# GridFire: gridfire::GraphEngine Class Reference

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gridfire::GraphEngine Class Referencefinal

A reaction network engine that uses a graph-based representation. More...

`#include <engine_graph.h>`

Inheritance diagram for gridfire::GraphEngine:

## Classes

class | AtomicReverseRate
struct | constants
struct | PrecomputedReaction

## Public Member Functions

| GraphEngine (const fourdst::composition::Composition &composition, BuildDepthType=NetworkBuildDepth::Full)
| Constructs a GraphEngine from a composition.
| GraphEngine (const fourdst::composition::Composition &composition, const partition::PartitionFunction &partitionFunction, BuildDepthType buildDepth=NetworkBuildDepth::Full)
| GraphEngine (const reaction::ReactionSet &reactions)
| Constructs a GraphEngine from a set of reactions.
std::expected< StepDerivatives< double >, expectations::StaleEngineError > | calculateRHSAndEnergy (const fourdst::composition::Composition &comp, double T9, double rho) const override
| Calculates the right-hand side (dY/dt) and energy generation rate.
EnergyDerivatives | calculateEpsDerivatives (const fourdst::composition::Composition &comp, double T9, double rho) const override
| Calculate the derivatives of the energy generation rate with respect to T and rho.
void | generateJacobianMatrix (const fourdst::composition::Composition &comp, double T9, double rho) const override
| Generates the Jacobian matrix for the current state.
void | generateJacobianMatrix (const fourdst::composition::Composition &comp, 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 fourdst::composition::Composition &comp, double T9, 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::ReactionSet & | getNetworkReactions () const override
| Gets the set of logical reactions in the network.
void | setNetworkReactions (const reaction::ReactionSet &reactions) override
double | getJacobianMatrixEntry (const fourdst::atomic::Species &rowSpecies, const fourdst::atomic::Species &colSpecies) const override
| Gets an entry from the previously generated Jacobian matrix.
int | getStoichiometryMatrixEntry (const fourdst::atomic::Species &species, const reaction::Reaction &reaction) const override
| Gets an entry from the stoichiometry matrix.
std::expected< std::unordered_map< fourdst::atomic::Species, double >, expectations::StaleEngineError > | getSpeciesTimescales (const fourdst::composition::Composition &comp, 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 fourdst::composition::Composition &comp, 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 model) override
| Sets the electron screening model for reaction rate calculations.
screening::ScreeningType | getScreeningModel () const override
| Gets the current electron screening model.
void | setPrecomputation (bool precompute)
| Sets whether to precompute reaction rates.
bool | isPrecomputationEnabled () const
| Checks if precomputation of reaction rates is enabled.
const partition::PartitionFunction & | getPartitionFunction () const
| Gets the partition function used for reaction rate calculations.
double | calculateReverseRate (const reaction::Reaction &reaction, double T9, double rho, const fourdst::composition::Composition &comp) const
| Calculates the reverse rate for a given reaction.
double | calculateReverseRateTwoBody (const reaction::Reaction &reaction, const double T9, const double forwardRate, const double expFactor) const
| Calculates the reverse rate for a two-body reaction.
double | calculateReverseRateTwoBodyDerivative (const reaction::Reaction &reaction, double T9, double rho, const fourdst::composition::Composition &comp, double reverseRate) const
bool | isUsingReverseReactions () const
| Checks if reverse reactions are enabled.
void | setUseReverseReactions (bool useReverse)
| Sets whether to use reverse reactions in the engine.
size_t | getSpeciesIndex (const fourdst::atomic::Species &species) const override
| Gets the index of a species in the network.
std::vector< double > | mapNetInToMolarAbundanceVector (const NetIn &netIn) const override
| Maps the NetIn object to a vector of molar abundances.
PrimingReport | primeEngine (const NetIn &netIn) override
| Prepares the engine for calculations with initial conditions.
BuildDepthType | getDepth () const override
| Gets the depth of the network.
void | rebuild (const fourdst::composition::Composition &comp, const BuildDepthType depth) override
| Rebuilds the reaction network based on a new composition.
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 () const
| Records the AD tape for the right-hand side of the ODE.
void | recordEpsADTape () const
void | collectAtomicReverseRateAtomicBases ()
void | precomputeNetwork ()
bool | validateConservation () const
| Validates mass and charge conservation across all reactions.
StepDerivatives< double > | calculateAllDerivativesUsingPrecomputation (const fourdst::composition::Composition &comp, 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, T Ye, T mue) const
| Calculates the molar reaction flow for a given reaction.
template<IsArithmeticOrAD T>
T | calculateReverseMolarReactionFlow (const T T9, const T rho, std::vector< T > screeningFactors, const std::vector< T > &Y, size_t reactionIndex, const reaction::Reaction &reaction) const
template<IsArithmeticOrAD T>
StepDerivatives< T > | calculateAllDerivatives (const std::vector< T > &Y_in, T T9, T rho, T Ye, T mue) const
| Calculates all derivatives (dY/dt) and the energy generation rate.

