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feat(weak): major weak rate progress

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Major weak rate progress which includes: A refactor of many of the public interfaces for GridFire Engines to use composition objects as opposed to raw abundance vectors. This helps prevent index mismatch errors. Further, the weak reaction class has been expanded with the majority of an implimentation, including an atomic_base derived class to allow for proper auto diff tracking of the interpolated table results. Some additional changes are that the version of fourdst and libcomposition have been bumped to versions with smarter caching of intermediate vectors and a few bug fixes.
This commit is contained in:
Emily Boudreaux
2025-10-07 15:16:03 -04:00
parent 4f1c260444
commit 8a0b5b2c36
53 changed files with 2310 additions and 1759 deletions
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87
src/include/gridfire/engine/views/engine_adaptive.h
View File

@@ -88,7 +88,7 @@ namespace gridfire {
/**
* @brief Calculates the right-hand side (dY/dt) and energy generation for the active species.
*
* @param Y_culled A vector of abundances for the active species.
* @param comp The current composition of the system.
* @param T9 The temperature in units of 10^9 K.
* @param rho The density in g/cm^3.
* @return A StepDerivatives struct containing the derivatives of the active species and the
@@ -102,21 +102,29 @@ namespace gridfire {
* @see AdaptiveEngineView::update()
*/
[[nodiscard]] std::expected<StepDerivatives<double>, expectations::StaleEngineError> calculateRHSAndEnergy(
const std::vector<double> &Y_culled,
const double T9,
const double rho
const fourdst::composition::Composition& comp,
double T9,
double rho
) const override;
/**
*
* @param comp The current composition of the system.
* @param T9 The temperature in units of 10^9 K.
* @param rho The density in g/cm^3.
* @return A struct containing the derivatives of the energy generation rate with respect to temperature and density.
*/
[[nodiscard]] EnergyDerivatives calculateEpsDerivatives(
const std::vector<double> &Y_culled,
const double T9,
const double rho
const fourdst::composition::Composition& comp,
double T9,
double rho
) const override;
/**
* @brief Generates the Jacobian matrix for the active species.
*
* @param Y_dynamic A vector of abundances for the active species.
* @param comp The current composition of the system.
* @param T9 The temperature in units of 10^9 K.
* @param rho The density in g/cm^3.
*
@@ -127,16 +135,16 @@ namespace gridfire {
* @see AdaptiveEngineView::update()
*/
void generateJacobianMatrix(
const std::vector<double> &Y_dynamic,
const double T9,
const double rho
const fourdst::composition::Composition &comp,
double T9,
double rho
) const override;
/**
* @brief Gets an entry from the Jacobian matrix for the active species.
*
* @param i_culled The row index (species index) in the culled matrix.
* @param j_culled The column index (species index) in the culled matrix.
* @param rowSpecies The species corresponding to the row index in the culled species list.
* @param colSpecies The species corresponding to the column index in the culled species list
* @return The value of the Jacobian matrix at (i_culled, j_culled).
*
* This method maps the culled indices to the full network indices and calls the base engine
@@ -147,8 +155,8 @@ namespace gridfire {
* @see AdaptiveEngineView::update()
*/
[[nodiscard]] double getJacobianMatrixEntry(
const int i_culled,
const int j_culled
const fourdst::atomic::Species& rowSpecies,
const fourdst::atomic::Species& colSpecies
) const override;
/**
@@ -165,8 +173,8 @@ namespace gridfire {
/**
* @brief Gets an entry from the stoichiometry matrix for the active species and reactions.
*
* @param speciesIndex_culled The index of the species in the culled species list.
* @param reactionIndex_culled The index of the reaction in the culled reaction list.
* @param species The species for which to get the stoichiometric coefficient.
* @param reaction The reaction for which to get the stoichiometric coefficient.
* @return The stoichiometric coefficient for the given species and reaction.
