A Lattice that is based on one particle per word, with sites strided per particle. More...

#include <IntLattice.h>

Inheritance diagram for lm::rdme::IntLattice:

Collaboration diagram for lm::rdme::IntLattice:

Public Member Functions
virtual site_t	getMaxSiteType () const
	Get the maximum number of site types possible in the lattice.
virtual particle_t	getMaxParticle () const
	Get the maximum number of particle types possible in the lattice.
virtual site_size_t	getMaxOccupancy () const
	Get the maximum number of particles that can live in a site.
	IntLattice (lattice_coord_t size, si_dist_t spacing, uint particlesPerSite)
	IntLattice (lattice_size_t xSize, lattice_size_t ySize, lattice_size_t zSize, si_dist_t spacing, uint particlesPerSite)
virtual	~IntLattice ()
virtual void	getNeighboringSites (lattice_size_t index, lattice_size_t *neighboringIndices)
	Get the sites that are neighbor to the indicated site.
virtual site_t	getSiteType (lattice_size_t x, lattice_size_t y, lattice_size_t z) const
	Get the site type at the specified location.
virtual site_t	getSiteType (lattice_size_t index) const
	Get the site type at the specified location.
virtual void	setSiteType (lattice_size_t x, lattice_size_t y, lattice_size_t z, site_t siteType)
	Set the site type at the specified location.
virtual void	setSiteType (lattice_size_t index, site_t site)
	Set the site type at the specified location.
virtual void *	getSiteTypes ()
virtual site_size_t	getOccupancy (lattice_size_t x, lattice_size_t y, lattice_size_t z) const
	Get the number of particles in the specified lattice site.
virtual site_size_t	getOccupancy (lattice_size_t subvolume) const
	Get the number of particles in the specified lattice site.
virtual particle_t	getParticle (lattice_size_t x, lattice_size_t y, lattice_size_t z, site_size_t particleIndex) const
	Get the particle at the specified site with at the specified number in the particle list.
virtual particle_t	getParticle (lattice_size_t subvolume, site_size_t particleIndex) const
	Get the particle at the specified site with at the specified number in the particle list.
virtual void	addParticle (lattice_size_t x, lattice_size_t y, lattice_size_t z, particle_t particle)
	Add a particle to the specified site.
virtual void	addParticle (lattice_size_t subvolume, particle_t particle)
	Add a particle to the specified site.
virtual void	removeParticles (lattice_size_t x, lattice_size_t y, lattice_size_t z)
	Remove a particle to the specified site.
virtual void	removeParticles (lattice_size_t subvolume)
	Remove a particle to the specified site.
virtual void	removeAllParticles ()
	Empty all particles from the specified site.
virtual std::map< particle_t, uint >	getParticleCounts ()
	Get the number of each particle type in the lattice.
virtual std::vector< particle_loc_t >	findParticles (particle_t minParticleType, particle_t maxParticleType)
	Get the number of the specified particles types in the lattice.
virtual void	setFromRowMajorByteData (void *buffer, size_t bufferSize)
virtual void	setFromRowMajorData (void *buffer, size_t bufferSize)
virtual void	setSitesFromRowMajorByteData (void *buffer, size_t bufferSize)
virtual void	getParticleLatticeView (uint32_t *particleLattice, int Nw, int Nz, int Ny, int Nx, int Np)
virtual void	getSiteLatticeView (uint8_t *siteLattice, int Nz, int Ny, int Nx)
virtual size_t	getLatticeMemorySize () const
Public Member Functions inherited from lm::rdme::Lattice
	Lattice (lattice_coord_t size, si_dist_t spacing)
	Create a Lattice object.
	Lattice (lattice_size_t xSize, lattice_size_t ySize, lattice_size_t zSize, si_dist_t spacing)
	Create a Lattice object.
virtual	~Lattice ()
	Destroy the Lattice object.
virtual lattice_coord_t	getSize () const
	Get size of the Lattice.
virtual lattice_size_t	getXSize () const
	Get x dimension of the Lattice.
virtual lattice_size_t	getYSize () const
	Get y dimension of the Lattice.
virtual lattice_size_t	getZSize () const
	Get z dimension of the Lattice.
virtual lattice_size_t	getNumberSites () const
	Get total number of sites in the Lattice.
virtual si_dist_t	getSpacing () const
	Get spacing between lattice sites.
std::vector< lattice_coord_t >	getNearbySites (lattice_size_t xc, lattice_size_t yc, lattice_size_t zc, uint minDistance, uint maxDistance)
	Get a list of sites near the specified site within a certain distance.
virtual void	print () const
	Print the lattice to the console.

Static Public Member Functions
static void	nativeSerialize (void destBuffer, void lattice, size_t latticeSize)
static void	copyNativeToRowMajor (void destBuffer, void sourceBuffer, lattice_size_t xSize, lattice_size_t ySize, lattice_size_t zSize, uint particlesPerSite, size_t bufferSize)
static void	copyRowMajorToNative (void destBuffer, void sourceBuffer, lattice_size_t xSize, lattice_size_t ySize, lattice_size_t zSize, uint particlesPerSite, size_t bufferSize)
static void	copySitesRowMajorByteToNative (void destBuffer, void sourceBuffer, lattice_size_t xSize, lattice_size_t ySize, lattice_size_t zSize, size_t bufferSize)
Static Public Member Functions inherited from lm::rdme::Lattice
static void	rowMajorByteSerialize (void destBuffer, void lattice, size_t bufferSize)
static void	rowMajorIntSerialize (void destBuffer, void lattice, size_t bufferSize)
static void	rowMajorByteSerializeSites (void destBuffer, void lattice, size_t bufferSize)

