CellGPU: Simple2DActiveCell Class Reference

Data structures and functions for simple active-brownian-particle-like motion. More...

#include <Simple2DActiveCell.h>

Inheritance diagram for Simple2DActiveCell:

[legend]

Public Member Functions
	Simple2DActiveCell ()
	A simple constructor. More...

void	initializeSimple2DActiveCell (int n)
	initialize class' data structures and set default values More...

void	setv0Dr (Dscalar v0new, Dscalar drnew)
	Set uniform motility. More...

void	setCellMotility (vector< Dscalar > &v0s, vector< Dscalar > &drs)
	Set non-uniform cell motilites. More...

void	setCellDirectorsRandomly ()
	Set random cell directors (for active cell models) More...

virtual int	getNumberOfDegreesOfFreedom ()
	get the number of degrees of freedom, defaulting to the number of cells

virtual void	cellDivision (const vector< int > &parameters, const vector< Dscalar > &dParams={})
	Divide cell...vector should be cell index i, vertex 1 and vertex 2. More...

virtual void	cellDeath (int cellIndex)
	Kill the indexed cell. More...

Dscalar	vicsekOrderParameter (Dscalar2 &vParallel, Dscalar2 &vPerpendicular)
	measure the viscek order parameter N^-1 {v_i}{\|v_i}

Dscalar	vicsekOrderParameterDirector (Dscalar2 &vParallel, Dscalar2 &vPerpendicular)
	measure the viscek order parameter N^-1 {v_i}{\|v_i} from the director only

void	initializeSimple2DCell (int n)
	initialize class' data structures and set default values More...

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.

virtual void	setCPU (bool a)=0

virtual void	computeForces ()
	do everything necessary to compute forces in the current model

virtual void	computeGeometry ()
	call either the computeGeometryCPU or GPU routines for the current model More...

virtual void	computeGeometryCPU ()
	let computeGeometryCPU be defined in derived classes

virtual void	computeGeometryGPU ()
	let computeGeometryGPU be defined in derived classes

virtual Dscalar	computeEnergy ()
	do everything necessary to compute the energy for the current model

Dscalar	computeKineticEnergy ()
	Call masses and velocities to get the total kinetic energy. More...

Dscalar4	computeKineticPressure ()
	Call masses and velocities to get the average kinetic contribution to the pressure tensor. More...

virtual void	getForces (GPUArray< Dscalar2 > &forces)
	copy the models current set of forces to the variable

virtual void	moveDegreesOfFreedom (GPUArray< Dscalar2 > &displacements, Dscalar scale=1.)
	move the degrees of freedom

virtual void	enforceTopology ()
	Do everything necessary to update or enforce the topology in the current model.

void	setCellPreferencesUniform (Dscalar A0, Dscalar P0)
	Set uniform cell area and perimeter preferences. More...

void	setCellPreferences (vector< Dscalar2 > &AreaPeriPreferences)
	Set cell area and perimeter preferences according to input vector. More...

void	setCellPositionsRandomly ()
	Set random cell positions, and set the periodic box to a square with average cell area=1. More...

void	setCellPositions (vector< Dscalar2 > newCellPositions)
	Set cell positions according to a user-specified vector. More...

void	setVertexPositions (vector< Dscalar2 > newVertexPositions)
	Set vertex positions according to a user-specified vector. More...

Dscalar	setCellVelocitiesMaxwellBoltzmann (Dscalar T)
	Set velocities via a temperature. The return value is the total kinetic energy. More...

Dscalar	setVertexVelocitiesMaxwellBoltzmann (Dscalar T)
	Set velocities via a temperature for the vertex degrees of freedom. More...

void	setModuliUniform (Dscalar newKA, Dscalar newKP)
	set uniform moduli for all cells More...

void	setCellTypeUniform (int i)
	Set all cells to the same "type". More...

void	setCellType (vector< int > &types)
	Set cells to different "type". More...

void	setVertexTopologyFromCells (vector< vector< int > > cellVertexIndices)
	An uncomfortable function to allow the user to set vertex topology "by hand". More...

virtual gpubox &	returnBox ()
	return the gpubox

void	setBox (BoxPtr _box)
	This can be used, but should not normally be. This re-assigns the pointer.

virtual vector< int > &	returnItt ()
	return the base "itt" re-indexing vector

virtual GPUArray< Dscalar2 > &	returnModuli ()
	Return a reference to moduli.

virtual GPUArray< Dscalar2 > &	returnAreaPeri ()
	Return a reference to AreaPeri array.

virtual GPUArray< Dscalar2 > &	returnAreaPeriPreferences ()
	Return a reference to AreaPeriPreferences.

virtual GPUArray< Dscalar2 > &	returnVelocities ()
	Return a reference to velocities on cells. VertexModelBase will instead return vertexVelocities.

virtual GPUArray< Dscalar2 > &	returnPositions ()
	Return a reference to Positions on cells.