*
* This method maps the culled indices to the full network indices and calls the base engine
@@ -177,15 +185,15 @@ namespace gridfire {
* @see AdaptiveEngineView::update()
*/
[[nodiscard]] int getStoichiometryMatrixEntry(
const int speciesIndex_culled,
const int reactionIndex_culled
const fourdst::atomic::Species& species,
const reaction::Reaction& reaction
) const override;
/**
* @brief Calculates the molar reaction flow for a given reaction in the active network.
*
* @param reaction The reaction for which to calculate the flow.
* @param Y_culled Vector of current abundances for the active species.
* @param comp Composition object containing current abundances.
* @param T9 Temperature in units of 10^9 K.
* @param rho Density in g/cm^3.
* @return Molar flow rate for the reaction (e.g., mol/g/s).
@@ -198,7 +206,7 @@ namespace gridfire {
*/
[[nodiscard]] double calculateMolarReactionFlow(
const reaction::Reaction &reaction,
const std::vector<double> &Y_culled,
const fourdst::composition::Composition &comp,
double T9,
double rho
) const override;
@@ -215,7 +223,7 @@ namespace gridfire {
/**
* @brief Computes timescales for all active species in the network.
*
* @param Y_culled Vector of current abundances for the active species.
* @param comp Composition object containing current abundances.
* @param T9 Temperature in units of 10^9 K.
* @param rho Density in g/cm^3.
* @return Map from Species to their characteristic timescales (s).
@@ -226,13 +234,13 @@ namespace gridfire {
* @throws std::runtime_error If the AdaptiveEngineView is stale (i.e., `update()` has not been called).
*/
[[nodiscard]] std::expected<std::unordered_map<fourdst::atomic::Species, double>, expectations::StaleEngineError> getSpeciesTimescales(
const std::vector<double> &Y_culled,
const fourdst::composition::Composition &comp,
double T9,
double rho
) const override;
[[nodiscard]] std::expected<std::unordered_map<fourdst::atomic::Species, double>, expectations::StaleEngineError> getSpeciesDestructionTimescales(
const std::vector<double> &Y,
const fourdst::composition::Composition &comp,
double T9,
double rho
) const override;
@@ -391,21 +399,18 @@ namespace gridfire {
* full network.
*
* @param netIn The current network input, containing temperature, density, and composition.
* @param out_Y_Full A vector that will be populated with the molar abundances of all species in the full network.
* @return A vector of ReactionFlow structs, each containing a pointer to a reaction and its calculated flow rate.
* @return A pair with the first element a vector of ReactionFlow structs, each containing a pointer to a reaction and its calculated flow rate and the second being a composition object where species which were not present in netIn but are present in the definition of the base engine are registered but have 0 mass fraction.
*
* @par Algorithm:
* 1. Clears and reserves space in `out_Y_Full`.
* 2. Iterates through all species in the base engine's network.
* 3. For each species, it retrieves the molar abundance from `netIn.composition`. If the species is not found, its abundance is set to 0.0.
* 4. Converts the temperature from Kelvin to T9.
* 5. Iterates through all reactions in the base engine's network.
* 6. For each reaction, it calls the base engine's `calculateMolarReactionFlow` to get the flow rate.
* 7. Stores the reaction pointer and its flow rate in a `ReactionFlow` struct and adds it to the returned vector.
* 1. Iterates through all species in the base engine's network.
* 2. For each species, it retrieves the molar abundance from `netIn.composition`. If the species is not found, its abundance is set to 0.0.
* 3. Converts the temperature from Kelvin to T9.
* 4. Iterates through all reactions in the base engine's network.
* 5. For each reaction, it calls the base engine's `calculateMolarReactionFlow` to get the flow rate.
* 6. Stores the reaction pointer and its flow rate in a `ReactionFlow` struct and adds it to the returned vector.
*/
std::vector<ReactionFlow> calculateAllReactionFlows(
const NetIn& netIn,
std::vector<double>& out_Y_Full
std::pair<std::vector<ReactionFlow>, fourdst::composition::Composition> calculateAllReactionFlows(
const NetIn& netIn
) const;
/**
* @brief Finds all species that are reachable from the initial fuel through the reaction network.
