An engine view that uses a user-defined reaction network from a file. More...

#include <engine_defined.h>

Inheritance diagram for gridfire::FileDefinedEngineView:

Public Member Functions
	FileDefinedEngineView (DynamicEngine &baseEngine, const std::string &fileName, const io::NetworkFileParser &parser)
	Constructs a FileDefinedEngineView.

const DynamicEngine &	getBaseEngine () const override
	Gets the base engine.

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

StepDerivatives< double >	calculateRHSAndEnergy (const std::vector< double > &Y_defined, const double T9, const double rho) const override
	Calculates the right-hand side (dY/dt) and energy generation for the active species.

void	generateJacobianMatrix (const std::vector< double > &Y_defined, const double T9, const double rho) override
	Generates the Jacobian matrix for the active species.

double	getJacobianMatrixEntry (const int i_defined, const int j_defined) const override
	Gets an entry from the Jacobian matrix for the active species.

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

int	getStoichiometryMatrixEntry (const int speciesIndex_defined, const int reactionIndex_defined) const override
	Gets an entry from the stoichiometry matrix for the active species and reactions.

double	calculateMolarReactionFlow (const reaction::Reaction &reaction, const std::vector< double > &Y_defined, const double T9, const double rho) const override
	Calculates the molar reaction flow for a given reaction in the active network.

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

std::unordered_map< fourdst::atomic::Species, double >	getSpeciesTimescales (const std::vector< double > &Y_defined, const double T9, const double rho) const override
	Computes timescales for all active species in the network.

void	update (const NetIn &netIn) override
	Updates the engine view if it is marked as stale.

void	setNetworkFile (const std::string &fileName)
	Sets a new network file to define the active reactions.

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.

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

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

Private Types
using	Config = fourdst::config::Config

using	LogManager = fourdst::logging::LogManager

Private Member Functions
void	buildFromFile (const std::string &fileName)
	Builds the active species and reaction sets from a file.

std::vector< size_t >	constructSpeciesIndexMap () const
	Constructs the species index map.

std::vector< size_t >	constructReactionIndexMap () const
	Constructs the reaction index map.

std::vector< double >	mapViewToFull (const std::vector< double > &defined) const
	Maps a vector of culled abundances to a vector of full abundances.

std::vector< double >	mapFullToView (const std::vector< double > &full) const
	Maps a vector of full abundances to a vector of culled abundances.

size_t	mapViewToFullSpeciesIndex (size_t definedSpeciesIndex) const
	Maps a culled species index to a full species index.

size_t	mapViewToFullReactionIndex (size_t definedReactionIndex) const
	Maps a culled reaction index to a full reaction index.

void	validateNetworkState () const
	Validates that the FileDefinedEngineView is not stale.

Private Attributes
Config &	m_config = Config::getInstance()
	A reference to the singleton Config instance.

quill::Logger *	m_logger = LogManager::getInstance().getLogger("log")
	A pointer to the logger instance.

DynamicEngine &	m_baseEngine
	The underlying engine to which this view delegates calculations.

std::string	m_fileName
	Parser for the network file.

const io::NetworkFileParser &	m_parser
	Active species in the defined engine.

std::vector< fourdst::atomic::Species >	m_activeSpecies
	Active reactions in the defined engine.

reaction::LogicalReactionSet	m_activeReactions
	Maps indices of active species to indices in the full network.

std::vector< size_t >	m_speciesIndexMap
	Maps indices of active reactions to indices in the full network.

std::vector< size_t >	m_reactionIndexMap

bool	m_isStale = true
	A flag indicating whether the view is stale and needs to be updated.

Detailed Description

An engine view that uses a user-defined reaction network from a file.

This class implements an EngineView that restricts the reaction network to a specific set of reactions defined in an external file. It acts as a filter or a view on a larger, more comprehensive base engine. The file provides a list of reaction identifiers, and this view will only consider those reactions and the species involved in them.

This is useful for focusing on a specific sub-network for analysis, debugging, or performance reasons, without modifying the underlying full network.

