SteadyState Class Reference

#include <SteadyState.h>

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List of all members.

Public Member Functions
	SteadyState ()
	~SteadyState ()
Id	getStoich () const
void	setStoich (Id s)
bool	badStoichiometry () const
bool	isInitialized () const
unsigned int	getRank () const
unsigned int	getNumVarPools () const
unsigned int	getNiter () const
unsigned int	getMaxIter () const
void	setMaxIter (unsigned int value)
string	getStatus () const
double	getConvergenceCriterion () const
void	setConvergenceCriterion (double value)
double	getTotal (const unsigned int i) const
void	setTotal (const unsigned int i, double val)
double	getEigenvalue (const unsigned int i) const
void	setEigenvalue (double val, const unsigned int i)
unsigned int	getStateType () const
unsigned int	getNnegEigenvalues () const
unsigned int	getNposEigenvalues () const
unsigned int	getSolutionStatus () const
void	setupMatrix ()
void	settleFunc ()
void	resettleFunc ()
void	settle (bool forceSetup)
void	showMatricesFunc ()
void	showMatrices ()
void	randomizeInitialCondition (const Eref &e)
void	classifyState (const double *T)
Static Public Member Functions
static void	assignY (double *S)
static void	setMolN (double y, unsigned int i)
static const Cinfo *	initCinfo ()
Static Public Attributes
static const double	EPSILON = 1e-9
static const double	DELTA = 1e-6

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Constructor & Destructor Documentation

SteadyState::SteadyState

(

)

SteadyState::~SteadyState

(

)

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Member Function Documentation

void SteadyState::assignY

(

double *

S

)

[static]

bool SteadyState::badStoichiometry

(

)

const

Referenced by initCinfo().

void SteadyState::classifyState

(

const double *

T

)

This does the iteration, using the specified method. First try gsl_multiroot_fsolver_hybrids If that doesn't work try gsl_multiroot_fsolver_dnewton Returns the gsl status.

References DELTA, EPSILON, Stoich::getKsolve(), isNaN(), and VoxelPools::updateRates().

Referenced by settle().

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double SteadyState::getConvergenceCriterion

(

)

const

Referenced by initCinfo().

double SteadyState::getEigenvalue

(

const unsigned int

i

)

const

Referenced by initCinfo().

unsigned int SteadyState::getMaxIter

(

)

const

Referenced by initCinfo().

unsigned int SteadyState::getNiter

(

)

const

Referenced by initCinfo().

unsigned int SteadyState::getNnegEigenvalues

(

)

const

Referenced by initCinfo().

unsigned int SteadyState::getNposEigenvalues

(

)

const

Referenced by initCinfo().

unsigned int SteadyState::getNumVarPools

(

)

const

Referenced by initCinfo().

unsigned int SteadyState::getRank

(

)

const

Referenced by initCinfo().

unsigned int SteadyState::getSolutionStatus

(

)

const

Referenced by initCinfo().

unsigned int SteadyState::getStateType

(

)

const

Referenced by initCinfo().

string SteadyState::getStatus

(

)

const

Referenced by initCinfo().

Id SteadyState::getStoich

(

)

const

Referenced by initCinfo().

double SteadyState::getTotal

(

const unsigned int

i

)

const

Referenced by initCinfo().

const Cinfo * SteadyState::initCinfo

(

)

[static]

This picks up the entire Stoich data structure static Finfo* gslShared[] = { new SrcFinfo( "reinitSrc", Ftype0::global() ), new DestFinfo( "assignStoich", Ftype1< void* >::global(), RFCAST( &SteadyState::assignStoichFunc ) ), new DestFinfo( "setMolN", Ftype2< double, unsigned int >::global(), RFCAST( &SteadyState::setMolN ) ), new SrcFinfo( "requestYsrc", Ftype0::global() ), new DestFinfo( "assignY", Ftype1< double* >::global(), RFCAST( &SteadyState::assignY ) ), };

These are the fields of the SteadyState class

References badStoichiometry(), getConvergenceCriterion(), getEigenvalue(), getMaxIter(), getNiter(), getNnegEigenvalues(), getNposEigenvalues(), getNumVarPools(), getRank(), getSolutionStatus(), getStateType(), getStatus(), getStoich(), getTotal(), Neutral::initCinfo(), isInitialized(), randomizeInitialCondition(), resettleFunc(), setConvergenceCriterion(), setMaxIter(), setStoich(), settle(), settleFunc(), setTotal(), setupMatrix(), and showMatrices().

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bool SteadyState::isInitialized

(

)

const

Referenced by initCinfo().

void SteadyState::randomizeInitialCondition

(

const Eref &

me

)

Generates a new set of values for the S vector that is a) random and b) obeys the conservation rules.

References EPSILON, reac_info::rank, and y.

Referenced by initCinfo().

void SteadyState::resettleFunc

(

)

References settle().

Referenced by initCinfo().

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void SteadyState::setConvergenceCriterion

(

double

value

)

Referenced by initCinfo().

void SteadyState::setEigenvalue	(	double	val,
		const unsigned int	i
	)

void SteadyState::setMaxIter

(

unsigned int

value

)

Referenced by initCinfo().

static void SteadyState::setMolN	(	double	y,
		unsigned int	i
	)			[static]

void SteadyState::setStoich

(

Id

s

)

References Element::cinfo(), Eref::data(), Id::element(), Id::eref(), Stoich::getCompartment(), Stoich::getNumCoreRates(), Stoich::getRateTerms(), Cinfo::isA(), VoxelPools::setStoich(), VoxelPoolsBase::setVolume(), and VoxelPools::updateAllRateTerms().

Referenced by initCinfo().

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void SteadyState::settle

(

bool

forceSetup

)

The settle function computes the steady state nearest the initial conditions.

References classifyState(), reac_info::convergenceCriterion, reac_info::nIter, reac_info::num_mols, reac_info::num_reacs, reac_info::nVec, reac_info::pool, reac_info::rank, and reac_info::T.

Referenced by initCinfo(), resettleFunc(), and settleFunc().

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void SteadyState::settleFunc

(

)

References settle().

Referenced by initCinfo().

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void SteadyState::setTotal	(	const unsigned int	i,
		double	val
	)

Referenced by initCinfo().

void SteadyState::setupMatrix

(

)

Referenced by initCinfo().

void SteadyState::showMatrices

(

)

Referenced by initCinfo().

void SteadyState::showMatricesFunc

(

)

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Member Data Documentation

const double SteadyState::DELTA = 1e-6 [static]

Referenced by classifyState().

const double SteadyState::EPSILON = 1e-9 [static]

Referenced by classifyState(), and randomizeInitialCondition().

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

• ksolve/SteadyState.h
• ksolve/SteadyState.cpp