This class handles operations involving the stoichiometric coefficients on one side of a reaction (reactant or product) for a set of reactions comprising a reaction mechanism. More...

#include <StoichManager.h>

Detailed Description

This class handles operations involving the stoichiometric coefficients on one side of a reaction (reactant or product) for a set of reactions comprising a reaction mechanism.

This class is used by class Kinetics, which contains three instances of this class (one to handle operations on the reactions, one for the products of reversible reactions, and one for the products of irreversible reactions).

This class is designed for use with elementary reactions, or at least ones with integral stoichiometric coefficients. Let \( M(i) \) be the number of molecules on the product or reactant side of reaction number i.

\[ r_i = \sum_m^{M_i} s_{k_{m,i}} \]

To understand the operations performed by this class, let \( N_{k,i} \) denote the stoichiometric coefficient of species k on one side (reactant or product) in reaction i. Then N is a sparse K by I matrix of stoichiometric coefficients.

The following matrix operations may be carried out with a vector S of length K, and a vector R of length I:

\( S = S + N R \) (incrementSpecies)
\( S = S - N R \) (decrementSpecies)
\( R = R + N^T S \) (incrementReaction)
\( R = R - N^T S \) (decrementReaction)

The actual implementation, however, does not compute these quantities by matrix multiplication. A faster algorithm is used that makes use of the fact that the integer-valued N matrix is very sparse, and the non-zero terms are small positive integers.

\[ S_k = R_{i1} + \dots + R_{iM} \]

where M is the number of molecules, and \( i(m) \) is the See Stoichiometry

Definition at line 588 of file StoichManager.h.

Public Member Functions
	StoichManagerN ()
	Constructor for the StoichManagerN class.

void	resizeCoeffs (size_t nSpc, size_t nRxn)
	Resize the sparse coefficient matrix.

void	add (size_t rxn, const vector< size_t > &k)
	Add a single reaction to the list of reactions that this stoichiometric manager object handles.

void	add (size_t rxn, const vector< size_t > &k, const vector< double > &order)

void	add (size_t rxn, const vector< size_t > &k, const vector< double > &order, const vector< double > &stoich)
	Add a single reaction to the list of reactions that this stoichiometric manager object handles.

void	multiply (const double input, double output) const

void	incrementSpecies (const double input, double output) const

void	decrementSpecies (const double input, double output) const

void	incrementReactions (const double input, double output) const

void	decrementReactions (const double input, double output) const

const Eigen::SparseMatrix< double > &	stoichCoeffs () const
	Return matrix containing stoichiometric coefficients.

Eigen::SparseMatrix< double >	derivatives (const double conc, const double rates)
	Calculate derivatives with respect to species concentrations.

void	scale (const double in, double out, double factor) const
	Scale input by reaction order and factor.

Private Attributes
bool	m_ready
	Boolean flag indicating whether object is fully configured.

vector< C1 >	m_c1_list

vector< C2 >	m_c2_list

vector< C3 >	m_c3_list

vector< C_AnyN >	m_cn_list

SparseTriplets	m_coeffList
	Sparse matrices for stoichiometric coefficients.

Eigen::SparseMatrix< double >	m_stoichCoeffs

vector< int >	m_outerIndices
	Storage indicies used to build derivatives.

vector< int >	m_innerIndices

vector< double >	m_values

Constructor & Destructor Documentation

◆ StoichManagerN()

StoichManagerN ( )

inline

Constructor for the StoichManagerN class.

Definition at line 594 of file StoichManager.h.

Member Function Documentation

◆ resizeCoeffs()

void resizeCoeffs	(	size_t	nSpc,
		size_t	nRxn
	)

inline

Resize the sparse coefficient matrix.

Definition at line 600 of file StoichManager.h.

◆ add() [1/3]

void add	(	size_t	rxn,
		const vector< size_t > &	k
	)

inline

Add a single reaction to the list of reactions that this stoichiometric manager object handles.

This function is the same as the add() function below. However, the order of each species in the power list expression is set to one automatically.

Definition at line 646 of file StoichManager.h.

◆ add() [2/3]

void add	(	size_t	rxn,
		const vector< size_t > &	k,
		const vector< double > &	order
	)

inline

Definition at line 652 of file StoichManager.h.

