productMass) * AMU2MeV;
}
uint64_t Reaction::hash(const uint64_t seed) const {
return XXHash64::hash(m_id.data(), m_id.size(), seed);
}
LogicalReaction::LogicalReaction(const std::vector<Reaction>& reactants) :
Reaction(reactants.front().peName(),
reactants.front().peName(),
reactants.front().chapter(),
reactants.front().reactants(),
reactants.front().products(),
reactants.front().qValue(),
reactants.front().sourceLabel(),
reactants.front().rateCoefficients(),
reactants.front().is_reverse()) {
m_sources.reserve(reactants.size());
m_rates.reserve(reactants.size());
for (const auto& reaction : reactants) {
if (std::abs(std::abs(reaction.qValue()) - std::abs(m_qValue)) > 1e-6) {
LOG_ERROR(
m_logger,
"LogicalReaction constructed with reactions having different Q-values. Expected {} got {}.",
m_qValue,
reaction.qValue()
);
m_logger -> flush_log();
throw std::runtime_error("LogicalReaction constructed with reactions having different Q-values. Expected " + std::to_string(m_qValue) + " got " + std::to_string(reaction.qValue()) + " (difference : " + std::to_string(std::abs(reaction.qValue() - m_qValue)) + ").");
}
m_sources.push_back(std::string(reaction.sourceLabel()));
m_rates.push_back(reaction.rateCoefficients());
}
}
void LogicalReaction::add_reaction(const Reaction& reaction) {
if (reaction.peName() != m_id) {
LOG_ERROR(m_logger, "Cannot add reaction with different peName to LogicalReaction. Expected {} got {}.", m_id, reaction.peName());
m_logger -> flush_log();
throw std::runtime_error("Cannot add reaction with different peName to LogicalReaction. Expected " + std::string(m_id) + " got " + std::string(reaction.peName()) + ".");
}
for (const auto& source : m_sources) {
if (source == reaction.sourceLabel()) {
LOG_ERROR(m_logger, "Cannot add reaction with duplicate source label {} to LogicalReaction.", reaction.sourceLabel());
m_logger -> flush_log();
throw std::runtime_error("Cannot add reaction with duplicate source label " + std::string(reaction.sourceLabel()) + " to LogicalReaction.");
}
}
if (std::abs(reaction.qValue() - m_qValue) > 1e-6) {
LOG_ERROR(m_logger, "LogicalReaction constructed with reactions having different Q-values. Expected {} got {}.", m_qValue, reaction.qValue());
m_logger -> flush_log();
throw std::runtime_error("LogicalReaction constructed with reactions having different Q-values. Expected " + std::to_string(m_qValue) + " got " + std::to_string(reaction.qValue()) + ".");
}
m_sources.push_back(std::string(reaction.sourceLabel()));
m_rates.push_back(reaction.rateCoefficients());
}
double LogicalReaction::calculate_rate(const double T9) const {
return calculate_rate<double>(T9);
}
double LogicalReaction::calculate_forward_rate_log_derivative(const double T9) const {
constexpr double r_p13 = 1.0 / 3.0;
constexpr double r_p53 = 5.0 / 3.0;
constexpr double r_p23 = 2.0 / 3.0;
constexpr double r_p43 = 4.0 / 3.0;
double totalRate = 0.0;
double totalRateDerivative = 0.0;
const double T9_m1 = 1.0 / T9;
const double T913 = std::pow(T9, r_p13);
const double T953 = std::pow(T9, r_p53);
const double logT9 = std::log(T9);
const double T9_m1_sq = T9_m1 * T9_m1;
const double T9_m23 = std::pow(T9, -r_p23);
const double T9_m43 = std::pow(T9, -r_p43);
const double T9_p23 = std::pow(T9, r_p23);
for (const auto& coeffs : m_rates) {
const double exponent = coeffs.a0 +
coeffs.a1 * T9_m1 +
coeffs.a2 / T913 +
coeffs.a3 * T913 +
coeffs.a4 * T9 +
coeffs.a5 * T953 +
coeffs.a6 * logT9;
const double individualRate = std::exp(exponent);
const double d_exponent_T9 =
-coeffs.a1 * T9_m1_sq
- r_p13 * coeffs.a2 * T9_m43
+ r_p13 * coeffs.a3 * T9_m23
+ coeffs.a4
+ r_p53 * coeffs.a5 * T9_p23
+ coeffs.a6 * T9_m1;
const double individualRateDerivative = individualRate * d_exponent_T9;
totalRate += individualRate;
totalRateDerivative += individualRateDerivative;
}
if (totalRate == 0.0) {
return 0.0; // Avoid division by zero
}
return totalRateDerivative / totalRate;
}
CppAD::AD<double> LogicalReaction::calculate_rate(const CppAD::AD<double> T9) const {
return calculate_rate<CppAD::AD<double>>(T9);
}
LogicalReactionSet packReactionSetToLogicalReactionSet(const ReactionSet& reactionSet) {
std::unordered_map<std::string_view, std::vector<Reaction>> groupedReactions;
for (const auto& reaction: reactionSet) {
groupedReactions[reaction.peName()].push_back(reaction);
}
std::vector<LogicalReaction> reactions;
reactions.reserve(groupedReactions.size());
for (const auto &reactionsGroup: groupedReactions | std::views::values) {
LogicalReaction logicalReaction(reactionsGroup);
reactions.push_back(logicalReaction);
}
return LogicalReactionSet(std::move(reactions));
}
}
namespace std {
template<>
struct hash<gridfire::reaction::Reaction> {
size_t operator()(const gridfire::reaction::Reaction& r) const noexcept {
return r.hash(0);
}
};
template<>
struct hash<gridfire::reaction::ReactionSet> {
size_t operator()(const gridfire::reaction::ReactionSet& s) const noexcept {
return s.hash(0);
}
};
template<>
struct hash<gridfire::reaction::LogicalReactionSet> {
size_t operator()(const gridfire::reaction::LogicalReactionSet& s) const noexcept {
return s.hash(0);
}
};
} // namespace std
gridfire::reaction::LogicalReaction
Represents a "logical" reaction that aggregates rates from multiple sources.