virtual GPUArray< Dscalar2 > &	returnForces ()
	Return a reference to forces on cells.

virtual GPUArray< Dscalar > &	returnMasses ()
	Return a reference to Masses on cells.

virtual GPUArray< Dscalar > &	returnOtherData ()
	Return other data just returns the masses; in this class it's not needed.

void	setDeltaT (Dscalar dt)
	Set the simulation time stepsize.

void	getCellNeighs (int idx, int &nNeighs, vector< int > &neighs)

Dscalar	getMaxForce ()
	Get the maximum force on a cell.

void	reportMeanCellForce (bool verbose)
	Report the current average force on each cell. More...

void	reportMeanVertexForce (bool verbose=false)
	Report the current average force per vertex...should be close to zero.

void	reportAP (bool verbose=false)
	report the current total area, and optionally the area and perimeter for each cell

Dscalar	reportq ()
	Report the average value of p/sqrt(A) for the cells in the system. More...

Dscalar	reportVarq ()
	Report the variance of p/sqrt(A) for the cells in the system. More...

Dscalar2	reportVarAP ()
	Report the variance of A and P for the cells in the system. More...

Dscalar	reportMeanP ()
	Report the mean value of the perimeter. More...

virtual void	getDynMatEntries (vector< int2 > &rcs, vector< Dscalar > &vals, Dscalar unstress=1.0, Dscalar stress=1.0)
	Do whatever is necessary to get lists of dynamical matrix elements.

virtual void	spatialSorting ()
	do everything necessary to perform a Hilbert sort

virtual void	setTime (Dscalar time)
	set the time

Public Attributes
GPUArray< Dscalar >	cellDirectors
	An array of angles (relative to the x-axis) that the cell directors point.

GPUArray< Dscalar >	cellDirectorForces
	An array of forces acting on the cell directors.

Dscalar	v0
	velocity of cells in mono-motile systems

Dscalar	Dr
	rotational diffusion of cell directors in mono-motile systems

GPUArray< Dscalar2 >	Motility
	The motility parameters (v0 and Dr) for each cell.

int	Ncells
	Number of cells in the simulation.

int	Nvertices
	Number of vertices.

GPUArray< Dscalar2 >	cellPositions
	Cell positions... not used for computation, but can track, e.g., MSD of cell centers.

GPUArray< Dscalar2 >	vertexPositions
	Position of the vertices.

GPUArray< Dscalar2 >	cellVelocities
	The velocity vector of cells (only relevant if the equations of motion use it)

GPUArray< Dscalar >	cellMasses
	The masses of the cells.

GPUArray< Dscalar2 >	vertexVelocities
	The velocity vector of vertices (only relevant if the equations of motion use it)

GPUArray< Dscalar >	vertexMasses
	The masses of the vertices.

GPUArray< int >	vertexNeighbors
	VERTEX neighbors of every vertex. More...

GPUArray< int >	vertexCellNeighbors
	Cell neighbors of every vertex. More...

Index2D	n_idx
	A 2dIndexer for computing where in the GPUArray to look for a given cell's vertices.

GPUArray< int >	cellNeighborNum
	The number of CELL neighbors of each cell. For simple models this is the same as cellVertexNum, but does not have to be.

GPUArray< int >	cellNeighbors
	CELL neighbors of every cell.

GPUArray< int >	cellVertexNum
	The number of vertices defining each cell. More...

GPUArray< Dscalar2 >	vertexForces
	an array containing net force on each vertex

GPUArray< Dscalar2 >	cellForces
	an array containing net force on each cell

GPUArray< int >	cellType
	An array of integers labeling cell type...an easy way of determining if cells are different. More...

Index2D	cellTypeIndexer
	A indexer for turning a pair of cells into a 1-D index.

Dscalar	Energy
	The current potential energy of the system; only updated when an explicit energy calculation is called (i.e. not by default each timestep)

Dscalar	KineticEnergy
	The current kinetic energy of the system; only updated when an explicit calculation is called.

vector< int >	tagToIdx
	To write consistent files...the cell that started the simulation as index i has current index tagToIdx[i]. More...

vector< int >	tagToIdxVertex
	To write consistent files...the vertex that started the simulation as index i has current index tagToIdx[i].

BoxPtr	Box
	the box defining the periodic domain

int	Timestep
	Count the number of times "performTimeStep" has been called.

Dscalar	deltaT
	The time stepsize of the simulation.

bool	forcesUpToDate
	Are the forces (and hence, the geometry) up-to-date?

