A reaction network engine that uses a graph-based representation. More...
#include <engine_graph.h>
Classes | |
| class | AtomicReverseRate |
| struct | constants |
| struct | PrecomputedReaction |
Public Member Functions | |
| GraphEngine (const fourdst::composition::Composition &composition, const BuildDepthType=NetworkBuildDepth::Full) | |
| Constructs a GraphEngine from a composition. | |
| GraphEngine (const fourdst::composition::Composition &composition, const partition::PartitionFunction &partitionFunction, const BuildDepthType buildDepth=NetworkBuildDepth::Full) | |
| GraphEngine (const reaction::LogicalReactionSet &reactions) | |
| Constructs a GraphEngine from a set of reactions. | |
| std::expected< StepDerivatives< double >, expectations::StaleEngineError > | calculateRHSAndEnergy (const std::vector< double > &Y, const double T9, const double rho) const override |
| Calculates the right-hand side (dY/dt) and energy generation rate. | |
| void | generateJacobianMatrix (const std::vector< double > &Y_dynamic, const double T9, const double rho) const override |
| Generates the Jacobian matrix for the current state. | |
| void | generateJacobianMatrix (const std::vector< double > &Y_dynamic, double T9, double rho, const SparsityPattern &sparsityPattern) const override |
| void | generateStoichiometryMatrix () override |
| Generates the stoichiometry matrix for the network. | |
| double | calculateMolarReactionFlow (const reaction::Reaction &reaction, const std::vector< double > &Y, const double T9, const double rho) const override |
| Calculates the molar reaction flow for a given reaction. | |
| const std::vector< fourdst::atomic::Species > & | getNetworkSpecies () const override |
| Gets the list of species in the network. | |
| const reaction::LogicalReactionSet & | getNetworkReactions () const override |
| Gets the set of logical reactions in the network. | |
| void | setNetworkReactions (const reaction::LogicalReactionSet &reactions) override |
| double | getJacobianMatrixEntry (const int i, const int j) const override |
| Gets an entry from the previously generated Jacobian matrix. | |
| int | getStoichiometryMatrixEntry (const int speciesIndex, const int reactionIndex) const override |
| Gets an entry from the stoichiometry matrix. | |
| std::expected< std::unordered_map< fourdst::atomic::Species, double >, expectations::StaleEngineError > | getSpeciesTimescales (const std::vector< double > &Y, double T9, double rho) const override |
| Computes timescales for all species in the network. | |
| std::expected< std::unordered_map< fourdst::atomic::Species, double >, expectations::StaleEngineError > | getSpeciesDestructionTimescales (const std::vector< double > &Y, double T9, double rho) const override |
| fourdst::composition::Composition | update (const NetIn &netIn) override |
| Update the internal state of the engine. | |
| bool | isStale (const NetIn &netIn) override |
| bool | involvesSpecies (const fourdst::atomic::Species &species) const |
| Checks if a given species is involved in the network. | |
| void | exportToDot (const std::string &filename) const |
| Exports the network to a DOT file for visualization. | |
| void | exportToCSV (const std::string &filename) const |
| Exports the network to a CSV file for analysis. | |
| void | setScreeningModel (screening::ScreeningType) override |
| Set the electron screening model. | |
| screening::ScreeningType | getScreeningModel () const override |
| Get the current electron screening model. | |
| void | setPrecomputation (bool precompute) |
| bool | isPrecomputationEnabled () const |
| const partition::PartitionFunction & | getPartitionFunction () const |
| double | calculateReverseRate (const reaction::Reaction &reaction, double T9) const |
| double | calculateReverseRateTwoBody (const reaction::Reaction &reaction, const double T9, const double forwardRate, const double expFactor) const |
| double | calculateReverseRateTwoBodyDerivative (const reaction::Reaction &reaction, const double T9, const double reverseRate) const |
| bool | isUsingReverseReactions () const |
| void | setUseReverseReactions (bool useReverse) |
| int | getSpeciesIndex (const fourdst::atomic::Species &species) const override |
| std::vector< double > | mapNetInToMolarAbundanceVector (const NetIn &netIn) const override |
| PrimingReport | primeEngine (const NetIn &netIn) override |
| BuildDepthType | getDepth () const override |
| void | rebuild (const fourdst::composition::Composition &comp, const BuildDepthType depth) override |
 Public Member Functions inherited from gridfire::Engine | |
| virtual | ~Engine ()=default |