@@ -436,7 +441,7 @@ namespace gridfire {
*
* @param allFlows A vector of all reactions and their flow rates.
* @param reachableSpecies A set of all species reachable from the initial fuel.
* @param Y_full A vector of molar abundances for all species in the full network.
* @param comp The current composition of the system.
* @param maxFlow The maximum reaction flow rate in the network.
* @return A vector of pointers to the reactions that have been kept after culling.
*
@@ -450,15 +455,15 @@ namespace gridfire {
[[nodiscard]] std::vector<const reaction::Reaction*> cullReactionsByFlow(
const std::vector<ReactionFlow>& allFlows,
const std::unordered_set<fourdst::atomic::Species>& reachableSpecies,
const std::vector<double>& Y_full,
const fourdst::composition::Composition& comp,
double maxFlow
) const;
typedef std::pair<std::unordered_set<const reaction::Reaction*>, std::unordered_set<fourdst::atomic::Species>> RescueSet;
[[nodiscard]] RescueSet rescueEdgeSpeciesDestructionChannel(
const std::vector<double>& Y_full,
const double T9,
const double rho,
const fourdst::composition::Composition& comp,
double T9,
double rho,
const std::vector<fourdst::atomic::Species>& activeSpecies,
const reaction::ReactionSet& activeReactions
) const;

58
src/include/gridfire/engine/views/engine_defined.h
View File

@@ -29,7 +29,7 @@ namespace gridfire{
/**
* @brief Calculates the right-hand side (dY/dt) and energy generation for the active species.
*
* @param Y_defined A vector of abundances for the active species.
* @param comp A Composition object containing the current composition of the system
* @param T9 The temperature in units of 10^9 K.
* @param rho The density in g/cm^3.
* @return A StepDerivatives struct containing the derivatives of the active species and the
@@ -38,44 +38,44 @@ namespace gridfire{
* @throws std::runtime_error If the view is stale (i.e., `update()` has not been called after `setNetworkFile()`).
*/
[[nodiscard]] std::expected<StepDerivatives<double>, expectations::StaleEngineError> calculateRHSAndEnergy(
const std::vector<double>& Y_defined,
const double T9,
const double rho
const fourdst::composition::Composition& comp,
double T9,
double rho
) const override;
[[nodiscard]] EnergyDerivatives calculateEpsDerivatives(
const std::vector<double> &Y,
const double T9,
const double rho
const fourdst::composition::Composition& comp,
double T9,
double rho
) const override;
/**
* @brief Generates the Jacobian matrix for the active species.
*
* @param Y_dynamic A vector of abundances for the active species.
* @param comp A Composition object containing the current composition of the system
* @param T9 The temperature in units of 10^9 K.
* @param rho The density in g/cm^3.
*
* @throws std::runtime_error If the view is stale.
*/
void generateJacobianMatrix(
const std::vector<double>& Y_dynamic,
const fourdst::composition::Composition& comp,
const double T9,
const double rho
) const override;
/**
* @brief Gets an entry from the Jacobian matrix for the active species.
*
* @param i_defined The row index (species index) in the defined matrix.
* @param j_defined The column index (species index) in the defined matrix.
* @return The value of the Jacobian matrix at (i_defined, j_defined).
* @param rowSpecies The species corresponding to the row index.
* @param colSpecies The species corresponding to the column index.
* @return The value of the Jacobian matrix at (row species index, col species index).
*
* @throws std::runtime_error If the view is stale.
* @throws std::out_of_range If an index is out of bounds.
*/
[[nodiscard]] double getJacobianMatrixEntry(
const int i_defined,
const int j_defined
const fourdst::atomic::Species& rowSpecies,
const fourdst::atomic::Species& colSpecies
) const override;
/**
* @brief Generates the stoichiometry matrix for the active reactions and species.
@@ -86,22 +86,22 @@ namespace gridfire{
/**
* @brief Gets an entry from the stoichiometry matrix for the active species and reactions.
*
* @param speciesIndex_defined The index of the species in the defined species list.
* @param reactionIndex_defined The index of the reaction in the defined reaction list.
