#include <CMESolver.h>

Inheritance diagram for lm::cme::CMESolver:

Collaboration diagram for lm::cme::CMESolver:

Classes
struct	CompetitiveMMPropensityArgs
struct	FirstOrderPropensityArgs
struct	FPTTracking
struct	KHillPropensityArgs
struct	KHillTransportPropensityArgs
struct	MichaelisMentenPropensityArgs
struct	NoncompetitiveMMPropensityArgs
struct	PropensityArgs
struct	SecondOrderPropensityArgs
struct	SecondOrderSelfPropensityArgs
struct	SpeciesLimit
struct	TrackedParameter
struct	UncompetitiveMMPropensityArgs
struct	ZerothOrderHeavisidePropensityArgs
struct	ZerothOrderPropensityArgs

Public Member Functions
	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	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 ()

Static Protected Member Functions
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)

Protected Attributes
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

Constructor & Destructor Documentation

◆ CMESolver()

lm::cme::CMESolver::CMESolver ( RandomGenerator::Distributions neededDists )

Here is the caller graph for this function:

◆ ~CMESolver()

lm::cme::CMESolver::~CMESolver ( )

virtual

Here is the call graph for this function:

Member Function Documentation

◆ addToParameterTrackingList()

void lm::cme::CMESolver::addToParameterTrackingList ( pair< string, double * > parameter )

virtual

Here is the caller graph for this function:

◆ allocateModel()

void lm::cme::CMESolver::allocateModel	(	uint	numberSpecies,
		uint	numberReactions )

protectedvirtual

Reimplemented in lm::rdme::NextSubvolumeSolver.

Here is the caller graph for this function:

◆ buildModel()

void lm::cme::CMESolver::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

Reimplemented in lm::cme::FluctuatingNRSolver, lm::cme::GillespieDSolver, lm::cme::NextReactionSolver, lm::MpdRdmeSolverExtended, lm::rdme::IntMpdRdmeSolver, lm::rdme::IntMpdRdmeSolverExtended, lm::rdme::MGPUIntMpdRdmeSolver, lm::rdme::MGPUMpdRdmeSolver, lm::rdme::MpdRdmeSolver, lm::rdme::MPIMpdRdmeSolver, and MpdRdmeSolver.

Here is the call graph for this function:

Here is the caller graph for this function:

◆ competitiveMMPropensity()

double lm::cme::CMESolver::competitiveMMPropensity	(	double	time,
		uint *	speciesCounts,
		void *	pargs )

staticprotected

Here is the caller graph for this function:

◆ destroyModel()

void lm::cme::CMESolver::destroyModel ( )

protectedvirtual

Reimplemented in lm::cme::FluctuatingNRSolver, lm::cme::GillespieDSolver, lm::cme::NextReactionSolver, and lm::rdme::NextSubvolumeSolver.

Here is the caller graph for this function:

◆ firstOrderPropensity()

double lm::cme::CMESolver::firstOrderPropensity	(	double	time,
		uint *	speciesCounts,
		void *	pargs )

staticprotected

Here is the caller graph for this function:

◆ generateTrajectory()

virtual void lm::cme::CMESolver::generateTrajectory ( )

pure virtual

Actually run the simulation.

Implements lm::me::MESolver.

Implemented in lm::cme::GillespieDSolver, lm::cme::HillSwitch, lm::cme::NextReactionSolver, lm::cme::SelfRegulatingGeneSwitch, lm::cme::TwoStateExpression, lm::cme::TwoStateHillLoopSwitch, lm::cme::TwoStateHillSwitch, lm::MpdRdmeSolverExtended, lm::rdme::IntMpdRdmeSolver, lm::rdme::MGPUIntMpdRdmeSolver, lm::rdme::MGPUMpdRdmeSolver, lm::rdme::MpdRdmeSolver, lm::rdme::MpdTestHarness, lm::rdme::MPIMpdRdmeSolver, lm::rdme::NextSubvolumeSolver, and MpdRdmeSolver.

◆ getReactionRateConstantsView()

void lm::cme::CMESolver::getReactionRateConstantsView	(	int	reactionNumber,
		double **	rates,
		int *	rateConstantCount )

virtual

◆ getSpeciesCountView()

void lm::cme::CMESolver::getSpeciesCountView	(	uint **	counts,
		int *	number )

virtual

◆ hookSimulation()

int lm::cme::CMESolver::hookSimulation ( double time )

protectedvirtual

Reimplemented in lm::cme::GillespieDSolver, and lm::cme::NextReactionSolver.

◆ initialize()

void lm::cme::CMESolver::initialize	(	unsigned int	replicate,
		map< string, string > *	parameters,
		ResourceAllocator::ComputeResources *	resources )

virtual

Initialize the simulation.