Dscalar	currentTime
	a time variable for keeping track of the simulation variable (for databases)

Protected Member Functions
void	spatiallySortVerticesAndCellActivity ()
	call the Simple2DCell spatial vertex sorter, and re-index arrays of cell activity More...

void	spatiallySortCellsAndCellActivity ()
	call the Simple2DCell spatial cell sorter, and re-index arrays of cell activity More...

void	initializeCellSorting ()
	set the size of the cell-sorting structures, initialize lists simply More...

void	initializeVertexSorting ()
	set the size of the vertex-sorting structures, initialize lists simply More...

void	reIndexCellArray (GPUArray< int > &array)
	Re-index cell arrays after a spatial sorting has occured. More...

void	reIndexCellArray (GPUArray< Dscalar > &array)
	why use templates when you can type more? More...

void	reIndexCellArray (GPUArray< Dscalar2 > &array)
	why use templates when you can type more? More...

void	reIndexVertexArray (GPUArray< int > &array)
	Re-index vertex after a spatial sorting has occured.

void	reIndexVertexArray (GPUArray< Dscalar > &array)
	why use templates when you can type more?

void	reIndexVertexArray (GPUArray< Dscalar2 > &array)
	why use templates when you can type more? More...

void	spatiallySortCells ()
	Perform a spatial sorting of the cells to try to maintain data locality. More...

void	spatiallySortVertices ()
	Perform a spatial sorting of the vertices to try to maintain data locality. More...

Protected Attributes
bool	GPUcompute
	Compute aspects of the model on the GPU.

bool	Reproducible
	A flag that determines whether the GPU RNG is the same every time.

noiseSource	noise
	A source of noise for random cell initialization.

Dscalar	KA
	the area modulus

Dscalar	KP
	The perimeter modulus.

GPUArray< Dscalar2 >	Moduli
	The area and perimeter moduli of each cell. CURRENTLY NOT SUPPORTED, BUT EASY TO IMPLEMENT.

GPUArray< Dscalar2 >	AreaPeri
	The current area and perimeter of each cell.

GPUArray< Dscalar2 >	AreaPeriPreferences
	The area and perimeter preferences of each cell.

GPUArray< int >	cellVertices
	A structure that indexes the vertices defining each cell. More...

int	vertexMax
	An upper bound for the maximum number of neighbors that any cell has.

GPUArray< Dscalar2 >	voroCur
	3*Nvertices length array of the position of vertices around cells More...

GPUArray< Dscalar4 >	voroLastNext

vector< int >	itt
	A map between cell index and the spatially sorted version. More...

vector< int >	tti
	A temporary structure that inverts itt.

vector< int >	idxToTag
	A temporary structure that inverse tagToIdx.

vector< int >	ittVertex
	A map between vertex index and the spatially sorted version.

vector< int >	ttiVertex
	A temporary structure that inverts itt.

vector< int >	idxToTagVertex
	A temporary structure that inverse tagToIdx.

GPUArray< Dscalar2 >	displacements
	An array of displacements used only for the equations of motion.

Detailed Description

Data structures and functions for simple active-brownian-particle-like motion.

A class defining the simplest aspects of a 2D system in which particles have a constant velocity along a director which rotates with gaussian noise

Constructor & Destructor Documentation

◆ Simple2DActiveCell()

Simple2DActiveCell::Simple2DActiveCell ( )

A simple constructor.

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

References Simple2DCell::setDeltaT(), and Simple2DCell::Timestep.

Member Function Documentation

◆ initializeSimple2DActiveCell()

void Simple2DActiveCell::initializeSimple2DActiveCell ( int n )

initialize class' data structures and set default values

Initialize the data structures to the size specified by n, and set default values, and call Simple2DCell's initilization routine.

◆ setv0Dr()

void Simple2DActiveCell::setv0Dr	(	Dscalar	v0new,
		Dscalar	drnew
	)

virtual

Set uniform motility.

Parameters

v0new	the new value of velocity for all cells
drnew	the new value of the rotational diffusion of cell directors for all cells

Implements Simple2DCell.

◆ setCellMotility()

void Simple2DActiveCell::setCellMotility	(	vector< Dscalar > &	v0s,
		vector< Dscalar > &	drs
	)

Set non-uniform cell motilites.

Parameters

v0s	the per-particle vector of what all velocities will be
drs	the per-particle vector of what all rotational diffusions will be

References cellDirectors, Simple2DCell::cellVelocities, ArrayHandle< T >::data, access_location::host, Motility, Simple2DCell::Ncells, access_mode::overwrite, access_mode::read, and GPUArray< T >::resize().

◆ setCellDirectorsRandomly()

void Simple2DActiveCell::setCellDirectorsRandomly ( )

Set random cell directors (for active cell models)

Assign cell directors via a simple, reproducible RNG

References cellDirectorForces, cellDirectors, Simple2DCell::cellVelocities, ArrayHandle< T >::data, noiseSource::getRealUniform(), access_location::host, Simple2DCell::Ncells, Simple2DCell::noise, access_mode::overwrite, noiseSource::Reproducible, Simple2DCell::Reproducible, and GPUArray< T >::resize().

