System Jacobians that use Eigen sparse matrices for storage. More...

#include <EigenSparseJacobian.h>

Inheritance diagram for EigenSparseJacobian:

Detailed Description

System Jacobians that use Eigen sparse matrices for storage.

Definition at line 16 of file EigenSparseJacobian.h.

Public Member Functions
void	initialize (size_t networkSize) override
	Called during setup for any processes that need to be completed prior to setup functions used in sundials.

void	reset () override
	Reset parameters as needed.

void	setValue (size_t row, size_t col, double value) override
	Set a value at the specified row and column of the jacobian triplet vector.

void	updatePreconditioner () override
	Transform Jacobian vector and write into preconditioner, P = (I - gamma * J)

void	updateTransient (double rdt, int *mask) override
	Update the diagonal terms in the Jacobian by using the transient mask \( \alpha \).

Eigen::SparseMatrix< double >	jacobian ()
	Return underlying Jacobian matrix.

Eigen::SparseMatrix< double >	matrix ()
	Return the internal preconditioner matrix.

void	printPreconditioner () override
	Print preconditioner contents.

void	printJacobian ()
	Print jacobian contents.

Public Member Functions inherited from SystemJacobian
virtual const string	type () const =0
	Derived type, corresponding to names registered with SystemJacobianFactory.

virtual void	setValue (size_t row, size_t col, double value)
	Set a value at the specified row and column of the jacobian triplet vector.

virtual void	stateAdjustment (vector< double > &state)
	Adjust the state vector based on the preconditioner, e.g., Adaptive preconditioning uses a strictly positive composition when preconditioning which is handled by this function.

string	preconditionerSide () const
	Get preconditioner application side for CVODES.

virtual void	setPreconditionerSide (const string &preconSide)
	For iterative solvers, set the side where the preconditioner is applied.

virtual void	updatePreconditioner ()
	Transform Jacobian vector and write into preconditioner, P = (I - gamma * J)

virtual void	updateTransient (double rdt, int *mask)
	Update the diagonal terms in the Jacobian by using the transient mask \( \alpha \).

virtual void	solve (const size_t stateSize, double rhs_vector, double output)
	Solve a linear system using the system matrix M

virtual void	setup ()
	Perform preconditioner specific post-reactor setup operations such as factorize.

virtual void	reset ()
	Reset parameters as needed.

virtual void	initialize (size_t networkSize)
	Called during setup for any processes that need to be completed prior to setup functions used in sundials.

virtual void	setBandwidth (size_t bw)
	Used to provide system bandwidth for implementations that use banded matrix storage.

virtual void	printPreconditioner ()
	Print preconditioner contents.

virtual void	setGamma (double gamma)
	Set gamma used in preconditioning.

virtual double	gamma ()
	Get gamma used in preconditioning.

virtual void	setAbsoluteTolerance (double atol)
	Set the absolute tolerance in the solver outside of the network initialization.

virtual int	info () const
	Get latest status of linear solver.

double	elapsedTime () const
	Elapsed CPU time spent computing the Jacobian elements.

void	updateElapsed (double evalTime)
	Increase the elapsed time by the specified time.

int	nEvals () const
	Number of Jacobian evaluations.

void	incrementEvals ()
	Increment the number of times the Jacobian has been evaluated.

int	age () const
	Number of times 'incrementAge' has been called since the last evaluation.

void	incrementAge ()
	Increment the Jacobian age.

void	setAge (int age)
	Set the Jacobian age.

void	clearStats ()
	Clear collected stats about number of Jacobian evaluations, CPU time spent on Jacobian updates, and the number of Newton steps that have been taken since updating the Jacobian.

Protected Attributes
vector< Eigen::Triplet< double > >	m_jac_trips
	Vector of triples representing the jacobian used in preconditioning.

Eigen::SparseMatrix< double >	m_identity
	Storage of appropriately sized identity matrix for making the preconditioner.

Eigen::SparseMatrix< double >	m_matrix
	Container that is the sparse preconditioner.

