Open Qmin: Simulation Class Reference

Open Qmin 0.8.0

GPU-accelerated Q-tensor-based liquid crystal simulations

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

#include <simulation.h>

Inheritance diagram for Simulation:

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Collaboration diagram for Simulation:

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Public Member Functions
void	setConfiguration (ConfigPtr _config)
	Pass in a reference to the configuration. More...

virtual void	computeForces ()
	Call the force computer to compute the forces. More...

virtual void	moveParticles (GPUArray< dVec > &displacements, scalar scale=1.0)
	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 More...

void	addUpdater (UpdaterPtr _upd)
	Add an updater. More...

void	addUpdater (UpdaterPtr _upd, ConfigPtr _config)
	Add an updater with a reference to a configuration. More...

void	addForce (ForcePtr _force)
	Add a force computer configuration. More...

void	addForce (ForcePtr _force, ConfigPtr _config)
	Add a force computer configuration. More...

void	clearForceComputers ()
	Clear out the vector of forceComputes. More...

void	clearUpdaters ()
	Clear out the vector of updaters. More...

scalar	getMaxForce ()
	A utility function that just checks the first updater for a max force. More...

virtual scalar	computePotentialEnergy (bool verbose=false)
	compute the potential energy associated with all of the forces More...

virtual scalar	computeKineticEnergy (bool verbose=false)
	compute the kinetic energy More...

virtual scalar	computeEnergy (bool verbose=false)
	compute the total energy More...

virtual void	computePressureTensor (MatrixDxD &P)
	compute the pressure tensor More...

void	setIntegrationTimestep (scalar 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	setNThreads (int n)
	work with openMP threads More...

void	setBox (BoxPtr _box)
	This changes the contents of the Box pointed to by Box to match that of _box. More...

void	setSortPeriod (int sp)
	Set the time between spatial sorting operations. More...

virtual void	setCurrentTime (scalar _cTime)
	reset the simulation clock More...

virtual void	setCurrentTimestep (int _cTime)
	reset the simulation clock counter More...

virtual void	sumUpdaterData (vector< scalar > &data)
	manipulate data from updaters More...

Public Attributes
vector< WeakUpdaterPtr >	updaters
	A vector of updaters that the simulation will loop through. More...

vector< WeakForcePtr >	forceComputers
	A vector of force computes the simulation will loop through. More...

WeakConfigPtr	configuration
	The configuration of particles. More...

BoxPtr	Box
	The domain of the simulation. More...

int	integerTimestep
	An integer that keeps track of how often performTimestep has been called. More...

scalar	Time
	The current simulation time. More...

scalar	integrationTimestep
	The dt of a time step. More...

bool	useGPU
	A flag controlling whether to use the GPU. More...

int	myRank
	integer for this rank More...

int	nRanks
	total number of ranks More...

int	NActive = 0
	some measure of the number of active degrees of freedom More...

Protected Attributes
int	sortPeriod
	Determines how frequently the spatial sorter be called...once per sortPeriod Timesteps. When sortPeriod < 0 no sorting occurs. More...

bool	spatialSortThisStep
	A flag that determins if a spatial sorting is due to occur this Timestep. More...

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.

Member Function Documentation

◆ setConfiguration()

void Simulation::setConfiguration ( ConfigPtr _config )

Pass in a reference to the configuration.

Set a pointer to the configuration

References basicSimulation::Box, and basicSimulation::configuration.

◆ computeForces()

void Simulation::computeForces ( )

virtual

Call the force computer to compute the forces.

Calls all force computers, and evaluate the self force calculation if the model demands it

Implements basicSimulation.

References basicSimulation::configuration, and forceComputers.

◆ moveParticles()

void Simulation::moveParticles	(	GPUArray< dVec > &	displacements,
		scalar	scale = `1.0`
	)

virtual

Call the configuration to move particles around.

Calls the configuration to displace the degrees of freedom

Implements basicSimulation.

References basicSimulation::configuration.

◆ 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 basicSimulation::integerTimestep, basicSimulation::integrationTimestep, basicSimulation::Time, and updaters.

◆ getPointer()

shared_ptr<Simulation> Simulation::getPointer ( )

inline

return a shared pointer to this Simulation

Referenced by addUpdater().

◆ addUpdater() [1/2]

void Simulation::addUpdater ( UpdaterPtr _upd )

inline

Add an updater.

References updaters.

◆ addUpdater() [2/2]

void Simulation::addUpdater	(	UpdaterPtr	_upd,
		ConfigPtr	_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 getPointer(), and updaters.

◆ addForce() [1/2]

void Simulation::addForce ( ForcePtr _force )

inline

Add a force computer configuration.

References forceComputers.

◆ addForce() [2/2]

void Simulation::addForce	(	ForcePtr	_force,
		ConfigPtr	_config
	)

Add a force computer configuration.

Add a pointer to the list of force computers, and give that FC a reference to the model...

References forceComputers.

◆ clearForceComputers()

void Simulation::clearForceComputers ( )

inline

Clear out the vector of forceComputes.

References forceComputers.

◆ clearUpdaters()

void Simulation::clearUpdaters ( )

inline

Clear out the vector of updaters.

References updaters.

◆ getMaxForce()

scalar Simulation::getMaxForce ( )

inline

A utility function that just checks the first updater for a max force.

References updaters.

◆ computePotentialEnergy()

scalar Simulation::computePotentialEnergy ( bool verbose = false )

virtual

compute the potential energy associated with all of the forces

Reimplemented from basicSimulation.

References forceComputers, and scalar.

Referenced by computeEnergy().

◆ computeKineticEnergy()

scalar Simulation::computeKineticEnergy ( bool verbose = false )

virtual

compute the kinetic energy

Reimplemented from basicSimulation.

References basicSimulation::configuration.

Referenced by computeEnergy().

◆ computeEnergy()

virtual scalar Simulation::computeEnergy ( bool verbose = false )

inlinevirtual

compute the total energy

References computeKineticEnergy(), and computePotentialEnergy().

◆ computePressureTensor()

void Simulation::computePressureTensor ( MatrixDxD & P )

virtual

compute the pressure tensor

References for(), forceComputers, make_dVec(), and MatrixDxD::mat.

◆ setIntegrationTimestep()

void Simulation::setIntegrationTimestep ( scalar dt )

Set the simulation timestep.

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

References basicSimulation::integrationTimestep, and updaters.

◆ 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 basicSimulation::configuration, forceComputers, updaters, and basicSimulation::useGPU.

◆ 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.

◆ setNThreads()

void Simulation::setNThreads ( int n )

work with openMP threads

References basicSimulation::configuration, forceComputers, n, and updaters.

◆ setBox()

void basicSimulation::setBox ( BoxPtr _box )

inherited

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...

References basicSimulation::Box, and basicSimulation::configuration.

◆ setSortPeriod()

void basicSimulation::setSortPeriod ( int sp )

inlineinherited

Set the time between spatial sorting operations.

References basicSimulation::sortPeriod.

◆ setCurrentTime()

void basicSimulation::setCurrentTime ( scalar _cTime )

virtualinherited

reset the simulation clock

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

References basicSimulation::Time.

◆ setCurrentTimestep()

virtual void basicSimulation::setCurrentTimestep ( int _cTime )

inlinevirtualinherited

reset the simulation clock counter

References basicSimulation::integerTimestep.

◆ sumUpdaterData()

virtual void basicSimulation::sumUpdaterData ( vector< scalar > & data )

inlinevirtualinherited

manipulate data from updaters

Reimplemented in multirankSimulation.

Member Data Documentation

◆ updaters

vector<WeakUpdaterPtr> Simulation::updaters

A vector of updaters that the simulation will loop through.

Referenced by addUpdater(), clearUpdaters(), getMaxForce(), performTimestep(), setCPUOperation(), setIntegrationTimestep(), setNThreads(), and setReproducible().

