GssaSystem Class Reference

#include <GssaSystem.h>

Collaboration diagram for GssaSystem:

Public Member Functions
	GssaSystem ()

Public Attributes
vector< vector< unsigned int > >	dependency
vector< vector< unsigned int > >	dependentMathExpn
bool	honorMassConservation = true
bool	isReady = false
vector< vector< unsigned int > >	ratesDependentOnPool
Stoich *	stoich
KinSparseMatrix	transposeN
	Transpose of stoichiometry matrix. More...
bool	useRandInit = true

Detailed Description

Definition at line 19 of file GssaSystem.h.

Constructor & Destructor Documentation

GssaSystem::GssaSystem ( )

inline

Definition at line 22 of file GssaSystem.h.

        : stoich(0), useRandInit(true), isReady(false), honorMassConservation(true)
    {;}

Member Data Documentation

vector< vector< unsigned int > > GssaSystem::dependency

Definition at line 25 of file GssaSystem.h.

Referenced by GssaVoxelPools::advance(), Gsolve::fillIncrementFuncDep(), Gsolve::fillMmEnzDep(), Gsolve::fillPoolFuncDep(), Gsolve::makeReacDepsUnique(), and Gsolve::rebuildGssaSystem().

vector< vector< unsigned int > > GssaSystem::dependentMathExpn

Definition at line 26 of file GssaSystem.h.

Referenced by Gsolve::fillIncrementFuncDep(), and Gsolve::fillPoolFuncDep().

bool GssaSystem::honorMassConservation = true

Definition at line 54 of file GssaSystem.h.

bool GssaSystem::isReady = false

Flag: True when all initialization is done.

Definition at line 49 of file GssaSystem.h.

Referenced by Gsolve::rebuildGssaSystem(), Gsolve::reinit(), Gsolve::setN(), Gsolve::setNinit(), Gsolve::setNumAllVoxels(), Gsolve::setNumPools(), Gsolve::setNvec(), and Gsolve::setStoich().

vector< vector< unsigned int > > GssaSystem::ratesDependentOnPool

Definition at line 27 of file GssaSystem.h.

Stoich* GssaSystem::stoich

Definition at line 31 of file GssaSystem.h.

Referenced by GssaVoxelPools::advance(), GssaVoxelPools::refreshAtot(), GssaVoxelPools::reinit(), Gsolve::setStoich(), GssaVoxelPools::updateDependentMathExpn(), and GssaVoxelPools::updateReacVelocities().

KinSparseMatrix GssaSystem::transposeN

Transpose of stoichiometry matrix.

Definition at line 30 of file GssaSystem.h.

Referenced by GssaVoxelPools::advance(), Gsolve::fillIncrementFuncDep(), Gsolve::fillMmEnzDep(), Gsolve::fillPoolFuncDep(), and Gsolve::rebuildGssaSystem().

bool GssaSystem::useRandInit = true

Flag: True when using probabilistic (random) rounding. When initializing the mol# from floating-point Sinit values, we have two options. One is to look at each Sinit, and round to the nearest integer. The other is to look at each Sinit, and probabilistically round up or down depending on the value. For example, if we had a Sinit value of 1.49, this would always be rounded to 1.0 if the flag is false, and would be rounded to 1.0 and 2.0 in the ratio 51:49 if the flag is true.

Definition at line 44 of file GssaSystem.h.

Referenced by Gsolve::getRandInit(), GssaVoxelPools::reinit(), and Gsolve::setRandInit().

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

• moose-core/ksolve/GssaSystem.h