Parameters

replicate	Replicate number out of total replicates
parameters	A map of all the parameters for the simulation
A	list of resources assigned to the simulation

Implements lm::me::MESolver.

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

Here is the call graph for this function:

◆ kHillPropensity()

double lm::cme::CMESolver::kHillPropensity	(	double	time,
		uint *	speciesCounts,
		void *	pargs )

staticprotected

Here is the caller graph for this function:

◆ kHillTransportPropensity()

double lm::cme::CMESolver::kHillTransportPropensity	(	double	time,
		uint *	speciesCounts,
		void *	pargs )

staticprotected

Here is the call graph for this function:

Here is the caller graph for this function:

◆ michaelisMentenPropensity()

double lm::cme::CMESolver::michaelisMentenPropensity	(	double	time,
		uint *	speciesCounts,
		void *	pargs )

staticprotected

Here is the caller graph for this function:

◆ noncompetitiveMMPropensity()

double lm::cme::CMESolver::noncompetitiveMMPropensity	(	double	time,
		uint *	speciesCounts,
		void *	pargs )

staticprotected

Here is the caller graph for this function:

◆ onBeginTrajectory()

int lm::cme::CMESolver::onBeginTrajectory ( )

protectedvirtual

Reimplemented in lm::cme::GillespieDSolver.

◆ onEndTrajectory()

int lm::cme::CMESolver::onEndTrajectory ( )

protectedvirtual

Reimplemented in lm::cme::GillespieDSolver.

◆ queueRecordedParameters()

void lm::cme::CMESolver::queueRecordedParameters ( bool flush = false )

protectedvirtual

Here is the call graph for this function:

Here is the caller graph for this function:

◆ reachedSpeciesLimit()

bool lm::cme::CMESolver::reachedSpeciesLimit ( )

inlineprotected

Here is the caller graph for this function:

◆ recordParameters()

double lm::cme::CMESolver::recordParameters	(	double	nextRecordTime,
		double	recordInterval,
		double	simulationTime )

protectedvirtual

Here is the call graph for this function:

Here is the caller graph for this function:

◆ secondOrderPropensity()

double lm::cme::CMESolver::secondOrderPropensity	(	double	time,
		uint *	speciesCounts,
		void *	pargs )

staticprotected

Here is the caller graph for this function:

◆ secondOrderSelfPropensity()

double lm::cme::CMESolver::secondOrderSelfPropensity	(	double	time,
		uint *	speciesCounts,
		void *	pargs )

staticprotected

Here is the caller graph for this function:

◆ setFptTrackingList()

void lm::cme::CMESolver::setFptTrackingList ( list< uint > speciesList )

virtual

Here is the caller graph for this function:

◆ setModelPropensityFunction()

void lm::cme::CMESolver::setModelPropensityFunction	(	uint	reaction,
		double(*	propensityFunction )(double time, uint speciesCounts, void args),
		void *	propensityFunctionArg )

virtual

Here is the caller graph for this function:

◆ setReactionModel()

void lm::cme::CMESolver::setReactionModel ( lm::io::ReactionModel * reactionModel )

virtual

Reimplemented in lm::cme::FluctuatingNRSolver, and lm::cme::LacHillSwitch.

Here is the call graph for this function:

◆ setReactionRateCME()

void lm::cme::CMESolver::setReactionRateCME	(	unsigned int	reactionId,
		double	rate )

virtual

◆ setSpeciesLowerLimit()

void lm::cme::CMESolver::setSpeciesLowerLimit	(	uint	species,
		uint	limit )

virtual

Here is the caller graph for this function:

◆ setSpeciesUpperLimit()

void lm::cme::CMESolver::setSpeciesUpperLimit	(	uint	species,
		uint	limit )

virtual

Here is the caller graph for this function:

◆ uncompetitiveMMPropensity()

double lm::cme::CMESolver::uncompetitiveMMPropensity	(	double	time,
		uint *	speciesCounts,
		void *	pargs )

staticprotected

Here is the caller graph for this function:

◆ updateSpeciesCounts()

void lm::cme::CMESolver::updateSpeciesCounts ( uint r )

inlineprotected

Here is the caller graph for this function:

◆ zerothOrderHeavisidePropensity()

double lm::cme::CMESolver::zerothOrderHeavisidePropensity	(	double	time,
		uint *	speciesCounts,
		void *	pargs )

staticprotected

Here is the caller graph for this function:

◆ zerothOrderPropensity()

double lm::cme::CMESolver::zerothOrderPropensity	(	double	time,
		uint *	speciesCounts,
		void *	pargs )

staticprotected

Here is the caller graph for this function:

Member Data Documentation

◆ D

uint* lm::cme::CMESolver::D

protected

◆ dependentReactions

uint** lm::cme::CMESolver::dependentReactions

protected

◆ dependentSpecies

uint** lm::cme::CMESolver::dependentSpecies

protected

◆ dependentSpeciesChange

int** lm::cme::CMESolver::dependentSpeciesChange

protected

◆ fptTrackedSpecies

FPTTracking* lm::cme::CMESolver::fptTrackedSpecies

protected

◆ initialSpeciesCounts

uint* lm::cme::CMESolver::initialSpeciesCounts

protected

◆ neededDists

RandomGenerator::Distributions lm::cme::CMESolver::neededDists

protected

◆ numberDependentReactions

uint* lm::cme::CMESolver::numberDependentReactions

protected

◆ numberDependentSpecies

uint* lm::cme::CMESolver::numberDependentSpecies

protected

◆ numberFptTrackedSpecies

uint lm::cme::CMESolver::numberFptTrackedSpecies

protected

◆ numberReactions

uint lm::cme::CMESolver::numberReactions

protected

◆ numberSpecies

uint lm::cme::CMESolver::numberSpecies

protected

◆ numberSpeciesLimits

uint lm::cme::CMESolver::numberSpeciesLimits

protected

◆ numberSpeciesToTrack

uint lm::cme::CMESolver::numberSpeciesToTrack

protected

◆ parameters

map<string,string>* lm::cme::CMESolver::parameters

protected

◆ propensityArgs

list<PropensityArgs *> lm::cme::CMESolver::propensityArgs

protected

◆ propensityFunctionArgs

void** lm::cme::CMESolver::propensityFunctionArgs

protected

◆ propensityFunctions

void** lm::cme::CMESolver::propensityFunctions

protected

◆ reactionTypes

uint* lm::cme::CMESolver::reactionTypes

protected

◆ replicate

unsigned int lm::cme::CMESolver::replicate

protected

◆ resources

ResourceAllocator::ComputeResources* lm::cme::CMESolver::resources

protected

◆ rng

RandomGenerator* lm::cme::CMESolver::rng

protected

◆ S

int* lm::cme::CMESolver::S

protected

◆ speciesCounts

uint* lm::cme::CMESolver::speciesCounts

protected

◆ speciesLimits

SpeciesLimit* lm::cme::CMESolver::speciesLimits

protected

◆ trackedParameters

list<TrackedParameter> lm::cme::CMESolver::trackedParameters

protected

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

/data2/LM_zls_github/Lattice-Microbes/src/cme/CMESolver.h
/data2/LM_zls_github/Lattice-Microbes/src/cme/CMESolver.cpp

Classes

Public Member Functions

Protected Member Functions

Static Protected Member Functions

Protected Attributes

Constructor & Destructor Documentation

◆ CMESolver()

◆ ~CMESolver()

Member Function Documentation

◆ addToParameterTrackingList()

◆ allocateModel()

◆ buildModel()

◆ competitiveMMPropensity()

◆ destroyModel()

◆ firstOrderPropensity()

◆ generateTrajectory()

◆ getReactionRateConstantsView()

◆ getSpeciesCountView()

◆ hookSimulation()

◆ initialize()

◆ kHillPropensity()

◆ kHillTransportPropensity()

◆ michaelisMentenPropensity()

◆ noncompetitiveMMPropensity()

◆ onBeginTrajectory()

◆ onEndTrajectory()

◆ queueRecordedParameters()

◆ reachedSpeciesLimit()

◆ recordParameters()

◆ secondOrderPropensity()

◆ secondOrderSelfPropensity()

◆ setFptTrackingList()

◆ setModelPropensityFunction()

◆ setReactionModel()

◆ setReactionRateCME()

◆ setSpeciesLowerLimit()

◆ setSpeciesUpperLimit()

◆ uncompetitiveMMPropensity()

◆ updateSpeciesCounts()

◆ zerothOrderHeavisidePropensity()

◆ zerothOrderPropensity()

Member Data Documentation

◆ D

◆ dependentReactions

◆ dependentSpecies

◆ dependentSpeciesChange

◆ fptTrackedSpecies

◆ initialSpeciesCounts

◆ neededDists

◆ numberDependentReactions

◆ numberDependentSpecies

◆ numberFptTrackedSpecies

◆ numberReactions

◆ numberSpecies

◆ numberSpeciesLimits

◆ numberSpeciesToTrack

◆ parameters

◆ propensityArgs

◆ propensityFunctionArgs

◆ propensityFunctions

◆ reactionTypes

◆ replicate

◆ resources

◆ rng

◆ S

◆ speciesCounts

◆ speciesLimits

◆ trackedParameters