◆ cellDivision()

void Simple2DActiveCell::cellDivision	(	const vector< int > &	parameters,
		const vector< Dscalar > &	dParams = `{}`
	)

virtual

Divide cell...vector should be cell index i, vertex 1 and vertex 2.

This function supports cellDivisions, updating data structures in Simple2DActiveCell This function will first call Simple2DCell's routine, and then grows the cellDirectors and Motility arrays, and assign the new cell (the last element of those arrays) the values of the cell given by parameters[0] Note that dParams does nothing

Reimplemented from Simple2DCell.

Reimplemented in vertexModelBase, and voronoiModelBase.

References cellDirectors, Simple2DCell::cellDivision(), ArrayHandle< T >::data, noiseSource::getRealUniform(), Motility, Simple2DCell::Ncells, Simple2DCell::noise, noiseSource::Reproducible, and Simple2DCell::Reproducible.

Referenced by getNumberOfDegreesOfFreedom().

◆ cellDeath()

void Simple2DActiveCell::cellDeath ( int cellIndex )

virtual

Kill the indexed cell.

This function supports cellDeath, updating the data structures in Simple2DActiveCell. This function will first call Simple2DCell's routine, then modify the cellDirectors and Motility arrays

Reimplemented from Simple2DCell.

Reimplemented in vertexModelBase, and voronoiModelBase.

References Simple2DCell::cellDeath(), cellDirectors, and Motility.

Referenced by voronoiModelBase::cellDeath(), and getNumberOfDegreesOfFreedom().

◆ spatiallySortVerticesAndCellActivity()

void Simple2DActiveCell::spatiallySortVerticesAndCellActivity ( )

protected

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

Calls the spatial vertex sorting routine in Simple2DCell, and re-indexes the arrays for the cell RNGS, as well as the cell motility and cellDirector arrays

References cellDirectors, Motility, Simple2DCell::reIndexCellArray(), and Simple2DCell::spatiallySortVertices().

Referenced by vertexModelBase::spatialSorting().

◆ spatiallySortCellsAndCellActivity()

void Simple2DActiveCell::spatiallySortCellsAndCellActivity ( )

protected

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

Calls the spatial vertex sorting routine in Simple2DCell, and re-indexes the arrays for the cell RNGS, as well as the cell motility and cellDirector arrays

References cellDirectors, Motility, Simple2DCell::reIndexCellArray(), and Simple2DCell::spatiallySortCells().

Referenced by voronoiModelBase::spatialSorting().

◆ initializeSimple2DCell()

void Simple2DCell::initializeSimple2DCell ( int n )

inherited

initialize class' data structures and set default values

Initialize the data structures to the size specified by n, and set default values.

◆ computeGeometry()

void Simple2DCell::computeGeometry ( )

virtualinherited

call either the computeGeometryCPU or GPU routines for the current model

Simply call either the CPU or GPU routine in the current or derived model

References Simple2DCell::computeGeometryCPU(), Simple2DCell::computeGeometryGPU(), and Simple2DCell::GPUcompute.

Referenced by VertexQuadraticEnergyWithTension::computeForces(), VoronoiQuadraticEnergyWithTension::computeForces(), VertexQuadraticEnergy::computeForces(), VoronoiQuadraticEnergy::computeForces(), and Simple2DCell::computeForces().

◆ computeKineticEnergy()

Dscalar Simple2DCell::computeKineticEnergy ( )

inherited

Call masses and velocities to get the total kinetic energy.

E = 0.5*m_i v_i^2

◆ computeKineticPressure()

Dscalar4 Simple2DCell::computeKineticPressure ( )

inherited

Call masses and velocities to get the average kinetic contribution to the pressure tensor.

P_ab = m_i v_{ib}v_{ia}

◆ setCellPreferencesUniform()

void Simple2DCell::setCellPreferencesUniform	(	Dscalar	A0,
		Dscalar	P0
	)

inherited

Set uniform cell area and perimeter preferences.

Generically believe that cells in 2D have a notion of a preferred area and perimeter

Referenced by Simple2DCell::enforceTopology().

◆ setCellPreferences()

void Simple2DCell::setCellPreferences ( vector< Dscalar2 > & APPref )

inherited

Set cell area and perimeter preferences according to input vector.

Set the Area and Perimeter preferences to the input vector

References Simple2DCell::AreaPeriPreferences, ArrayHandle< T >::data, access_location::host, Simple2DCell::Ncells, access_mode::overwrite, and GPUArray< T >::resize().

◆ setCellPositionsRandomly()

void Simple2DCell::setCellPositionsRandomly ( )

inherited

Set random cell positions, and set the periodic box to a square with average cell area=1.

Resize the box so that every cell has, on average, area = 1, and place cells via either a simple, reproducible RNG or a non-reproducible RNG

References Simple2DCell::cellPositions, Simple2DCell::Ncells, and GPUArray< T >::resize().

