#include <MPIMpdRdmeSolver.h>

Inheritance diagram for lm::rdme::MPIMpdRdmeSolver:

Collaboration diagram for lm::rdme::MPIMpdRdmeSolver:

Public Member Functions
	MPIMpdRdmeSolver ()
virtual	~MPIMpdRdmeSolver ()
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.
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 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, ByteLattice lattice, lm::io::Lattice latticeDataSet)
virtual void	recordSpeciesCounts (double time, ByteLattice lattice, lm::io::SpeciesCounts speciesCountsDataSet)
virtual void	writeSpeciesCounts (lm::io::SpeciesCounts *speciesCountsDataSet)
virtual int	run_next_timestep (uint32_t timestep)
virtual uint64_t	getTimestepSeed (uint32_t timestep, uint32_t substep)
virtual void	copyModelsToDevice ()
virtual void	initialize_decomposition ()
virtual void	prepare_gpu ()
virtual void	calculateXLaunchParameters (dim3 gridSize, dim3 threadBlockSize, const unsigned int maxXBlockSize, const unsigned int latticeXSize, const unsigned int latticeYSize, const unsigned int latticeZSize)
virtual void	calculateYLaunchParameters (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 (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 (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
void *	cudaOverflowList
double	tau
uint32_t	overflowTimesteps
uint32_t	overflowListUses
unsigned int *	model_reactionOrders
unsigned int *	model_reactionSites
unsigned int *	model_D1
unsigned int *	model_D2
int8_t *	model_S
float *	model_T
uint8_t *	model_RL
float *	model_reactionRates
int	world_size
int	rank
ZDivMPIGPUMapper *	mapper
ResourceAllocator::ComputeResources *	resources
int	timesteps_to_run
uint32_t	absolute_timestep
int	gpu
int	ngpus
bool	lattice_synched
unsigned int *	dLattice
unsigned int *	dLatticeTmp
uint8_t *	dSites
cudaStream_t	stream1
cudaStream_t	stream2
cudaEvent_t	x_finish
cudaEvent_t	diffusion_finished
cudaEvent_t	rx_finish
unsigned int *	h_overflows
unsigned int *	d_overflows
dim3	grid_x
dim3	grid_y
dim3	grid_z
dim3	grid_r
dim3	threads_x
dim3	threads_y
dim3	threads_z
dim3	threads_r
SegmentDescriptor_s *	segment
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

◆ MPIMpdRdmeSolver()

lm::rdme::MPIMpdRdmeSolver::MPIMpdRdmeSolver ( )

◆ ~MPIMpdRdmeSolver()

virtual lm::rdme::MPIMpdRdmeSolver::~MPIMpdRdmeSolver ( )

virtual

Member Function Documentation

◆ allocateLattice()

virtual void lm::rdme::MPIMpdRdmeSolver::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::MPIMpdRdmeSolver::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::MPIMpdRdmeSolver::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::MPIMpdRdmeSolver::calculateReactionLaunchParameters	(	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::MPIMpdRdmeSolver::calculateXLaunchParameters	(	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::MPIMpdRdmeSolver::calculateYLaunchParameters	(	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::MPIMpdRdmeSolver::calculateZLaunchParameters	(	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

◆ copyModelsToDevice()

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

protectedvirtual

◆ generateTrajectory()

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

virtual

Actually run the simulation.

Implements lm::cme::CMESolver.

◆ getTimestepSeed()

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

protectedvirtual

◆ initialize()

virtual void lm::rdme::MPIMpdRdmeSolver::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.

◆ initialize_decomposition()

virtual void lm::rdme::MPIMpdRdmeSolver::initialize_decomposition ( )

protectedvirtual

◆ needsDiffusionModel()

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

inlinevirtual

Tells whether the solver needs a reaction model.

Implements lm::me::MESolver.

◆ needsReactionModel()

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

inlinevirtual

Tells whether the solver needs a reaction model.

Implements lm::me::MESolver.

◆ prepare_gpu()

virtual void lm::rdme::MPIMpdRdmeSolver::prepare_gpu ( )

protectedvirtual

◆ recordSpeciesCounts()

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

protectedvirtual

◆ run_next_timestep()

virtual int lm::rdme::MPIMpdRdmeSolver::run_next_timestep ( uint32_t timestep )

protectedvirtual

◆ writeLatticeData()

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

protectedvirtual

◆ writeSpeciesCounts()

