Open Qmin: multirankQTensorLatticeModel Class Reference

#include <multirankQTensorLatticeModel.h>

Inheritance diagram for multirankQTensorLatticeModel:

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Collaboration diagram for multirankQTensorLatticeModel:

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Public Member Functions
	multirankQTensorLatticeModel (int lx, int ly, int lz, bool _xHalo, bool _yHalo, bool _zHalo, bool _useGPU=false, bool _neverGPU=false)

virtual scalar	getClassSize ()
	return size of data in class in GB More...

void	determineBufferLayout ()

int3	indexToPosition (int idx)
	given an 0 <= index < totalSites, return the local lattice position More...

int	positionToIndex (int3 &pos)
	given a local lattice position, return the index in the expanded data arrays More...

int	positionToIndex (int px, int py, int pz)

void	getBufferInt3FromIndex (int idx, int3 &pos, int directionType, bool sending)

void	prepareSendingBuffer (int directionType=-1)
	Fill the appropriate part of the sending buffer...if GPU, fill it all in one function call. More...

void	readReceivingBuffer (int directionType=-1)
	Fill the appropriate part of data from the receiving buffer...if GPU, fill it all in one function call. More...

virtual int	getNeighbors (int target, vector< int > &neighbors, int &neighs, int stencilType=0)
	this implementation knows that extra neighbors are after N in the data arrays More...

virtual void	moveParticles (GPUArray< dVec > &displacements, scalar scale=1.)
	(possibly) need to rewrite how the Q tensors update with respect to a displacement call More...

virtual void	moveParticles (GPUArray< dVec > &dofs, GPUArray< dVec > &displacements, scalar scale=1.)
	move a different GPU array according to the same rules More...

void	setNematicQTensorRandomly (noiseSource &noise, scalar s0, bool globallyAligned=false)
	initialize each d.o.f., also passing in the value of the nematicity More...

void	getAverageEigenvalues ()
	get field-averaged eigenvalues More...

void	createBoundaryFromFile (string fname, bool verbose=false)
	import a boundary object from a (carefully prepared) text file More...

void	createSimpleFlatWallNormal (int plane, int xyz, boundaryObject &bObj)
	create a flat wall at the specified location, on either an x,y, or z plane, with anchoring given by the boundary object More...

void	createSimpleFlatWallZNormal (int zPlane, boundaryObject &bObj)
	create a flat wall (with z-normal) at the specified location, with anchoring given by the boundary object More...

void	createSimpleSpherialColloid (scalar3 center, scalar radius, boundaryObject &bObj)
	create a spherical colloid with anchoring given by the boundary object (with surface normal the director direction) More...

void	computeDefectMeasures (int defectType)
	compute different measures of whether a site is a defect More...

void	setSpinsRandomly (noiseSource &noise)
	initialize each d.o.f. to be a unit spin on the sphere More...

void	sliceIndices (bool _s=true)
	decide to slice sites More...

int	latticeSiteToLinearIndex (const int3 &target)
	given a triple, determine what More...

virtual void	fillNeighborLists (int stencilType=0)
	store the neighbors of each lattice site. The i'th neighbor of site j is given by neighboringSites[neighborIndex(i,j)] More...

virtual dVec	averagePosition ()
	return the mean spin More...

virtual void	displaceBoundaryObject (int objectIndex, int motionDirection, int magnitude)
	Displace a boundary object (and surface sites) by one of the six primitive cubic lattice directions. More...

void	createBoundaryObject (vector< int > &latticeSites, boundaryType _type, scalar Param1, scalar Param2)
	assign a collection of lattice sites to a new boundaryObject More...

void	initializeSimpleModel (int n)
	initialize the size of the basic data structure arrays More...

virtual void	setGPU (bool _useGPU=true)
	Enforce GPU operation. More...

virtual int	getNumberOfParticles ()
	get the number of degrees of freedom, defaulting to the number of cells More...

virtual void	computeForces (bool zeroOutForces=false)
	do everything unusual to compute additional forces... by default, sets forces to zero More...

void	setParticlePositions (GPUArray< dVec > &newPositions)

void	setParticlePositions (vector< dVec > &newPositions)

void	setParticlePositionsRandomly (noiseSource &noise)

scalar	setVelocitiesMaxwellBoltzmann (scalar T, noiseSource &noise)
	Set velocities via a temperature. The return value is the total kinetic energy. More...

virtual scalar	computeKineticEnergy (bool verbose=false)
	compute the current KE More...

virtual scalar	computeInstantaneousTemperature (bool fixedMomentum=true)
	compute the dimension-dependent instantaneous temperature More...

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

virtual GPUArray< dVec > &	returnPositions ()
	return a reference to the GPUArray of positions More...

virtual GPUArray< dVec > &	returnForces ()
	return a reference to the GPUArray of the current forces More...

virtual GPUArray< int > &	returnTypes ()
	return a reference to the GPUArray of the integer types More...

virtual GPUArray< dVec > &	returnVelocities ()
	return a reference to the GPUArray of the current velocities More...

virtual GPUArray< scalar > &	returnDefectMeasures ()
	return a reference to the GPUArray of the current defects More...

virtual void	setNThreads (int n)
	allow for setting multiple threads More...

virtual void	freeGPUArrays (bool freeVelocities, bool freeRadii, bool freeMasses)
	some situations do not require us to maintain various data structures More...

Public Attributes
int	totalSites
	N is the number of sites controlled, totalSites includes halo sites. More...

bool	xHalo

bool	yHalo

bool	zHalo

int	myRank

int3	latticeSites

vector< int2 >	transferStartStopIndexes
	list of start/stop elements in the transfer arrays for the halo sites More...

GPUArray< int >	intTransferBufferSend

GPUArray< scalar >	doubleTransferBufferSend

GPUArray< int >	intTransferBufferReceive

GPUArray< scalar >	doubleTransferBufferReceive

Index3D	latticeIndex
	indexer for lattice sites More...

Index2D	neighborIndex
	indexer for neighbors More...

GPUArray< int >	neighboringSites
	List of neighboring lattice sites. More...

GPUArray< boundaryObject >	boundaries
	list of the non-bulk objects in the simulations More...

vector< GPUArray< int > >	boundarySites
	A vector that keeps track of the sites associated with each boundary object. More...

vector< GPUArray< int > >	surfaceSites
	A vector that keeps track of the surface sites associated with each boundary object. More...

vector< int >	boundaryState
	A vector of flags that specifies the state of each boundary object...most schemes will be 0 = fixed boundary, 1 = movable boudnary. More...

vector< scalar3 >	boundaryForce
	The force (from integrating the stress tensor) on each object. More...

GPUArray< pair< int, dVec > >	boundaryMoveAssist1
	An assist vector that can keep track of changes to boundary sites during a move. First element is the index a Qtensor (second ) will move to. More...

GPUArray< pair< int, dVec > >	boundaryMoveAssist2
	An assist vector that can keep track of changes to surface sites during a move. First element is the index a Qtensor (second ) will move to. More...

bool	selfForceCompute
	Does this model have a special force it needs to compute itself? More...

BoxPtr	Box
	The space in which the particles live. More...

bool	forcesComputed
	Are the forces current? set to false after every call to moveParticles. set to true after the SIMULATION calls computeForces. More...

GPUArray< scalar >	defectMeasures
	scalars that can represent different defect measures More...

bool	neverGPU
	Whereas useGPU can be turned on and off, neverGPU is fixed. More...

Protected Member Functions
void	initializeNSites ()
	a utility function for initialization More...

Protected Attributes
bool	sliceSites
	should we use a memory-efficient slicing scheme? More...

int	L
	lattice sites per edge More...

bool	normalizeSpins
	normalize vector length when moving spins? More...

shared_ptr< kernelTuner >	moveParticlesTuner
	performance for the moveParticles kernel More...

int	N
	The number of particles. More...

int	nThreads =1
	number of threads to use More...

GPUArray< dVec >	positions
	particle positions More...

GPUArray< dVec >	velocities
	particle velocities More...

GPUArray< dVec >	forces
	Forces on particles. More...

GPUArray< int >	types
	particle types More...

bool	useGPU
	particle radii More...

Detailed Description

In the nomenclature of multi-rank models, the "type" of lattice sites corresponds to: -2 --> sites that might be communicated to other ranks (this value can be overwritten) -1 --> sites that border at least one boundary (colloid, wall, etc.) 0 --> bulk sites [positive number] --> sites that are part of a boundary object

Constructor & Destructor Documentation

◆ multirankQTensorLatticeModel()

multirankQTensorLatticeModel::multirankQTensorLatticeModel	(	int	lx,
		int	ly,
		int	lz,
		bool	_xHalo,
		bool	_yHalo,
		bool	_zHalo,
		bool	_useGPU = `false`,
		bool	_neverGPU = `false`
	)

Member Function Documentation

◆ getClassSize()

virtual scalar multirankQTensorLatticeModel::getClassSize ( )

inlinevirtual

return size of data in class in GB

Reimplemented from qTensorLatticeModel.

References doubleTransferBufferReceive, doubleTransferBufferSend, qTensorLatticeModel::getClassSize(), GPUArray< T >::getNumElements(), intTransferBufferReceive, intTransferBufferSend, scalar, and transferStartStopIndexes.

◆ determineBufferLayout()

void multirankQTensorLatticeModel::determineBufferLayout ( )

During halo site communication, each rank will first completely fill the send buffer, and then send/receives within the buffers will be performed. Finally, the entire receive buffer will be transfered into the expanded data arrays. To facilitate this, a specific layout of the transfer buffers will be adopted for easy package/send/receive patterns: the x = 0 face will be the first (Ly*Lz) elemetents, followed by the other faces, the edges, and finally the 8 corners.

References doubleTransferBufferReceive, doubleTransferBufferSend, intTransferBufferReceive, intTransferBufferSend, latticeSites, GPUArray< T >::resize(), and transferStartStopIndexes.

Referenced by multirankQTensorLatticeModel().

◆ indexToPosition()

int3 multirankQTensorLatticeModel::indexToPosition ( int idx )

given an 0 <= index < totalSites, return the local lattice position

References getBufferInt3FromIndex(), idx, Index3D::inverseIndex(), cubicLattice::latticeIndex, simpleModel::N, totalSites, and transferStartStopIndexes.

