Gsolve Class Reference

#include <Gsolve.h>

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Collaboration diagram for Gsolve:

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List of all members.

Public Member Functions
	Gsolve ()
	~Gsolve ()
Id	getStoich () const
void	setStoich (Id stoich)
Id	getCompartment () const
	Inherited from ZombiePoolInterface.
void	setCompartment (Id compt)
	Assigns compartment.
unsigned int	getNumLocalVoxels () const
	Number of voxels here. pools_.size() == getNumLocalVoxels.
unsigned int	getNumAllVoxels () const
void	setNumAllVoxels (unsigned int num)
void	setNumPools (unsigned int num)
unsigned int	getNumPools () const
	Inherited.
VoxelPoolsBase *	pools (unsigned int i)
	Inherited.
double	volume (unsigned int i) const
	Inherited.
vector< double >	getNvec (unsigned int voxel) const
	Returns the vector of pool Num at the specified voxel.
void	setNvec (unsigned int voxel, vector< double > vec)
void	process (const Eref &e, ProcPtr p)
void	reinit (const Eref &e, ProcPtr p)
void	initProc (const Eref &e, ProcPtr p)
void	initReinit (const Eref &e, ProcPtr p)
void	updateVoxelVol (vector< double > vols)
void	rebuildGssaSystem ()
void	fillMmEnzDep ()
void	fillMathDep ()
void	insertMathDepReacs (unsigned int mathDepIndex, unsigned int firedReac)
void	makeReacDepsUnique ()
unsigned int	getPoolIndex (const Eref &e) const
	Return pool index, using Stoich ptr to do lookup.
unsigned int	getVoxelIndex (const Eref &e) const
void	setDsolve (Id dsolve)
void	setN (const Eref &e, double v)
	Set # of molecules in given pool and voxel. Varies with time.
double	getN (const Eref &e) const
	Get # of molecules in given pool and voxel. Varies with time.
void	setNinit (const Eref &e, double v)
	Set initial # of molecules in given pool and voxel. Bdry cond.
double	getNinit (const Eref &e) const
	get initial # of molecules in given pool and voxel. Bdry cond.
void	setDiffConst (const Eref &e, double v)
	Diffusion constant: Only one per pool, voxel number is ignored.
double	getDiffConst (const Eref &e) const
	Diffusion constant: Only one per pool, voxel number is ignored.
void	getBlock (vector< double > &values) const
void	setBlock (const vector< double > &values)
void	updateRateTerms (unsigned int index)
bool	getRandInit () const
void	setRandInit (bool val)
	Flag: set true if randomized round to integers is to be done.
Static Public Member Functions
static SrcFinfo2< Id, vector < double > > *	xComptOut ()
static const Cinfo *	initCinfo ()

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Constructor & Destructor Documentation

Gsolve::Gsolve

(

)

Gsolve::~Gsolve

(

)

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Member Function Documentation

void Gsolve::fillMathDep

(

)

Fill in dependency list for all MathExpns on reactions. Note that when a MathExpn updates, it alters a further molecule, that may be a substrate for another reaction. So we need to also add further dependent reactions. In principle we might also cascade to deeper MathExpns. Later.

References c, GssaSystem::dependency, GssaSystem::dependentMathExpn, Stoich::funcs(), Stoich::getNumAllPools(), Stoich::getNumBufPools(), Stoich::getNumFuncs(), Stoich::getNumProxyPools(), Stoich::getNumRates(), Stoich::getNumVarPools(), FuncTerm::getReactantIndex(), SparseMatrix< T >::getRow(), Stoich::getStoichiometryMatrix(), and GssaSystem::transposeN.

Referenced by rebuildGssaSystem().

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void Gsolve::fillMmEnzDep

(

)

Fill in dependency list for all MMEnzs on reactions. The dependencies of MMenz products are already in the system, so here we just need to add cases where any reaction product is the Enz of an MMEnz.

References GssaSystem::dependency, Stoich::getNumRates(), RateTerm::getReactants(), SparseMatrix< T >::getRow(), Stoich::rates(), and GssaSystem::transposeN.

Referenced by rebuildGssaSystem().

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void Gsolve::getBlock

(

vector< double > &

values

)

const [virtual]

Gets block of data. The first 4 entries are passed in on the 'values' vector: the start voxel, numVoxels, start pool#, numPools. These are followed by numVoxels * numPools of data values which are filled in by the function. We assert that the entire requested block is present in this ZombiePoolInterface. The block is organized as an array of arrays of voxels; values[pool#][voxel#]

Note that numVoxels and numPools are the number in the current block, not the upper limit of the block. So values.size() == 4 + numPools * numVoxels.

Implements ZombiePoolInterface.

Referenced by process().

Id Gsolve::getCompartment

(

)

const

Inherited from ZombiePoolInterface.

