ThirdBodyCalc Class Reference

Calculate and apply third-body effects on reaction rates, including non- unity third-body efficiencies. More...

#include <ThirdBodyCalc.h>

Detailed Description

Calculate and apply third-body effects on reaction rates, including non- unity third-body efficiencies.

Definition at line 19 of file ThirdBodyCalc.h.

Public Member Functions
void	install (size_t rxnNumber, const map< size_t, double > &efficiencies, double default_efficiency, bool mass_action)
	Install reaction that uses third-body effects in ThirdBodyCalc manager.
void	resizeCoeffs (size_t nSpc, size_t nRxn)
	Resize the sparse coefficient matrix.
void	update (const vector< double > &conc, double ctot, double *concm) const
	Update third-body concentrations in full vector.
void	multiply (double *output, const double *concm)
	Multiply output with effective third-body concentration.
Eigen::SparseMatrix< double >	derivatives (const double *product)
	Calculate derivatives with respect to species concentrations.
void	scale (const double *in, double *out, double factor) const
	Scale entries involving third-body collider in law of mass action by factor.
void	scaleM (const double *in, double *out, const double *concm, double factor) const
	Scale entries involving third-body collider in rate expression by third-body concentration and factor.
bool	empty () const
	Return boolean indicating whether ThirdBodyCalc is empty.

Protected Attributes
vector< size_t >	m_reaction_index
	Indices of reactions that use third-bodies within vector of concentrations.
vector< size_t >	m_mass_action_index
	Indices within m_reaction_index of reactions that consider third-body effects in the law of mass action.
vector< size_t >	m_no_mass_action_index
	Indices within m_reaction_index of reactions that consider third-body effects in the rate expression.
vector< vector< size_t > >	m_species
	m_species[i][j] is the index of the j-th species in reaction i.
vector< vector< double > >	m_eff
	m_eff[i][j] is the efficiency of the j-th species in reaction i.
vector< double >	m_default
	The default efficiency for each reaction.
vector< Eigen::Triplet< double > >	m_efficiencyList
	Sparse efficiency matrix (compensated for defaults) Each triplet corresponds to (reaction index, species index, efficiency)
Eigen::SparseMatrix< double >	m_multipliers
	Sparse derivative multiplier matrix.

Member Function Documentation

install()

void install ( size_t rxnNumber, const map< size_t, double > & efficiencies, double default_efficiency, bool mass_action )

inline

Install reaction that uses third-body effects in ThirdBodyCalc manager.

Definition at line 23 of file ThirdBodyCalc.h.

resizeCoeffs()

void resizeCoeffs ( size_t nSpc, size_t nRxn )

inline

Resize the sparse coefficient matrix.

Definition at line 47 of file ThirdBodyCalc.h.

update()

void update ( const vector< double > & conc, double ctot, double * concm ) const

inline

Update third-body concentrations in full vector.

Definition at line 75 of file ThirdBodyCalc.h.

multiply()

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

inline

Multiply output with effective third-body concentration.

Definition at line 86 of file ThirdBodyCalc.h.

derivatives()

Eigen::SparseMatrix< double > derivatives ( const double * product )

inline

Calculate derivatives with respect to species concentrations.

Parameters

product

Product of law of mass action and rate terms.

Definition at line 97 of file ThirdBodyCalc.h.

scale()

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

inline

Scale entries involving third-body collider in law of mass action by factor.

Definition at line 103 of file ThirdBodyCalc.h.

scaleM()

void scaleM ( const double * in, double * out, const double * concm, double factor ) const

inline

Scale entries involving third-body collider in rate expression by third-body concentration and factor.

Definition at line 112 of file ThirdBodyCalc.h.

empty()

bool empty ( ) const

inline

Return boolean indicating whether ThirdBodyCalc is empty.

Definition at line 122 of file ThirdBodyCalc.h.

Member Data Documentation

m_reaction_index

vector<size_t> m_reaction_index

protected

Indices of reactions that use third-bodies within vector of concentrations.

Definition at line 128 of file ThirdBodyCalc.h.

m_mass_action_index

vector<size_t> m_mass_action_index

protected

Indices within m_reaction_index of reactions that consider third-body effects in the law of mass action.

Definition at line 132 of file ThirdBodyCalc.h.

m_no_mass_action_index

vector<size_t> m_no_mass_action_index

protected

Indices within m_reaction_index of reactions that consider third-body effects in the rate expression.

Definition at line 136 of file ThirdBodyCalc.h.

m_species

vector<vector<size_t> > m_species

protected

m_species[i][j] is the index of the j-th species in reaction i.

Definition at line 139 of file ThirdBodyCalc.h.

m_eff

vector<vector<double> > m_eff

protected

m_eff[i][j] is the efficiency of the j-th species in reaction i.

Definition at line 142 of file ThirdBodyCalc.h.

m_default

vector<double> m_default

protected

The default efficiency for each reaction.

Definition at line 145 of file ThirdBodyCalc.h.

m_efficiencyList

vector<Eigen::Triplet<double> > m_efficiencyList

protected

Sparse efficiency matrix (compensated for defaults) Each triplet corresponds to (reaction index, species index, efficiency)

Definition at line 149 of file ThirdBodyCalc.h.

m_multipliers

Eigen::SparseMatrix<double> m_multipliers

protected

Sparse derivative multiplier matrix.

Definition at line 152 of file ThirdBodyCalc.h.

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

• ThirdBodyCalc.h