Referenced by multirankQTensorLatticeModel().

◆ positionToIndex() [1/2]

int multirankQTensorLatticeModel::positionToIndex ( int3 & pos )

given a local lattice position, return the index in the expanded data arrays

Given the buffer layout below, determine the data array index of a given position

References cubicLattice::latticeIndex, latticeSites, simpleModel::N, ordered(), transferStartStopIndexes, xHalo, yHalo, and zHalo.

Referenced by getNeighbors(), positionToIndex(), and prepareSendingBuffer().

◆ positionToIndex() [2/2]

int multirankQTensorLatticeModel::positionToIndex	(	int	px,
		int	py,
		int	pz
	)

inline

References positionToIndex().

◆ getBufferInt3FromIndex()

void multirankQTensorLatticeModel::getBufferInt3FromIndex	(	int	idx,
		int3 &	pos,
		int	directionType,
		bool	sending
	)

Meant to be used with idx in (transferStartStopIndexes[directionType].x to ".y)

Parameters

idx	the linear index in between 0 and the maximum number of extended sites
pos	gets filled with the right lattice position, with correct send/receive dependence
directionType	an int specifying the type of face/edge/corner. See comments in determingBufferLayout() for the mapping between 0 and 25 to the possibilities
sending	flag the either restricts pos to be withing 0 and latticeSites, or the halo sites if fase

References idx, index, latticeSites, and transferStartStopIndexes.

Referenced by indexToPosition(), and prepareSendingBuffer().

◆ prepareSendingBuffer()

void multirankQTensorLatticeModel::prepareSendingBuffer ( int directionType = -1 )

Fill the appropriate part of the sending buffer...if GPU, fill it all in one function call.

References ArrayHandle< T >::data, access_location::device, doubleTransferBufferSend, getBufferInt3FromIndex(), gpu_prepareSendingBuffer(), access_location::host, intTransferBufferSend, cubicLattice::latticeIndex, latticeSites, simpleModel::positions, positionToIndex(), access_mode::read, access_mode::readwrite, transferStartStopIndexes, simpleModel::types, and simpleModel::useGPU.

◆ readReceivingBuffer()

void multirankQTensorLatticeModel::readReceivingBuffer ( int directionType = -1 )

Fill the appropriate part of data from the receiving buffer...if GPU, fill it all in one function call.

References ArrayHandle< T >::data, access_location::device, doubleTransferBufferReceive, gpu_copyReceivingBuffer(), access_location::host, intTransferBufferReceive, simpleModel::N, simpleModel::positions, access_mode::read, access_mode::readwrite, transferStartStopIndexes, simpleModel::types, and simpleModel::useGPU.

◆ getNeighbors()

int multirankQTensorLatticeModel::getNeighbors	(	int	target,
		vector< int > &	neighbors,
		int &	neighs,
		int	stencilType = `0`
	)

virtual

this implementation knows that extra neighbors are after N in the data arrays

Reimplemented from cubicLattice.

References Index3D::inverseIndex(), cubicLattice::latticeIndex, positionToIndex(), and cubicLattice::sliceSites.

◆ moveParticles() [1/2]

void qTensorLatticeModel::moveParticles	(	GPUArray< dVec > &	displacements,
		scalar	scale = `1.`
	)

virtualinherited

(possibly) need to rewrite how the Q tensors update with respect to a displacement call

Reimplemented from cubicLattice.

References ArrayHandle< T >::data, access_location::device, gpu_update_qTensor(), access_location::host, cubicLattice::moveParticlesTuner, simpleModel::N, simpleModel::positions, access_mode::read, access_mode::readwrite, and simpleModel::useGPU.

◆ moveParticles() [2/2]

void cubicLattice::moveParticles	(	GPUArray< dVec > &	dofs,
		GPUArray< dVec > &	displacements,
		scalar	scale = `1.`
	)

virtualinherited

move a different GPU array according to the same rules

References ArrayHandle< T >::data, access_location::device, gpu_update_spins(), access_location::host, simpleModel::N, norm(), cubicLattice::normalizeSpins, access_mode::read, access_mode::readwrite, scalar, and simpleModel::useGPU.

◆ setNematicQTensorRandomly()

void qTensorLatticeModel::setNematicQTensorRandomly	(	noiseSource &	noise,
		scalar	s0,
		bool	globallyAligned = `false`
	)

inherited

initialize each d.o.f., also passing in the value of the nematicity

References ArrayHandle< T >::data, access_location::device, noiseSource::getRealUniform(), gpu_set_random_nematic_qTensors(), access_location::host, noiseSource::initialize(), noiseSource::initializeGPURNGs(), n, simpleModel::N, PI, simpleModel::positions, qTensorFromDirector(), access_mode::read, access_mode::readwrite, noiseSource::RNGs, scalar, scalar3, simpleModel::types, and simpleModel::useGPU.

◆ getAverageEigenvalues()

void qTensorLatticeModel::getAverageEigenvalues ( )

inherited

get field-averaged eigenvalues

References ArrayHandle< T >::data, eigenvaluesOfQ(), access_location::host, n, simpleModel::N, simpleModel::positions, access_mode::read, scalar, and simpleModel::types.