The view maintains mappings between the indices of its active (defined) species and reactions and the corresponding indices in the full network of the base engine. All calculations are delegated to the base engine after mapping the inputs from the view's context to the full network context, and the results are mapped back.

Definition at line 36 of file engine_defined.h.

Member Typedef Documentation

◆ Config

using gridfire::FileDefinedEngineView::Config = fourdst::config::Config

private

Definition at line 223 of file engine_defined.h.

◆ LogManager

using gridfire::FileDefinedEngineView::LogManager = fourdst::logging::LogManager

private

Definition at line 224 of file engine_defined.h.

Constructor & Destructor Documentation

◆ FileDefinedEngineView()

gridfire::FileDefinedEngineView::FileDefinedEngineView	(	DynamicEngine &	baseEngine,
		const std::string &	fileName,
		const io::NetworkFileParser &	parser )

explicit

Constructs a FileDefinedEngineView.

Parameters

baseEngine	The underlying DynamicEngine to which this view delegates calculations.
fileName	The path to the file that defines the reaction network for this view.
parser	A reference to a parser object capable of parsing the network file.

Usage Example:: MyParser parser;

DynamicEngine baseEngine(...);

FileDefinedEngineView view(baseEngine, "my_network.net", parser);

gridfire::DynamicEngine
Abstract class for engines supporting Jacobian and stoichiometry operations.
Definition engine_abstract.h:121

gridfire::FileDefinedEngineView::FileDefinedEngineView
FileDefinedEngineView(DynamicEngine &baseEngine, const std::string &fileName, const io::NetworkFileParser &parser)
Constructs a FileDefinedEngineView.
Definition engine_defined.cpp:8

Postcondition: The view is initialized with the reactions and species from the specified file.

Exceptions

std::runtime_error If a reaction from the file is not found in the base engine.

Definition at line 8 of file engine_defined.cpp.

Member Function Documentation

◆ buildFromFile()

void gridfire::FileDefinedEngineView::buildFromFile ( const std::string & fileName )

private

Builds the active species and reaction sets from a file.

This method uses the provided parser to read reaction names from the given file. It then finds these reactions in the base engine's full network and populates the m_activeReactions and m_activeSpecies members. Finally, it constructs the index maps for the active sets.

Parameters

fileName The path to the network definition file.

Postcondition

m_activeReactions and m_activeSpecies are populated.
m_speciesIndexMap and m_reactionIndexMap are constructed.
m_isStale is set to false.

Exceptions

std::runtime_error If a reaction from the file is not found in the base engine.

Definition at line 208 of file engine_defined.cpp.

◆ calculateMolarReactionFlow()

double gridfire::FileDefinedEngineView::calculateMolarReactionFlow	(	const reaction::Reaction &	reaction,
		const std::vector< double > &	Y_defined,
		const double	T9,
		const double	rho ) const

overridevirtual

Calculates the molar reaction flow for a given reaction in the active network.

Parameters

reaction	The reaction for which to calculate the flow.
Y_defined	Vector of current abundances for the active species.
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).

Exceptions

std::runtime_error If the view is stale or if the reaction is not in the active set.

Implements gridfire::DynamicEngine.

Definition at line 85 of file engine_defined.cpp.

◆ calculateRHSAndEnergy()

StepDerivatives< double > gridfire::FileDefinedEngineView::calculateRHSAndEnergy	(	const std::vector< double > &	Y_defined,
		const double	T9,
		const double	rho ) const

overridevirtual

Calculates the right-hand side (dY/dt) and energy generation for the active species.

Parameters

Y_defined	A vector of abundances for the active species.
T9	The temperature in units of 10^9 K.
rho	The density in g/cm^3.

Returns: A StepDerivatives struct containing the derivatives of the active species and the nuclear energy generation rate.

Exceptions

std::runtime_error If the view is stale (i.e., update() has not been called after setNetworkFile()).

Implements gridfire::Engine.

