#include <NextSubvolumeSolver.h>

Inheritance diagram for lm::rdme::NextSubvolumeSolver:

Collaboration diagram for lm::rdme::NextSubvolumeSolver:

Public Member Functions
	NextSubvolumeSolver ()
	NextSubvolumeSolver (RandomGenerator::Distributions neededDists)
virtual	~NextSubvolumeSolver ()
virtual bool	needsReactionModel ()
	Tells whether the solver needs a reaction model.
virtual bool	needsDiffusionModel ()
	Tells whether the solver needs a reaction model.
virtual void	buildDiffusionModel (const uint numberSiteTypesA, const double DFA, const uint RLA, lattice_size_t latticeXSize, lattice_size_t latticeYSize, lattice_size_t latticeZSize, site_size_t particlesPerSite, unsigned int bytes_per_particle, si_dist_t latticeSpacing, const uint8_t latticeData, const uint8_t latticeSitesData, bool rowMajorData=true)
virtual void	generateTrajectory ()
	Actually run the simulation.
Public Member Functions inherited from lm::rdme::RDMESolver
	RDMESolver (RandomGenerator::Distributions neededDists)
virtual	~RDMESolver ()
virtual void	setDiffusionModel (DiffusionModel dm, const uint8_t lattice, size_t latticeSize, const uint8_t *latticeSites, size_t latticeSitesSize)
Public Member Functions inherited from lm::cme::CMESolver
	CMESolver (RandomGenerator::Distributions neededDists)
virtual	~CMESolver ()
virtual void	initialize (unsigned int replicate, map< string, string > parameters, ResourceAllocator::ComputeResources resources)
	Initialize the simulation.
virtual void	setReactionModel (lm::io::ReactionModel *reactionModel)
virtual void	buildModel (const uint numberSpecies, const uint numberReactions, const uint initialSpeciesCounts, const uint reactionTypesA, const double k, const int S, const uint *D, const uint kCols=1)
virtual void	setModelPropensityFunction (uint reaction, double(propensityFunction)(double time, uint speciesCounts, void args), void propensityFunctionArg)
virtual void	setSpeciesUpperLimit (uint species, uint limit)
virtual void	setSpeciesLowerLimit (uint species, uint limit)
virtual void	setFptTrackingList (list< uint > speciesList)
virtual void	addToParameterTrackingList (pair< string, double * >parameter)
virtual void	setReactionRateCME (unsigned int reactionId, double rate)
virtual void	getSpeciesCountView (uint *counts, int number)
virtual void	getReactionRateConstantsView (int reactionNumber, double *rates, int rateConstantCount)
Public Member Functions inherited from lm::me::MESolver
	MESolver ()
	Create the MESolver.
virtual	~MESolver ()

Protected Member Functions
virtual void	allocateModel (uint numberSpecies, uint numberReactions)
virtual void	destroyModel ()
virtual void	destroyDiffusionModel ()
virtual void	checkSpeciesCountsAgainstLattice ()
virtual void	writeLatticeData (double time, ByteLattice lattice, lm::io::Lattice latticeDataSet)
virtual void	recordSpeciesCounts (double time, lm::io::SpeciesCounts *speciesCountsDataSet)
virtual void	writeSpeciesCounts (lm::io::SpeciesCounts *speciesCountsDataSet)
virtual int	updateAllSubvolumePropensities (si_time_t time, int rngNext, double *expRngValues)
virtual int	updateSubvolumePropensity (si_time_t time, lattice_size_t s, int rngNext, double *expRngValues)
virtual double	calculateSubvolumePropensity (si_time_t time, lattice_size_t s)
virtual int	performSubvolumeReaction (si_time_t time, lattice_size_t s, int rngNext, double uniRngValues, bool affectedNeighbor, lattice_size_t *neighborSubvolume)
virtual void	updateCurrentSubvolumeSpeciesCounts (uint r)
virtual void	updateSpeciesCountsForSubvolume (lattice_size_t subvolume)
void	updateSubvolumeWithSpeciesCounts (lattice_size_t subvolume)
void	addParticles (lattice_size_t subvolume, particle_t particle, uint count)
Protected Member Functions inherited from lm::rdme::RDMESolver
virtual void	allocateDiffusionModel (uint numberSiteTypesA, lattice_size_t latticeXSize, lattice_size_t latticeYSize, lattice_size_t latticeZSize, site_size_t particlesPerSite, unsigned int bytes_per_particle, si_dist_t latticeSpacing)
virtual void	allocateLattice (lattice_size_t latticeXSize, lattice_size_t latticeYSize, lattice_size_t latticeZSize, site_size_t particlesPerSite, unsigned int bytes_per_particle, si_dist_t latticeSpacing)
virtual void	setLatticeData (const uint8_t *latticeData)
virtual void	setLatticeSitesData (const uint8_t *latticeSitesData)
Protected Member Functions inherited from lm::cme::CMESolver
virtual double	recordParameters (double nextRecordTime, double recordInterval, double simulationTime)
virtual void	queueRecordedParameters (bool flush=false)
void	updateSpeciesCounts (uint r)
bool	reachedSpeciesLimit ()
virtual int	hookSimulation (double time)
virtual int	onBeginTrajectory ()
virtual int	onEndTrajectory ()