◆ createBoundaryFromFile()

void qTensorLatticeModel::createBoundaryFromFile	(	string	fname,
		bool	verbose = `false`
	)

inherited

import a boundary object from a (carefully prepared) text file

Reads a carefully prepared text file to create a new boundary object... The first line must be a single integer specifying the number of objects to be read in.

Each subsequent block must be formatted as follows (with no additional lines between the blocks): The first line MUST be formatted as a b c d where a=0 means homeotropic, a=1 means degeneratePlanar b is a scalar setting the anchoring strength c is the preferred value of S0 d is an integer specifying the number of sites.

Every subsequent line MUST be x y z Qxx Qxy Qxz Qyy Qyz, where x y z are the integer lattice sites, and the Q-tensor components correspond to the desired anchoring conditions. For homeotropic boundaries, Q^B = 3 S_0/2*(\nu^s \nu^s - \delta_{ab}/3), where \nu^s is the locally preferred director. For degenerate planar anchoring the boundary site should be, Q^B[0] = \hat{nu}_x Q^B[1] = \hat{nu}_y Q^B[2] = \hat{nu}_z where \nu^s = {Cos[[Phi]] Sin[[theta]], Sin[[Phi]] Sin[[theta]], Cos[[theta]]} is the direction to which the LC should try to be orthogonal

References cubicLattice::createBoundaryObject(), ArrayHandle< T >::data, degeneratePlanar, homeotropic, cubicLattice::latticeIndex, simpleModel::positions, scalar, Index3D::sizes, and wrap().

◆ createSimpleFlatWallNormal()

void qTensorLatticeModel::createSimpleFlatWallNormal	(	int	plane,
		int	xyz,
		boundaryObject &	bObj
	)

inherited

create a flat wall at the specified location, on either an x,y, or z plane, with anchoring given by the boundary object

References boundaryObject::boundary, cubicLattice::createBoundaryObject(), ArrayHandle< T >::data, degeneratePlanar, homeotropic, cubicLattice::latticeIndex, boundaryObject::P1, boundaryObject::P2, simpleModel::positions, scalar, Index3D::sizes, and UNWRITTENCODE.

◆ createSimpleFlatWallZNormal()

void qTensorLatticeModel::createSimpleFlatWallZNormal	(	int	zPlane,
		boundaryObject &	bObj
	)

inherited

create a flat wall (with z-normal) at the specified location, with anchoring given by the boundary object

◆ createSimpleSpherialColloid()

void qTensorLatticeModel::createSimpleSpherialColloid	(	scalar3	center,
		scalar	radius,
		boundaryObject &	bObj
	)

inherited

create a spherical colloid with anchoring given by the boundary object (with surface normal the director direction)

References boundaryObject::boundary, cubicLattice::createBoundaryObject(), ArrayHandle< T >::data, degeneratePlanar, homeotropic, cubicLattice::latticeIndex, norm(), boundaryObject::P1, boundaryObject::P2, simpleModel::positions, qTensorFromDirector(), scalar, scalar3, Index3D::sizes, UNWRITTENCODE, and wrap().

◆ computeDefectMeasures()

void qTensorLatticeModel::computeDefectMeasures ( int defectType )

inherited

compute different measures of whether a site is a defect

defectType==0 stores the largest eigenvalue of Q at each site defectType==1 stores the determinant of Q each site defectType==2 stores the (Tr(Q^2))^3-54 det(Q)^2 at each site

References ArrayHandle< T >::data, simpleModel::defectMeasures, determinantOfQ(), access_location::device, eigenvaluesOfQ(), gpu_get_qtensor_DefectMeasures(), access_location::host, simpleModel::N, access_mode::overwrite, simpleModel::positions, access_mode::read, scalar, TrQ2(), simpleModel::types, and simpleModel::useGPU.

◆ setSpinsRandomly()

void cubicLattice::setSpinsRandomly ( noiseSource & noise )

inherited

initialize each d.o.f. to be a unit spin on the sphere

References ArrayHandle< T >::data, access_location::device, dot(), noiseSource::getRealNormal(), gpu_set_random_spins(), noiseSource::initialize(), noiseSource::initializeGPURNGs(), simpleModel::N, access_mode::overwrite, simpleModel::positions, access_mode::readwrite, noiseSource::RNGs, scalar, and simpleModel::useGPU.

◆ sliceIndices()

void cubicLattice::sliceIndices ( bool _s = true )

inlineinherited

decide to slice sites

References cubicLattice::sliceSites.

◆ latticeSiteToLinearIndex()

int cubicLattice::latticeSiteToLinearIndex ( const int3 & target )

inherited

given a triple, determine what

References cubicLattice::latticeIndex, and cubicLattice::sliceSites.

◆ fillNeighborLists()

void cubicLattice::fillNeighborLists ( int stencilType = 0 )

virtualinherited

store the neighbors of each lattice site. The i'th neighbor of site j is given by neighboringSites[neighborIndex(i,j)]

stencilType here has the same meaning as in "getNeighbors" function

References ArrayHandle< T >::data, cubicLattice::getNeighbors(), simpleModel::N, cubicLattice::neighborIndex, cubicLattice::neighboringSites, and GPUArray< T >::resize().

