Ksolve Class Reference

#include <Ksolve.h>

Inheritance diagram for Ksolve:

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Collaboration diagram for Ksolve:

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List of all members.

Public Member Functions
	Ksolve ()
	~Ksolve ()
string	getMethod () const
void	setMethod (string method)
double	getEpsAbs () const
	Assigns Absolute tolerance for integration.
void	setEpsAbs (double val)
double	getEpsRel () const
	Assigns Relative tolerance for integration.
void	setEpsRel (double val)
Id	getStoich () const
	Assigns Stoich object to Ksolve.
void	setStoich (Id stoich)
Id	getDsolve () const
	Inherited from ZombiePoolInterface.
void	setDsolve (Id dsolve)
	Assigns the diffusion solver. Used by the reac solvers.
unsigned int	getNumLocalVoxels () const
	Inherited from ZombiePoolInterface.
unsigned int	getNumAllVoxels () const
void	setNumAllVoxels (unsigned int num)
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)
double	getEstimatedDt () const
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)
unsigned int	getPoolIndex (const Eref &e) const
	Return pool index, using Stoich ptr to do lookup.
unsigned int	getVoxelIndex (const Eref &e) const
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	setNumPools (unsigned int num)
unsigned int	getNumPools () const
	gets number of pools (species) handled by system.
VoxelPoolsBase *	pools (unsigned int i)
	Return a pointer to the specified VoxelPool.
double	volume (unsigned int i) const
	Return volume of voxel i.
void	getBlock (vector< double > &values) const
void	setBlock (const vector< double > &values)
void	matchJunctionVols (vector< double > &vols, Id otherCompt) const
void	updateRateTerms (unsigned int index)
void	setupXfer (Id myKsolve, Id otherKsolve, unsigned int numProxyMols, const vector< VoxelJunction > &vj)
void	assignXferIndex (unsigned int numProxyMols, unsigned int xferCompt, const vector< vector< unsigned int > > &voxy)
void	assignXferVoxels (unsigned int xferCompt)
unsigned int	assignProxyPools (const map< Id, vector< Id > > &xr, Id myKsolve, Id otherKsolve, Id otherComptId)
void	buildCrossReacVolScaling (Id otherKsolve, const vector< VoxelJunction > &vj)
void	print () const
Static Public Member Functions
static SrcFinfo2< Id, vector < double > > *	xComptOut ()
static const Cinfo *	initCinfo ()

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Constructor & Destructor Documentation

Ksolve::Ksolve

(

)

Ksolve::~Ksolve

(

)

---

Member Function Documentation

unsigned int Ksolve::assignProxyPools	(	const map< Id, vector< Id > > &	xr,
		Id	myKsolve,
		Id	otherKsolve,
		Id	otherComptId
	)

Reimplemented from ZombiePoolInterface.

void Ksolve::assignXferIndex	(	unsigned int	numProxyMols,
		unsigned int	xferCompt,
		const vector< vector< unsigned int > > &	voxy
	)

Reimplemented from ZombiePoolInterface.

void Ksolve::assignXferVoxels

(

unsigned int

xferCompt

)

Figures out which voxels are involved in cross-compt reactions. Stores in the appropriate xfer_ entry.

Reimplemented from ZombiePoolInterface.

void Ksolve::buildCrossReacVolScaling	(	Id	otherKsolve,
		const vector< VoxelJunction > &	vj
	)

void Ksolve::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().

double Ksolve::getDiffConst

(

const Eref &

e

)

const [virtual]

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

Implements ZombiePoolInterface.

Id Ksolve::getDsolve

(

)

const

Inherited from ZombiePoolInterface.

Assigns Dsolve object to Ksolve.

double Ksolve::getEpsAbs

(

)

const

Assigns Absolute tolerance for integration.

Referenced by initCinfo().

double Ksolve::getEpsRel

(

)

const

Assigns Relative tolerance for integration.

Referenced by initCinfo().

double Ksolve::getEstimatedDt

(

)

const

This does a quick and dirty estimate of the timestep suitable for this sytem

References EPSILON, Stoich::getNumAllPools(), Stoich::getNumProxyPools(), and Stoich::getNumRates().

Referenced by initCinfo().