Definition at line 29 of file engine_defined.cpp.

◆ constructReactionIndexMap()

std::vector< size_t > gridfire::FileDefinedEngineView::constructReactionIndexMap ( ) const

private

Constructs the reaction index map.

Returns: A vector mapping defined reaction indices to full reaction indices.

This method creates a map from the indices of the active reactions to the indices of the corresponding reactions in the full network.

Exceptions

std::runtime_error If an active reaction is not found in the base engine's reaction list.

Definition at line 176 of file engine_defined.cpp.

◆ constructSpeciesIndexMap()

std::vector< size_t > gridfire::FileDefinedEngineView::constructSpeciesIndexMap ( ) const

private

Constructs the species index map.

Returns: A vector mapping defined species indices to full species indices.

This method creates a map from the indices of the active species to the indices of the corresponding species in the full network.

Exceptions

std::runtime_error If an active species is not found in the base engine's species list.

Definition at line 147 of file engine_defined.cpp.

◆ generateJacobianMatrix()

void gridfire::FileDefinedEngineView::generateJacobianMatrix	(	const std::vector< double > &	Y_defined,
		const double	T9,
		const double	rho )

overridevirtual

Generates the Jacobian matrix for the active species.

Parameters

Y_defined	A vector of abundances for the active species.
T9	The temperature in units of 10^9 K.
rho	The density in g/cm^3.

Exceptions

std::runtime_error If the view is stale.

Implements gridfire::DynamicEngine.

Definition at line 45 of file engine_defined.cpp.

◆ generateStoichiometryMatrix()

void gridfire::FileDefinedEngineView::generateStoichiometryMatrix ( )

overridevirtual

Generates the stoichiometry matrix for the active reactions and species.

Exceptions

std::runtime_error If the view is stale.

Implements gridfire::DynamicEngine.

Definition at line 68 of file engine_defined.cpp.

◆ getBaseEngine()

const DynamicEngine & gridfire::FileDefinedEngineView::getBaseEngine ( ) const

overridevirtual

Gets the base engine.

Returns: A const reference to the base engine.

Implements gridfire::EngineView< DynamicEngine >.

Definition at line 21 of file engine_defined.cpp.

◆ getJacobianMatrixEntry()

double gridfire::FileDefinedEngineView::getJacobianMatrixEntry	(	const int	i_defined,
		const int	j_defined ) const

overridevirtual

Gets an entry from the Jacobian matrix for the active species.

Parameters

i_defined	The row index (species index) in the defined matrix.
j_defined	The column index (species index) in the defined matrix.

Returns: The value of the Jacobian matrix at (i_defined, j_defined).

Exceptions

std::runtime_error	If the view is stale.
std::out_of_range	If an index is out of bounds.

Implements gridfire::DynamicEngine.

Definition at line 56 of file engine_defined.cpp.

◆ getNetworkReactions()

const reaction::LogicalReactionSet & gridfire::FileDefinedEngineView::getNetworkReactions ( ) const

overridevirtual

Gets the set of active logical reactions in the network.

Returns: Reference to the LogicalReactionSet containing all active reactions.

Exceptions

std::runtime_error If the view is stale.

Implements gridfire::DynamicEngine.

Definition at line 102 of file engine_defined.cpp.

◆ getNetworkSpecies()

const std::vector< Species > & gridfire::FileDefinedEngineView::getNetworkSpecies ( ) const

overridevirtual

Gets the list of active species in the network defined by the file.

Returns: A const reference to the vector of active species.

Implements gridfire::Engine.

Definition at line 25 of file engine_defined.cpp.

◆ getScreeningModel()

screening::ScreeningType gridfire::FileDefinedEngineView::getScreeningModel ( ) const

nodiscardoverridevirtual

Gets the screening model from the base engine.

Returns: The current screening model type.

Implements gridfire::DynamicEngine.

Definition at line 143 of file engine_defined.cpp.