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

protectedvirtual

Member Data Documentation

◆ absolute_timestep

uint32_t lm::rdme::MPIMpdRdmeSolver::absolute_timestep

protected

◆ cudaOverflowList

void* lm::rdme::MPIMpdRdmeSolver::cudaOverflowList

protected

◆ d_overflows

unsigned int * lm::rdme::MPIMpdRdmeSolver::d_overflows

protected

◆ diffusion_finished

cudaEvent_t lm::rdme::MPIMpdRdmeSolver::diffusion_finished

protected

◆ dLattice

unsigned int* lm::rdme::MPIMpdRdmeSolver::dLattice

protected

◆ dLatticeTmp

unsigned int * lm::rdme::MPIMpdRdmeSolver::dLatticeTmp

protected

◆ dSites

uint8_t* lm::rdme::MPIMpdRdmeSolver::dSites

protected

◆ gpu

int lm::rdme::MPIMpdRdmeSolver::gpu

protected

◆ grid_r

dim3 lm::rdme::MPIMpdRdmeSolver::grid_r

protected

◆ grid_x

dim3 lm::rdme::MPIMpdRdmeSolver::grid_x

protected

◆ grid_y

dim3 lm::rdme::MPIMpdRdmeSolver::grid_y

protected

◆ grid_z

dim3 lm::rdme::MPIMpdRdmeSolver::grid_z

protected

◆ h_overflows

unsigned int* lm::rdme::MPIMpdRdmeSolver::h_overflows

protected

◆ lattice_synched

bool lm::rdme::MPIMpdRdmeSolver::lattice_synched

protected

◆ mapper

ZDivMPIGPUMapper* lm::rdme::MPIMpdRdmeSolver::mapper

protected

◆ model_D1

unsigned int* lm::rdme::MPIMpdRdmeSolver::model_D1

protected

◆ model_D2

unsigned int* lm::rdme::MPIMpdRdmeSolver::model_D2

protected

◆ model_reactionOrders

unsigned int* lm::rdme::MPIMpdRdmeSolver::model_reactionOrders

protected

◆ model_reactionRates

float* lm::rdme::MPIMpdRdmeSolver::model_reactionRates

protected

◆ model_reactionSites

unsigned int* lm::rdme::MPIMpdRdmeSolver::model_reactionSites

protected

◆ model_RL

uint8_t* lm::rdme::MPIMpdRdmeSolver::model_RL

protected

◆ model_S

int8_t* lm::rdme::MPIMpdRdmeSolver::model_S

protected

◆ model_T

float* lm::rdme::MPIMpdRdmeSolver::model_T

protected

◆ ngpus

int lm::rdme::MPIMpdRdmeSolver::ngpus

protected

◆ overflowListUses

uint32_t lm::rdme::MPIMpdRdmeSolver::overflowListUses

protected

◆ overflowTimesteps

uint32_t lm::rdme::MPIMpdRdmeSolver::overflowTimesteps

protected

◆ rank

int lm::rdme::MPIMpdRdmeSolver::rank

protected

◆ resources

ResourceAllocator::ComputeResources* lm::rdme::MPIMpdRdmeSolver::resources

protected

◆ rx_finish

cudaEvent_t lm::rdme::MPIMpdRdmeSolver::rx_finish

protected

◆ seed

uint32_t lm::rdme::MPIMpdRdmeSolver::seed

protected

◆ segment

SegmentDescriptor_s* lm::rdme::MPIMpdRdmeSolver::segment

protected

◆ stream1

cudaStream_t lm::rdme::MPIMpdRdmeSolver::stream1

protected

◆ stream2

cudaStream_t lm::rdme::MPIMpdRdmeSolver::stream2

protected

◆ tau

double lm::rdme::MPIMpdRdmeSolver::tau

protected

◆ threads_r

dim3 lm::rdme::MPIMpdRdmeSolver::threads_r

protected

◆ threads_x

dim3 lm::rdme::MPIMpdRdmeSolver::threads_x

protected

◆ threads_y

dim3 lm::rdme::MPIMpdRdmeSolver::threads_y

protected

◆ threads_z

dim3 lm::rdme::MPIMpdRdmeSolver::threads_z

protected

◆ timesteps_to_run

int lm::rdme::MPIMpdRdmeSolver::timesteps_to_run

protected

◆ world_size

int lm::rdme::MPIMpdRdmeSolver::world_size

protected

◆ x_finish

cudaEvent_t lm::rdme::MPIMpdRdmeSolver::x_finish

protected

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

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

Public Member Functions

Protected Member Functions

Protected Attributes

Additional Inherited Members

Constructor & Destructor Documentation

◆ MPIMpdRdmeSolver()

◆ ~MPIMpdRdmeSolver()

Member Function Documentation

◆ allocateLattice()

◆ buildDiffusionModel()

◆ buildModel()

◆ calculateReactionLaunchParameters()

◆ calculateXLaunchParameters()

◆ calculateYLaunchParameters()

◆ calculateZLaunchParameters()

◆ copyModelsToDevice()

◆ generateTrajectory()

◆ getTimestepSeed()

◆ initialize()

◆ initialize_decomposition()

◆ needsDiffusionModel()

◆ needsReactionModel()

◆ prepare_gpu()

◆ recordSpeciesCounts()

◆ run_next_timestep()

◆ writeLatticeData()

◆ writeSpeciesCounts()

Member Data Documentation

◆ absolute_timestep

◆ cudaOverflowList

◆ d_overflows

◆ diffusion_finished

◆ dLattice

◆ dLatticeTmp

◆ dSites

◆ gpu

◆ grid_r

◆ grid_x

◆ grid_y

◆ grid_z

◆ h_overflows

◆ lattice_synched

◆ mapper

◆ model_D1

◆ model_D2

◆ model_reactionOrders

◆ model_reactionRates

◆ model_reactionSites

◆ model_RL

◆ model_S

◆ model_T

◆ ngpus

◆ overflowListUses

◆ overflowTimesteps

◆ rank

◆ resources

◆ rx_finish

◆ seed

◆ segment

◆ stream1

◆ stream2

◆ tau

◆ threads_r

◆ threads_x

◆ threads_y

◆ threads_z

◆ timesteps_to_run

◆ world_size

◆ x_finish