◆ add() [3/3]

void add	(	size_t	rxn,
		const vector< size_t > &	k,
		const vector< double > &	order,
		const vector< double > &	stoich
	)

inline

Add a single reaction to the list of reactions that this stoichiometric manager object handles.

Parameters

rxn	Reaction index of the current reaction. This is used as an index into vectors which have length n_total_rxn.
k	This is a vector of integer values specifying the species indices. The length of this vector species the number of different species in the description. The value of the entries are the species indices. These are used as indexes into vectors which have length n_total_species.
order	This is a vector of the same length as vector k. The order is used for the routine power(), which produces a power law expression involving the species vector.
stoich	This is used to handle fractional stoichiometric coefficients on the product side of irreversible reactions.

Definition at line 673 of file StoichManager.h.

◆ multiply()

void multiply	(	const double *	input,
		double *	output
	)		const

inline

Definition at line 722 of file StoichManager.h.

◆ incrementSpecies()

void incrementSpecies	(	const double *	input,
		double *	output
	)		const

inline

Definition at line 729 of file StoichManager.h.

◆ decrementSpecies()

void decrementSpecies	(	const double *	input,
		double *	output
	)		const

inline

Definition at line 736 of file StoichManager.h.

◆ incrementReactions()

void incrementReactions	(	const double *	input,
		double *	output
	)		const

inline

Definition at line 743 of file StoichManager.h.

◆ decrementReactions()

void decrementReactions	(	const double *	input,
		double *	output
	)		const

inline

Definition at line 750 of file StoichManager.h.

◆ stoichCoeffs()

const Eigen::SparseMatrix< double > & stoichCoeffs ( ) const

inline

Return matrix containing stoichiometric coefficients.

Definition at line 758 of file StoichManager.h.

◆ derivatives()

Eigen::SparseMatrix< double > derivatives	(	const double *	conc,
		const double *	rates
	)

inline

Calculate derivatives with respect to species concentrations.

The species derivative is the term of the Jacobian that accounts for species products in the law of mass action. As StoichManagerN does not account for third bodies or rate constants that depend on species concentrations, corresponding derivatives are not included.

Parameters

conc	Species concentration.
rates	Rates-of-progress.

Definition at line 780 of file StoichManager.h.

◆ scale()

void scale	(	const double *	in,
		double *	out,
		double	factor
	)		const

inline

Scale input by reaction order and factor.

Definition at line 795 of file StoichManager.h.

Member Data Documentation

◆ m_ready

bool m_ready

private

Boolean flag indicating whether object is fully configured.

Definition at line 804 of file StoichManager.h.

◆ m_c1_list

vector<C1> m_c1_list

private

Definition at line 806 of file StoichManager.h.

◆ m_c2_list

vector<C2> m_c2_list

private

Definition at line 807 of file StoichManager.h.

◆ m_c3_list

vector<C3> m_c3_list

private

Definition at line 808 of file StoichManager.h.

◆ m_cn_list

vector<C_AnyN> m_cn_list

private

Definition at line 809 of file StoichManager.h.

◆ m_coeffList

SparseTriplets m_coeffList

private

Sparse matrices for stoichiometric coefficients.

Definition at line 812 of file StoichManager.h.

◆ m_stoichCoeffs

Eigen::SparseMatrix<double> m_stoichCoeffs

private

Definition at line 813 of file StoichManager.h.

◆ m_outerIndices

vector<int> m_outerIndices

private

Storage indicies used to build derivatives.

Definition at line 816 of file StoichManager.h.

◆ m_innerIndices

vector<int> m_innerIndices

private

Definition at line 817 of file StoichManager.h.

◆ m_values

vector<double> m_values

private

Definition at line 818 of file StoichManager.h.

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

StoichManager.h

Detailed Description

Public Member Functions

Private Attributes

Constructor & Destructor Documentation

◆ StoichManagerN()

Member Function Documentation

◆ resizeCoeffs()

◆ add() [1/3]

◆ add() [2/3]

◆ add() [3/3]

◆ multiply()

◆ incrementSpecies()

◆ decrementSpecies()

◆ incrementReactions()

◆ decrementReactions()

◆ stoichCoeffs()

◆ derivatives()

◆ scale()

Member Data Documentation

◆ m_ready

◆ m_c1_list

◆ m_c2_list

◆ m_c3_list

◆ m_cn_list

◆ m_coeffList

◆ m_stoichCoeffs

◆ m_outerIndices

◆ m_innerIndices

◆ m_values