◆ getSpeciesTimescales()

std::unordered_map< Species, double > gridfire::FileDefinedEngineView::getSpeciesTimescales	(	const std::vector< double > &	Y_defined,
		const double	T9,
		const double	rho ) const

overridevirtual

Computes timescales for all active species in the network.

Parameters

Y_defined	Vector of current abundances for the active species.
T9	Temperature in units of 10^9 K.
rho	Density in g/cm^3.

Returns: Map from Species to their characteristic timescales (s).

Exceptions

std::runtime_error If the view is stale.

Implements gridfire::DynamicEngine.

Definition at line 108 of file engine_defined.cpp.

◆ getStoichiometryMatrixEntry()

int gridfire::FileDefinedEngineView::getStoichiometryMatrixEntry	(	const int	speciesIndex_defined,
		const int	reactionIndex_defined ) const

overridevirtual

Gets an entry from the stoichiometry matrix for the active species and reactions.

Parameters

speciesIndex_defined	The index of the species in the defined species list.
reactionIndex_defined	The index of the reaction in the defined reaction list.

Returns: The stoichiometric coefficient for the given species and reaction.

Exceptions

std::runtime_error	If the view is stale.
std::out_of_range	If an index is out of bounds.

Implements gridfire::DynamicEngine.

Definition at line 74 of file engine_defined.cpp.

◆ mapFullToView()

std::vector< double > gridfire::FileDefinedEngineView::mapFullToView ( const std::vector< double > & full ) const

private

Maps a vector of full abundances to a vector of culled abundances.

Parameters

full	A vector of abundances for the full network.

Returns: A vector of abundances for the active species, with the abundances of the active species copied from the full vector.

Definition at line 276 of file engine_defined.cpp.

◆ mapViewToFull()

std::vector< double > gridfire::FileDefinedEngineView::mapViewToFull ( const std::vector< double > & defined ) const

private

Maps a vector of culled abundances to a vector of full abundances.

Parameters

defined A vector of abundances for the active species.

Returns: A vector of abundances for the full network, with the abundances of the active species copied from the defined vector.

Definition at line 267 of file engine_defined.cpp.

◆ mapViewToFullReactionIndex()

size_t gridfire::FileDefinedEngineView::mapViewToFullReactionIndex ( size_t definedReactionIndex ) const

private

Maps a culled reaction index to a full reaction index.

Parameters

definedReactionIndex The index of the reaction in the defined reaction list.

Returns: The index of the corresponding reaction in the full network.

Exceptions

std::out_of_range If the defined index is out of bounds for the reaction index map.

Definition at line 294 of file engine_defined.cpp.

◆ mapViewToFullSpeciesIndex()

size_t gridfire::FileDefinedEngineView::mapViewToFullSpeciesIndex ( size_t definedSpeciesIndex ) const

private

Maps a culled species index to a full species index.

Parameters

definedSpeciesIndex The index of the species in the defined species list.

Returns: The index of the corresponding species in the full network.

Exceptions

std::out_of_range If the defined index is out of bounds for the species index map.

Definition at line 285 of file engine_defined.cpp.

◆ setNetworkFile()

void gridfire::FileDefinedEngineView::setNetworkFile ( const std::string & fileName )

Sets a new network file to define the active reactions.

Parameters

fileName The path to the new network definition file.

Usage Example:: view.setNetworkFile("another_network.net");

view.update(netIn); // Must be called before using the view again

Postcondition: The view is marked as stale. update() must be called before further use.

Definition at line 133 of file engine_defined.cpp.

◆ setScreeningModel()

void gridfire::FileDefinedEngineView::setScreeningModel ( screening::ScreeningType model )

overridevirtual

Sets the screening model for the base engine.

Parameters

model The screening model to set.

Implements gridfire::DynamicEngine.

Definition at line 139 of file engine_defined.cpp.

◆ update()

void gridfire::FileDefinedEngineView::update ( const NetIn & netIn )

overridevirtual

Updates the engine view if it is marked as stale.

