#include <MpdRdmeSolver.h>

Inheritance diagram for MpdRdmeSolver:

Collaboration diagram for MpdRdmeSolver:

Public Member Functions
	MpdRdmeSolver ()
virtual	~MpdRdmeSolver ()
virtual void	initialize (unsigned int replicate, map< string, string > parameters, ResourceAllocator::ComputeResources resources)
	Initialize the simulation.
virtual bool	needsReactionModel ()
	Tells whether the solver needs a reaction model.
virtual bool	needsDiffusionModel ()
	Tells whether the solver needs a reaction model.
virtual void	buildModel (const uint numberSpeciesA, const uint numberReactionsA, const uint initialSpeciesCountsA, const uint reactionTypeA, const double kA, const int SA, const uint *DA, const uint kCols=1)
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)
virtual void	generateTrajectory ()
	Actually run the simulation.
virtual void	setReactionRate (unsigned int rxid, float rate)
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	setReactionModel (lm::io::ReactionModel *reactionModel)
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 int	onBeginTrajectory (CudaByteLattice *lattice)
virtual int	onEndTrajectory (CudaByteLattice *lattice)
virtual int	onWriteLattice (double time, CudaByteLattice *lattice)
virtual void	allocateLattice (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)
virtual void	writeLatticeData (double time, CudaByteLattice lattice, lm::io::Lattice latticeDataSet)
virtual void	writeLatticeSites (double time, CudaByteLattice *lattice)
virtual void	recordSpeciesCounts (double time, CudaByteLattice lattice, lm::io::SpeciesCounts speciesCountsDataSet)
virtual void	writeSpeciesCounts (lm::io::SpeciesCounts *speciesCountsDataSet)
virtual int	hookSimulation (double time, CudaByteLattice *lattice)
virtual void	hookCheckSimulation (double time, CudaByteLattice *lattice)
virtual void	runTimestep (CudaByteLattice *lattice, uint32_t timestep)
virtual uint64_t	getTimestepSeed (uint32_t timestep, uint32_t substep)
virtual void	computePropensities ()
virtual void	copyModelsToDevice ()
virtual void	calculateXLaunchParameters (unsigned int gridXSize, dim3 gridSize, dim3 *threadBlockSize, const unsigned int maxXBlockSize, const unsigned int latticeXSize, const unsigned int latticeYSize, const unsigned int latticeZSize)
virtual void	calculateYLaunchParameters (unsigned int gridXSize, dim3 gridSize, dim3 *threadBlockSize, const unsigned int blockXSize, const unsigned int blockYSize, const unsigned int latticeXSize, const unsigned int latticeYSize, const unsigned int latticeZSize)
virtual void	calculateZLaunchParameters (unsigned int gridXSize, dim3 gridSize, dim3 *threadBlockSize, const unsigned int blockXSize, const unsigned int blockZSize, const unsigned int latticeXSize, const unsigned int latticeYSize, const unsigned int latticeZSize)
virtual void	calculateReactionLaunchParameters (unsigned int gridXSize, dim3 gridSize, dim3 *threadBlockSize, const unsigned int blockXSize, const unsigned int blockYSize, const unsigned int latticeXSize, const unsigned int latticeYSize, const unsigned int latticeZSize)
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	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
uint32_t	seed
double	tau
bool	reactionModelModified
void *	cudaOverflowList
cudaStream_t	cudaStream
uint32_t	overflowTimesteps
uint32_t	overflowListUses
int	overflow_handling
float *	model_reactionRates
size_t	zeroOrderSize
size_t	firstOrderSize
size_t	secondOrderSize
float *	zeroOrder
float *	firstOrder
float *	secondOrder
float *	propZeroOrder
float *	propFirstOrder
float *	propSecondOrder
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

◆ MpdRdmeSolver()

lm::rdme::MpdRdmeSolver::MpdRdmeSolver ( )

◆ ~MpdRdmeSolver()

virtual lm::rdme::MpdRdmeSolver::~MpdRdmeSolver ( )

virtual

Member Function Documentation

◆ allocateLattice()

virtual void lm::rdme::MpdRdmeSolver::allocateLattice	(	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 )

protectedvirtual

Reimplemented from lm::rdme::RDMESolver.

◆ buildDiffusionModel()

virtual void lm::rdme::MpdRdmeSolver::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 from lm::rdme::RDMESolver.