◆ averagePosition()

virtual dVec cubicLattice::averagePosition ( )

inlinevirtualinherited

return the mean spin

References ArrayHandle< T >::data, simpleModel::N, simpleModel::positions, and simpleModel::types.

◆ displaceBoundaryObject()

void cubicLattice::displaceBoundaryObject	(	int	objectIndex,
		int	motionDirection,
		int	magnitude
	)

virtualinherited

Displace a boundary object (and surface sites) by one of the six primitive cubic lattice directions.

This function moves an object, shifting the type of lattice sites over on the lattice. Surface sites are also moved. Sites that change from being part of the boundary to a surface site adopt the average state of the neighboring sites that weren't formerly part of the boundary object. This function makes use of the fact that primitive translations will not change the total number of boundary or surface sites associated with each object

Parameters

objectIndex	The position in the vector of boundarySites and surfaceSites that the desired object to move is in
motionDirection	Which way to move the object. Follows same convention as lattice neighbors for stencilType=0
magnitude	number of lattice sites to move in the given direction

Reimplemented from simpleModel.

References cubicLattice::boundaryMoveAssist1, cubicLattice::boundaryMoveAssist2, cubicLattice::boundarySites, ArrayHandle< T >::data, access_location::device, gpu_copy_boundary_object(), gpu_move_boundary_object(), access_location::host, cubicLattice::neighborIndex, cubicLattice::neighboringSites, access_mode::overwrite, simpleModel::positions, access_mode::read, access_mode::readwrite, cubicLattice::surfaceSites, simpleModel::types, and simpleModel::useGPU.

◆ createBoundaryObject()

void cubicLattice::createBoundaryObject	(	vector< int > &	latticeSites,
		boundaryType	_type,
		scalar	Param1,
		scalar	Param2
	)

inherited

◆ initializeNSites()

void cubicLattice::initializeNSites ( )

protectedinherited

a utility function for initialization

References cubicLattice::boundaries, cubicLattice::boundaryMoveAssist1, cubicLattice::boundaryMoveAssist2, simpleModel::initializeSimpleModel(), cubicLattice::moveParticlesTuner, simpleModel::N, cubicLattice::neighboringSites, simpleModel::neverGPU, and GPUArray< T >::noGPU.

Referenced by cubicLattice::cubicLattice().

◆ initializeSimpleModel()

void simpleModel::initializeSimpleModel ( int n )

inherited

initialize the size of the basic data structure arrays

actually set the array sizes. positions, velocities, forces are zero masses are set to unity

References simpleModel::defectMeasures, simpleModel::forces, make_dVec(), n, simpleModel::N, simpleModel::neverGPU, GPUArray< T >::noGPU, simpleModel::positions, GPUArray< T >::resize(), simpleModel::selfForceCompute, simpleModel::types, and simpleModel::velocities.

Referenced by cubicLattice::initializeNSites(), simpleModel::setParticlePositions(), and simpleModel::simpleModel().

◆ setGPU()

virtual void simpleModel::setGPU ( bool _useGPU = true )

inlinevirtualinherited

Enforce GPU operation.

References simpleModel::useGPU.

◆ getNumberOfParticles()

virtual int simpleModel::getNumberOfParticles ( )

inlinevirtualinherited

get the number of degrees of freedom, defaulting to the number of cells

References simpleModel::N.

◆ computeForces()

void simpleModel::computeForces ( bool zeroOutForces = false )

virtualinherited

do everything unusual to compute additional forces... by default, sets forces to zero

References ArrayHandle< T >::data, simpleModel::forces, gpu_set_array(), simpleModel::N, and simpleModel::useGPU.

◆ setParticlePositions() [1/2]

void simpleModel::setParticlePositions ( GPUArray< dVec > & newPositions )

inherited

References simpleModel::Box, ArrayHandle< T >::data, GPUArray< T >::getNumElements(), simpleModel::initializeSimpleModel(), simpleModel::N, and simpleModel::positions.

◆ setParticlePositions() [2/2]

void simpleModel::setParticlePositions ( vector< dVec > & newPositions )

inherited

References simpleModel::Box, ArrayHandle< T >::data, simpleModel::initializeSimpleModel(), simpleModel::N, and simpleModel::positions.

◆ setParticlePositionsRandomly()

void simpleModel::setParticlePositionsRandomly ( noiseSource & noise )

inherited

References simpleModel::Box, ArrayHandle< T >::data, noiseSource::getRealUniform(), simpleModel::N, and simpleModel::positions.

◆ setVelocitiesMaxwellBoltzmann()

scalar simpleModel::setVelocitiesMaxwellBoltzmann	(	scalar	T,
		noiseSource &	noise
	)

inherited

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

References ArrayHandle< T >::data, dot(), noiseSource::getRealNormal(), simpleModel::N, scalar, and simpleModel::velocities.

◆ computeKineticEnergy()

scalar simpleModel::computeKineticEnergy ( bool verbose = false )

virtualinherited

compute the current KE

References ArrayHandle< T >::data, dot(), simpleModel::N, scalar, and simpleModel::velocities.