| Virtual destructor. | |
Static Public Member Functions | |
| static std::unordered_map< fourdst::atomic::Species, int > | getNetReactionStoichiometry (const reaction::Reaction &reaction) |
| Gets the net stoichiometry for a given reaction. | |
Private Member Functions | |
| void | syncInternalMaps () |
| Synchronizes the internal maps. | |
| void | collectNetworkSpecies () |
| Collects the unique species in the network. | |
| void | populateReactionIDMap () |
| Populates the reaction ID map. | |
| void | populateSpeciesToIndexMap () |
| Populates the species-to-index map. | |
| void | reserveJacobianMatrix () const |
| Reserves space for the Jacobian matrix. | |
| void | recordADTape () |
| Records the AD tape for the right-hand side of the ODE. | |
| void | collectAtomicReverseRateAtomicBases () |
| void | precomputeNetwork () |
| bool | validateConservation () const |
| Validates mass and charge conservation across all reactions. | |
| void | validateComposition (const fourdst::composition::Composition &composition, double culling, double T9) |
| Validates the composition against the current reaction set. | |
| StepDerivatives< double > | calculateAllDerivativesUsingPrecomputation (const std::vector< double > &Y_in, const std::vector< double > &bare_rates, const std::vector< double > &bare_reverse_rates, double T9, double rho) const |
| template<IsArithmeticOrAD T> | |
| T | calculateMolarReactionFlow (const reaction::Reaction &reaction, const std::vector< T > &Y, const T T9, const T rho) const |
| Calculates the molar reaction flow for a given reaction. | |
| template<IsArithmeticOrAD T> | |
| T | calculateReverseMolarReactionFlow (T T9, T rho, std::vector< T > screeningFactors, std::vector< T > Y, size_t reactionIndex, const reaction::LogicalReaction &reaction) const |
| template<IsArithmeticOrAD T> | |
| StepDerivatives< T > | calculateAllDerivatives (const std::vector< T > &Y_in, T T9, T rho) const |
| Calculates all derivatives (dY/dt) and the energy generation rate. | |
| StepDerivatives< double > | calculateAllDerivatives (const std::vector< double > &Y_in, const double T9, const double rho) const |
| Calculates all derivatives (dY/dt) and the energy generation rate (double precision). | |
| StepDerivatives< ADDouble > | calculateAllDerivatives (const std::vector< ADDouble > &Y_in, const ADDouble &T9, const ADDouble &rho) const |
| Calculates all derivatives (dY/dt) and the energy generation rate (automatic differentiation). | |
Private Attributes | |
| Config & | m_config = Config::getInstance() |
| quill::Logger * | m_logger = LogManager::getInstance().getLogger("log") |
| constants | m_constants |
| reaction::LogicalReactionSet | 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. | |
| std::unordered_map< std::string_view, fourdst::atomic::Species > | m_networkSpeciesMap |
| Map from species name to Species object. | |
| std::unordered_map< fourdst::atomic::Species, size_t > | m_speciesToIndexMap |
| Map from species to their index in the stoichiometry matrix. | |
| boost::numeric::ublas::compressed_matrix< int > | m_stoichiometryMatrix |
| Stoichiometry matrix (species x reactions). | |
| boost::numeric::ublas::compressed_matrix< double > | m_jacobianMatrix |
| Jacobian matrix (species x species). | |
| CppAD::ADFun< double > | m_rhsADFun |
| CppAD function for the right-hand side of the ODE. | |
| CppAD::sparse_jac_work | m_jac_work |
| Work object for sparse Jacobian calculations. | |
| CppAD::sparse_rc< std::vector< size_t > > | m_full_jacobian_sparsity_pattern |
| Full sparsity pattern for the Jacobian matrix. | |
| std::vector< std::unique_ptr< AtomicReverseRate > > | m_atomicReverseRates |
| screening::ScreeningType | m_screeningType = screening::ScreeningType::BARE |
| Screening type for the reaction network. Default to no screening. | |
| std::unique_ptr< screening::ScreeningModel > | m_screeningModel = screening::selectScreeningModel(m_screeningType) |
| bool | m_usePrecomputation = true |
| Flag to enable or disable using precomputed reactions for efficiency. Mathematically, this should not change the results. Generally end users should not need to change this. | |
| bool | m_useReverseReactions = true |
| Flag to enable or disable reverse reactions. If false, only forward reactions are considered. | |
| BuildDepthType | m_depth |
| std::vector< PrecomputedReaction > | m_precomputedReactions |
| Precomputed reactions for efficiency. | |
| std::unique_ptr< partition::PartitionFunction > | m_partitionFunction |
| Partition function for the network. | |
Detailed Description
A reaction network engine that uses a graph-based representation.
