Lattice Microbes 2.5
This is for whole cell modeling
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lm::cme::GillespieDSolver Class Reference

#include <GillespieDSolver.h>

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Public Member Functions

 GillespieDSolver ()
virtual ~GillespieDSolver ()
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 numberSpecies, const uint numberReactions, const uint *initialSpeciesCounts, const uint *reactionType, const double *k, const int *S, const uint *D, const uint kCols=1)
virtual void generateTrajectory ()
 Actually run the simulation.
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 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 destroyModel ()
void updateAllPropensities (double time)
void updatePropensities (double time, uint r)
virtual int hookSimulation (double time)
virtual int onBeginTrajectory ()
virtual int onEndTrajectory ()
Protected Member Functions inherited from lm::cme::CMESolver
virtual void allocateModel (uint numberSpecies, uint numberReactions)
virtual double recordParameters (double nextRecordTime, double recordInterval, double simulationTime)
virtual void queueRecordedParameters (bool flush=false)
void updateSpeciesCounts (uint r)
bool reachedSpeciesLimit ()

Protected Attributes

double * propensities
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

◆ GillespieDSolver()

lm::cme::GillespieDSolver::GillespieDSolver ( )
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◆ ~GillespieDSolver()

lm::cme::GillespieDSolver::~GillespieDSolver ( )
virtual

Member Function Documentation

◆ buildModel()

void lm::cme::GillespieDSolver::buildModel ( const uint numberSpecies,
const uint numberReactions,
const uint * initialSpeciesCounts,
const uint * reactionType,
const double * k,
const int * S,
const uint * D,
const uint kCols = 1 )
virtual

Reimplemented from lm::cme::CMESolver.

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◆ destroyModel()

void lm::cme::GillespieDSolver::destroyModel ( )
protectedvirtual

Reimplemented from lm::cme::CMESolver.

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◆ generateTrajectory()

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

Actually run the simulation.

Implements lm::cme::CMESolver.

Reimplemented in lm::cme::HillSwitch, lm::cme::TwoStateExpression, lm::cme::TwoStateHillLoopSwitch, and lm::cme::TwoStateHillSwitch.

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◆ hookSimulation()

int lm::cme::GillespieDSolver::hookSimulation ( double time)
protectedvirtual

Reimplemented from lm::cme::CMESolver.

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◆ needsDiffusionModel()

virtual bool lm::cme::GillespieDSolver::needsDiffusionModel ( )
inlinevirtual

Tells whether the solver needs a reaction model.

Implements lm::me::MESolver.

Reimplemented in lm::cme::HillSwitch, lm::cme::TwoStateExpression, lm::cme::TwoStateHillLoopSwitch, and lm::cme::TwoStateHillSwitch.

◆ needsReactionModel()

virtual bool lm::cme::GillespieDSolver::needsReactionModel ( )
inlinevirtual

Tells whether the solver needs a reaction model.

Implements lm::me::MESolver.

Reimplemented in lm::cme::HillSwitch, lm::cme::TwoStateExpression, lm::cme::TwoStateHillLoopSwitch, and lm::cme::TwoStateHillSwitch.

◆ onBeginTrajectory()

int lm::cme::GillespieDSolver::onBeginTrajectory ( )
protectedvirtual

Reimplemented from lm::cme::CMESolver.

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◆ onEndTrajectory()

int lm::cme::GillespieDSolver::onEndTrajectory ( )
protectedvirtual

Reimplemented from lm::cme::CMESolver.

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◆ updateAllPropensities()

void lm::cme::GillespieDSolver::updateAllPropensities ( double time)
inlineprotected
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◆ updatePropensities()

void lm::cme::GillespieDSolver::updatePropensities ( double time,
uint r )
inlineprotected
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Member Data Documentation

◆ propensities

double* lm::cme::GillespieDSolver::propensities
protected
The documentation for this class was generated from the following files: