Provides a view of a DynamicEngine filtered to reactions involving a specified priming species. More...

#include <engine_priming.h>

Inheritance diagram for gridfire::engine::NetworkPrimingEngineView:

Collaboration diagram for gridfire::engine::NetworkPrimingEngineView:

Public Member Functions
	NetworkPrimingEngineView (const std::string &primingSymbol, GraphEngine &baseEngine)
	Constructs the view by looking up the priming species by symbol.

	NetworkPrimingEngineView (const fourdst::atomic::Species &primingSpecies, GraphEngine &baseEngine)
	Constructs the view using an existing Species object.

Public Member Functions inherited from gridfire::engine::DefinedEngineView
	DefinedEngineView (const std::vector< std::string > &peNames, GraphEngine &baseEngine)

const DynamicEngine &	getBaseEngine () const override
	Get the base engine associated with this defined engine view.

const std::vector< fourdst::atomic::Species > &	getNetworkSpecies () const override
	Gets the list of active species in the network defined by the file.

std::expected< StepDerivatives< double >, engine::EngineStatus >	calculateRHSAndEnergy (const fourdst::composition::CompositionAbstract &comp, double T9, double rho) const override
	Calculates the right-hand side (dY/dt) and energy generation for the active species.

EnergyDerivatives	calculateEpsDerivatives (const fourdst::composition::CompositionAbstract &comp, double T9, double rho) const override
	Calculate the derivatives of the energy generation rate with respect to T and rho.

NetworkJacobian	generateJacobianMatrix (const fourdst::composition::CompositionAbstract &comp, double T9, double rho) const override
	Generates the Jacobian matrix for the active species.

NetworkJacobian	generateJacobianMatrix (const fourdst::composition::CompositionAbstract &comp, double T9, double rho, const std::vector< fourdst::atomic::Species > &activeSpecies) const override
	Generates the Jacobian matrix for the active species.

NetworkJacobian	generateJacobianMatrix (const fourdst::composition::CompositionAbstract &comp, double T9, double rho, const SparsityPattern &sparsityPattern) const override
	Generates the Jacobian matrix for a given sparsity pattern.

void	generateStoichiometryMatrix () override
	Generates the stoichiometry matrix for the active reactions and species.

int	getStoichiometryMatrixEntry (const fourdst::atomic::Species &species, const reaction::Reaction &reaction) const override
	Gets an entry from the stoichiometry matrix for the active species and reactions.

double	calculateMolarReactionFlow (const reaction::Reaction &reaction, const fourdst::composition::CompositionAbstract &comp, double T9, double rho) const override
	Calculates the molar reaction flow for a given reaction in the active network.

const reaction::ReactionSet &	getNetworkReactions () const override
	Gets the set of active logical reactions in the network.

void	setNetworkReactions (const reaction::ReactionSet &reactions) override
	Sets the active reactions in the network.

std::expected< std::unordered_map< fourdst::atomic::Species, double >, engine::EngineStatus >	getSpeciesTimescales (const fourdst::composition::CompositionAbstract &comp, double T9, double rho) const override
	Computes timescales for all active species in the network.

std::expected< std::unordered_map< fourdst::atomic::Species, double >, engine::EngineStatus >	getSpeciesDestructionTimescales (const fourdst::composition::CompositionAbstract &comp, double T9, double rho) const override
	Computes destruction timescales for all active species in the network.

fourdst::composition::Composition	update (const NetIn &netIn) override
	Updates the engine view if it is marked as stale.

bool	isStale (const NetIn &netIn) override
	Checks if the engine view is stale.

void	setScreeningModel (screening::ScreeningType model) override
	Sets the screening model for the base engine.

screening::ScreeningType	getScreeningModel () const override
	Gets the screening model from the base engine.

size_t	getSpeciesIndex (const fourdst::atomic::Species &species) const override
	Maps a species from the full network to its index in the defined active network.

std::vector< double >	mapNetInToMolarAbundanceVector (const NetIn &netIn) const override
	Map from a NetIn object to a vector of molar abundances for the active species.

PrimingReport	primeEngine (const NetIn &netIn) override
	Prime the engine view for calculations. This will delegate to the base engine.

fourdst::composition::Composition	collectComposition (const fourdst::composition::CompositionAbstract &comp, double T9, double rho) const override
	Collects a Composition object from the base engine.