This method checks if the view is stale (e.g., after setNetworkFile was called). If it is, it rebuilds the active network from the currently set file. The netIn parameter is not used by this implementation but is required by the interface.

Parameters

netIn The current network input (unused).

Postcondition: If the view was stale, it is rebuilt and is no longer stale.

Implements gridfire::DynamicEngine.

Definition at line 127 of file engine_defined.cpp.

◆ validateNetworkState()

void gridfire::FileDefinedEngineView::validateNetworkState ( ) const

private

Validates that the FileDefinedEngineView is not stale.

Exceptions

std::runtime_error If the view is stale (i.e., update() has not been called after the view was made stale).

Definition at line 303 of file engine_defined.cpp.

Member Data Documentation

◆ m_activeReactions

reaction::LogicalReactionSet gridfire::FileDefinedEngineView::m_activeReactions

private

Maps indices of active species to indices in the full network.

Definition at line 240 of file engine_defined.h.

◆ m_activeSpecies

std::vector<fourdst::atomic::Species> gridfire::FileDefinedEngineView::m_activeSpecies

private

Active reactions in the defined engine.

Definition at line 238 of file engine_defined.h.

◆ m_baseEngine

DynamicEngine& gridfire::FileDefinedEngineView::m_baseEngine

private

The underlying engine to which this view delegates calculations.

Name of the file defining the reaction set considered by the engine view.

Definition at line 231 of file engine_defined.h.

◆ m_config

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

private

A reference to the singleton Config instance.

Definition at line 226 of file engine_defined.h.

◆ m_fileName

std::string gridfire::FileDefinedEngineView::m_fileName

private

Parser for the network file.

Definition at line 233 of file engine_defined.h.

◆ m_isStale

bool gridfire::FileDefinedEngineView::m_isStale = true

private

A flag indicating whether the view is stale and needs to be updated.

Definition at line 248 of file engine_defined.h.

◆ m_logger

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

private

A pointer to the logger instance.

Definition at line 228 of file engine_defined.h.

◆ m_parser

const io::NetworkFileParser& gridfire::FileDefinedEngineView::m_parser

private

Active species in the defined engine.

Definition at line 235 of file engine_defined.h.

◆ m_reactionIndexMap

std::vector<size_t> gridfire::FileDefinedEngineView::m_reactionIndexMap

private

Definition at line 245 of file engine_defined.h.

◆ m_speciesIndexMap

std::vector<size_t> gridfire::FileDefinedEngineView::m_speciesIndexMap

private

Maps indices of active reactions to indices in the full network.

Definition at line 243 of file engine_defined.h.

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

src/network/include/gridfire/engine/views/engine_defined.h
src/network/lib/engine/views/engine_defined.cpp

Public Member Functions

Private Types

Private Member Functions

Private Attributes

Detailed Description

Member Typedef Documentation

◆ Config

◆ LogManager

Constructor & Destructor Documentation

◆ FileDefinedEngineView()

Member Function Documentation

◆ buildFromFile()

◆ calculateMolarReactionFlow()

◆ calculateRHSAndEnergy()

◆ constructReactionIndexMap()

◆ constructSpeciesIndexMap()

◆ generateJacobianMatrix()

◆ generateStoichiometryMatrix()

◆ getBaseEngine()

◆ getJacobianMatrixEntry()

◆ getNetworkReactions()

◆ getNetworkSpecies()

◆ getScreeningModel()

◆ getSpeciesTimescales()

◆ getStoichiometryMatrixEntry()

◆ mapFullToView()

◆ mapViewToFull()

◆ mapViewToFullReactionIndex()

◆ mapViewToFullSpeciesIndex()

◆ setNetworkFile()

◆ setScreeningModel()

◆ update()

◆ validateNetworkState()

Member Data Documentation

◆ m_activeReactions

◆ m_activeSpecies

◆ m_baseEngine

◆ m_config

◆ m_fileName

◆ m_isStale

◆ m_logger

◆ m_parser

◆ m_reactionIndexMap

◆ m_speciesIndexMap