The GraphEngine class implements the DynamicEngine interface using a graph-based representation of the reaction network. It uses sparse matrices for efficient storage and computation of the stoichiometry and Jacobian matrices. Automatic differentiation (AD) is used to calculate the Jacobian matrix.
The engine supports:
- Calculation of the right-hand side (dY/dt) and energy generation rate.
- Generation and access to the Jacobian matrix.
- Generation and access to the stoichiometry matrix.
- Calculation of molar reaction flows.
- Access to the set of logical reactions in the network.
- Computation of timescales for each species.
- Exporting the network to DOT and CSV formats for visualization and analysis.
- See also
- engine_abstract.h
Definition at line 101 of file engine_graph.h.
Constructor & Destructor Documentation
◆ GraphEngine() [1/3]
|
explicit |
Constructs a GraphEngine from a composition.
- Parameters
-
composition The composition of the material.
This constructor builds the reaction network from the given composition using the build_reaclib_nuclear_network function.
- See also
- build_reaclib_nuclear_network
Definition at line 34 of file engine_graph.cpp.
◆ GraphEngine() [2/3]
|
explicit |
Definition at line 39 of file engine_graph.cpp.
◆ GraphEngine() [3/3]
|
explicit |
Constructs a GraphEngine from a set of reactions.
- Parameters
-
reactions The set of reactions to use in the network.
This constructor uses the given set of reactions to construct the reaction network.
Definition at line 50 of file engine_graph.cpp.
Member Function Documentation
◆ calculateAllDerivatives() [1/3]
|
nodiscardprivate |
Calculates all derivatives (dY/dt) and the energy generation rate (automatic differentiation).
- Parameters
-
Y_in Vector of current abundances for all species. T9 Temperature in units of 10^9 K. rho Density in g/cm^3.
- Returns
- StepDerivatives<ADDouble> containing dY/dt and energy generation rate.
This method calculates the time derivatives of all species and the specific nuclear energy generation rate for the current state using automatic differentiation.
Definition at line 616 of file engine_graph.cpp.
◆ calculateAllDerivatives() [2/3]
|
nodiscardprivate |
Calculates all derivatives (dY/dt) and the energy generation rate (double precision).
- Parameters
-
Y_in Vector of current abundances for all species. T9 Temperature in units of 10^9 K. rho Density in g/cm^3.
- Returns
- StepDerivatives<double> containing dY/dt and energy generation rate.
This method calculates the time derivatives of all species and the specific nuclear energy generation rate for the current state using double precision arithmetic.
Definition at line 608 of file engine_graph.cpp.
◆ calculateAllDerivatives() [3/3]
|
nodiscardprivate |
Calculates all derivatives (dY/dt) and the energy generation rate.
- Template Parameters
-
T The numeric type to use for the calculation.