◆ forceComputers

vector<WeakForcePtr> Simulation::forceComputers

A vector of force computes the simulation will loop through.

Referenced by addForce(), clearForceComputers(), computeForces(), computePotentialEnergy(), computePressureTensor(), setCPUOperation(), and setNThreads().

◆ configuration

WeakConfigPtr basicSimulation::configuration

inherited

The configuration of particles.

Referenced by computeForces(), computeKineticEnergy(), moveParticles(), basicSimulation::setBox(), setConfiguration(), setCPUOperation(), and setNThreads().

◆ Box

BoxPtr basicSimulation::Box

inherited

The domain of the simulation.

Referenced by basicSimulation::basicSimulation(), basicSimulation::setBox(), setConfiguration(), and multirankSimulation::setConfiguration().

◆ integerTimestep

int basicSimulation::integerTimestep

inherited

An integer that keeps track of how often performTimestep has been called.

Referenced by performTimestep(), multirankSimulation::performTimestep(), and basicSimulation::setCurrentTimestep().

◆ Time

scalar basicSimulation::Time

inherited

The current simulation time.

Referenced by performTimestep(), multirankSimulation::performTimestep(), and basicSimulation::setCurrentTime().

◆ integrationTimestep

scalar basicSimulation::integrationTimestep

inherited

The dt of a time step.

Referenced by performTimestep(), multirankSimulation::performTimestep(), setIntegrationTimestep(), and multirankSimulation::setIntegrationTimestep().

◆ useGPU

bool basicSimulation::useGPU

inherited

A flag controlling whether to use the GPU.

Referenced by multirankSimulation::communicateHaloSitesRoutine(), multirankSimulation::computeForces(), setCPUOperation(), multirankSimulation::setCPUOperation(), and multirankSimulation::synchronizeAndTransferBuffers().

◆ myRank

int basicSimulation::myRank

inherited

integer for this rank

Referenced by multirankSimulation::multirankSimulation(), and multirankSimulation::setRankTopology().

◆ nRanks

int basicSimulation::nRanks

inherited

total number of ranks

Referenced by multirankSimulation::communicateHaloSitesRoutine(), multirankSimulation::setRankTopology(), multirankSimulation::sumUpdaterData(), and multirankSimulation::synchronizeAndTransferBuffers().

◆ NActive

int basicSimulation::NActive = 0

inherited

some measure of the number of active degrees of freedom

Referenced by multirankSimulation::computePotentialEnergy(), and multirankSimulation::finalizeObjects().

◆ sortPeriod

int basicSimulation::sortPeriod

protectedinherited

Determines how frequently the spatial sorter be called...once per sortPeriod Timesteps. When sortPeriod < 0 no sorting occurs.

Referenced by basicSimulation::setSortPeriod().

◆ spatialSortThisStep

bool basicSimulation::spatialSortThisStep

protectedinherited

A flag that determins if a spatial sorting is due to occur this Timestep.

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

Public Member Functions

Public Attributes

Protected Attributes

Detailed Description

Member Function Documentation

◆ setConfiguration()

◆ computeForces()

◆ moveParticles()

◆ performTimestep()

◆ getPointer()

◆ addUpdater() [1/2]

◆ addUpdater() [2/2]

◆ addForce() [1/2]

◆ addForce() [2/2]

◆ clearForceComputers()

◆ clearUpdaters()

◆ getMaxForce()

◆ computePotentialEnergy()

◆ computeKineticEnergy()

◆ computeEnergy()

◆ computePressureTensor()

◆ setIntegrationTimestep()

◆ setCPUOperation()

◆ setReproducible()

◆ setNThreads()

◆ setBox()

◆ setSortPeriod()

◆ setCurrentTime()

◆ setCurrentTimestep()

◆ sumUpdaterData()

Member Data Documentation

◆ updaters

◆ forceComputers

◆ configuration

◆ Box

◆ integerTimestep

◆ Time

◆ integrationTimestep

◆ useGPU

◆ myRank

◆ nRanks

◆ NActive

◆ sortPeriod

◆ spatialSortThisStep