* @param species The species for which to get the stoichiometric coefficient.
* @param reaction The reaction for which to get the stoichiometric coefficient.
* @return The stoichiometric coefficient for the given species and reaction.
*
* @throws std::runtime_error If the view is stale.
* @throws std::out_of_range If an index is out of bounds.
*/
[[nodiscard]] int getStoichiometryMatrixEntry(
const int speciesIndex_defined,
const int reactionIndex_defined
const fourdst::atomic::Species& species,
const reaction::Reaction& reaction
) const override;
/**
* @brief Calculates the molar reaction flow for a given reaction in the active network.
*
* @param reaction The reaction for which to calculate the flow.
* @param Y_defined Vector of current abundances for the active species.
* @param comp A Composition object containing the current composition of the system
* @param T9 Temperature in units of 10^9 K.
* @param rho Density in g/cm^3.
* @return Molar flow rate for the reaction (e.g., mol/g/s).
@@ -110,9 +110,9 @@ namespace gridfire{
*/
[[nodiscard]] double calculateMolarReactionFlow(
const reaction::Reaction& reaction,
const std::vector<double>& Y_defined,
const double T9,
const double rho
const fourdst::composition::Composition& comp,
double T9,
double rho
) const override;
/**
* @brief Gets the set of active logical reactions in the network.
@@ -127,7 +127,7 @@ namespace gridfire{
/**
* @brief Computes timescales for all active species in the network.
*
* @param Y_defined Vector of current abundances for the active species.
* @param comp A Composition object containing the current composition of the system
* @param T9 Temperature in units of 10^9 K.
* @param rho Density in g/cm^3.
* @return Map from Species to their characteristic timescales (s).
@@ -135,15 +135,15 @@ namespace gridfire{
* @throws std::runtime_error If the view is stale.
*/
[[nodiscard]] std::expected<std::unordered_map<fourdst::atomic::Species, double>, expectations::StaleEngineError> getSpeciesTimescales(
const std::vector<double>& Y_defined,
const double T9,
const double rho
const fourdst::composition::Composition& comp,
double T9,
double rho
) const override;
[[nodiscard]] std::expected<std::unordered_map<fourdst::atomic::Species, double>, expectations::StaleEngineError> getSpeciesDestructionTimescales(
const std::vector<double>& Y_defined,
const double T9,
const double rho
const fourdst::composition::Composition& comp,
double T9,
double rho
) const override;
/**

153
src/include/gridfire/engine/views/engine_multiscale.h
View File

@@ -206,7 +206,7 @@ namespace gridfire {
/**
* @brief Calculates the right-hand side (dY/dt) and energy generation.
*
* @param Y_full Vector of current molar abundances for all species in the base engine.
* @param comp The current composition.
* @param T9 Temperature in units of 10^9 K.
* @param rho Density in g/cm^3.
* @return A `std::expected` containing `StepDerivatives<double>` on success, or a
@@ -231,21 +231,21 @@ namespace gridfire {
* (T9, rho, Y_full). This indicates `update()` was not called recently enough.
*/
[[nodiscard]] std::expected<StepDerivatives<double>, expectations::StaleEngineError> calculateRHSAndEnergy(
const std::vector<double> &Y_full,
const fourdst::composition::Composition& comp,
double T9,
double rho
) const override;
[[nodiscard]] EnergyDerivatives calculateEpsDerivatives(
const std::vector<double> &Y,
const double T9,
const double rho
const fourdst::composition::Composition& comp,
double T9,
double rho
) const override;
/**
* @brief Generates the Jacobian matrix for the current state.
*
* @param Y_full Vector of current molar abundances.
* @param comp The current composition.
* @param T9 Temperature in units of 10^9 K.
* @param rho Density in g/cm^3.
*
@@ -266,7 +266,7 @@ namespace gridfire {
* without a valid partition.
*/
void generateJacobianMatrix(
const std::vector<double> &Y_full,
const fourdst::composition::Composition& comp,
double T9,
double rho
) const override;
@@ -274,8 +274,8 @@ namespace gridfire {
/**
* @brief Gets an entry from the previously generated Jacobian matrix.