◆ buildModel()

virtual void lm::rdme::MpdRdmeSolver::buildModel	(	const uint	numberSpeciesA,
		const uint	numberReactionsA,
		const uint *	initialSpeciesCountsA,
		const uint *	reactionTypeA,
		const double *	kA,
		const int *	SA,
		const uint *	DA,
		const uint	kCols = 1 )

virtual

Reimplemented from lm::cme::CMESolver.

◆ calculateReactionLaunchParameters()

virtual void lm::rdme::MpdRdmeSolver::calculateReactionLaunchParameters	(	unsigned int *	gridXSize,
		dim3 *	gridSize,
		dim3 *	threadBlockSize,
		const unsigned int	blockXSize,
		const unsigned int	blockYSize,
		const unsigned int	latticeXSize,
		const unsigned int	latticeYSize,
		const unsigned int	latticeZSize )

protectedvirtual

◆ calculateXLaunchParameters()

virtual void lm::rdme::MpdRdmeSolver::calculateXLaunchParameters	(	unsigned int *	gridXSize,
		dim3 *	gridSize,
		dim3 *	threadBlockSize,
		const unsigned int	maxXBlockSize,
		const unsigned int	latticeXSize,
		const unsigned int	latticeYSize,
		const unsigned int	latticeZSize )

protectedvirtual

◆ calculateYLaunchParameters()

virtual void lm::rdme::MpdRdmeSolver::calculateYLaunchParameters	(	unsigned int *	gridXSize,
		dim3 *	gridSize,
		dim3 *	threadBlockSize,
		const unsigned int	blockXSize,
		const unsigned int	blockYSize,
		const unsigned int	latticeXSize,
		const unsigned int	latticeYSize,
		const unsigned int	latticeZSize )

protectedvirtual

◆ calculateZLaunchParameters()

virtual void lm::rdme::MpdRdmeSolver::calculateZLaunchParameters	(	unsigned int *	gridXSize,
		dim3 *	gridSize,
		dim3 *	threadBlockSize,
		const unsigned int	blockXSize,
		const unsigned int	blockZSize,
		const unsigned int	latticeXSize,
		const unsigned int	latticeYSize,
		const unsigned int	latticeZSize )

protectedvirtual

◆ computePropensities()

virtual void lm::rdme::MpdRdmeSolver::computePropensities ( )

protectedvirtual

◆ copyModelsToDevice()

virtual void lm::rdme::MpdRdmeSolver::copyModelsToDevice ( )

protectedvirtual

◆ generateTrajectory()

virtual void lm::rdme::MpdRdmeSolver::generateTrajectory ( )

virtual

Actually run the simulation.

Implements lm::cme::CMESolver.

◆ getTimestepSeed()

virtual uint64_t lm::rdme::MpdRdmeSolver::getTimestepSeed	(	uint32_t	timestep,
		uint32_t	substep )

protectedvirtual

◆ hookCheckSimulation()

virtual void lm::rdme::MpdRdmeSolver::hookCheckSimulation	(	double	time,
		CudaByteLattice *	lattice )

protectedvirtual

◆ hookSimulation()

virtual int lm::rdme::MpdRdmeSolver::hookSimulation	(	double	time,
		CudaByteLattice *	lattice )

protectedvirtual

◆ initialize()

virtual void lm::rdme::MpdRdmeSolver::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

Reimplemented from lm::cme::CMESolver.

◆ needsDiffusionModel()

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

inlinevirtual

Tells whether the solver needs a reaction model.

Implements lm::me::MESolver.

◆ needsReactionModel()

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

inlinevirtual

Tells whether the solver needs a reaction model.

Implements lm::me::MESolver.

◆ onBeginTrajectory()

virtual int lm::rdme::MpdRdmeSolver::onBeginTrajectory ( CudaByteLattice * lattice )

protectedvirtual

◆ onEndTrajectory()

virtual int lm::rdme::MpdRdmeSolver::onEndTrajectory ( CudaByteLattice * lattice )

protectedvirtual

◆ onWriteLattice()

virtual int lm::rdme::MpdRdmeSolver::onWriteLattice	(	double	time,
		CudaByteLattice *	lattice )

protectedvirtual

◆ recordSpeciesCounts()

virtual void lm::rdme::MpdRdmeSolver::recordSpeciesCounts	(	double	time,
		CudaByteLattice *	lattice,
		lm::io::SpeciesCounts *	speciesCountsDataSet )

protectedvirtual

◆ runTimestep()