Definition reaction.h:310
gridfire::reaction::LogicalReaction::add_reaction
void add_reaction(const Reaction &reaction)
Adds another Reaction source to this logical reaction.
Definition reaction.cpp:192
gridfire::reaction::LogicalReaction::calculate_rate
double calculate_rate(const double T9) const override
Calculates the total reaction rate by summing all source rates.
Definition reaction.cpp:214
gridfire::reaction::LogicalReaction::LogicalReaction
LogicalReaction(const std::vector< Reaction > &reactions)
Constructs a LogicalReaction from a vector of Reaction objects.
Definition reaction.cpp:163
gridfire::reaction::LogicalReaction::m_sources
std::vector< std::string > m_sources
List of source labels.
Definition reaction.h:372
gridfire::reaction::LogicalReaction::m_rates
std::vector< RateCoefficientSet > m_rates
List of rate coefficient sets from each source.
Definition reaction.h:373
gridfire::reaction::LogicalReaction::calculate_forward_rate_log_derivative
virtual double calculate_forward_rate_log_derivative(const double T9) const override
Definition reaction.cpp:218
gridfire::reaction::Reaction
Represents a single nuclear reaction from a specific data source.
Definition reaction.h:72
gridfire::reaction::Reaction::m_sourceLabel
std::string m_sourceLabel
Source label for the rate data (e.g., "wc12w", "st08").
Definition reaction.h:270
gridfire::reaction::Reaction::product_species
std::unordered_set< fourdst::atomic::Species > product_species() const
Gets a set of all unique product species.
Definition reaction.cpp:106
gridfire::reaction::Reaction::contains_product
bool contains_product(const fourdst::atomic::Species &species) const
Checks if the reaction involves a given species as a product.
Definition reaction.cpp:82
gridfire::reaction::Reaction::id
std::string_view id() const
Gets the unique identifier of the reaction.
Definition reaction.h:204
gridfire::reaction::Reaction::m_reverse
bool m_reverse
Flag indicating if this is a reverse reaction rate.
Definition reaction.h:272
gridfire::reaction::Reaction::reactants
const std::vector< fourdst::atomic::Species > & reactants() const
Gets the vector of reactant species.
Definition reaction.h:216
gridfire::reaction::Reaction::m_chapter
int m_chapter
Chapter number from the REACLIB database, defining the reaction structure.
Definition reaction.h:266
gridfire::reaction::Reaction::num_species
size_t num_species() const
Gets the number of unique species involved in the reaction.
Definition reaction.cpp:129
gridfire::reaction::Reaction::calculate_forward_rate_log_derivative
virtual double calculate_forward_rate_log_derivative(const double T9) const
Definition reaction.cpp:47
gridfire::reaction::Reaction::sourceLabel
std::string_view sourceLabel() const
Gets the source label for the rate data.
Definition reaction.h:134
gridfire::reaction::Reaction::m_products
std::vector< fourdst::atomic::Species > m_products
Products of the reaction.
Definition reaction.h:269
gridfire::reaction::Reaction::m_qValue
double m_qValue
Q-value of the reaction in MeV.
Definition reaction.h:267
gridfire::reaction::Reaction::m_id
std::string m_id
Unique identifier for the reaction (e.g., "h1+h1=>h2+e+nu").
Definition reaction.h:264
gridfire::reaction::Reaction::chapter
int chapter() const
Gets the REACLIB chapter number.