- Parameters
-
Y_in Vector of current abundances for all species. T9 Temperature in units of 10^9 K. rho Density in g/cm^3.
- Returns
- StepDerivatives<T> containing dY/dt and energy generation rate.
This method calculates the time derivatives of all species and the specific nuclear energy generation rate for the current state.
Definition at line 745 of file engine_graph.h.
◆ calculateAllDerivativesUsingPrecomputation()
|
nodiscardprivate |
Definition at line 470 of file engine_graph.cpp.
◆ calculateMolarReactionFlow() [1/2]
|
nodiscardoverridevirtual |
Calculates the molar reaction flow for a given reaction.
- Parameters
-
reaction The reaction for which to calculate the flow. Y Vector of current abundances. T9 Temperature in units of 10^9 K. rho Density in g/cm^3.
- Returns
- Molar flow rate for the reaction (e.g., mol/g/s).
This method computes the net rate at which the given reaction proceeds under the current state.
Implements gridfire::DynamicEngine.
Definition at line 645 of file engine_graph.cpp.
◆ calculateMolarReactionFlow() [2/2]
|
private |
Calculates the molar reaction flow for a given reaction.
- Template Parameters
-
T The numeric type to use for the calculation.
- Parameters
-
reaction The reaction for which to calculate the flow. Y Vector of current abundances. T9 Temperature in units of 10^9 K. rho Density in g/cm^3.
- Returns
- Molar flow rate for the reaction (e.g., mol/g/s).
This method computes the net rate at which the given reaction proceeds under the current state.
Definition at line 826 of file engine_graph.h.
◆ calculateReverseMolarReactionFlow()
|
private |
Definition at line 667 of file engine_graph.h.
◆ calculateReverseRate()
|
nodiscard |
Definition at line 262 of file engine_graph.cpp.
◆ calculateReverseRateTwoBody()
|
nodiscard |
Definition at line 291 of file engine_graph.cpp.
◆ calculateReverseRateTwoBodyDerivative()
|
nodiscard |
Definition at line 368 of file engine_graph.cpp.
◆ calculateRHSAndEnergy()
|
nodiscardoverridevirtual |
Calculates the right-hand side (dY/dt) and energy generation rate.
- Parameters
-
Y Vector of current abundances for all species. T9 Temperature in units of 10^9 K. rho Density in g/cm^3.
- Returns
- StepDerivatives<double> containing dY/dt and energy generation rate.
This method calculates the time derivatives of all species and the specific nuclear energy generation rate for the current state.
- See also
- StepDerivatives
Implements gridfire::Engine.
Definition at line 57 of file engine_graph.cpp.
◆ collectAtomicReverseRateAtomicBases()
|
private |
Definition at line 969 of file engine_graph.cpp.
◆ collectNetworkSpecies()
|
private |
Collects the unique species in the network.
This method collects the unique species in the network from the reactants and products of all reactions.
Definition at line 106 of file engine_graph.cpp.
◆ exportToCSV()
| void gridfire::GraphEngine::exportToCSV | ( | const std::string & | filename | ) | const |
Exports the network to a CSV file for analysis.
- Parameters
-
filename The name of the CSV file to create.
This method generates a CSV file containing information about the reactions in the network, including the reactants, products, Q-value, and reaction rate coefficients.
- Exceptions
-
std::runtime_error If the file cannot be opened for writing.
Example usage:
Definition at line 810 of file engine_graph.cpp.
◆ exportToDot()
| void gridfire::GraphEngine::exportToDot | ( | const std::string & | filename | ) | const |
Exports the network to a DOT file for visualization.
- Parameters
-
filename The name of the DOT file to create.
This method generates a DOT file that can be used to visualize the reaction network as a graph. The DOT file can be converted to a graphical image using Graphviz.
- Exceptions
-
std::runtime_error If the file cannot be opened for writing.
Example usage:
Definition at line 762 of file engine_graph.cpp.
◆ generateJacobianMatrix() [1/2]
|
overridevirtual |
Generates the Jacobian matrix for the current state.