Protected Attributes
lattice_size_t	numberSubvolumes
double *	reactionPropensities
double	latticeSpacingSquared
ReactionQueue *	reactionQueue
uint *	currentSubvolumeSpeciesCounts
Protected Attributes inherited from lm::rdme::RDMESolver
uint	numberSiteTypes
double *	DF
uint *	RL
Lattice *	lattice
Protected Attributes inherited from lm::cme::CMESolver
RandomGenerator::Distributions	neededDists
unsigned int	replicate
map< string, string > *	parameters
ResourceAllocator::ComputeResources *	resources
RandomGenerator *	rng
uint	numberSpecies
uint	numberSpeciesToTrack
uint	numberReactions
uint *	initialSpeciesCounts
uint *	speciesCounts
uint *	reactionTypes
int *	S
uint *	D
void **	propensityFunctions
void **	propensityFunctionArgs
list< PropensityArgs * >	propensityArgs
uint	numberSpeciesLimits
SpeciesLimit *	speciesLimits
uint	numberFptTrackedSpecies
FPTTracking *	fptTrackedSpecies
list< TrackedParameter >	trackedParameters
uint *	numberDependentSpecies
uint **	dependentSpecies
int **	dependentSpeciesChange
uint *	numberDependentReactions
uint **	dependentReactions

Additional Inherited Members
Static Protected Member Functions inherited from lm::cme::CMESolver
static double	zerothOrderPropensity (double time, uint speciesCounts, void pargs)
static double	firstOrderPropensity (double time, uint speciesCounts, void pargs)
static double	secondOrderPropensity (double time, uint speciesCounts, void pargs)
static double	secondOrderSelfPropensity (double time, uint speciesCounts, void pargs)
static double	kHillPropensity (double time, uint speciesCounts, void pargs)
static double	kHillTransportPropensity (double time, uint speciesCounts, void pargs)
static double	zerothOrderHeavisidePropensity (double time, uint speciesCounts, void pargs)
static double	michaelisMentenPropensity (double time, uint speciesCounts, void pargs)
static double	competitiveMMPropensity (double time, uint speciesCounts, void pargs)
static double	uncompetitiveMMPropensity (double time, uint speciesCounts, void pargs)
static double	noncompetitiveMMPropensity (double time, uint speciesCounts, void pargs)

Constructor & Destructor Documentation

◆ NextSubvolumeSolver() [1/2]

lm::rdme::NextSubvolumeSolver::NextSubvolumeSolver ( )

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◆ NextSubvolumeSolver() [2/2]

lm::rdme::NextSubvolumeSolver::NextSubvolumeSolver ( RandomGenerator::Distributions neededDists )

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◆ ~NextSubvolumeSolver()

lm::rdme::NextSubvolumeSolver::~NextSubvolumeSolver ( )

virtual

Member Function Documentation

◆ addParticles()

void lm::rdme::NextSubvolumeSolver::addParticles	(	lattice_size_t	subvolume,
		particle_t	particle,
		uint	count )

protected

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◆ allocateModel()

void lm::rdme::NextSubvolumeSolver::allocateModel	(	uint	numberSpecies,
		uint	numberReactions )

protectedvirtual

Reimplemented from lm::cme::CMESolver.

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◆ buildDiffusionModel()

void lm::rdme::NextSubvolumeSolver::buildDiffusionModel	(	const uint	numberSiteTypesA,
		const double *	DFA,
		const uint *	RLA,
		lattice_size_t	latticeXSize,
		lattice_size_t	latticeYSize,
		lattice_size_t	latticeZSize,
		site_size_t	particlesPerSite,
		unsigned int	bytes_per_particle,
		si_dist_t	latticeSpacing,
		const uint8_t *	latticeData,
		const uint8_t *	latticeSitesData,
		bool	rowMajorData = true )

virtual

Reimplemented from lm::rdme::RDMESolver.

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◆ calculateSubvolumePropensity()

double lm::rdme::NextSubvolumeSolver::calculateSubvolumePropensity	(	si_time_t	time,
		lattice_size_t	s )

protectedvirtual

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◆ checkSpeciesCountsAgainstLattice()

void lm::rdme::NextSubvolumeSolver::checkSpeciesCountsAgainstLattice ( )

protectedvirtual

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◆ destroyDiffusionModel()

void lm::rdme::NextSubvolumeSolver::destroyDiffusionModel ( )

protectedvirtual

Reimplemented from lm::rdme::RDMESolver.

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◆ destroyModel()

void lm::rdme::NextSubvolumeSolver::destroyModel ( )

protectedvirtual

Reimplemented from lm::cme::CMESolver.

