#include <RDMESolver.h>

Inheritance diagram for lm::rdme::RDMESolver:

Collaboration diagram for lm::rdme::RDMESolver:

Public Member Functions
	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)
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, const unsigned int bytes_per_particle, si_dist_t latticeSpacing, const uint8_t latticeData, const uint8_t latticeSitesData, bool rowMajorData=true)
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	generateTrajectory ()=0
	Actually run the simulation.
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 ()
virtual bool	needsReactionModel ()=0
	Tells whether the solver needs a reaction model.
virtual bool	needsDiffusionModel ()=0
	Tells whether the solver needs a reaction model.

Protected Member Functions
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)
virtual void	destroyDiffusionModel ()
Protected Member Functions inherited from lm::cme::CMESolver
virtual void	allocateModel (uint numberSpecies, uint numberReactions)
virtual void	destroyModel ()
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
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

◆ RDMESolver()

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

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◆ ~RDMESolver()

lm::rdme::RDMESolver::~RDMESolver ( )

virtual

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Member Function Documentation

◆ allocateDiffusionModel()

void lm::rdme::RDMESolver::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 )

protectedvirtual

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◆ allocateLattice()

void lm::rdme::RDMESolver::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 )

protectedvirtual

Reimplemented in lm::MpdRdmeSolverExtended, lm::rdme::IntMpdRdmeSolver, lm::rdme::MGPUIntMpdRdmeSolver, lm::rdme::MGPUMpdRdmeSolver, lm::rdme::MpdRdmeSolver, lm::rdme::MPIMpdRdmeSolver, and MpdRdmeSolver.

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◆ buildDiffusionModel()

void lm::rdme::RDMESolver::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,
		const unsigned int	bytes_per_particle,
		si_dist_t	latticeSpacing,
		const uint8_t *	latticeData,
		const uint8_t *	latticeSitesData,
		bool	rowMajorData = true )

virtual

Reimplemented in lm::MpdRdmeSolverExtended, lm::rdme::IntMpdRdmeSolver, lm::rdme::IntMpdRdmeSolverExtended, lm::rdme::MGPUIntMpdRdmeSolver, lm::rdme::MGPUMpdRdmeSolver, lm::rdme::MpdRdmeSolver, lm::rdme::MPIMpdRdmeSolver, lm::rdme::NextSubvolumeSolver, and MpdRdmeSolver.

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◆ destroyDiffusionModel()

void lm::rdme::RDMESolver::destroyDiffusionModel ( )

protectedvirtual

Reimplemented in lm::rdme::NextSubvolumeSolver.

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◆ setDiffusionModel()

void lm::rdme::RDMESolver::setDiffusionModel	(	DiffusionModel *	dm,
		const uint8_t *	lattice,
		size_t	latticeSize,
		const uint8_t *	latticeSites,
		size_t	latticeSitesSize )

virtual

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◆ setLatticeData()

void lm::rdme::RDMESolver::setLatticeData ( const uint8_t * latticeData )

protectedvirtual

Reimplemented in lm::rdme::IntMpdRdmeSolver, and lm::rdme::MGPUIntMpdRdmeSolver.

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◆ setLatticeSitesData()

void lm::rdme::RDMESolver::setLatticeSitesData ( const uint8_t * latticeSitesData )

protectedvirtual

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Member Data Documentation

◆ DF

double* lm::rdme::RDMESolver::DF

protected

◆ lattice

Lattice* lm::rdme::RDMESolver::lattice

protected

◆ numberSiteTypes

uint lm::rdme::RDMESolver::numberSiteTypes

protected

◆ RL

uint* lm::rdme::RDMESolver::RL

protected

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

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

Public Member Functions

Protected Member Functions

Protected Attributes

Additional Inherited Members

Constructor & Destructor Documentation

◆ RDMESolver()

◆ ~RDMESolver()

Member Function Documentation

◆ allocateDiffusionModel()

◆ allocateLattice()

◆ buildDiffusionModel()

◆ destroyDiffusionModel()

◆ setDiffusionModel()

◆ setLatticeData()

◆ setLatticeSitesData()

Member Data Documentation

◆ DF

◆ lattice

◆ numberSiteTypes

◆ RL