- Parameters
-
Y_dynamic Vector of current abundances. T9 Temperature in units of 10^9 K. rho Density in g/cm^3.
This method computes and stores the Jacobian matrix (∂(dY/dt)_i/∂Y_j) for the current state using automatic differentiation. The matrix can then be accessed via getJacobianMatrixEntry().
- See also
- getJacobianMatrixEntry()
Implements gridfire::DynamicEngine.
Definition at line 654 of file engine_graph.cpp.
◆ generateJacobianMatrix() [2/2]
|
overridevirtual |
Reimplemented from gridfire::DynamicEngine.
Definition at line 687 of file engine_graph.cpp.
◆ generateStoichiometryMatrix()
|
overridevirtual |
Generates the stoichiometry matrix for the network.
This method computes and stores the stoichiometry matrix, which encodes the net change of each species in each reaction.
Implements gridfire::DynamicEngine.
Definition at line 567 of file engine_graph.cpp.
◆ getDepth()
|
nodiscardoverridevirtual |
Reimplemented from gridfire::DynamicEngine.
Definition at line 456 of file engine_graph.cpp.
◆ getJacobianMatrixEntry()
|
nodiscardoverridevirtual |
Gets an entry from the previously generated Jacobian matrix.
- Parameters
-
i Row index (species index). j Column index (species index).
- Returns
- Value of the Jacobian matrix at (i, j).
The Jacobian must have been generated by generateJacobianMatrix() before calling this.
- See also
- generateJacobianMatrix()
Implements gridfire::DynamicEngine.
Definition at line 744 of file engine_graph.cpp.
◆ getNetReactionStoichiometry()
|
staticnodiscard |
Gets the net stoichiometry for a given reaction.
- Parameters
-
reaction The reaction for which to get the stoichiometry.
- Returns
- Map of species to their stoichiometric coefficients.
Definition at line 749 of file engine_graph.cpp.
◆ getNetworkReactions()
|
nodiscardoverridevirtual |
Gets the set of logical reactions in the network.
- Returns
- Reference to the LogicalReactionSet containing all reactions.
Implements gridfire::DynamicEngine.
Definition at line 168 of file engine_graph.cpp.
◆ getNetworkSpecies()
|
nodiscardoverridevirtual |
Gets the list of species in the network.
- Returns
- Vector of Species objects representing all network species.
Implements gridfire::Engine.
Definition at line 162 of file engine_graph.cpp.
◆ getPartitionFunction()
|
nodiscard |
Definition at line 641 of file engine_graph.cpp.
◆ getScreeningModel()
|
nodiscardoverridevirtual |
Get the current electron screening model.
- Returns
- The currently active screening model type.
- Usage Example:
- screening::ScreeningType currentModel = myEngine.getScreeningModel();
Implements gridfire::DynamicEngine.
Definition at line 629 of file engine_graph.cpp.
◆ getSpeciesDestructionTimescales()
|
nodiscardoverridevirtual |
Implements gridfire::DynamicEngine.
Definition at line 883 of file engine_graph.cpp.
◆ getSpeciesIndex()
|
nodiscardoverridevirtual |
Implements gridfire::DynamicEngine.
Definition at line 417 of file engine_graph.cpp.
◆ getSpeciesTimescales()
|
nodiscardoverridevirtual |
Computes timescales for all species in the network.
- Parameters
-
Y Vector of current abundances. T9 Temperature in units of 10^9 K. rho Density in g/cm^3.
- Returns
- Map from Species to their characteristic timescales (s).
This method estimates the timescale for abundance change of each species, which can be used for timestep control or diagnostics.
Implements gridfire::DynamicEngine.
Definition at line 864 of file engine_graph.cpp.
◆ getStoichiometryMatrixEntry()
|
nodiscardoverridevirtual |
Gets an entry from the stoichiometry matrix.
- Parameters
-
speciesIndex Index of the species. reactionIndex Index of the reaction.
- Returns
- Stoichiometric coefficient for the species in the reaction.
The stoichiometry matrix must have been generated by generateStoichiometryMatrix().
- See also
- generateStoichiometryMatrix()
Implements gridfire::DynamicEngine.
Definition at line 755 of file engine_graph.cpp.
◆ involvesSpecies()
|
nodiscard |
Checks if a given species is involved in the network.
- Parameters
-
species The species to check.
- Returns
- True if the species is involved in the network, false otherwise.
Definition at line 179 of file engine_graph.cpp.
◆ isPrecomputationEnabled()
|
nodiscard |
Definition at line 637 of file engine_graph.cpp.
◆ isStale()
|
overridevirtual |
Implements gridfire::DynamicEngine.
Definition at line 920 of file engine_graph.cpp.
◆ isUsingReverseReactions()
|
nodiscard |
Definition at line 409 of file engine_graph.cpp.
◆ mapNetInToMolarAbundanceVector()
|
nodiscardoverridevirtual |
Implements gridfire::DynamicEngine.
Definition at line 421 of file engine_graph.cpp.
◆ populateReactionIDMap()
|
private |
Populates the reaction ID map.
This method populates the reaction ID map, which maps reaction IDs to REACLIBReaction objects.
Definition at line 135 of file engine_graph.cpp.
◆ populateSpeciesToIndexMap()
|
private |
Populates the species-to-index map.
This method populates the species-to-index map, which maps species to their index in the stoichiometry matrix.
Definition at line 144 of file engine_graph.cpp.
◆ precomputeNetwork()
|
private |
Definition at line 982 of file engine_graph.cpp.
◆ primeEngine()
|
nodiscardoverridevirtual |
Implements gridfire::DynamicEngine.
Definition at line 429 of file engine_graph.cpp.
◆ rebuild()
|
overridevirtual |
Reimplemented from gridfire::DynamicEngine.
Definition at line 460 of file engine_graph.cpp.
◆ recordADTape()
|
private |
Records the AD tape for the right-hand side of the ODE.
This method records the AD tape for the right-hand side of the ODE, which is used to calculate the Jacobian matrix using automatic differentiation.
- Exceptions
-
std::runtime_error If there are no species in the network.
Definition at line 924 of file engine_graph.cpp.
◆ reserveJacobianMatrix()
|
private |
Reserves space for the Jacobian matrix.
This method reserves space for the Jacobian matrix, which is used to store the partial derivatives of the right-hand side of the ODE with respect to the species abundances.
Definition at line 151 of file engine_graph.cpp.
◆ setNetworkReactions()
|
overridevirtual |
Implements gridfire::DynamicEngine.
Definition at line 174 of file engine_graph.cpp.
◆ setPrecomputation()
| void gridfire::GraphEngine::setPrecomputation | ( | bool | precompute | ) |
Definition at line 633 of file engine_graph.cpp.
◆ setScreeningModel()
|
overridevirtual |
Set the electron screening model.
- Parameters
-
model The type of screening model to use for reaction rate calculations.
This method allows changing the screening model at runtime. Screening corrections account for the electrostatic shielding of nuclei by electrons, which affects reaction rates in dense stellar plasmas.
- Usage Example:
- myEngine.setScreeningModel(screening::ScreeningType::WEAK);
- Postcondition
- The engine will use the specified screening model for subsequent rate calculations.
Implements gridfire::DynamicEngine.
Definition at line 624 of file engine_graph.cpp.
◆ setUseReverseReactions()
| void gridfire::GraphEngine::setUseReverseReactions | ( | bool | useReverse | ) |
Definition at line 413 of file engine_graph.cpp.
◆ syncInternalMaps()
|
private |
Synchronizes the internal maps.
This method synchronizes the internal maps used by the engine, including the species map, reaction ID map, and species-to-index map. It also generates the stoichiometry matrix and records the AD tape.
Definition at line 81 of file engine_graph.cpp.
◆ update()
|
overridevirtual |
Update the internal state of the engine.
- Parameters
-
netIn A struct containing the current network input, such as temperature, density, and composition.
