gridfire::engine::NetworkJacobian Class Reference

A wrapper class for handling the network Jacobian matrix. More...

#include <jacobian.h>

Collaboration diagram for gridfire::engine::NetworkJacobian:

Public Member Functions
	NetworkJacobian (const Eigen::SparseMatrix< double > &jacobianMatrix, const std::function< fourdst::atomic::Species(size_t)> &indexToSpeciesFunc)
	Constructs a NetworkJacobian with the given sparse matrix and species index mapping function.
	NetworkJacobian (const NetworkJacobian &jacobian)
	Copy constructor for NetworkJacobian.
	NetworkJacobian (NetworkJacobian &&jacobian) noexcept
	Copy assignment operator for NetworkJacobian.
NetworkJacobian &	operator= (NetworkJacobian &&jacobian) noexcept
	Move constructor for NetworkJacobian.
double	operator() (const fourdst::atomic::Species &row, const fourdst::atomic::Species &col) const
	Accesses the value at the specified row and column corresponding to the given species.
double	operator() (size_t i, size_t j) const
	Accesses the value at the specified row and column indices.
void	set (const fourdst::atomic::Species &row, const fourdst::atomic::Species &col, double value)
	Sets the value at the specified row and column corresponding to the given species.
void	set (size_t i, size_t j, double value)
	Sets the value at the specified row and column indices.
void	set (const JacobianEntry &entry)
	Sets the value in the Jacobian matrix based on a JacobianEntry.
std::tuple< size_t, size_t >	shape () const
	Retrieves the shape of the Jacobian matrix as a tuple (rows, columns).
size_t	rank () const
	Retrieves the rank of the Jacobian matrix.
size_t	nnz () const
	Get the number of non-zero entries in the Jacobian matrix.
bool	singular () const
	Checks if the Jacobian matrix is singular.
std::vector< JacobianEntry >	infs () const
	Retrieves all entries in the Jacobian matrix that are infinite.
std::vector< JacobianEntry >	nans () const
	Retrieves all entries in the Jacobian matrix that are NaN (Not a Number).
Eigen::SparseMatrix< double >	data () const
	Provides access to the underlying sparse matrix data.
const std::unordered_map< fourdst::atomic::Species, size_t > &	mapping () const
	Provides access to the species-to-index mapping.
void	to_csv (const std::string &filename) const
	Exports the Jacobian matrix to a CSV file.

Private Attributes
Eigen::SparseMatrix< double >	m_jacobianMatrix
std::unordered_map< fourdst::atomic::Species, size_t >	m_speciesToIndexMap
std::optional< size_t >	m_rank = std::nullopt

Detailed Description

A wrapper class for handling the network Jacobian matrix.

This class encapsulates an Eigen::SparseMatrix to represent the Jacobian matrix of a reaction network. It provides methods for accessing and modifying matrix entries using species identifiers, as well as utility functions for analyzing the matrix (e.g., checking for singularity, counting non-zero entries).

Constructor & Destructor Documentation

NetworkJacobian() [1/3]

gridfire::engine::NetworkJacobian::NetworkJacobian ( const Eigen::SparseMatrix< double > &  jacobianMatrix, const std::function< fourdst::atomic::Species(size_t)> &  indexToSpeciesFunc  )

explicit

Constructs a NetworkJacobian with the given sparse matrix and species index mapping function.

Parameters

jacobianMatrix	The sparse matrix representing the Jacobian.
indexToSpeciesFunc	A function that maps matrix indices to species identifiers.

NetworkJacobian() [2/3]

gridfire::engine::NetworkJacobian::NetworkJacobian

(

const NetworkJacobian &

jacobian

)

Copy constructor for NetworkJacobian.

Parameters

jacobian

The NetworkJacobian instance to copy from.

NetworkJacobian() [3/3]

gridfire::engine::NetworkJacobian::NetworkJacobian ( NetworkJacobian &&  jacobian )

noexcept

Copy assignment operator for NetworkJacobian.

Parameters

jacobian

The NetworkJacobian instance to copy from.

Returns

Reference to the assigned NetworkJacobian instance.