## Private Attributes

Config & | m_config = Config::getInstance()
quill::Logger * | m_logger = LogManager::getInstance().getLogger("log")
constants | m_constants
rates::weak::WeakRateInterpolator | m_weakRateInterpolator
| Interpolator for weak reaction rates.
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.
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.
std::unordered_map< size_t, fourdst::atomic::Species > | m_indexToSpeciesMap
| Map from index to species 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::ADFun< double > | m_epsADFun
| CppAD function for the energy generation rate.
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

## Constructor & Destructor Documentation

## GraphEngine() [1/3]

gridfire::GraphEngine::GraphEngine | ( | const fourdst::composition::Composition & | composition,
|  | BuildDepthType | buildDepth = NetworkBuildDepth::Full )

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

## GraphEngine() [2/3]

gridfire::GraphEngine::GraphEngine | ( | const fourdst::composition::Composition & | composition,
|  | const partition::PartitionFunction & | partitionFunction,
|  | BuildDepthType | buildDepth = NetworkBuildDepth::Full )

explicit

## GraphEngine() [3/3]

gridfire::GraphEngine::GraphEngine | ( | const reaction::ReactionSet & | reactions | ) |

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.

## Member Function Documentation

## calculateAllDerivatives()

template<IsArithmeticOrAD T>

StepDerivatives< T > gridfire::GraphEngine::calculateAllDerivatives | ( | const std::vector< T > & | Y_in,
|  | T | T9,
|  | T | rho,
|  | T | Ye,
|  | T | mue ) const

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 molar abundances for all species in the network.
  T9 | Temperature in units of 10^9 K.
  rho | Density in g/cm^3.
  Ye |
  mue |

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.

## calculateAllDerivativesUsingPrecomputation()

StepDerivatives< double > gridfire::GraphEngine::calculateAllDerivativesUsingPrecomputation | ( | const fourdst::composition::Composition & | comp,
|  | const std::vector< double > & | bare_rates,
|  | const std::vector< double > & | bare_reverse_rates,
|  | double | T9,
|  | double | rho ) const

nodiscardprivate

## calculateEpsDerivatives()

EnergyDerivatives gridfire::GraphEngine::calculateEpsDerivatives | ( | const fourdst::composition::Composition & | comp,
|  | double | T9,
|  | double | rho ) const

nodiscardoverridevirtual

Calculate the derivatives of the energy generation rate with respect to T and rho.

Parameters

  comp | Composition object containing current abundances.
  T9 | Temperature in units of 10^9 K.
  rho | Density in g/cm^3.

Returns
  EnergyDerivatives containing dEps/dT and dEps/dRho.

This method computes the partial derivatives of the specific nuclear energy generation rate with respect to temperature and density for the current state.

Implements gridfire::DynamicEngine.

## calculateMolarReactionFlow() [1/2]

double gridfire::GraphEngine::calculateMolarReactionFlow | ( | const reaction::Reaction & | reaction,
|  | const fourdst::composition::Composition & | comp,
|  | double | T9,
|  | double | rho ) const

nodiscardoverridevirtual

Calculates the molar reaction flow for a given reaction.

Parameters

  reaction | The reaction for which to calculate the flow.
  comp | Composition object containing 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.

## calculateMolarReactionFlow() [2/2]

template<IsArithmeticOrAD T>

T gridfire::GraphEngine::calculateMolarReactionFlow | ( | const reaction::Reaction & | reaction,
|  | const std::vector< T > & | Y,
|  | const T | T9,
|  | const T | rho,
|  | T | Ye,
|  | T | mue ) const

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 molar abundances for all species in the network.
  T9 | Temperature in units of 10^9 K.
  rho | Density in g/cm^3.
  Ye |
  mue |

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.