*
* @param i_full Row index (species index) in the full network.
* @param j_full Column index (species index) in the full network.
* @param rowSpecies Species corresponding to the row index (i_full).
* @param colSpecies Species corresponding to the column index (j_full).
* @return Value of the Jacobian matrix at (i_full, j_full).
*
* @par Purpose
@@ -289,8 +289,8 @@ namespace gridfire {
* @pre `generateJacobianMatrix()` must have been called for the current state.
*/
[[nodiscard]] double getJacobianMatrixEntry(
int i_full,
int j_full
const fourdst::atomic::Species& rowSpecies,
const fourdst::atomic::Species& colSpecies
) const override;
/**
@@ -308,8 +308,8 @@ namespace gridfire {
/**
* @brief Gets an entry from the stoichiometry matrix.
*
* @param speciesIndex Index of the species in the full network.
* @param reactionIndex Index of the reaction in the full network.
* @param species Species to look up stoichiometry for.
* @param reaction Reaction to find.
* @return Stoichiometric coefficient for the species in the reaction.
*
* @par Purpose
@@ -321,15 +321,15 @@ namespace gridfire {
* @pre `generateStoichiometryMatrix()` must have been called.
*/
[[nodiscard]] int getStoichiometryMatrixEntry(
int speciesIndex,
int reactionIndex
const fourdst::atomic::Species& species,
const reaction::Reaction& reaction
) const override;
/**
* @brief Calculates the molar reaction flow for a given reaction.
*
* @param reaction The reaction for which to calculate the flow.
* @param Y_full Vector of current molar abundances for the full network.
* @param comp The current composition.
* @param T9 Temperature in units of 10^9 K.
* @param rho Density in g/cm^3.
* @return Molar flow rate for the reaction (e.g., mol/g/s).
@@ -349,7 +349,7 @@ namespace gridfire {
*/
[[nodiscard]] double calculateMolarReactionFlow(
const reaction::Reaction &reaction,
const std::vector<double> &Y_full,
const fourdst::composition::Composition& comp,
double T9,
double rho
) const override;
@@ -385,7 +385,7 @@ namespace gridfire {
/**
* @brief Computes timescales for all species in the network.
*
* @param Y Vector of current molar abundances for the full network.
* @param comp The current composition.
* @param T9 Temperature in units of 10^9 K.
* @param rho Density in g/cm^3.
* @return A `std::expected` containing a map from `Species` to their characteristic
@@ -403,7 +403,7 @@ namespace gridfire {
* @throws StaleEngineError If the QSE cache misses.
*/
[[nodiscard]] std::expected<std::unordered_map<fourdst::atomic::Species, double>, expectations::StaleEngineError> getSpeciesTimescales(
const std::vector<double> &Y,
const fourdst::composition::Composition& comp,
double T9,
double rho
) const override;
@@ -411,7 +411,7 @@ namespace gridfire {
/**
* @brief Computes destruction timescales for all species in the network.
*
* @param Y Vector of current molar abundances for the full network.
* @param comp The current composition.
* @param T9 Temperature in units of 10^9 K.
* @param rho Density in g/cm^3.
* @return A `std::expected` containing a map from `Species` to their characteristic
@@ -429,7 +429,7 @@ namespace gridfire {
* @throws StaleEngineError If the QSE cache misses.
*/
[[nodiscard]] std::expected<std::unordered_map<fourdst::atomic::Species, double>, expectations::StaleEngineError> getSpeciesDestructionTimescales(
const std::vector<double> &Y,
const fourdst::composition::Composition& comp,
double T9,
double rho
) const override;
@@ -516,7 +516,7 @@ namespace gridfire {
*
* @param timescale_pools A vector of vectors of species indices, where each inner vector
* represents a timescale pool.
* @param Y Vector of current molar abundances for the full network.
* @param comp Vector of current molar abundances for the full network.
* @param T9 Temperature in units of 10^9 K.