◆ setCellPositions()

void Simple2DCell::setCellPositions ( vector< Dscalar2 > newCellPositions )

inherited

Set cell positions according to a user-specified vector.

Does not update any other lists – it is the user's responsibility to maintain topology, etc, when using this function.

References Simple2DCell::cellPositions, ArrayHandle< T >::data, GPUArray< T >::getNumElements(), access_location::host, Simple2DCell::Ncells, access_mode::overwrite, and GPUArray< T >::resize().

◆ setVertexPositions()

void Simple2DCell::setVertexPositions ( vector< Dscalar2 > newVertexPositions )

inherited

Set vertex positions according to a user-specified vector.

Does not update any other lists – it is the user's responsibility to maintain topology, etc, when using this function.

References ArrayHandle< T >::data, GPUArray< T >::getNumElements(), access_location::host, Simple2DCell::Nvertices, access_mode::overwrite, GPUArray< T >::resize(), and Simple2DCell::vertexPositions.

◆ setCellVelocitiesMaxwellBoltzmann()

Dscalar Simple2DCell::setCellVelocitiesMaxwellBoltzmann ( Dscalar T )

inherited

Set velocities via a temperature. The return value is the total kinetic energy.

Set the cell velocities by drawing from a Maxwell-Boltzmann distribution, and then make sure there is no net momentum. The return value is the total kinetic energy

◆ setVertexVelocitiesMaxwellBoltzmann()

Dscalar Simple2DCell::setVertexVelocitiesMaxwellBoltzmann ( Dscalar T )

inherited

Set velocities via a temperature for the vertex degrees of freedom.

Set the vertex velocities by drawing from a Maxwell-Boltzmann distribution, and then make sure there is no net momentum. The return value is the total kinetic energy.

◆ setModuliUniform()

void Simple2DCell::setModuliUniform	(	Dscalar	newKA,
		Dscalar	newKP
	)

inherited

set uniform moduli for all cells

set all cell K_A, K_P preferences to uniform values. PLEASE NOTE that as an optimization this data is not actually used at the moment, but the code could be trivially altered to use this

◆ setCellTypeUniform()

void Simple2DCell::setCellTypeUniform ( int i )

inherited

Set all cells to the same "type".

set all cell types to i

References Simple2DCell::cellType, ArrayHandle< T >::data, access_location::host, Simple2DCell::Ncells, access_mode::overwrite, and GPUArray< T >::resize().

◆ setCellType()

void Simple2DCell::setCellType ( vector< int > & types )

inherited

Set cells to different "type".

Parameters

types a vector of integers that the cell types will be set to

References Simple2DCell::cellType, ArrayHandle< T >::data, access_location::host, Simple2DCell::Ncells, access_mode::overwrite, and GPUArray< T >::resize().

◆ setVertexTopologyFromCells()

void Simple2DCell::setVertexTopologyFromCells ( vector< vector< int > > cellVertexIndices )

inherited

An uncomfortable function to allow the user to set vertex topology "by hand".

This function allows a user to set the vertex topology by hand. The user is responsible for making sure the input topology is sensible. DMS NOTE – this functionality has not been thoroughly tested

Precondition: Nvertices and vertex positions are already set

Parameters

cellVertexIndices a vector of vector of ints. Each vector of ints must correspond to the counter-clockwise ordering of vertices that make up the cell, and every vertex should appear at most three times in different cells

References Simple2DCell::cellVertexNum, Simple2DCell::cellVertices, ArrayHandle< T >::data, access_location::host, Simple2DCell::n_idx, Simple2DCell::Ncells, Simple2DCell::Nvertices, access_mode::overwrite, GPUArray< T >::resize(), Simple2DCell::vertexCellNeighbors, Simple2DCell::vertexMax, and Simple2DCell::vertexNeighbors.

◆ initializeCellSorting()

void Simple2DCell::initializeCellSorting ( )

protectedinherited

set the size of the cell-sorting structures, initialize lists simply

Sets the size of itt, tti, idxToTag, and tagToIdx, and sets all of them so that array[i] = i, i.e., unsorted

Precondition: Ncells is determined

References Simple2DCell::idxToTag, Simple2DCell::itt, Simple2DCell::Ncells, Simple2DCell::tagToIdx, and Simple2DCell::tti.

◆ initializeVertexSorting()

void Simple2DCell::initializeVertexSorting ( )

protectedinherited

set the size of the vertex-sorting structures, initialize lists simply

Sets the size of ittVertex, ttiVertex, idxToTagVertex, and tagToIdxVertex,and sets all of them so that array[i] = i, i.e., things are unsorted

Precondition: Nvertices is determined

References Simple2DCell::idxToTagVertex, Simple2DCell::ittVertex, Simple2DCell::Nvertices, Simple2DCell::tagToIdxVertex, and Simple2DCell::ttiVertex.