## calculateReverseMolarReactionFlow()

template<IsArithmeticOrAD T>

T gridfire::GraphEngine::calculateReverseMolarReactionFlow | ( | const T | T9,
|  | const T | rho,
|  | std::vector< T > | screeningFactors,
|  | const std::vector< T > & | Y,
|  | size_t | reactionIndex,
|  | const reaction::Reaction & | reaction ) const

private

## calculateReverseRate()

double gridfire::GraphEngine::calculateReverseRate | ( | const reaction::Reaction & | reaction,
|  | double | T9,
|  | double | rho,
|  | const fourdst::composition::Composition & | comp ) const

nodiscard

Calculates the reverse rate for a given reaction.

Parameters

  reaction | The reaction for which to calculate the reverse rate.
  T9 | Temperature in units of 10^9 K.
  rho |
  comp | Composition object containing current abundances.

Returns
  Reverse rate for the reaction (e.g., mol/g/s).

This method computes the reverse rate based on the forward rate and thermodynamic properties of the reaction.

## calculateReverseRateTwoBody()

double gridfire::GraphEngine::calculateReverseRateTwoBody | ( | const reaction::Reaction & | reaction,
|  | const double | T9,
|  | const double | forwardRate,
|  | const double | expFactor ) const

nodiscard

Calculates the reverse rate for a two-body reaction.

Parameters

  reaction | The reaction for which to calculate the reverse rate.
  T9 | Temperature in units of 10^9 K.
  forwardRate | The forward rate of the reaction.
  expFactor | Exponential factor for the reaction.

Returns
  Reverse rate for the two-body reaction (e.g., mol/g/s).

This method computes the reverse rate using the forward rate and thermodynamic properties of the reaction.

## calculateReverseRateTwoBodyDerivative()

double gridfire::GraphEngine::calculateReverseRateTwoBodyDerivative | ( | const reaction::Reaction & | reaction,
|  | double | T9,
|  | double | rho,
|  | const fourdst::composition::Composition & | comp,
|  | double | reverseRate ) const

nodiscard

## calculateRHSAndEnergy()

std::expected< StepDerivatives< double >, expectations::StaleEngineError > gridfire::GraphEngine::calculateRHSAndEnergy | ( | const fourdst::composition::Composition & | comp,
|  | double | T9,
|  | double | rho ) const

nodiscardoverridevirtual

Calculates the right-hand side (dY/dt) and energy generation rate.

Parameters

  comp | Composition object containing current abundances.
  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.

## collectAtomicReverseRateAtomicBases()

void gridfire::GraphEngine::collectAtomicReverseRateAtomicBases | ( |  | ) |

private

## collectNetworkSpecies()

void gridfire::GraphEngine::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.

## 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:

engine.exportToCSV("network.csv");

## 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:

engine.exportToDot("network.dot");

## generateJacobianMatrix() [1/2]

void gridfire::GraphEngine::generateJacobianMatrix | ( | const fourdst::composition::Composition & | comp,
|  | double | T9,
|  | double | rho ) const

overridevirtual

Generates the Jacobian matrix for the current state.

Parameters

  comp | Composition object containing 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.

## generateJacobianMatrix() [2/2]

void gridfire::GraphEngine::generateJacobianMatrix | ( | const fourdst::composition::Composition & | comp,
|  | double | T9,
|  | double | rho,
|  | const SparsityPattern & | sparsityPattern ) const

overridevirtual

Reimplemented from gridfire::DynamicEngine.

## generateStoichiometryMatrix()

void gridfire::GraphEngine::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.

## getDepth()

BuildDepthType gridfire::GraphEngine::getDepth | ( |  | ) | const

nodiscardoverridevirtual

Gets the depth of the network.

Returns
  The build depth of the network.

This method returns the current build depth of the reaction network, which indicates how many levels of reactions are included in the network.

Reimplemented from gridfire::DynamicEngine.

## getJacobianMatrixEntry()

double gridfire::GraphEngine::getJacobianMatrixEntry | ( | const fourdst::atomic::Species & | rowSpecies,
|  | const fourdst::atomic::Species & | colSpecies ) const

nodiscardoverridevirtual

Gets an entry from the previously generated Jacobian matrix.