SpeciesStatus	getSpeciesStatus (const fourdst::atomic::Species &species) const override
	Gets the status of a species in the active network.

Public Member Functions inherited from gridfire::engine::DynamicEngine
virtual BuildDepthType	getDepth () const
	Get the depth of the network.

virtual void	rebuild (const fourdst::composition::CompositionAbstract &comp, BuildDepthType depth)
	Rebuild the network with a specified depth.

Public Member Functions inherited from gridfire::engine::Engine
virtual	~Engine ()=default
	Virtual destructor.

Public Member Functions inherited from gridfire::engine::EngineView< DynamicEngine >
virtual	~EngineView ()=default
	Virtual destructor.

Private Member Functions
std::vector< std::string >	constructPrimingReactionSet (const fourdst::atomic::Species &primingSpecies, const GraphEngine &baseEngine) const
	Constructs the set of reaction names that involve the priming species.

Private Attributes
quill::Logger *	m_logger = LogManager::getInstance().getLogger("log")

fourdst::atomic::Species	m_primingSpecies
	The priming species, if specified.

Additional Inherited Members
Protected Attributes inherited from gridfire::engine::DefinedEngineView
bool	m_isStale = true

GraphEngine &	m_baseEngine

Detailed Description

Provides a view of a DynamicEngine filtered to reactions involving a specified priming species.

This view constructs a subset of the network reactions from the base engine that contain the given priming species and delegates all engine operations to the underlying engine.

See implementation in engine_priming.cpp for details on reaction set construction.

Note: Throws std::runtime_error if no priming reactions are found for the species.

Constructor & Destructor Documentation

◆ NetworkPrimingEngineView() [1/2]

gridfire::engine::NetworkPrimingEngineView::NetworkPrimingEngineView	(	const std::string &	primingSymbol,
		GraphEngine &	baseEngine
	)

Constructs the view by looking up the priming species by symbol.

Parameters

primingSymbol	Symbol string of the species to prime.
baseEngine	Reference to the base DynamicEngine to wrap.

Precondition: primingSymbol must correspond to a valid species in atomic::species registry.

Postcondition: The view will contain only reactions that involve the priming species.

Exceptions

std::out_of_range	If primingSymbol is not found in the species registry.
std::runtime_error	If no reactions contain the priming species.

◆ NetworkPrimingEngineView() [2/2]

gridfire::engine::NetworkPrimingEngineView::NetworkPrimingEngineView	(	const fourdst::atomic::Species &	primingSpecies,
		GraphEngine &	baseEngine
	)

Constructs the view using an existing Species object.

Parameters

primingSpecies	The species object to prime.
baseEngine	Reference to the base DynamicEngine to wrap.

Precondition: primingSpecies must be valid and present in the network of baseEngine.

Postcondition: The view will contain only reactions that involve the priming species.

Exceptions

std::runtime_error If no reactions contain the priming species.

Member Function Documentation

◆ constructPrimingReactionSet()

std::vector< std::string > gridfire::engine::NetworkPrimingEngineView::constructPrimingReactionSet	(	const fourdst::atomic::Species &	primingSpecies,
		const GraphEngine &	baseEngine
	)		const

private

Constructs the set of reaction names that involve the priming species.

Parameters

primingSpecies	Species for which to collect priming reactions.
baseEngine	Base engine containing the full network of reactions.

Precondition: baseEngine.getNetworkReactions() returns a valid iterable set of reactions.

Postcondition: Returns a vector of unique reaction name strings containing the priming species.

Returns: Vector of reaction name strings containing the priming species.

Exceptions

std::runtime_error If no reactions involve the priming species.

Member Data Documentation

◆ m_logger

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

private

◆ m_primingSpecies

fourdst::atomic::Species gridfire::engine::NetworkPrimingEngineView::m_primingSpecies

private

The priming species, if specified.

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

src/include/gridfire/engine/views/engine_priming.h
src/lib/engine/views/engine_priming.cpp

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ NetworkPrimingEngineView() [1/2]

◆ NetworkPrimingEngineView() [2/2]

Member Function Documentation

◆ constructPrimingReactionSet()

Member Data Documentation

◆ m_logger

◆ m_primingSpecies