* @param rho Density in g/cm^3.
* @return A vector of vectors of species indices, where each inner vector represents a
@@ -531,9 +531,9 @@ namespace gridfire {
* It then finds the connected components within that graph using a Breadth-First Search (BFS).
* The resulting components from all pools are collected and returned.
*/
std::vector<std::vector<size_t>> analyzeTimescalePoolConnectivity(
const std::vector<std::vector<size_t>> &timescale_pools,
const std::vector<double> &Y,
std::vector<std::vector<fourdst::atomic::Species>> analyzeTimescalePoolConnectivity(
const std::vector<std::vector<fourdst::atomic::Species>> &timescale_pools,
const fourdst::composition::Composition &comp,
double T9,
double rho
) const;
@@ -541,7 +541,7 @@ namespace gridfire {
/**
* @brief Partitions the network into dynamic and algebraic (QSE) groups based on timescales.
*
* @param Y Vector of current molar abundances for the full network.
* @param comp Vector of current molar abundances for the full network.
* @param T9 Temperature in units of 10^9 K.
* @param rho Density in g/cm^3.
*
@@ -567,7 +567,7 @@ namespace gridfire {
* partitioning.
*/
void partitionNetwork(
const std::vector<double>& Y,
const fourdst::composition::Composition &comp,
double T9,
double rho
);
@@ -605,9 +605,9 @@ namespace gridfire {
*/
void exportToDot(
const std::string& filename,
const std::vector<double>& Y,
const double T9,
const double rho
const fourdst::composition::Composition &Y,
double T9,
double rho
) const;
/**
@@ -679,7 +679,7 @@ namespace gridfire {
/**
* @brief Equilibrates the network by partitioning and solving for QSE abundances.
*
* @param Y Vector of current molar abundances for the full network.
* @param comp Vector of current molar abundances for the full network.
* @param T9 Temperature in units of 10^9 K.
* @param rho Density in g/cm^3.
* @return A new composition object with the equilibrated abundances.
@@ -698,7 +698,7 @@ namespace gridfire {
* @post The engine's internal partition is updated. A new composition object is returned.
*/
fourdst::composition::Composition equilibrateNetwork(
const std::vector<double> &Y,
const fourdst::composition::Composition &comp,
double T9,
double rho
);
@@ -730,11 +730,10 @@ namespace gridfire {
* in quasi-steady-state equilibrium with each other.
*/
struct QSEGroup {
std::set<size_t> species_indices; ///< Indices of all species in this group.
bool is_in_equilibrium = false; ///< Flag set by flux analysis.
std::set<size_t> algebraic_indices; ///< Indices of algebraic species in this group.
std::set<size_t> seed_indices; ///< Indices of dynamic species in this group.
double mean_timescale; ///< Mean timescale of the group.
bool is_in_equilibrium = false; ///< Flag set by flux analysis.
std::set<fourdst::atomic::Species> algebraic_species; ///< Algebraic species in this group.
std::set<fourdst::atomic::Species> seed_species; ///< Dynamic species in this group.
double mean_timescale; ///< Mean timescale of the group.
/**
* @brief Less-than operator for QSEGroup, used for sorting.
@@ -761,9 +760,7 @@ namespace gridfire {
*/
bool operator!=(const QSEGroup& other) const;
std::string toString() const;
std::string toString(const DynamicEngine &engine) const;
[[nodiscard]] [[maybe_unused]] std::string toString() const;
};
/**
@@ -802,11 +799,11 @@ namespace gridfire {
/**
* @brief Indices of the species to solve for in the QSE group.
*/
const std::vector<size_t>& m_qse_solve_indices;
const std::set<fourdst::atomic::Species>& m_qse_solve_species;
/**
* @brief Initial abundances of all species in the full network.
*/
const std::vector<double>& m_Y_full_initial;
const fourdst::composition::Composition& m_initial_comp;
/**
* @brief Temperature in units of 10^9 K.
*/
@@ -820,41 +817,49 @@ namespace gridfire {
*/
const Eigen::VectorXd& m_Y_scale;
/**
* @brief Mapping from species to their indices in the QSE solve vector.