Protected Attributes inherited from SystemJacobian
size_t	m_dim
	Dimension of the system.

double	m_gamma = 1.0
	gamma value used in M = I - gamma*J

bool	m_init = false
	bool saying whether or not the system is initialized

double	m_atol = 0
	Absolute tolerance of the ODE solver.

double	m_elapsed = 0.0
	Elapsed CPU time taken to compute the Jacobian.

int	m_nevals = 0
	Number of Jacobian evaluations.

int	m_age = 100000
	Age of the Jacobian (times incrementAge() has been called)

string	m_precon_side = "none"
	For iterative solvers, side of the system to apply the preconditioner on.

Additional Inherited Members
Protected Member Functions inherited from SystemJacobian
virtual void	factorize ()
	Factorize the system matrix.

Member Function Documentation

◆ initialize()

void initialize ( size_t networkSize )

overridevirtual

Called during setup for any processes that need to be completed prior to setup functions used in sundials.

Parameters

networkSize the number of variables in the associated reactor network

Reimplemented from SystemJacobian.

Definition at line 12 of file EigenSparseJacobian.cpp.

◆ reset()

void reset ( )

overridevirtual

Reset parameters as needed.

Reimplemented from SystemJacobian.

Definition at line 30 of file EigenSparseJacobian.cpp.

◆ setValue()

void setValue	(	size_t	row,
		size_t	col,
		double	value
	)

overridevirtual

Set a value at the specified row and column of the jacobian triplet vector.

Parameters

row	row in the jacobian matrix
col	column in the jacobian matrix
value	value of the element at row and col

Reimplemented from SystemJacobian.

Definition at line 36 of file EigenSparseJacobian.cpp.

◆ updatePreconditioner()

void updatePreconditioner ( )

overridevirtual

Transform Jacobian vector and write into preconditioner, P = (I - gamma * J)

Reimplemented from SystemJacobian.

Definition at line 41 of file EigenSparseJacobian.cpp.

◆ updateTransient()

void updateTransient	(	double	rdt,
		int *	mask
	)

overridevirtual

Update the diagonal terms in the Jacobian by using the transient mask \( \alpha \).

Parameters

rdt	Reciprocal of the time step [1/s]
mask	Mask for transient terms: 1 if transient, 0 if algebraic.

Reimplemented from SystemJacobian.

Definition at line 51 of file EigenSparseJacobian.cpp.

◆ matrix()

Eigen::SparseMatrix< double > matrix ( )

inline

Return the internal preconditioner matrix.

Definition at line 31 of file EigenSparseJacobian.h.

◆ printPreconditioner()

void printPreconditioner ( )

overridevirtual

Print preconditioner contents.

Reimplemented from SystemJacobian.

Definition at line 68 of file EigenSparseJacobian.cpp.

◆ printJacobian()

void printJacobian ( )

Print jacobian contents.

Definition at line 75 of file EigenSparseJacobian.cpp.

Member Data Documentation

◆ m_jac_trips

vector<Eigen::Triplet<double> > m_jac_trips

protected

Vector of triples representing the jacobian used in preconditioning.

Definition at line 43 of file EigenSparseJacobian.h.

◆ m_identity

Eigen::SparseMatrix<double> m_identity

protected

Storage of appropriately sized identity matrix for making the preconditioner.

Definition at line 46 of file EigenSparseJacobian.h.

◆ m_matrix

Eigen::SparseMatrix<double> m_matrix

protected

Container that is the sparse preconditioner.

Definition at line 49 of file EigenSparseJacobian.h.

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

Detailed Description

Public Member Functions

Protected Attributes

Additional Inherited Members

Member Function Documentation

◆ initialize()

◆ reset()

◆ setValue()

◆ updatePreconditioner()

◆ updateTransient()

◆ matrix()

◆ printPreconditioner()

◆ printJacobian()

Member Data Documentation

◆ m_jac_trips

◆ m_identity

◆ m_matrix