◆ computeInstantaneousTemperature()

scalar simpleModel::computeInstantaneousTemperature ( bool fixedMomentum = true )

virtualinherited

compute the dimension-dependent instantaneous temperature

References ArrayHandle< T >::data, dot(), simpleModel::N, scalar, and simpleModel::velocities.

◆ spatialSorting()

virtual void simpleModel::spatialSorting ( )

inlinevirtualinherited

do everything necessary to perform a Hilbert sort

◆ returnPositions()

virtual GPUArray<dVec>& simpleModel::returnPositions ( )

inlinevirtualinherited

return a reference to the GPUArray of positions

References simpleModel::positions.

◆ returnForces()

virtual GPUArray<dVec>& simpleModel::returnForces ( )

inlinevirtualinherited

return a reference to the GPUArray of the current forces

References simpleModel::forces.

◆ returnTypes()

virtual GPUArray<int>& simpleModel::returnTypes ( )

inlinevirtualinherited

return a reference to the GPUArray of the integer types

References simpleModel::types.

◆ returnVelocities()

virtual GPUArray<dVec>& simpleModel::returnVelocities ( )

inlinevirtualinherited

return a reference to the GPUArray of the current velocities

References simpleModel::velocities.

◆ returnDefectMeasures()

virtual GPUArray<scalar>& simpleModel::returnDefectMeasures ( )

inlinevirtualinherited

return a reference to the GPUArray of the current defects

◆ setNThreads()

virtual void simpleModel::setNThreads ( int n )

inlinevirtualinherited

allow for setting multiple threads

References n, and simpleModel::nThreads.

◆ freeGPUArrays()

virtual void simpleModel::freeGPUArrays	(	bool	freeVelocities,
		bool	freeRadii,
		bool	freeMasses
	)

inlinevirtualinherited

some situations do not require us to maintain various data structures

Member Data Documentation

◆ totalSites

int multirankQTensorLatticeModel::totalSites

N is the number of sites controlled, totalSites includes halo sites.

Referenced by indexToPosition(), and multirankQTensorLatticeModel().

◆ xHalo

bool multirankQTensorLatticeModel::xHalo

Referenced by multirankQTensorLatticeModel(), and positionToIndex().

◆ yHalo

bool multirankQTensorLatticeModel::yHalo

Referenced by multirankQTensorLatticeModel(), and positionToIndex().

◆ zHalo

bool multirankQTensorLatticeModel::zHalo

Referenced by multirankQTensorLatticeModel(), and positionToIndex().

◆ myRank

int multirankQTensorLatticeModel::myRank

◆ latticeSites

int3 multirankQTensorLatticeModel::latticeSites

Referenced by determineBufferLayout(), getBufferInt3FromIndex(), multirankQTensorLatticeModel(), positionToIndex(), and prepareSendingBuffer().

◆ transferStartStopIndexes

vector<int2> multirankQTensorLatticeModel::transferStartStopIndexes

list of start/stop elements in the transfer arrays for the halo sites

Referenced by determineBufferLayout(), getBufferInt3FromIndex(), getClassSize(), indexToPosition(), multirankQTensorLatticeModel(), positionToIndex(), prepareSendingBuffer(), and readReceivingBuffer().

◆ intTransferBufferSend

GPUArray<int> multirankQTensorLatticeModel::intTransferBufferSend

Referenced by determineBufferLayout(), getClassSize(), multirankQTensorLatticeModel(), and prepareSendingBuffer().

◆ doubleTransferBufferSend

GPUArray<scalar> multirankQTensorLatticeModel::doubleTransferBufferSend

Referenced by determineBufferLayout(), getClassSize(), multirankQTensorLatticeModel(), and prepareSendingBuffer().

◆ intTransferBufferReceive

GPUArray<int> multirankQTensorLatticeModel::intTransferBufferReceive

Referenced by determineBufferLayout(), getClassSize(), multirankQTensorLatticeModel(), and readReceivingBuffer().

◆ doubleTransferBufferReceive

GPUArray<scalar> multirankQTensorLatticeModel::doubleTransferBufferReceive

Referenced by determineBufferLayout(), getClassSize(), multirankQTensorLatticeModel(), and readReceivingBuffer().

◆ latticeIndex

Index3D cubicLattice::latticeIndex

inherited

indexer for lattice sites

Referenced by qTensorLatticeModel::createBoundaryFromFile(), qTensorLatticeModel::createSimpleFlatWallNormal(), qTensorLatticeModel::createSimpleFlatWallZNormal(), qTensorLatticeModel::createSimpleSpherialColloid(), cubicLattice::cubicLattice(), cubicLattice::getNeighbors(), getNeighbors(), indexToPosition(), cubicLattice::latticeSiteToLinearIndex(), positionToIndex(), and prepareSendingBuffer().

◆ neighborIndex

Index2D cubicLattice::neighborIndex

inherited

indexer for neighbors

Referenced by cubicLattice::displaceBoundaryObject(), and cubicLattice::fillNeighborLists().

◆ neighboringSites

GPUArray<int> cubicLattice::neighboringSites

inherited

List of neighboring lattice sites.