*/
const std::unordered_map<fourdst::atomic::Species, size_t> m_qse_solve_species_index_map;
/**
* @brief Constructs an EigenFunctor.
*
* @param view The MultiscalePartitioningEngineView instance.
* @param qse_solve_indices Indices of the species to solve for in the QSE group.
* @param Y_full_initial Initial abundances of all species.
* @param qse_solve_species Species to solve for in the QSE group.
* @param initial_comp Initial abundances of all species in the full network.
* @param T9 Temperature in units of 10^9 K.
* @param rho Density in g/cm^3.
* @param Y_scale Scaling factors for the species abundances.
* @param qse_solve_species_index_map Mapping from species to their indices in the QSE solve vector.
*/
EigenFunctor(
MultiscalePartitioningEngineView& view,
const std::vector<size_t>& qse_solve_indices,
const std::vector<double>& Y_full_initial,
const std::set<fourdst::atomic::Species>& qse_solve_species,
const fourdst::composition::Composition& initial_comp,
const double T9,
const double rho,
const Eigen::VectorXd& Y_scale
const Eigen::VectorXd& Y_scale,
const std::unordered_map<fourdst::atomic::Species, size_t>& qse_solve_species_index_map
) :
m_view(&view),
m_qse_solve_indices(qse_solve_indices),
m_Y_full_initial(Y_full_initial),
m_qse_solve_species(qse_solve_species),
m_initial_comp(initial_comp),
m_T9(T9),
m_rho(rho),
m_Y_scale(Y_scale) {}
m_Y_scale(Y_scale),
m_qse_solve_species_index_map(qse_solve_species_index_map){}
/**
* @brief Gets the number of output values from the functor (size of the residual vector).
* @return The number of algebraic species being solved.
*/
[[nodiscard]] size_t values() const { return m_qse_solve_indices.size(); }
[[nodiscard]] size_t values() const { return m_qse_solve_species.size(); }
/**
* @brief Gets the number of input values to the functor (size of the variable vector).
* @return The number of algebraic species being solved.
*/
[[nodiscard]] size_t inputs() const { return m_qse_solve_indices.size(); }
[[nodiscard]] size_t inputs() const { return m_qse_solve_species.size(); }
/**
* @brief Evaluates the functor's residual vector `f_qse = dY_alg/dt`.
@@ -981,23 +986,15 @@ namespace gridfire {
* @brief The simplified set of species presented to the solver (the "slow" species).
*/
std::vector<fourdst::atomic::Species> m_dynamic_species;
/**
* @brief Indices mapping the dynamic species back to the base engine's full species list.
*/
std::vector<size_t> m_dynamic_species_indices;
/**
* @brief Species that are treated as algebraic (in QSE) in the QSE groups.
*/
std::vector<fourdst::atomic::Species> m_algebraic_species;
/**
* @breif Stateful storage of the current algebraic species abundances. This is updated every time the update method is called.
* @brief Map from species to their calculated abundances in the QSE state.
*/
std::vector<double> m_Y_algebraic;
/**
* @brief Indices of algebraic species in the full network.
*/
std::vector<size_t> m_algebraic_species_indices;
std::unordered_map<fourdst::atomic::Species, double> m_algebraic_abundances;
/**
* @brief Indices of all species considered active in the current partition (dynamic + algebraic).
@@ -1029,7 +1026,7 @@ namespace gridfire {
/**
* @brief Partitions the network by timescale.
*
* @param Y_full Vector of current molar abundances for all species.
* @param comp Vector of current molar abundances for all species.
* @param T9 Temperature in units of 10^9 K.
* @param rho Density in g/cm^3.
* @return A vector of vectors of species indices, where each inner vector represents a
@@ -1044,8 +1041,8 @@ namespace gridfire {
* a gap between consecutive timescales that is larger than a predefined threshold
* (e.g., a factor of 100).