Definition reaction.h:128
gridfire::reaction::Reaction::m_peName
std::string m_peName
Name of the reaction in (projectile, ejectile) notation (e.g. "p(p,g)d").
Definition reaction.h:265
gridfire::reaction::Reaction::products
const std::vector< fourdst::atomic::Species > & products() const
Gets the vector of product species.
Definition reaction.h:222
gridfire::reaction::Reaction::m_logger
quill::Logger * m_logger
Definition reaction.h:263
gridfire::reaction::Reaction::peName
virtual std::string_view peName() const
Gets the reaction name in (projectile, ejectile) notation.
Definition reaction.h:122
gridfire::reaction::Reaction::all_species
std::unordered_set< fourdst::atomic::Species > all_species() const
Gets a set of all unique species involved in the reaction.
Definition reaction.cpp:91
gridfire::reaction::Reaction::Reaction
Reaction(const std::string_view id, const std::string_view peName, const int chapter, const std::vector< fourdst::atomic::Species > &reactants, const std::vector< fourdst::atomic::Species > &products, const double qValue, const std::string_view label, const RateCoefficientSet &sets, const bool reverse=false)
Constructs a Reaction object.
Definition reaction.cpp:19
gridfire::reaction::Reaction::reactant_species
std::unordered_set< fourdst::atomic::Species > reactant_species() const
Gets a set of all unique reactant species.
Definition reaction.cpp:98
gridfire::reaction::Reaction::rateCoefficients
const RateCoefficientSet & rateCoefficients() const
Gets the set of rate coefficients.
Definition reaction.h:140
gridfire::reaction::Reaction::m_reactants
std::vector< fourdst::atomic::Species > m_reactants
Reactants of the reaction.
Definition reaction.h:268
gridfire::reaction::Reaction::excess_energy
double excess_energy() const
Calculates the excess energy from the mass difference of reactants and products.
Definition reaction.cpp:144
gridfire::reaction::Reaction::m_rateCoefficients
RateCoefficientSet m_rateCoefficients
The seven rate coefficients.
Definition reaction.h:271
gridfire::reaction::Reaction::is_reverse
bool is_reverse() const
Checks if this is a reverse reaction rate.
Definition reaction.h:228
gridfire::reaction::Reaction::contains
bool contains(const fourdst::atomic::Species &species) const
Checks if the reaction involves a given species as a reactant or product.
Definition reaction.cpp:68
gridfire::reaction::Reaction::contains_reactant
bool contains_reactant(const fourdst::atomic::Species &species) const
Checks if the reaction involves a given species as a reactant.
Definition reaction.cpp:73
gridfire::reaction::Reaction::qValue
double qValue() const
Gets the Q-value of the reaction.
Definition reaction.h:210
gridfire::reaction::Reaction::stoichiometry
std::unordered_map< fourdst::atomic::Species, int > stoichiometry() const
Gets a map of all species to their stoichiometric coefficients.
Definition reaction.cpp:133
gridfire::reaction::Reaction::calculate_rate
virtual double calculate_rate(const double T9) const
Calculates the reaction rate for a given temperature.
Definition reaction.cpp:39
gridfire::reaction::Reaction::hash
uint64_t hash(uint64_t seed=0) const
Computes a hash for the reaction based on its ID.
Definition reaction.cpp:157
gridfire::reaction
Definition reaction.h:25
gridfire::reaction::LogicalReactionSet
TemplatedReactionSet< LogicalReaction > LogicalReactionSet
A set of logical reactions.
Definition reaction.h:563
gridfire::reaction::packReactionSetToLogicalReactionSet
LogicalReactionSet packReactionSetToLogicalReactionSet(const ReactionSet &reactionSet)
Definition reaction.cpp:273
gridfire::reaction::ReactionSet
TemplatedReactionSet< Reaction > ReactionSet
A set of reactions, typically from a single source like REACLIB.
Definition reaction.h:562
gridfire
Definition engine_abstract.h:31
std
STL namespace.
reaction.h
Defines classes for representing and managing nuclear reactions.
gridfire::reaction::RateCoefficientSet
Holds the seven coefficients for the REACLIB rate equation.
Definition reaction.h:33
std::hash< gridfire::reaction::LogicalReactionSet >::operator()
size_t operator()(const gridfire::reaction::LogicalReactionSet &s) const noexcept
Definition reaction.cpp:308
std::hash< gridfire::reaction::Reaction >::operator()
size_t operator()(const gridfire::reaction::Reaction &r) const noexcept
Definition reaction.cpp:294
std::hash< gridfire::reaction::ReactionSet >::operator()
size_t operator()(const gridfire::reaction::ReactionSet &s) const noexcept
Definition reaction.cpp:301