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string Ksolve::getMethod

(

)

const

Assigns integration method

Referenced by initCinfo().

double Ksolve::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 Ksolve::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 Ksolve::getNumAllVoxels

(

)

const

Referenced by initCinfo().

unsigned int Ksolve::getNumLocalVoxels

(

)

const [virtual]

Inherited from ZombiePoolInterface.

Implements ZombiePoolInterface.

Referenced by initCinfo(), and process().

unsigned int Ksolve::getNumPools

(

)

const [virtual]

gets number of pools (species) handled by system.

Implements ZombiePoolInterface.

Referenced by initCinfo().

vector< double > Ksolve::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 Ksolve::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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Id Ksolve::getStoich

(

)

const

Assigns Stoich object to Ksolve.

References ZombiePoolInterface::stoich_.

Referenced by initCinfo().

unsigned int Ksolve::getVoxelIndex

(

const Eref &

e

)

const

References Eref::dataIndex(), and OFFNODE.

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

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const Cinfo * Ksolve::initCinfo

(

)

[static]

References ZombiePoolInterface::getCompartment(), getEpsAbs(), getEpsRel(), getEstimatedDt(), getMethod(), getNumAllVoxels(), getNumLocalVoxels(), getNumPools(), getNvec(), getStoich(), init(), Neutral::initCinfo(), initProc(), initReinit(), process(), reinit(), ZombiePoolInterface::setCompartment(), setEpsAbs(), setEpsRel(), setMethod(), setNumAllVoxels(), setNumPools(), setNvec(), updateVoxelVol(), ZombiePoolInterface::xComptIn(), and xComptOut().

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

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

Referenced by initCinfo().

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void Ksolve::matchJunctionVols	(	vector< double > &	vols,
		Id	otherCompt
	)			const

Reimplemented from ZombiePoolInterface.

VoxelPoolsBase * Ksolve::pools

(

unsigned int

i

)

[virtual]

Return a pointer to the specified VoxelPool.

Implements ZombiePoolInterface.

void Ksolve::print

(

)

const

References ZombiePoolInterface::compartment_, Stoich::getKsolve(), Id::path(), ZombiePoolInterface::stoich_, and ZombiePoolInterface::xfer_.

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

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

Referenced by initCinfo().

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

References ProcInfo::dt, Stoich::getNumProxyPools(), ZombiePoolInterface::isBuilt_, XferInfo::lastValues, XferInfo::values, ZombiePoolInterface::xfer_, XferInfo::xferPoolIdx, and XferInfo::xferVoxel.

Referenced by initCinfo().

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

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

Implements ZombiePoolInterface.

void Ksolve::setDsolve

(

Id

dsolve

)

[virtual]

Assigns the diffusion solver. Used by the reac solvers.

Implements ZombiePoolInterface.

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

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void Ksolve::setEpsAbs

(

double

val

)

Referenced by initCinfo().

void Ksolve::setEpsRel

(

double

val

)

Referenced by initCinfo().

void Ksolve::setMethod

(

string

method

)

Referenced by initCinfo().

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

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

Implements ZombiePoolInterface.

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

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

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

Implements ZombiePoolInterface.

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

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void Ksolve::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.

Referenced by initCinfo().

void Ksolve::setNumPools

(

unsigned int

num

)

[virtual]

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

Implements ZombiePoolInterface.

Referenced by initCinfo().

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

Referenced by initCinfo().

void Ksolve::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(), OdeSystem::epsAbs, OdeSystem::epsRel, Id::eref(), Stoich::getNumAllPools(), Stoich::getNumProxyPools(), VoxelPools::gslFunc(), OdeSystem::initStepSize, Cinfo::isA(), ZombiePoolInterface::isBuilt_, and ZombiePoolInterface::stoich_.

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void Ksolve::setupXfer	(	Id	myKsolve,
		Id	otherKsolve,
		unsigned int	numProxyMols,
		const vector< VoxelJunction > &	vj
	)

Reimplemented from ZombiePoolInterface.

void Ksolve::updateRateTerms

(

unsigned int

index

)

[virtual]

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

updateRateTerms obtains the latest parameters for the rates_ vector, and has each of the pools update its parameters including rescaling for volumes.

Implements ZombiePoolInterface.

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

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void Ksolve::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 Ksolve::volume

(

unsigned int

i

)

const [virtual]

Return volume of voxel i.

Implements ZombiePoolInterface.

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

(

)

[static]

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

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

• ksolve/Ksolve.h
• ksolve/Ksolve.cpp