Reimplemented from ZombiePoolInterface.

References ZombiePoolInterface::compartment_.

Referenced by initCinfo().

double Gsolve::getDiffConst

(

const Eref &

e

)

const [virtual]

Diffusion constant: Only one per pool, voxel number is ignored.

Implements ZombiePoolInterface.

double Gsolve::getN

(

const Eref &

e

)

const [virtual]

Get # of molecules in given pool and voxel. Varies with time.

Implements ZombiePoolInterface.

References getPoolIndex(), getVoxelIndex(), and OFFNODE.

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double Gsolve::getNinit

(

const Eref &

e

)

const [virtual]

get initial # of molecules in given pool and voxel. Bdry cond.

Implements ZombiePoolInterface.

References getPoolIndex(), getVoxelIndex(), and OFFNODE.

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unsigned int Gsolve::getNumAllVoxels

(

)

const

Referenced by initCinfo().

unsigned int Gsolve::getNumLocalVoxels

(

)

const [virtual]

Number of voxels here. pools_.size() == getNumLocalVoxels.

Implements ZombiePoolInterface.

Referenced by initCinfo(), and process().

unsigned int Gsolve::getNumPools

(

)

const [virtual]

Inherited.

Implements ZombiePoolInterface.

Referenced by initCinfo().

vector< double > Gsolve::getNvec

(

unsigned int

voxel

)

const

Returns the vector of pool Num at the specified voxel.

References dummy().

Referenced by initCinfo().

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unsigned int Gsolve::getPoolIndex

(

const Eref &

er

)

const [virtual]

Return pool index, using Stoich ptr to do lookup.

Implements ZombiePoolInterface.

References Stoich::convertIdToPoolIndex(), and Eref::id().

Referenced by getN(), getNinit(), setN(), and setNinit().

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bool Gsolve::getRandInit

(

)

const

Flag: returns true if randomized round to integers is done.

References GssaSystem::useRandInit.

Referenced by initCinfo().

Id Gsolve::getStoich

(

)

const

References ZombiePoolInterface::stoich_.

Referenced by initCinfo().

unsigned int Gsolve::getVoxelIndex

(

const Eref &

e

)

const

References Eref::dataIndex(), and OFFNODE.

Referenced by getN(), getNinit(), setN(), and setNinit().

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const Cinfo * Gsolve::initCinfo

(

)

[static]

References getCompartment(), getNumAllVoxels(), getNumLocalVoxels(), getNumPools(), getNvec(), getRandInit(), getStoich(), init(), Neutral::initCinfo(), initProc(), initReinit(), process(), reinit(), setCompartment(), setNumAllVoxels(), setNumPools(), setNvec(), setRandInit(), setStoich(), updateVoxelVol(), ZombiePoolInterface::xComptIn(), and xComptOut().

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void Gsolve::initProc	(	const Eref &	e,
		ProcPtr	p
	)

References Eref::id(), XferInfo::ksolve, xComptOut(), ZombiePoolInterface::xfer_, XferInfo::xferPoolIdx, and XferInfo::xferVoxel.

Referenced by initCinfo().

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void Gsolve::initReinit	(	const Eref &	e,
		ProcPtr	p
	)

References Eref::id(), XferInfo::ksolve, XferInfo::lastValues, xComptOut(), ZombiePoolInterface::xfer_, XferInfo::xferPoolIdx, and XferInfo::xferVoxel.

Referenced by initCinfo().

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void Gsolve::insertMathDepReacs	(	unsigned int	mathDepIndex,
		unsigned int	firedReac
	)

Inserts reactions that depend on molecules modified by the specified MathExpn, into the dependency list. Later.

void Gsolve::makeReacDepsUnique

(

)

STL stuff follows, with the usual weirdness.

References GssaSystem::dependency, and Stoich::getNumRates().

Referenced by rebuildGssaSystem().

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VoxelPoolsBase * Gsolve::pools

(

unsigned int

i

)

[virtual]

Inherited.

Implements ZombiePoolInterface.

void Gsolve::process	(	const Eref &	e,
		ProcPtr	p
	)

References getBlock(), ZombiePoolInterface::getBlock(), getNumLocalVoxels(), Stoich::getNumVarPools(), XferInfo::lastValues, ZombiePoolInterface::setBlock(), setBlock(), ZombiePoolInterface::xfer_, XferInfo::xferPoolIdx, and XferInfo::xferVoxel.

Referenced by initCinfo().

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void Gsolve::rebuildGssaSystem

(

)

References Stoich::convertRatesToStochasticForm(), GssaSystem::dependency, fillMathDep(), fillMmEnzDep(), KinSparseMatrix::getGillespieDependence(), Stoich::getNumCoreRates(), Stoich::getNumProxyPools(), Stoich::getNumRates(), Stoich::getNumVarPools(), Stoich::getRateTerms(), Stoich::getStoichiometryMatrix(), GssaSystem::isReady, makeReacDepsUnique(), SparseMatrix< T >::transpose(), GssaSystem::transposeN, and KinSparseMatrix::truncateRow().