◆ reIndexCellArray() [1/3]

void Simple2DCell::reIndexCellArray ( GPUArray< int > & array )

protectedinherited

Re-index cell arrays after a spatial sorting has occured.

Re-indexes GPUarrays of ints

References ArrayHandle< T >::data, access_location::host, Simple2DCell::itt, Simple2DCell::Ncells, access_mode::read, and access_mode::readwrite.

Referenced by Simple2DCell::spatiallySortCells(), spatiallySortCellsAndCellActivity(), Simple2DCell::spatiallySortVertices(), spatiallySortVerticesAndCellActivity(), and voronoiModelBase::spatialSorting().

◆ reIndexCellArray() [2/3]

void Simple2DCell::reIndexCellArray ( GPUArray< Dscalar > & array )

protectedinherited

why use templates when you can type more?

Re-indexes GPUarrays of Dscalars

References ArrayHandle< T >::data, access_location::host, Simple2DCell::itt, Simple2DCell::Ncells, access_mode::read, and access_mode::readwrite.

◆ reIndexCellArray() [3/3]

void Simple2DCell::reIndexCellArray ( GPUArray< Dscalar2 > & array )

protectedinherited

why use templates when you can type more?

Always called after spatial sorting is performed, reIndexCellArray shuffles the order of an array based on the spatial sort order of the cells

References ArrayHandle< T >::data, access_location::host, Simple2DCell::itt, Simple2DCell::Ncells, access_mode::read, and access_mode::readwrite.

◆ reIndexVertexArray()

void Simple2DCell::reIndexVertexArray ( GPUArray< Dscalar2 > & array )

protectedinherited

why use templates when you can type more?

Called if the vertices need to be spatially sorted, reIndexVertexArray shuffles the order of an array based on the spatial sort order of the vertices

References ArrayHandle< T >::data, access_location::host, Simple2DCell::ittVertex, Simple2DCell::Nvertices, access_mode::read, and access_mode::readwrite.

◆ spatiallySortCells()

void Simple2DCell::spatiallySortCells ( )

protectedinherited

Perform a spatial sorting of the cells to try to maintain data locality.

take the current location of the cells and sort them according the their order along a 2D Hilbert curve

References Simple2DCell::AreaPeri, Simple2DCell::AreaPeriPreferences, Simple2DCell::Box, Simple2DCell::cellMasses, Simple2DCell::cellPositions, Simple2DCell::cellType, Simple2DCell::cellVelocities, ArrayHandle< T >::data, HilbertSorter::getIdx(), access_location::host, Simple2DCell::idxToTag, Simple2DCell::itt, Simple2DCell::Moduli, Simple2DCell::Ncells, access_mode::readwrite, Simple2DCell::reIndexCellArray(), Simple2DCell::tagToIdx, and Simple2DCell::tti.

Referenced by spatiallySortCellsAndCellActivity().

◆ spatiallySortVertices()

void Simple2DCell::spatiallySortVertices ( )

protectedinherited

Perform a spatial sorting of the vertices to try to maintain data locality.

take the current location of the vertices and sort them according the their order along a 2D Hilbert curve. This routine first sorts the vertices, and then uses the vertex sorting to derive a sorting of the cells

Postcondition: both the itt, tti,... and ittVertex, ttiVertex... arrays are correctly set

References Simple2DCell::AreaPeriPreferences, Simple2DCell::Box, Simple2DCell::cellPositions, Simple2DCell::cellType, Simple2DCell::cellVertexNum, Simple2DCell::cellVertices, ArrayHandle< T >::data, HilbertSorter::getIdx(), access_location::host, Simple2DCell::idxToTag, Simple2DCell::idxToTagVertex, Simple2DCell::itt, Simple2DCell::ittVertex, Simple2DCell::Moduli, Simple2DCell::n_idx, Simple2DCell::Ncells, Simple2DCell::Nvertices, access_mode::read, access_mode::readwrite, Simple2DCell::reIndexCellArray(), Simple2DCell::reIndexVertexArray(), Simple2DCell::tagToIdx, Simple2DCell::tagToIdxVertex, Simple2DCell::tti, Simple2DCell::ttiVertex, Simple2DCell::vertexCellNeighbors, Simple2DCell::vertexMasses, Simple2DCell::vertexNeighbors, Simple2DCell::vertexPositions, and Simple2DCell::vertexVelocities.

Referenced by spatiallySortVerticesAndCellActivity().

◆ reportMeanCellForce()

void Simple2DCell::reportMeanCellForce ( bool verbose )

virtualinherited

Report the current average force on each cell.

a utility/testing function...output the currently computed mean net force to screen.

Parameters

verbose if true also print out the force on each cell

Implements Simple2DModel.

References Simple2DCell::cellForces, Simple2DCell::cellPositions, access_location::host, and access_mode::read.