Parameters

  rowSpecies | Species corresponding to the row index (i).
  colSpecies | Species corresponding to the column index (j).

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.

## getNetReactionStoichiometry()

std::unordered_map< fourdst::atomic::Species, int > gridfire::GraphEngine::getNetReactionStoichiometry | ( | const reaction::Reaction & | reaction | ) |

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.

## getNetworkReactions()

const reaction::ReactionSet & gridfire::GraphEngine::getNetworkReactions | ( |  | ) | const

nodiscardoverridevirtual

Gets the set of logical reactions in the network.

Returns
  Reference to the LogicalReactionSet containing all reactions.

Implements gridfire::DynamicEngine.

## getNetworkSpecies()

const std::vector< fourdst::atomic::Species > & gridfire::GraphEngine::getNetworkSpecies | ( |  | ) | const

nodiscardoverridevirtual

Gets the list of species in the network.

Returns
  Vector of Species objects representing all network species.

Implements gridfire::Engine.

## getPartitionFunction()

const partition::PartitionFunction & gridfire::GraphEngine::getPartitionFunction | ( |  | ) | const

nodiscard

Gets the partition function used for reaction rate calculations.

Returns
  Reference to the PartitionFunction object.

This method provides access to the partition function used in the engine, which is essential for calculating thermodynamic properties and reaction rates.

## getScreeningModel()

screening::ScreeningType gridfire::GraphEngine::getScreeningModel | ( |  | ) | const

nodiscardoverridevirtual

Gets the current electron screening model.

Returns
  The currently active screening model type.

Example usage:

screening::ScreeningType currentModel = engine.getScreeningModel();
gridfire::screening::ScreeningType
ScreeningType
Enumerates the available plasma screening models.
Definition screening_types.h:15

Implements gridfire::DynamicEngine.

## getSpeciesDestructionTimescales()

std::expected< std::unordered_map< fourdst::atomic::Species, double >, expectations::StaleEngineError > gridfire::GraphEngine::getSpeciesDestructionTimescales | ( | const fourdst::composition::Composition & | comp,
|  | double | T9,
|  | double | rho ) const

nodiscardoverridevirtual

Implements gridfire::DynamicEngine.

## getSpeciesIndex()

size_t gridfire::GraphEngine::getSpeciesIndex | ( | const fourdst::atomic::Species & | species | ) | const

nodiscardoverridevirtual

Gets the index of a species in the network.

Parameters

  species | The species for which to get the index.

Returns
  Index of the species in the network, or -1 if not found.

This method returns the index of the given species in the network's species vector. If the species is not found, it returns -1.

Implements gridfire::DynamicEngine.

## getSpeciesTimescales()

std::expected< std::unordered_map< fourdst::atomic::Species, double >, expectations::StaleEngineError > gridfire::GraphEngine::getSpeciesTimescales | ( | const fourdst::composition::Composition & | comp,
|  | double | T9,
|  | double | rho ) const

nodiscardoverridevirtual

Computes timescales for all species in the network.

Parameters

  comp | Composition object containing 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.

## getStoichiometryMatrixEntry()

int gridfire::GraphEngine::getStoichiometryMatrixEntry | ( | const fourdst::atomic::Species & | species,
|  | const reaction::Reaction & | reaction ) const

nodiscardoverridevirtual

Gets an entry from the stoichiometry matrix.

Parameters

  species | Species to look up stoichiometry for.
  reaction | Reaction to find.

Returns
  Stoichiometric coefficient for the species in the reaction.

The stoichiometry matrix must have been generated by `generateStoichiometryMatrix()`.

See also
  generateStoichiometryMatrix()

Implements gridfire::DynamicEngine.

## involvesSpecies()

bool gridfire::GraphEngine::involvesSpecies | ( | const fourdst::atomic::Species & | species | ) | const

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.

## isPrecomputationEnabled()

bool gridfire::GraphEngine::isPrecomputationEnabled | ( |  | ) | const

nodiscard

Checks if precomputation of reaction rates is enabled.

Returns
  True if precomputation is enabled, false otherwise.

This method allows checking the current state of precomputation for reaction rates in the engine.