*/
std::vector<std::vector<size_t>> partitionByTimescale(
const std::vector<double> &Y_full,
std::vector<std::vector<fourdst::atomic::Species>> partitionByTimescale(
const fourdst::composition::Composition &comp,
double T9,
double rho
) const;
@@ -1054,7 +1051,7 @@ namespace gridfire {
* @brief Validates candidate QSE groups using flux analysis.
*
* @param candidate_groups A vector of candidate QSE groups.
* @param Y Vector of current molar abundances for the full network.
* @param comp Vector of current molar abundances for the full network.
* @param T9 Temperature in units of 10^9 K.
* @param rho Density in g/cm^3.
* @return A vector of validated QSE groups that meet the flux criteria.
@@ -1074,7 +1071,7 @@ namespace gridfire {
::
QSEGroup>> validateGroupsWithFluxAnalysis(
const std::vector<QSEGroup> &candidate_groups,
const std::vector<double> &Y,
const fourdst::composition::Composition &comp,
double T9,
double rho
) const;
@@ -1082,7 +1079,7 @@ namespace gridfire {
/**
* @brief Solves for the QSE abundances of the algebraic species in a given state.
*
* @param Y_full Vector of current molar abundances for all species in the base engine.
* @param comp Vector of current molar abundances for all species in the base engine.
* @param T9 Temperature in units of 10^9 K.
* @param rho Density in g/cm^3.
* @return A vector of molar abundances for the algebraic species.
@@ -1099,8 +1096,8 @@ namespace gridfire {
* @pre The input state (Y_full, T9, rho) must be a valid physical state.
* @post The algebraic species in the QSE cache are updated with the new equilibrium abundances.
*/
std::vector<double> solveQSEAbundances(
const std::vector<double> &Y_full,
fourdst::composition::Composition solveQSEAbundances(
const fourdst::composition::Composition &comp,
double T9,
double rho
);
@@ -1110,7 +1107,7 @@ namespace gridfire {
*
* @param pools A vector of vectors of species indices, where each inner vector represents a
* timescale pool.
* @param Y Vector of current molar abundances for the full network.
* @param comp Vector of current molar abundances for the full network.
* @param T9 Temperature in units of 10^9 K.
* @param rho Density in g/cm^3.
* @return The index of the pool with the largest (slowest) mean destruction timescale.
@@ -1123,8 +1120,8 @@ namespace gridfire {
* pool and returns the index of the pool with the maximum mean timescale.
*/
size_t identifyMeanSlowestPool(
const std::vector<std::vector<size_t>>& pools,
const std::vector<double> &Y,
const std::vector<std::vector<fourdst::atomic::Species>>& pools,
const fourdst::composition::Composition &comp,
double T9,
double rho
) const;
@@ -1144,8 +1141,8 @@ namespace gridfire {
* and one as a product), it adds edges between all reactants and products from
* that reaction that are also in the pool.
*/
std::unordered_map<size_t, std::vector<size_t>> buildConnectivityGraph(
const std::vector<size_t>& species_pool
std::unordered_map<fourdst::atomic::Species, std::vector<fourdst::atomic::Species>> buildConnectivityGraph(
const std::vector<fourdst::atomic::Species>& species_pool
) const;
/**
@@ -1153,7 +1150,7 @@ namespace gridfire {
*
* @param candidate_pools A vector of vectors of species indices, where each inner vector
* represents a connected pool of species with similar fast timescales.
* @param Y Vector of current molar abundances.
* @param comp Vector of current molar abundances.
* @param T9 Temperature in units of 10^9 K.
* @param rho Density in g/cm^3.
* @return A vector of `QSEGroup` structs, ready for flux validation.
@@ -1168,8 +1165,8 @@ namespace gridfire {
* @post A list of candidate `QSEGroup` objects is returned.
*/
std::vector<QSEGroup> constructCandidateGroups(
const std::vector<std::vector<size_t>>& candidate_pools,
const std::vector<double>& Y,
const std::vector<std::vector<fourdst::atomic::Species>>& candidate_pools,
const fourdst::composition::Composition &comp,
double T9,
double rho
) const;