Member Function Documentation

data()

Eigen::SparseMatrix< double > gridfire::engine::NetworkJacobian::data

(

)

const

Provides access to the underlying sparse matrix data.

Returns

The Eigen::SparseMatrix representing the Jacobian.

infs()

std::vector< JacobianEntry > gridfire::engine::NetworkJacobian::infs

(

)

const

Retrieves all entries in the Jacobian matrix that are infinite.

Returns

A vector of JacobianEntry representing infinite entries.

mapping()

const std::unordered_map< fourdst::atomic::Species, size_t > & gridfire::engine::NetworkJacobian::mapping

(

)

const

Provides access to the species-to-index mapping.

Returns

A constant reference to the species-to-index mapping.

nans()

std::vector< JacobianEntry > gridfire::engine::NetworkJacobian::nans

(

)

const

Retrieves all entries in the Jacobian matrix that are NaN (Not a Number).

Returns

A vector of JacobianEntry representing NaN entries.

nnz()

size_t gridfire::engine::NetworkJacobian::nnz

(

)

const

Get the number of non-zero entries in the Jacobian matrix.

Returns

The number of non-zero entries.

operator()() [1/2]

double gridfire::engine::NetworkJacobian::operator()	(	const fourdst::atomic::Species &	row,
		const fourdst::atomic::Species &	col
	)		const

Accesses the value at the specified row and column corresponding to the given species.

Parameters

row	Species for the row
col	Species for the column

Returns

value at the specified position

operator()() [2/2]

double gridfire::engine::NetworkJacobian::operator()	(	size_t	i,
		size_t	j
	)		const

Accesses the value at the specified row and column indices.

Parameters

i	Row index
j	Column index

Returns

value at the specified position

operator=()

NetworkJacobian & gridfire::engine::NetworkJacobian::operator= ( NetworkJacobian &&  jacobian )

noexcept

Move constructor for NetworkJacobian.

Parameters

jacobian

The NetworkJacobian instance to move from.

Returns

Reference to the assigned NetworkJacobian instance.

rank()

size_t gridfire::engine::NetworkJacobian::rank

(

)

const

Retrieves the rank of the Jacobian matrix.

Returns

The rank of the matrix.

Note

Rank is computed using QR decomposition and cached for efficiency. The rank is computed the first time this method is called and stored for subsequent calls. If any set operation is performed on the matrix, the cached rank is invalidated.

set() [1/3]

void gridfire::engine::NetworkJacobian::set	(	const fourdst::atomic::Species &	row,
		const fourdst::atomic::Species &	col,
		double	value
	)

Sets the value at the specified row and column corresponding to the given species.

Parameters

row	Row species
col	Column species
value	Value to set

set() [2/3]

void gridfire::engine::NetworkJacobian::set

(

const JacobianEntry &

entry

)

Sets the value in the Jacobian matrix based on a JacobianEntry.

Parameters

entry

The JacobianEntry containing row species, column species, and value.

set() [3/3]

void gridfire::engine::NetworkJacobian::set	(	size_t	i,
		size_t	j,
		double	value
	)

Sets the value at the specified row and column indices.

Parameters

i	Row index
j	Column index
value	Value to set

shape()

std::tuple< size_t, size_t > gridfire::engine::NetworkJacobian::shape

(

)

const

Retrieves the shape of the Jacobian matrix as a tuple (rows, columns).

Returns

A tuple containing the number of rows and columns.

singular()

bool gridfire::engine::NetworkJacobian::singular

(

)

const

Checks if the Jacobian matrix is singular.

Returns

True if the matrix is singular, false otherwise.

to_csv()

void gridfire::engine::NetworkJacobian::to_csv

(

const std::string &

filename

)

const

Exports the Jacobian matrix to a CSV file.

Parameters

filename

The name of the CSV file to export to.

Member Data Documentation

m_jacobianMatrix

Eigen::SparseMatrix<double> gridfire::engine::NetworkJacobian::m_jacobianMatrix

private

m_rank

std::optional<size_t> gridfire::engine::NetworkJacobian::m_rank = std::nullopt

mutableprivate

m_speciesToIndexMap

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

private

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

• src/include/gridfire/engine/types/jacobian.h
• src/lib/engine/types/jacobian.cpp