## isStale()

bool gridfire::GraphEngine::isStale | ( | const NetIn & | netIn | ) |

overridevirtual

Implements gridfire::DynamicEngine.

## isUsingReverseReactions()

bool gridfire::GraphEngine::isUsingReverseReactions | ( |  | ) | const

nodiscard

Checks if reverse reactions are enabled.

Returns
  True if reverse reactions are enabled, false otherwise.

This method allows checking whether the engine is configured to use reverse reactions in its calculations.

## mapNetInToMolarAbundanceVector()

std::vector< double > gridfire::GraphEngine::mapNetInToMolarAbundanceVector | ( | const NetIn & | netIn | ) | const

nodiscardoverridevirtual

Maps the NetIn object to a vector of molar abundances.

Parameters

  netIn | The NetIn object containing the input conditions.

Returns
  Vector of molar abundances corresponding to the species in the network.

This method converts the NetIn object into a vector of molar abundances for each species in the network, which can be used for further calculations.

Implements gridfire::DynamicEngine.

## populateReactionIDMap()

void gridfire::GraphEngine::populateReactionIDMap | ( |  | ) |

private

Populates the reaction ID map.

This method populates the reaction ID map, which maps reaction IDs to REACLIBReaction objects.

## populateSpeciesToIndexMap()

void gridfire::GraphEngine::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.

## precomputeNetwork()

void gridfire::GraphEngine::precomputeNetwork | ( |  | ) |

private

## primeEngine()

PrimingReport gridfire::GraphEngine::primeEngine | ( | const NetIn & | netIn | ) |

nodiscardoverridevirtual

Prepares the engine for calculations with initial conditions.

Parameters

  netIn | The input conditions for the network.

Returns
  PrimingReport containing information about the priming process.

This method initializes the engine with the provided input conditions, setting up reactions, species, and precomputing necessary data.

Implements gridfire::DynamicEngine.

## rebuild()

void gridfire::GraphEngine::rebuild | ( | const fourdst::composition::Composition & | comp,
|  | const BuildDepthType | depth )

overridevirtual

Rebuilds the reaction network based on a new composition.

Parameters

  comp | The new composition to use for rebuilding the network.
  depth | The build depth to use for the network.

This method rebuilds the reaction network using the provided composition and build depth. It updates all internal data structures accordingly.

Reimplemented from gridfire::DynamicEngine.

## recordADTape()

void gridfire::GraphEngine::recordADTape | ( |  | ) | const

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.

## recordEpsADTape()

void gridfire::GraphEngine::recordEpsADTape | ( |  | ) | const

private

## reserveJacobianMatrix()

void gridfire::GraphEngine::reserveJacobianMatrix | ( |  | ) | const

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.

## setNetworkReactions()

void gridfire::GraphEngine::setNetworkReactions | ( | const reaction::ReactionSet & | reactions | ) |

overridevirtual

Implements gridfire::DynamicEngine.

## setPrecomputation()

void gridfire::GraphEngine::setPrecomputation | ( | bool | precompute | ) |

Sets whether to precompute reaction rates.

Parameters

  precompute | True to enable precomputation, false to disable.

This method allows enabling or disabling precomputation of reaction rates for performance optimization. When enabled, reaction rates are computed once and stored for later use.

## setScreeningModel()

void gridfire::GraphEngine::setScreeningModel | ( | screening::ScreeningType | model | ) |

overridevirtual

Sets the electron screening model for reaction rate calculations.

Parameters

  model | The type of screening model to use.

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.

Implements gridfire::DynamicEngine.

## setUseReverseReactions()

void gridfire::GraphEngine::setUseReverseReactions | ( | bool | useReverse | ) |

Sets whether to use reverse reactions in the engine.

Parameters

  useReverse | True to enable reverse reactions, false to disable.

This method allows enabling or disabling reverse reactions in the engine. If disabled, only forward reactions will be considered in calculations.

## syncInternalMaps()

void gridfire::GraphEngine::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.

## update()

fourdst::composition::Composition gridfire::GraphEngine::update | ( | const NetIn & | netIn | ) |

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:
  NetIn input = { ... };
  myEngine.update(input);
  gridfire::NetIn
  Definition network.h:51

Postcondition
  The internal state of the engine is updated to reflect the new conditions.

