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refactor(reaction): refactored to an abstract reaction class in prep for weak reactions

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This commit is contained in:
Emily Boudreaux
2025-08-14 13:33:46 -04:00
parent d920a55ba6
commit 0b77f2e269
81 changed files with 1050041 additions and 913 deletions
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54
src/include/gridfire/engine/engine_graph.h
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@@ -25,16 +25,10 @@
#include "cppad/utility/sparse_rc.hpp"
#include "cppad/speed/sparse_jac_fun.hpp"
#include "procedures/priming.h"
#include "quill/LogMacros.h"
// PERF: The function getNetReactionStoichiometry returns a map of species to their stoichiometric coefficients for a given reaction.
// this makes extra copies of the species, which is not ideal and could be optimized further.
// Even more relevant is the member m_reactionIDMap which makes copies of a REACLIBReaction for each reaction ID.
// REACLIBReactions are quite large data structures, so this could be a performance bottleneck.
// static bool isF17 = false;
namespace gridfire {
/**
* @brief Alias for CppAD AD type for double precision.
@@ -128,7 +122,7 @@ namespace gridfire {
* This constructor uses the given set of reactions to construct the
* reaction network.
*/
explicit GraphEngine(const reaction::LogicalReactionSet &reactions);
explicit GraphEngine(const reaction::ReactionSet &reactions);
/**
* @brief Calculates the right-hand side (dY/dt) and energy generation rate.
@@ -212,9 +206,9 @@ namespace gridfire {
* @brief Gets the set of logical reactions in the network.
* @return Reference to the LogicalReactionSet containing all reactions.
*/
[[nodiscard]] const reaction::LogicalReactionSet& getNetworkReactions() const override;
[[nodiscard]] const reaction::ReactionSet& getNetworkReactions() const override;
void setNetworkReactions(const reaction::LogicalReactionSet& reactions) override;
void setNetworkReactions(const reaction::ReactionSet& reactions) override;
/**
* @brief Gets an entry from the previously generated Jacobian matrix.
@@ -394,6 +388,8 @@ namespace gridfire {
*
* @param reaction The reaction for which to calculate the reverse rate.
* @param T9 Temperature in units of 10^9 K.
* @param rho
* @param Y
* @return Reverse rate for the reaction (e.g., mol/g/s).
*
* This method computes the reverse rate based on the forward rate and
@@ -401,7 +397,7 @@ namespace gridfire {
*/
[[nodiscard]] double calculateReverseRate(
const reaction::Reaction &reaction,
double T9
double T9, double rho, const std::vector<double> &Y
) const;
/**
@@ -426,7 +422,7 @@ namespace gridfire {
[[nodiscard]] double calculateReverseRateTwoBodyDerivative(
const reaction::Reaction &reaction,
const double T9,
const double reverseRate
double rho, const std::vector<double> &Y, const double reverseRate
) const;
/**
@@ -458,8 +454,8 @@ namespace gridfire {
* This method returns the index of the given species in the network's
* species vector. If the species is not found, it returns -1.
*/
[[nodiscard]] int getSpeciesIndex(
const fourdst::atomic::Species& species
[[nodiscard]] size_t getSpeciesIndex(
const fourdst::atomic::Species &species
) const override;
/**
@@ -574,7 +570,7 @@ namespace gridfire {
constants m_constants;
reaction::LogicalReactionSet m_reactions; ///< Set of REACLIB reactions in the network.
reaction::ReactionSet m_reactions; ///< Set of REACLIB reactions in the network.
std::unordered_map<std::string_view, reaction::Reaction*> m_reactionIDMap; ///< Map from reaction ID to REACLIBReaction. //PERF: This makes copies of REACLIBReaction and could be a performance bottleneck.
std::vector<fourdst::atomic::Species> m_networkSpecies; ///< Vector of unique species in the network.
@@ -654,7 +650,7 @@ namespace gridfire {
*
* @throws std::runtime_error If there are no species in the network.
*/
void recordADTape();
void recordADTape() const;
void collectAtomicReverseRateAtomicBases();
@@ -708,7 +704,7 @@ namespace gridfire {
std::vector<T> screeningFactors,
std::vector<T> Y,
size_t reactionIndex,
const reaction::LogicalReaction &reaction
const reaction::Reaction &reaction
) const;
/**
@@ -776,7 +772,7 @@ namespace gridfire {
std::vector<T> screeningFactors,
std::vector<T> Y,
size_t reactionIndex,
const reaction::LogicalReaction &reaction
const reaction::Reaction &reaction
) const {
if (!m_useReverseReactions) {
return static_cast<T>(0.0); // If reverse reactions are not used, return zero
@@ -800,7 +796,7 @@ namespace gridfire {
}
} else {
// A,B If not calling with an AD type, calculate the reverse rate directly
reverseRateConstant = calculateReverseRate(reaction, T9);
reverseRateConstant = calculateReverseRate(reaction, T9, 0, {});
}
// C. Get product multiplicities
@@ -888,14 +884,18 @@ namespace gridfire {
calculateMolarReactionFlow<T>(reaction, Y, T9, rho);
// 2. Calculate reverse reaction rate
T reverseMolarFlow = calculateReverseMolarReactionFlow<T>(
T9,
rho,
screeningFactors,
Y,
reactionIndex,
reaction
);
T reverseMolarFlow = static_cast<T>(0.0);
// Do not calculate reverse flow for weak reactions
if (reaction.type() == reaction::ReactionType::LOGICAL_REACLIB || reaction.type() == reaction::ReactionType::REACLIB) {
reverseMolarFlow = calculateReverseMolarReactionFlow<T>(
T9,
rho,
screeningFactors,
Y,
reactionIndex,
reaction
);
}
const T molarReactionFlow = forwardMolarReactionFlow - reverseMolarFlow; // Net molar reaction flow
@@ -930,7 +930,7 @@ namespace gridfire {
const T zero = static_cast<T>(0.0);
// --- Calculate the molar reaction rate (in units of [s^-1][cm^3(N-1)][mol^(1-N)] for N reactants) ---
const T k_reaction = reaction.calculate_rate(T9);
const T k_reaction = reaction.calculate_rate(T9, rho, Y);
// --- Cound the number of each reactant species to account for species multiplicity ---
std::unordered_map<std::string, int> reactant_counts;