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◆ generateTrajectory()

void lm::rdme::NextSubvolumeSolver::generateTrajectory ( )

virtual

Actually run the simulation.

Implements lm::cme::CMESolver.

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◆ needsDiffusionModel()

virtual bool lm::rdme::NextSubvolumeSolver::needsDiffusionModel ( )

inlinevirtual

Tells whether the solver needs a reaction model.

Implements lm::me::MESolver.

◆ needsReactionModel()

virtual bool lm::rdme::NextSubvolumeSolver::needsReactionModel ( )

inlinevirtual

Tells whether the solver needs a reaction model.

Implements lm::me::MESolver.

◆ performSubvolumeReaction()

int lm::rdme::NextSubvolumeSolver::performSubvolumeReaction	(	si_time_t	time,
		lattice_size_t	s,
		int	rngNext,
		double *	uniRngValues,
		bool *	affectedNeighbor,
		lattice_size_t *	neighborSubvolume )

protectedvirtual

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◆ recordSpeciesCounts()

void lm::rdme::NextSubvolumeSolver::recordSpeciesCounts	(	double	time,
		lm::io::SpeciesCounts *	speciesCountsDataSet )

protectedvirtual

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◆ updateAllSubvolumePropensities()

int lm::rdme::NextSubvolumeSolver::updateAllSubvolumePropensities	(	si_time_t	time,
		int	rngNext,
		double *	expRngValues )

protectedvirtual

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◆ updateCurrentSubvolumeSpeciesCounts()

void lm::rdme::NextSubvolumeSolver::updateCurrentSubvolumeSpeciesCounts ( uint r )

protectedvirtual

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◆ updateSpeciesCountsForSubvolume()

void lm::rdme::NextSubvolumeSolver::updateSpeciesCountsForSubvolume ( lattice_size_t subvolume )

protectedvirtual

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◆ updateSubvolumePropensity()

int lm::rdme::NextSubvolumeSolver::updateSubvolumePropensity	(	si_time_t	time,
		lattice_size_t	s,
		int	rngNext,
		double *	expRngValues )

protectedvirtual

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◆ updateSubvolumeWithSpeciesCounts()

void lm::rdme::NextSubvolumeSolver::updateSubvolumeWithSpeciesCounts ( lattice_size_t subvolume )

protected

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◆ writeLatticeData()

void lm::rdme::NextSubvolumeSolver::writeLatticeData	(	double	time,
		ByteLattice *	lattice,
		lm::io::Lattice *	latticeDataSet )

protectedvirtual

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◆ writeSpeciesCounts()

void lm::rdme::NextSubvolumeSolver::writeSpeciesCounts ( lm::io::SpeciesCounts * speciesCountsDataSet )

protectedvirtual

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Member Data Documentation

◆ currentSubvolumeSpeciesCounts

uint* lm::rdme::NextSubvolumeSolver::currentSubvolumeSpeciesCounts

protected

◆ latticeSpacingSquared

double lm::rdme::NextSubvolumeSolver::latticeSpacingSquared

protected

◆ numberSubvolumes

lattice_size_t lm::rdme::NextSubvolumeSolver::numberSubvolumes

protected

◆ reactionPropensities

double* lm::rdme::NextSubvolumeSolver::reactionPropensities

protected

◆ reactionQueue

ReactionQueue* lm::rdme::NextSubvolumeSolver::reactionQueue

protected

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

/data2/LM_zls_github/Lattice-Microbes/src/rdme/NextSubvolumeSolver.h
/data2/LM_zls_github/Lattice-Microbes/src/rdme/NextSubvolumeSolver.cpp

Public Member Functions

Protected Member Functions

Protected Attributes

Additional Inherited Members

Constructor & Destructor Documentation

◆ NextSubvolumeSolver() [1/2]

◆ NextSubvolumeSolver() [2/2]

◆ ~NextSubvolumeSolver()

Member Function Documentation

◆ addParticles()

◆ allocateModel()

◆ buildDiffusionModel()

◆ calculateSubvolumePropensity()

◆ checkSpeciesCountsAgainstLattice()

◆ destroyDiffusionModel()

◆ destroyModel()

◆ generateTrajectory()

◆ needsDiffusionModel()

◆ needsReactionModel()

◆ performSubvolumeReaction()

◆ recordSpeciesCounts()

◆ updateAllSubvolumePropensities()

◆ updateCurrentSubvolumeSpeciesCounts()

◆ updateSpeciesCountsForSubvolume()

◆ updateSubvolumePropensity()

◆ updateSubvolumeWithSpeciesCounts()

◆ writeLatticeData()

◆ writeSpeciesCounts()

Member Data Documentation

◆ currentSubvolumeSpeciesCounts

◆ latticeSpacingSquared

◆ numberSubvolumes

◆ reactionPropensities

◆ reactionQueue