Simulation Class Reference

A class that ties together all the parts of a simulation. More...

#include <Simulation.h>

Inheritance diagram for Simulation:

Public Member Functions
	Simulation ()
	Initialize all the shared pointers, etc. More...
void	setConfiguration (ForcePtr _config)
	Pass in a reference to the configuration. More...
void	computeForces (GPUArray< Dscalar2 > &forces)
	Call the force computer to compute the forces. More...
void	moveDegreesOfFreedom (GPUArray< Dscalar2 > &displacements)
	Call the configuration to move particles around. More...
void	performTimestep ()
	Call every updater to advance one time step. More...
shared_ptr< Simulation >	getPointer ()
	return a shared pointer to this Simulation
void	addUpdater (UpdaterPtr _upd)
	Add an updater.
void	addUpdater (UpdaterPtr _upd, ForcePtr _config)
	Add an updater with a reference to a configuration. More...
void	clearUpdaters ()
	Clear out the vector of updaters.
void	setBox (BoxPtr _box)
	This changes the contents of the Box pointed to by Box to match that of _box. More...
void	setCellList (cellListGPU &_cl)
	Pass in a reference to the box.
void	setIntegrationTimestep (Dscalar dt)
	Set the simulation timestep. More...
void	setCPUOperation (bool setcpu)
	turn on CPU-only mode for all components More...
void	setReproducible (bool reproducible)
	Enforce reproducible dynamics. More...
void	setSortPeriod (int sp)
	Set the time between spatial sorting operations.
virtual void	setCurrentTime (Dscalar _cTime)
	reset the simulation clock More...
virtual void	setCurrentTimestep (int _cTime)
	reset the simulation clock counter

Public Attributes
WeakForcePtr	cellConfiguration
	The configuration of cells.
vector< WeakUpdaterPtr >	updaters
	A vector of updaters that the simulation will loop through.
BoxPtr	Box
	The domain of the simulation.
cellListGPU *	cellList
	A neighbor list assisting the simulation.
int	integerTimestep
	An integer that keeps track of how often performTimestep has been called.
Dscalar	Time
	The current simulation time.
Dscalar	integrationTimestep
	The dt of a time step.
bool	USE_GPU
	A flag controlling whether to use the GPU.

Protected Attributes
int	sortPeriod
	Determines how frequently the spatial sorter be called...once per sortPeriod Timesteps. When sortPeriod < 0 no sorting occurs.
bool	spatialSortThisStep
	A flag that determins if a spatial sorting is due to occur this Timestep.

Detailed Description

A class that ties together all the parts of a simulation.

Simulation objects should have a configuration set, and then at least one updater (such as an equation of motion). In addition to being a centralized object controlling the progression of a simulation of cell models, the Simulation class provides some interfaces to cell configuration and updater parameter setters.

Constructor & Destructor Documentation

Simulation()

Simulation::Simulation

(

)

Initialize all the shared pointers, etc.

Initialize all of the shared points, set default values of things

References Box.

Member Function Documentation

setConfiguration()

void Simulation::setConfiguration

(

ForcePtr

_config

)

Pass in a reference to the configuration.

Set a pointer to the configuratione, and give the configurationa reference to this

References Box, and cellConfiguration.

computeForces()

void Simulation::computeForces

(

GPUArray< Dscalar2 > &

forces

)

Call the force computer to compute the forces.

Calls the configuration to displace the degrees of freedom

References cellConfiguration, and GPUArray< T >::swap().

moveDegreesOfFreedom()

void Simulation::moveDegreesOfFreedom

(

GPUArray< Dscalar2 > &

displacements

)

Call the configuration to move particles around.

Calls the configuration to displace the degrees of freedom

References cellConfiguration.

performTimestep()

void Simulation::performTimestep

(

)

Call every updater to advance one time step.

Call all relevant functions to advance the system one time step; every sortPeriod also call the spatial sorting routine.

Postcondition

The simulation is advanced one time step

References cellConfiguration, integerTimestep, integrationTimestep, sortPeriod, Time, and updaters.

addUpdater()

void Simulation::addUpdater	(	UpdaterPtr	_upd,
		ForcePtr	_config
	)

Add an updater with a reference to a configuration.

Add a pointer to the list of updaters, and give that updater a reference to the model...

References updaters.

setBox()

void Simulation::setBox

(

BoxPtr

_box

)

This changes the contents of the Box pointed to by Box to match that of _box.

Set a new Box for the simulation...This is the function that should be called to propagate a change in the box dimensions throughout the simulation...By this time the Box pointed to in the Simulation is the same one pointed to by the BoxPtrs of Simple2DCell (and, in the Voronoi models, by DelaunayLoc and cellListGPU), so when we modify it the changes will run through the rest of the simulation components

Referenced by clearUpdaters().

setIntegrationTimestep()

void Simulation::setIntegrationTimestep

(

Dscalar

dt

)

Set the simulation timestep.

Postcondition

the cell configuration and e.o.m. timestep is set to the input value

Referenced by setCellList().

setCPUOperation()

void Simulation::setCPUOperation

(

bool

setcpu

)

turn on CPU-only mode for all components

Postcondition

the cell configuration and e.o.m. timestep is set to the input value

References cellConfiguration, updaters, and USE_GPU.

setReproducible()

void Simulation::setReproducible

(

bool

reproducible

)

Enforce reproducible dynamics.

Precondition

the updaters already know if the GPU will be used

Postcondition

the updaters are set to be reproducible if the boolean is true, otherwise the RNG is initialized

References updaters.

setCurrentTime()

void Simulation::setCurrentTime ( Dscalar  _cTime )

virtual

reset the simulation clock

Postcondition

the cell configuration and e.o.m. timestep is set to the input value

Referenced by setSortPeriod().

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

• Simulation.h
• Simulation.cpp