selfPropelledCellVertexDynamics Class Reference

A class that implements simple self-propelled particle dynamics in 2D. More...

#include <selfPropelledCellVertexDynamics.h>

Inheritance diagram for selfPropelledCellVertexDynamics:

Public Member Functions
	selfPropelledCellVertexDynamics (int Ncells, int Nvertices)
	base constructor sets default time step size More...
virtual void	integrateEquationsOfMotion ()
	the fundamental function that models will call, using vectors of different data structures More...
virtual void	integrateEquationsOfMotionCPU ()
	call the CPU routine to integrate the e.o.m. More...
virtual void	integrateEquationsOfMotionGPU ()
	call the GPU routine to integrate the e.o.m. More...
int	getNvertices ()
	Get the number of vertices.
int	getNcells ()
	Get the number of cells.
void	setNcells (int _n)
	Set the number of cells.
void	setNvertices (int _n)
	Set the number of vertices.
Dscalar	getMu ()
	Get the inverse friction constant, mu.
void	setMu (Dscalar _mu)
	Set the number of degrees of freedom of the equation of motion.
virtual void	spatialSorting ()
	call the Simple2DCell spatial vertex sorter, and re-index arrays of cell activity More...
virtual void	set2DModel (shared_ptr< Simple2DModel > _model)
	set the active model More...
int	getTimestep ()
	get the number of timesteps run
Dscalar	getTime ()
	get the current simulation time
virtual void	setDeltaT (Dscalar dt)
	Set the simulation time stepsize.
virtual void	performUpdate ()
	performUpdate just maps to integrateEquationsOfMotion
virtual void	setReproducible (bool rep)
	Set whether the source of noise should always use the same random numbers.
void	reIndexRNG (GPUArray< curandState > &array)
	re-index the any RNGs associated with the e.o.m.
virtual void	Update (int timestep)
	The fundamental function that a controlling Simulation can call.
void	setPeriod (int _p)
	set the period
void	setPhase (int _p)
	set the phase
virtual void	setGPU ()
	Enforce GPU-only operation. This is the default mode, so this method need not be called most of the time.
virtual void	setCPU ()
	Enforce CPU-only operation. Derived classes might have to do more work when the CPU mode is invoked.
int	getNdof ()
	Get the number of degrees of freedom of the equation of motion.
void	setNdof (int _n)
	Set the number of degrees of freedom of the equation of motion.

Public Attributes
int	Ncells
	In the mixed cell-vertex model, the equations of motion need to know the number of cells.
int	Nvertices
	In the mixed cell-vertex model, the equations of motion need to know the number of vertices (dof)
shared_ptr< Simple2DModel >	model
	A pointer to a Simple2DModel that the updater acts on.

Protected Member Functions
void	reIndexArray (GPUArray< int > &array)
	Re-index cell arrays after a spatial sorting has occured.
void	reIndexArray (GPUArray< Dscalar > &array)
	why use templates when you can type more?
void	reIndexArray (GPUArray< Dscalar2 > &array)
	why use templates when you can type more?

Protected Attributes
shared_ptr< Simple2DActiveCell >	activeModel
	A shared pointer to a simple active model.
Dscalar	mu
	The value of the inverse friction constant.
int	Timestep
	Count the number of integration timesteps.
Dscalar	deltaT
	The time stepsize of the simulation.
GPUArray< Dscalar2 >	displacements
	an internal GPUArray for holding displacements
noiseSource	noise
	A source of noise for the equation of motion.
int	Period
	The period of the updater... the updater will work every Period timesteps.
int	Phase
	The phase of the updater... the updater will work every Period timesteps offset by a phase.
bool	GPUcompute
	whether the updater does its work on the GPU or not
int	Ndof
	The number of degrees of freedom the equations of motion need to know about.
vector< int >	reIndexing
	a vector of the re-indexing information

Detailed Description

A class that implements simple self-propelled particle dynamics in 2D.

implements dr/dt = mu*F = 1/3 Sum(v_i {n}_i, where {n}_i = (cos(theta),sin(theta)), and d theta/dt = (brownian noise), and the sum is over the cells that neighbor the vertex

Constructor & Destructor Documentation

selfPropelledCellVertexDynamics()

selfPropelledCellVertexDynamics::selfPropelledCellVertexDynamics	(	int	_Ncells,
		int	_Nvertices
	)

base constructor sets default time step size

An extremely simple constructor that does nothing, but enforces default GPU operation

Parameters

the	number of points in the system (cells or particles)

References simpleEquationOfMotion::deltaT, simpleEquationOfMotion::displacements, updater::GPUcompute, noiseSource::initialize(), selfPropelledParticleDynamics::mu, Ncells, updater::Ndof, updaterWithNoise::noise, Nvertices, GPUArray< T >::resize(), and simpleEquationOfMotion::Timestep.

Member Function Documentation

integrateEquationsOfMotion()

void selfPropelledCellVertexDynamics::integrateEquationsOfMotion ( )

virtual

the fundamental function that models will call, using vectors of different data structures

Advances self-propelled dynamics with random noise in the director by one time step

Reimplemented from selfPropelledParticleDynamics.

References selfPropelledParticleDynamics::activeModel, simpleEquationOfMotion::displacements, updater::GPUcompute, noiseSource::initialize(), integrateEquationsOfMotionCPU(), integrateEquationsOfMotionGPU(), Ncells, updaterWithNoise::noise, Nvertices, GPUArray< T >::resize(), and simpleEquationOfMotion::Timestep.

integrateEquationsOfMotionCPU()

void selfPropelledCellVertexDynamics::integrateEquationsOfMotionCPU ( )

virtual

call the CPU routine to integrate the e.o.m.

Move every vertex according to the net force on it and its motility...CPU routine

Reimplemented from selfPropelledParticleDynamics.

References selfPropelledParticleDynamics::activeModel, simpleEquationOfMotion::displacements, access_location::host, access_mode::overwrite, access_mode::read, and access_mode::readwrite.

Referenced by integrateEquationsOfMotion().

integrateEquationsOfMotionGPU()

void selfPropelledCellVertexDynamics::integrateEquationsOfMotionGPU ( )

virtual

call the GPU routine to integrate the e.o.m.

The straightforward GPU implementation

Reimplemented from selfPropelledParticleDynamics.

References selfPropelledParticleDynamics::activeModel, ArrayHandle< T >::data, simpleEquationOfMotion::deltaT, access_location::device, simpleEquationOfMotion::displacements, gpu_spp_cellVertex_eom_integration(), selfPropelledParticleDynamics::mu, Ncells, updaterWithNoise::noise, Nvertices, access_mode::overwrite, access_mode::read, access_mode::readwrite, noiseSource::RNGs, and simpleEquationOfMotion::Timestep.

Referenced by integrateEquationsOfMotion().

spatialSorting()

void selfPropelledParticleDynamics::spatialSorting ( )

virtualinherited

call the Simple2DCell spatial vertex sorter, and re-index arrays of cell activity

When spatial sorting is performed, re-index the array of cuda RNGs... This function is currently commented out, for greater flexibility (i.e., to not require that the indexToTag (or Itt) be the re-indexing array), since that assumes cell and not particle-based dynamics

Reimplemented from updater.

set2DModel()

void selfPropelledParticleDynamics::set2DModel ( shared_ptr< Simple2DModel >  _model )

virtualinherited

set the active model

Set the shared pointer of the base class to passed variable; cast it as an active cell model

Reimplemented from updater.

References selfPropelledParticleDynamics::activeModel, and updater::model.

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

• selfPropelledCellVertexDynamics.h
• selfPropelledCellVertexDynamics.cpp