Referenced by cubicLattice::displaceBoundaryObject(), cubicLattice::fillNeighborLists(), cubicLattice::getClassSize(), and cubicLattice::initializeNSites().

◆ boundaries

GPUArray<boundaryObject> cubicLattice::boundaries

inherited

list of the non-bulk objects in the simulations

Referenced by cubicLattice::createBoundaryObject(), and cubicLattice::initializeNSites().

◆ boundarySites

vector<GPUArray<int> > cubicLattice::boundarySites

inherited

A vector that keeps track of the sites associated with each boundary object.

Referenced by cubicLattice::createBoundaryObject(), cubicLattice::displaceBoundaryObject(), and cubicLattice::getClassSize().

◆ surfaceSites

vector<GPUArray<int> > cubicLattice::surfaceSites

inherited

A vector that keeps track of the surface sites associated with each boundary object.

Referenced by cubicLattice::createBoundaryObject(), cubicLattice::displaceBoundaryObject(), and cubicLattice::getClassSize().

◆ boundaryState

vector<int> cubicLattice::boundaryState

inherited

A vector of flags that specifies the state of each boundary object...most schemes will be 0 = fixed boundary, 1 = movable boudnary.

Referenced by cubicLattice::createBoundaryObject(), and cubicLattice::getClassSize().

◆ boundaryForce

vector<scalar3> cubicLattice::boundaryForce

inherited

The force (from integrating the stress tensor) on each object.

Referenced by cubicLattice::createBoundaryObject().

◆ boundaryMoveAssist1

GPUArray<pair<int,dVec> > cubicLattice::boundaryMoveAssist1

inherited

An assist vector that can keep track of changes to boundary sites during a move. First element is the index a Qtensor (second ) will move to.

Referenced by cubicLattice::createBoundaryObject(), cubicLattice::displaceBoundaryObject(), cubicLattice::getClassSize(), and cubicLattice::initializeNSites().

◆ boundaryMoveAssist2

GPUArray<pair<int,dVec> > cubicLattice::boundaryMoveAssist2

inherited

An assist vector that can keep track of changes to surface sites during a move. First element is the index a Qtensor (second ) will move to.

Referenced by cubicLattice::createBoundaryObject(), cubicLattice::displaceBoundaryObject(), cubicLattice::getClassSize(), and cubicLattice::initializeNSites().

◆ sliceSites

bool cubicLattice::sliceSites

protectedinherited

should we use a memory-efficient slicing scheme?

Referenced by cubicLattice::cubicLattice(), cubicLattice::getNeighbors(), getNeighbors(), cubicLattice::latticeSiteToLinearIndex(), and cubicLattice::sliceIndices().

◆ L

int cubicLattice::L

protectedinherited

lattice sites per edge

Referenced by cubicLattice::cubicLattice().

◆ normalizeSpins

bool cubicLattice::normalizeSpins

protectedinherited

normalize vector length when moving spins?

Referenced by cubicLattice::cubicLattice(), cubicLattice::moveParticles(), and qTensorLatticeModel::qTensorLatticeModel().

◆ moveParticlesTuner

shared_ptr<kernelTuner> cubicLattice::moveParticlesTuner

protectedinherited

performance for the moveParticles kernel

Referenced by cubicLattice::initializeNSites(), and qTensorLatticeModel::moveParticles().

◆ selfForceCompute

bool simpleModel::selfForceCompute

inherited

Does this model have a special force it needs to compute itself?

Referenced by cubicLattice::cubicLattice(), and simpleModel::initializeSimpleModel().

◆ Box

BoxPtr simpleModel::Box

inherited

The space in which the particles live.

Referenced by cubicLattice::cubicLattice(), simpleModel::moveParticles(), simpleModel::setParticlePositions(), simpleModel::setParticlePositionsRandomly(), and simpleModel::simpleModel().

◆ forcesComputed

bool simpleModel::forcesComputed

inherited

Are the forces current? set to false after every call to moveParticles. set to true after the SIMULATION calls computeForces.

Referenced by simpleModel::moveParticles().

◆ defectMeasures

GPUArray<scalar> simpleModel::defectMeasures

inherited

scalars that can represent different defect measures

Referenced by qTensorLatticeModel::computeDefectMeasures(), simpleModel::getClassSize(), simpleModel::initializeSimpleModel(), and qTensorLatticeModel::qTensorLatticeModel().

◆ neverGPU

bool simpleModel::neverGPU

inherited

Whereas useGPU can be turned on and off, neverGPU is fixed.

Referenced by cubicLattice::createBoundaryObject(), cubicLattice::cubicLattice(), cubicLattice::initializeNSites(), simpleModel::initializeSimpleModel(), multirankQTensorLatticeModel(), and qTensorLatticeModel::qTensorLatticeModel().

◆ N

int simpleModel::N

protectedinherited

The number of particles.