Referenced by reinit().

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void Gsolve::reinit	(	const Eref &	e,
		ProcPtr	p
	)

References Stoich::getNumProxyPools(), GssaSystem::isReady, XferInfo::lastValues, rebuildGssaSystem(), XferInfo::values, ZombiePoolInterface::xfer_, XferInfo::xferPoolIdx, and XferInfo::xferVoxel.

Referenced by initCinfo().

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void Gsolve::setBlock

(

const vector< double > &

values

)

[virtual]

Sets block of data. The first 4 entries on the 'values' vector are the start voxel, numVoxels, start pool#, numPools. These are followed by numVoxels * numPools of data values.

Implements ZombiePoolInterface.

Referenced by process().

void Gsolve::setCompartment

(

Id

compartment

)

[virtual]

Assigns compartment.

Reimplemented from ZombiePoolInterface.

References Element::cinfo(), ZombiePoolInterface::compartment_, Id::element(), and Cinfo::isA().

Referenced by initCinfo().

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void Gsolve::setDiffConst	(	const Eref &	e,
		double	val
	)			[virtual]

Diffusion constant: Only one per pool, voxel number is ignored.

Implements ZombiePoolInterface.

void Gsolve::setDsolve

(

Id

dsolve

)

[virtual]

Inherited. Needed for reac-diff calculations so the Gsolve can orchestrate the data transfer between the itself and the diffusion solver.

Implements ZombiePoolInterface.

References Element::cinfo(), Eref::data(), Id::element(), Id::eref(), Cinfo::isA(), Cinfo::name(), and Id::path().

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void Gsolve::setN	(	const Eref &	e,
		double	val
	)			[virtual]

Set # of molecules in given pool and voxel. Varies with time.

Implements ZombiePoolInterface.

References Element::cinfo(), Eref::element(), getPoolIndex(), getVoxelIndex(), Cinfo::isA(), GssaSystem::isReady, and OFFNODE.

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void Gsolve::setNinit	(	const Eref &	e,
		double	val
	)			[virtual]

Set initial # of molecules in given pool and voxel. Bdry cond.

Implements ZombiePoolInterface.

References Element::cinfo(), Eref::element(), getPoolIndex(), getVoxelIndex(), Cinfo::isA(), GssaSystem::isReady, and OFFNODE.

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void Gsolve::setNumAllVoxels

(

unsigned int

num

)

[virtual]

Assigns the number of voxels used in the entire reac-diff system. Note that fewer than this may be used on any given node.

Implements ZombiePoolInterface.

References GssaSystem::isReady.

Referenced by initCinfo().

void Gsolve::setNumPools

(

unsigned int

num

)

[virtual]

Assigns number of different pools (chemical species) present in each voxel.

Implements ZombiePoolInterface.

References GssaSystem::isReady.

Referenced by initCinfo().

void Gsolve::setNvec	(	unsigned int	voxel,
		vector< double >	vec
	)

Referenced by initCinfo().

void Gsolve::setRandInit

(

bool

val

)

Flag: set true if randomized round to integers is to be done.

References GssaSystem::useRandInit.

Referenced by initCinfo().

void Gsolve::setStoich

(

Id

stoich

)

[virtual]

Informs the ZPI about the stoich, used during subsequent computations. Called to wrap up the model building. The Stoich does this call after it has set up its own path.

Implements ZombiePoolInterface.

References Element::cinfo(), Eref::data(), Id::element(), Id::eref(), Cinfo::isA(), GssaSystem::isReady, GssaSystem::stoich, and ZombiePoolInterface::stoich_.

Referenced by initCinfo().

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void Gsolve::updateRateTerms

(

unsigned int

index

)

[virtual]

Rescale specified voxel rate term following rate constant change or volume change. If index == ~0U then does all terms.

Implements ZombiePoolInterface.

References Stoich::getNumCoreRates(), and Stoich::getRateTerms().

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void Gsolve::updateVoxelVol

(

vector< double >

vols

)

Handles request to change volumes of voxels in this Ksolve, and all cascading effects of this. At this point it won't handle change in size of voxel array.

Referenced by initCinfo().

double Gsolve::volume

(

unsigned int

i

)

const [virtual]

Inherited.

Implements ZombiePoolInterface.

SrcFinfo2< Id, vector< double > > * Gsolve::xComptOut

(

)

[static]

Referenced by initCinfo(), initProc(), and initReinit().

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

• ksolve/Gsolve.h
• ksolve/Gsolve.cpp