virtual void lm::rdme::MpdRdmeSolver::runTimestep	(	CudaByteLattice *	lattice,
		uint32_t	timestep )

protectedvirtual

◆ setReactionRate()

virtual void lm::rdme::MpdRdmeSolver::setReactionRate	(	unsigned int	rxid,
		float	rate )

virtual

◆ writeLatticeData()

virtual void lm::rdme::MpdRdmeSolver::writeLatticeData	(	double	time,
		CudaByteLattice *	lattice,
		lm::io::Lattice *	latticeDataSet )

protectedvirtual

◆ writeLatticeSites()

virtual void lm::rdme::MpdRdmeSolver::writeLatticeSites	(	double	time,
		CudaByteLattice *	lattice )

protectedvirtual

◆ writeSpeciesCounts()

virtual void lm::rdme::MpdRdmeSolver::writeSpeciesCounts ( lm::io::SpeciesCounts * speciesCountsDataSet )

protectedvirtual

Member Data Documentation

◆ cudaOverflowList

void* lm::rdme::MpdRdmeSolver::cudaOverflowList

protected

◆ cudaStream

cudaStream_t lm::rdme::MpdRdmeSolver::cudaStream

protected

◆ firstOrder

float * lm::rdme::MpdRdmeSolver::firstOrder

protected

◆ firstOrderSize

size_t lm::rdme::MpdRdmeSolver::firstOrderSize

protected

◆ model_reactionRates

float* lm::rdme::MpdRdmeSolver::model_reactionRates

protected

◆ overflow_handling

int lm::rdme::MpdRdmeSolver::overflow_handling

protected

◆ overflowListUses

uint32_t lm::rdme::MpdRdmeSolver::overflowListUses

protected

◆ overflowTimesteps

uint32_t lm::rdme::MpdRdmeSolver::overflowTimesteps

protected

◆ propFirstOrder

float* lm::rdme::MpdRdmeSolver::propFirstOrder

protected

◆ propSecondOrder

float* lm::rdme::MpdRdmeSolver::propSecondOrder

protected

◆ propZeroOrder

float* lm::rdme::MpdRdmeSolver::propZeroOrder

protected

◆ reactionModelModified

bool lm::rdme::MpdRdmeSolver::reactionModelModified

protected

◆ secondOrder

float * lm::rdme::MpdRdmeSolver::secondOrder

protected

◆ secondOrderSize

size_t lm::rdme::MpdRdmeSolver::secondOrderSize

protected

◆ seed

uint32_t lm::rdme::MpdRdmeSolver::seed

protected

◆ tau

double lm::rdme::MpdRdmeSolver::tau

protected

◆ zeroOrder

float* lm::rdme::MpdRdmeSolver::zeroOrder

protected

◆ zeroOrderSize

size_t lm::rdme::MpdRdmeSolver::zeroOrderSize

protected

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

/data2/LM_zls_github/Lattice-Microbes/src/rdme/MpdRdmeSolver.h

Public Member Functions

Protected Member Functions

Protected Attributes

Additional Inherited Members

Constructor & Destructor Documentation

◆ MpdRdmeSolver()

◆ ~MpdRdmeSolver()

Member Function Documentation

◆ allocateLattice()

◆ buildDiffusionModel()

◆ buildModel()

◆ calculateReactionLaunchParameters()

◆ calculateXLaunchParameters()

◆ calculateYLaunchParameters()

◆ calculateZLaunchParameters()

◆ computePropensities()

◆ copyModelsToDevice()

◆ generateTrajectory()

◆ getTimestepSeed()

◆ hookCheckSimulation()

◆ hookSimulation()

◆ initialize()

◆ needsDiffusionModel()

◆ needsReactionModel()

◆ onBeginTrajectory()

◆ onEndTrajectory()

◆ onWriteLattice()

◆ recordSpeciesCounts()

◆ runTimestep()

◆ setReactionRate()

◆ writeLatticeData()

◆ writeLatticeSites()

◆ writeSpeciesCounts()

Member Data Documentation

◆ cudaOverflowList

◆ cudaStream

◆ firstOrder

◆ firstOrderSize

◆ model_reactionRates

◆ overflow_handling

◆ overflowListUses

◆ overflowTimesteps

◆ propFirstOrder

◆ propSecondOrder

◆ propZeroOrder

◆ reactionModelModified

◆ secondOrder

◆ secondOrderSize

◆ seed

◆ tau

◆ zeroOrder

◆ zeroOrderSize