lm::me::MESolver Class Reference

An abstract base class for all Master Equation solvers, this is essentially a representation of "the simulation instance". More...

#include <MESolver.h>

Inheritance diagram for lm::me::MESolver:

Public Member Functions
	MESolver ()
	Create the MESolver.
virtual	~MESolver ()
virtual void	initialize (unsigned int replicate, map< string, string > *parameters, ResourceAllocator::ComputeResources *resources)=0
	Initialize the simulation.
virtual bool	needsReactionModel ()=0
	Tells whether the solver needs a reaction model.
virtual bool	needsDiffusionModel ()=0
	Tells whether the solver needs a reaction model.
virtual void	generateTrajectory ()=0
	Actually run the simulation.

Detailed Description

An abstract base class for all Master Equation solvers, this is essentially a representation of "the simulation instance".

Constructor & Destructor Documentation

MESolver()

lm::me::MESolver::MESolver

(

)

Create the MESolver.

~MESolver()

lm::me::MESolver::~MESolver ( )

virtual

Member Function Documentation

generateTrajectory()

virtual void lm::me::MESolver::generateTrajectory ( )

pure virtual

Actually run the simulation.

Implemented in CMESolver, lm::cme::CMESolver, 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.

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initialize()

virtual void lm::me::MESolver::initialize ( unsigned int replicate, map< string, string > * parameters, ResourceAllocator::ComputeResources * resources )

pure 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

Implemented in CMESolver, lm::cme::CMESolver, lm::rdme::IntMpdRdmeSolver, lm::rdme::MGPUIntMpdRdmeSolver, lm::rdme::MGPUMpdRdmeSolver, lm::rdme::MpdRdmeSolver, lm::rdme::MPIMpdRdmeSolver, and MpdRdmeSolver.

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needsDiffusionModel()

virtual bool lm::me::MESolver::needsDiffusionModel ( )

pure virtual

Tells whether the solver needs a reaction model.

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

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needsReactionModel()

virtual bool lm::me::MESolver::needsReactionModel ( )

pure virtual

Tells whether the solver needs a reaction model.

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

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

• /data2/LM_zls_github/Lattice-Microbes/src/me/MESolver.h
• /data2/LM_zls_github/Lattice-Microbes/src/me/MESolver.cpp