Implements gridfire::DynamicEngine.

## validateConservation()

bool gridfire::GraphEngine::validateConservation | ( |  | ) | const

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.

## Member Data Documentation

## m_atomicReverseRates

std::vector<std::unique_ptr<AtomicReverseRate> > gridfire::GraphEngine::m_atomicReverseRates

private

## m_config

Config& gridfire::GraphEngine::m_config = Config::getInstance()

private

## m_constants

constants gridfire::GraphEngine::m_constants

private

## m_depth

BuildDepthType gridfire::GraphEngine::m_depth

private

## m_epsADFun

CppAD::ADFun<double> gridfire::GraphEngine::m_epsADFun

mutableprivate

CppAD function for the energy generation rate.

## m_full_jacobian_sparsity_pattern

CppAD::sparse_rc<std::vector<size_t> > gridfire::GraphEngine::m_full_jacobian_sparsity_pattern

private

Full sparsity pattern for the Jacobian matrix.

## m_indexToSpeciesMap

std::unordered_map<size_t, fourdst::atomic::Species> gridfire::GraphEngine::m_indexToSpeciesMap

private

Map from index to species in the stoichiometry matrix.

## m_jac_work

CppAD::sparse_jac_work gridfire::GraphEngine::m_jac_work

mutableprivate

Work object for sparse Jacobian calculations.

## m_jacobianMatrix

boost::numeric::ublas::compressed_matrix<double> gridfire::GraphEngine::m_jacobianMatrix

mutableprivate

Jacobian matrix (species x species).

## m_logger

quill::Logger* gridfire::GraphEngine::m_logger = LogManager::getInstance().getLogger("log")

private

## m_networkSpecies

std::vector<fourdst::atomic::Species> gridfire::GraphEngine::m_networkSpecies

private

Vector of unique species in the network.

## m_networkSpeciesMap

std::unordered_map<std::string_view, fourdst::atomic::Species> gridfire::GraphEngine::m_networkSpeciesMap

private

Map from species name to Species object.

## m_partitionFunction

std::unique_ptr<partition::PartitionFunction> gridfire::GraphEngine::m_partitionFunction

private

Partition function for the network.

## m_precomputedReactions

std::vector<PrecomputedReaction> gridfire::GraphEngine::m_precomputedReactions

private

Precomputed reactions for efficiency.

## m_reactionIDMap

std::unordered_map<std::string_view, reaction::Reaction*> gridfire::GraphEngine::m_reactionIDMap

private

Map from reaction ID to REACLIBReaction. //PERF: This makes copies of REACLIBReaction and could be a performance bottleneck.

## m_reactions

reaction::ReactionSet gridfire::GraphEngine::m_reactions

private

Set of REACLIB reactions in the network.

## m_rhsADFun

CppAD::ADFun<double> gridfire::GraphEngine::m_rhsADFun

mutableprivate

CppAD function for the right-hand side of the ODE.

## m_screeningModel

std::unique_ptr<screening::ScreeningModel> gridfire::GraphEngine::m_screeningModel = screening::selectScreeningModel(m_screeningType)

private

## m_screeningType

screening::ScreeningType gridfire::GraphEngine::m_screeningType = screening::ScreeningType::BARE

private

Screening type for the reaction network. Default to no screening.

## m_speciesToIndexMap

std::unordered_map<fourdst::atomic::Species, size_t> gridfire::GraphEngine::m_speciesToIndexMap

private

Map from species to their index in the stoichiometry matrix.

## m_stoichiometryMatrix

boost::numeric::ublas::compressed_matrix<int> gridfire::GraphEngine::m_stoichiometryMatrix

private

Stoichiometry matrix (species x reactions).

## m_usePrecomputation

bool gridfire::GraphEngine::m_usePrecomputation = true

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.

## m_useReverseReactions

bool gridfire::GraphEngine::m_useReverseReactions = true

private

Flag to enable or disable reverse reactions. If false, only forward reactions are considered.

## m_weakRateInterpolator

rates::weak::WeakRateInterpolator gridfire::GraphEngine::m_weakRateInterpolator

private

Interpolator for weak reaction rates.

The documentation for this class was generated from the following files:

- src/include/gridfire/engine/engine_graph.h
- src/lib/engine/engine_graph.cpp