◆ reportq()

Dscalar Simple2DCell::reportq ( )

virtualinherited

Report the average value of p/sqrt(A) for the cells in the system.

Returns the mean value of the shape parameter:

Implements Simple2DModel.

◆ reportVarq()

Dscalar Simple2DCell::reportVarq ( )

inherited

Report the variance of p/sqrt(A) for the cells in the system.

Returns the variance of the shape parameter:

◆ reportVarAP()

Dscalar2 Simple2DCell::reportVarAP ( )

inherited

Report the variance of A and P for the cells in the system.

Returns the variance of the A and P for the system:

◆ reportMeanP()

Dscalar Simple2DCell::reportMeanP ( )

inherited

Report the mean value of the perimeter.

Returns the mean value of the perimeter

Member Data Documentation

◆ vertexNeighbors

GPUArray<int> Simple2DCell::vertexNeighbors

inherited

VERTEX neighbors of every vertex.

in general, we have: vertexNeighbors[3*i], vertexNeighbors[3*i+1], and vertexNeighbors[3*i+2] contain the indices of the three vertices that are connected to vertex i

Referenced by vertexModelBase::cellDeath(), vertexModelBase::flipEdgesGPU(), Simple2DCell::setVertexTopologyFromCells(), Simple2DCell::spatiallySortVertices(), vertexModelBase::testAndPerformT1TransitionsCPU(), and vertexModelBase::testEdgesForT1GPU().

◆ vertexCellNeighbors

GPUArray<int> Simple2DCell::vertexCellNeighbors

inherited

Cell neighbors of every vertex.

in general, we have: vertexCellNeighbors[3*i], vertexCellNeighbors[3*i+1], and vertexCellNeighbors[3*i+2] contain the indices of the three cells are neighbors of vertex i

Referenced by vertexModelBase::cellDeath(), VertexQuadraticEnergy::computeForcesCPU(), VertexQuadraticEnergy::computeForcesGPU(), vertexModelBase::computeGeometryCPU(), vertexModelBase::computeGeometryGPU(), VertexQuadraticEnergyWithTension::computeVertexTensionForcesCPU(), vertexModelBase::flipEdgesGPU(), vertexModelBase::getCellVertexSetForT1(), Simple2DCell::setVertexTopologyFromCells(), Simple2DCell::spatiallySortVertices(), vertexModelBase::testAndPerformT1TransitionsCPU(), and vertexModelBase::testEdgesForT1GPU().

◆ cellVertexNum

GPUArray<int> Simple2DCell::cellVertexNum

inherited

The number of vertices defining each cell.

cellVertexNum[c] is an integer storing the number of vertices that make up the boundary of cell c.

Referenced by vertexModelBase::cellDeath(), vertexModelBase::computeGeometryCPU(), vertexModelBase::computeGeometryGPU(), VertexQuadraticEnergyWithTension::computeVertexTensionForcesCPU(), vertexModelBase::flipEdgesGPU(), vertexModelBase::getCellCentroidsCPU(), vertexModelBase::getCellPositionsCPU(), vertexModelBase::getCellPositionsGPU(), vertexModelBase::getCellVertexSetForT1(), vertexModelBase::growCellVerticesList(), vertexModelBase::reportNeighborsCell(), Simple2DCell::setVertexTopologyFromCells(), Simple2DCell::spatiallySortVertices(), vertexModelBase::testAndPerformT1TransitionsCPU(), and vertexModelBase::testEdgesForT1GPU().

◆ cellType

GPUArray<int> Simple2DCell::cellType

inherited

An array of integers labeling cell type...an easy way of determining if cells are different.

Please note that "type" is not meaningful unless it is used by child classes. That is, things like area/perimeter preferences, or motility, or whatever are neither set nor accessed by cell type, but rather by cell index! Thus, this is just an additional data structure that can be useful. For instance, the VoronoiTension2D classes uses the integers of cellType to determine when to apply an additional line tension between cells.

Referenced by Simple2DCell::cellDeath(), Simple2DCell::cellDivision(), VertexQuadraticEnergyWithTension::computeVertexTensionForcesCPU(), VoronoiQuadraticEnergyWithTension::computeVoronoiSimpleTensionForceSetsGPU(), VoronoiQuadraticEnergyWithTension::computeVoronoiTensionForceSetsGPU(), Simple2DCell::setCellType(), Simple2DCell::setCellTypeUniform(), Simple2DCell::spatiallySortCells(), and Simple2DCell::spatiallySortVertices().

◆ tagToIdx

vector<int> Simple2DCell::tagToIdx

inherited

To write consistent files...the cell that started the simulation as index i has current index tagToIdx[i].