This method is intended to be implemented by derived classes to update their internal state based on the provided network conditions. For example, an adaptive engine might use this to re-evaluate which reactions and species are active. For other engines that do not support manually updating, this method might do nothing.
- Usage Example:
- Postcondition
- The internal state of the engine is updated to reflect the new conditions.
Implements gridfire::DynamicEngine.
Definition at line 908 of file engine_graph.cpp.
◆ validateComposition()
|
private |
Validates the composition against the current reaction set.
- Parameters
-
composition The composition to validate. culling The culling threshold to use. T9 The temperature to use.
This method validates the composition against the current reaction set. If the composition is not compatible with the reaction set, the reaction set is rebuilt from the composition.
Definition at line 242 of file engine_graph.cpp.
◆ validateConservation()
|
nodiscardprivate |
Validates mass and charge conservation across all reactions.
- Returns
- True if all reactions conserve mass and charge, false otherwise.
This method checks that all reactions in the network conserve mass and charge. If any reaction does not conserve mass or charge, an error message is logged and false is returned.
Definition at line 187 of file engine_graph.cpp.
Member Data Documentation
◆ m_atomicReverseRates
|
private |
Definition at line 467 of file engine_graph.h.
◆ m_config
|
private |
Definition at line 448 of file engine_graph.h.
◆ m_constants
|
private |
Definition at line 451 of file engine_graph.h.
◆ m_depth
|
private |
Definition at line 476 of file engine_graph.h.
◆ m_full_jacobian_sparsity_pattern
|
private |
Full sparsity pattern for the Jacobian matrix.
Definition at line 465 of file engine_graph.h.
◆ m_jac_work
|
mutableprivate |
Work object for sparse Jacobian calculations.
Definition at line 464 of file engine_graph.h.
◆ m_jacobianMatrix
|
mutableprivate |
Jacobian matrix (species x species).
Definition at line 462 of file engine_graph.h.
◆ m_logger
|
private |
Definition at line 449 of file engine_graph.h.
◆ m_networkSpecies
|
private |
Vector of unique species in the network.
Definition at line 456 of file engine_graph.h.
◆ m_networkSpeciesMap
|
private |
Map from species name to Species object.
Definition at line 457 of file engine_graph.h.
◆ m_partitionFunction
|
private |
Partition function for the network.
Definition at line 479 of file engine_graph.h.
◆ m_precomputedReactions
|
private |
Precomputed reactions for efficiency.
Definition at line 478 of file engine_graph.h.
◆ m_reactionIDMap
|
private |
Map from reaction ID to REACLIBReaction. //PERF: This makes copies of REACLIBReaction and could be a performance bottleneck.
Definition at line 454 of file engine_graph.h.
◆ m_reactions
|
private |
Set of REACLIB reactions in the network.
Definition at line 453 of file engine_graph.h.
◆ m_rhsADFun
|
mutableprivate |
CppAD function for the right-hand side of the ODE.
Definition at line 463 of file engine_graph.h.
◆ m_screeningModel
|
private |
Definition at line 470 of file engine_graph.h.
◆ m_screeningType
|
private |
Screening type for the reaction network. Default to no screening.
Definition at line 469 of file engine_graph.h.
◆ m_speciesToIndexMap
|
private |
Map from species to their index in the stoichiometry matrix.
Definition at line 458 of file engine_graph.h.
◆ m_stoichiometryMatrix
|
private |
Stoichiometry matrix (species x reactions).
Definition at line 460 of file engine_graph.h.
◆ m_usePrecomputation
|
private |
Flag to enable or disable using precomputed reactions for efficiency. Mathematically, this should not change the results. Generally end users should not need to change this.
Definition at line 472 of file engine_graph.h.
◆ m_useReverseReactions
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private |
Flag to enable or disable reverse reactions. If false, only forward reactions are considered.
Definition at line 474 of file engine_graph.h.
The documentation for this class was generated from the following files:
- src/include/gridfire/engine/engine_graph.h
- src/lib/engine/engine_graph.cpp