Referenced by cubicLattice::averagePosition(), qTensorLatticeModel::computeDefectMeasures(), simpleModel::computeForces(), simpleModel::computeInstantaneousTemperature(), simpleModel::computeKineticEnergy(), cubicLattice::cubicLattice(), cubicLattice::fillNeighborLists(), qTensorLatticeModel::getAverageEigenvalues(), simpleModel::getNumberOfParticles(), indexToPosition(), cubicLattice::initializeNSites(), simpleModel::initializeSimpleModel(), cubicLattice::moveParticles(), qTensorLatticeModel::moveParticles(), simpleModel::moveParticles(), multirankQTensorLatticeModel(), positionToIndex(), qTensorLatticeModel::qTensorLatticeModel(), readReceivingBuffer(), qTensorLatticeModel::setNematicQTensorRandomly(), simpleModel::setParticlePositions(), simpleModel::setParticlePositionsRandomly(), cubicLattice::setSpinsRandomly(), simpleModel::setVelocitiesMaxwellBoltzmann(), and simpleModel::simpleModel().

◆ nThreads

int simpleModel::nThreads =1

protectedinherited

number of threads to use

Referenced by simpleModel::setNThreads().

◆ positions

GPUArray<dVec> simpleModel::positions

protectedinherited

particle positions

◆ velocities

GPUArray<dVec> simpleModel::velocities

protectedinherited

particle velocities

Referenced by simpleModel::computeInstantaneousTemperature(), simpleModel::computeKineticEnergy(), simpleModel::getClassSize(), simpleModel::initializeSimpleModel(), multirankQTensorLatticeModel(), simpleModel::returnVelocities(), and simpleModel::setVelocitiesMaxwellBoltzmann().

◆ forces

GPUArray<dVec> simpleModel::forces

protectedinherited

Forces on particles.

Referenced by simpleModel::computeForces(), simpleModel::getClassSize(), simpleModel::initializeSimpleModel(), multirankQTensorLatticeModel(), and simpleModel::returnForces().

◆ types

GPUArray<int> simpleModel::types

protectedinherited

particle types

Referenced by cubicLattice::averagePosition(), qTensorLatticeModel::computeDefectMeasures(), cubicLattice::createBoundaryObject(), cubicLattice::displaceBoundaryObject(), qTensorLatticeModel::getAverageEigenvalues(), simpleModel::getClassSize(), simpleModel::initializeSimpleModel(), multirankQTensorLatticeModel(), prepareSendingBuffer(), readReceivingBuffer(), simpleModel::returnTypes(), and qTensorLatticeModel::setNematicQTensorRandomly().

◆ useGPU

bool simpleModel::useGPU

protectedinherited

particle radii

particle masses Whether the GPU should be used to compute anything

Referenced by qTensorLatticeModel::computeDefectMeasures(), simpleModel::computeForces(), cubicLattice::cubicLattice(), cubicLattice::displaceBoundaryObject(), cubicLattice::moveParticles(), qTensorLatticeModel::moveParticles(), simpleModel::moveParticles(), prepareSendingBuffer(), readReceivingBuffer(), simpleModel::setGPU(), qTensorLatticeModel::setNematicQTensorRandomly(), and cubicLattice::setSpinsRandomly().

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

◆ multirankQTensorLatticeModel()

Member Function Documentation

◆ getClassSize()

◆ determineBufferLayout()

◆ indexToPosition()

◆ positionToIndex() [1/2]

◆ positionToIndex() [2/2]

◆ getBufferInt3FromIndex()

◆ prepareSendingBuffer()

◆ readReceivingBuffer()

◆ getNeighbors()

◆ moveParticles() [1/2]

◆ moveParticles() [2/2]

◆ setNematicQTensorRandomly()

◆ getAverageEigenvalues()

◆ createBoundaryFromFile()

◆ createSimpleFlatWallNormal()

◆ createSimpleFlatWallZNormal()

◆ createSimpleSpherialColloid()

◆ computeDefectMeasures()

◆ setSpinsRandomly()

◆ sliceIndices()

◆ latticeSiteToLinearIndex()

◆ fillNeighborLists()

◆ averagePosition()

◆ displaceBoundaryObject()

◆ createBoundaryObject()

◆ initializeNSites()

◆ initializeSimpleModel()

◆ setGPU()

◆ getNumberOfParticles()

◆ computeForces()

◆ setParticlePositions() [1/2]

◆ setParticlePositions() [2/2]

◆ setParticlePositionsRandomly()

◆ setVelocitiesMaxwellBoltzmann()

◆ computeKineticEnergy()

◆ computeInstantaneousTemperature()

◆ spatialSorting()

◆ returnPositions()

◆ returnForces()

◆ returnTypes()

◆ returnVelocities()

◆ returnDefectMeasures()

◆ setNThreads()

◆ freeGPUArrays()

Member Data Documentation

◆ totalSites

◆ xHalo

◆ yHalo

◆ zHalo

◆ myRank

◆ latticeSites

◆ transferStartStopIndexes

◆ intTransferBufferSend

◆ doubleTransferBufferSend

◆ intTransferBufferReceive

◆ doubleTransferBufferReceive

◆ latticeIndex

◆ neighborIndex

◆ neighboringSites

◆ boundaries

◆ boundarySites

◆ surfaceSites

◆ boundaryState

◆ boundaryForce

◆ boundaryMoveAssist1

◆ boundaryMoveAssist2

◆ sliceSites

◆ L

◆ normalizeSpins

◆ moveParticlesTuner

◆ selfForceCompute

◆ Box