The Hilbert sorting stuff makes keeping track of particles, and re-indexing things when particle number changes, a pain. Here's a description of the four relevant data structures. tagToIdx[i] = a. At the beginning of a simulation, a particle had index "i", meaning its current state was found in position "i" of all various data vectors and arrays. That same particle's data is now in position "a" of those data structures. Short version: "Where do I look to find info for what I orinally called partice i?" idxToTag[a] = i. That is, idxToTag just helps invert the tagToIdx list. idxToTag[tagToIdx[i]]=i The above two structures (and the vertex versions of them) tell you how to go back and forth between the current state of the system and the initial state of the system. What about going back and forth between the current sorted state and the previous sorted state? The "itt" and "tti" vectors give this information. The itt and tti vectors are completely overwritten each time a spatial sorting is called. By the way, I apologize if the nomenclature of "index" vs. "tag" is the opposite of what you, the reader of these code comments, might expect.

Referenced by Simple2DCell::cellDeath(), Simple2DCell::cellDivision(), Simple2DCell::initializeCellSorting(), Simple2DCell::spatiallySortCells(), and Simple2DCell::spatiallySortVertices().

◆ cellVertices

GPUArray<int> Simple2DCell::cellVertices

protectedinherited

A structure that indexes the vertices defining each cell.

cellVertices is a large, 1D array containing the vertices associated with each cell. It must be accessed with the help of the Index2D structure n_idx. the index of the kth vertex of cell c (where the ordering is counter-clockwise starting with a random vertex) is given by cellVertices[n_idx(k,c)];

◆ voroCur

GPUArray<Dscalar2> Simple2DCell::voroCur

protectedinherited

3*Nvertices length array of the position of vertices around cells

For both vertex and Voronoi models, it may help to save the relative position of the vertices around a cell, either for easy force computation or in the geometry routine, etc. voroCur.data[n_idx(nn,i)] gives the nth vertex, in CCW order, of cell i

Referenced by VertexQuadraticEnergy::computeForcesCPU(), VertexQuadraticEnergy::computeForcesGPU(), vertexModelBase::computeGeometryCPU(), voronoiModelBase::computeGeometryCPU(), vertexModelBase::computeGeometryGPU(), voronoiModelBase::computeGeometryGPU(), VertexQuadraticEnergyWithTension::computeVertexTensionForcesCPU(), VoronoiQuadraticEnergy::computeVoronoiForceSetsGPU(), VoronoiQuadraticEnergyWithTension::computeVoronoiSimpleTensionForceSetsGPU(), VoronoiQuadraticEnergyWithTension::computeVoronoiTensionForceSetsGPU(), and voronoiModelBase::resetLists().

◆ voroLastNext

GPUArray<Dscalar4> Simple2DCell::voroLastNext

protectedinherited

3*Nvertices length array of the position of the last and next vertices along the cell Similarly, voroLastNext.data[n_idx(nn,i)] gives the previous and next vertex of the same

◆ itt

vector<int> Simple2DCell::itt

protectedinherited

A map between cell index and the spatially sorted version.

sortedArray[i] = unsortedArray[itt[i]] after a hilbert sort

Referenced by Simple2DCell::cellDeath(), Simple2DCell::cellDivision(), Simple2DCell::initializeCellSorting(), Simple2DCell::reIndexCellArray(), Simple2DCell::returnItt(), Simple2DCell::spatiallySortCells(), and Simple2DCell::spatiallySortVertices().

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

Public Member Functions

Public Attributes

Protected Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

◆ Simple2DActiveCell()

Member Function Documentation

◆ initializeSimple2DActiveCell()

◆ setv0Dr()

◆ setCellMotility()

◆ setCellDirectorsRandomly()

◆ cellDivision()

◆ cellDeath()

◆ spatiallySortVerticesAndCellActivity()

◆ spatiallySortCellsAndCellActivity()

◆ initializeSimple2DCell()

◆ computeGeometry()

◆ computeKineticEnergy()

◆ computeKineticPressure()

◆ setCellPreferencesUniform()

◆ setCellPreferences()

◆ setCellPositionsRandomly()

◆ setCellPositions()

◆ setVertexPositions()

◆ setCellVelocitiesMaxwellBoltzmann()

◆ setVertexVelocitiesMaxwellBoltzmann()

◆ setModuliUniform()

◆ setCellTypeUniform()

◆ setCellType()

◆ setVertexTopologyFromCells()

◆ initializeCellSorting()

◆ initializeVertexSorting()

◆ reIndexCellArray() [1/3]

◆ reIndexCellArray() [2/3]

◆ reIndexCellArray() [3/3]

◆ reIndexVertexArray()

◆ spatiallySortCells()

◆ spatiallySortVertices()

◆ reportMeanCellForce()

◆ reportq()

◆ reportVarq()

◆ reportVarAP()

◆ reportMeanP()

Member Data Documentation

◆ vertexNeighbors

◆ vertexCellNeighbors

◆ cellVertexNum

◆ cellType

◆ tagToIdx

◆ cellVertices

◆ voroCur

◆ voroLastNext

◆ itt