Protected Member Functions
virtual void	allocateMemory ()
virtual void	deallocateMemory ()
virtual uint32_t *	getParticlesMemory ()
virtual uint8_t *	getSitesMemory ()

Protected Attributes
uint	wordsPerSite
uint32_t *	particles
uint8_t *	siteTypes
Protected Attributes inherited from lm::rdme::Lattice
lattice_coord_t	size
lattice_size_t	numberSites
si_dist_t	spacing

Friends
class	MGPUMpdRdmeSolver
class	MPIMpdRdmeSolver
class	MGPUIntMpdRdmeSolver

Detailed Description

A Lattice that is based on one particle per word, with sites strided per particle.

Constructor & Destructor Documentation

◆ IntLattice() [1/2]

lm::rdme::IntLattice::IntLattice	(	lattice_coord_t	size,
		si_dist_t	spacing,
		uint	particlesPerSite )

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◆ IntLattice() [2/2]

lm::rdme::IntLattice::IntLattice	(	lattice_size_t	xSize,
		lattice_size_t	ySize,
		lattice_size_t	zSize,
		si_dist_t	spacing,
		uint	particlesPerSite )

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◆ ~IntLattice()

lm::rdme::IntLattice::~IntLattice ( )

virtual

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Member Function Documentation

◆ addParticle() [1/2]

void lm::rdme::IntLattice::addParticle	(	lattice_size_t	index,
		particle_t	particle )

virtual

Add a particle to the specified site.

Implements lm::rdme::Lattice.

Reimplemented in lm::rdme::CudaIntLattice.

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◆ addParticle() [2/2]

void lm::rdme::IntLattice::addParticle	(	lattice_size_t	x,
		lattice_size_t	y,
		lattice_size_t	z,
		particle_t	particle )

virtual

Add a particle to the specified site.

Implements lm::rdme::Lattice.

Reimplemented in lm::rdme::CudaIntLattice.

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◆ allocateMemory()

void lm::rdme::IntLattice::allocateMemory ( )

protectedvirtual

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◆ copyNativeToRowMajor()

void lm::rdme::IntLattice::copyNativeToRowMajor	(	void *	destBuffer,
		void *	sourceBuffer,
		lattice_size_t	xSize,
		lattice_size_t	ySize,
		lattice_size_t	zSize,
		uint	particlesPerSite,
		size_t	bufferSize )

static

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◆ copyRowMajorToNative()

void lm::rdme::IntLattice::copyRowMajorToNative	(	void *	destBuffer,
		void *	sourceBuffer,
		lattice_size_t	xSize,
		lattice_size_t	ySize,
		lattice_size_t	zSize,
		uint	particlesPerSite,
		size_t	bufferSize )

static

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◆ copySitesRowMajorByteToNative()

void lm::rdme::IntLattice::copySitesRowMajorByteToNative	(	void *	destBuffer,
		void *	sourceBuffer,
		lattice_size_t	xSize,
		lattice_size_t	ySize,
		lattice_size_t	zSize,
		size_t	bufferSize )

static

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◆ deallocateMemory()

void lm::rdme::IntLattice::deallocateMemory ( )

protectedvirtual

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◆ findParticles()

std::vector< particle_loc_t > lm::rdme::IntLattice::findParticles	(	particle_t	minParticleType,
		particle_t	maxParticleType )

virtual

Get the number of the specified particles types in the lattice.

Implements lm::rdme::Lattice.

◆ getLatticeMemorySize()

size_t lm::rdme::IntLattice::getLatticeMemorySize ( ) const

virtual

Implements lm::rdme::Lattice.

◆ getMaxOccupancy()

site_size_t lm::rdme::IntLattice::getMaxOccupancy ( ) const

virtual

Get the maximum number of particles that can live in a site.

Implements lm::rdme::Lattice.

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◆ getMaxParticle()

particle_t lm::rdme::IntLattice::getMaxParticle ( ) const

virtual

Get the maximum number of particle types possible in the lattice.

Implements lm::rdme::Lattice.

◆ getMaxSiteType()

site_t lm::rdme::IntLattice::getMaxSiteType ( ) const

virtual

Get the maximum number of site types possible in the lattice.

Implements lm::rdme::Lattice.

◆ getNeighboringSites()

void lm::rdme::IntLattice::getNeighboringSites	(	lattice_size_t	index,
		lattice_size_t *	neighboringIndices )

virtual

Get the sites that are neighbor to the indicated site.

Parameters

index	Index of the site for which to get neighbors
neighboringIndicies	An array to hold the indicies of the neighbor sites

Implements lm::rdme::Lattice.

◆ getOccupancy() [1/2]

site_size_t lm::rdme::IntLattice::getOccupancy ( lattice_size_t index ) const

virtual

Get the number of particles in the specified lattice site.

Implements lm::rdme::Lattice.

◆ getOccupancy() [2/2]

site_size_t lm::rdme::IntLattice::getOccupancy	(	lattice_size_t	x,
		lattice_size_t	y,
		lattice_size_t	z ) const

virtual

Get the number of particles in the specified lattice site.

Implements lm::rdme::Lattice.

◆ getParticle() [1/2]

particle_t lm::rdme::IntLattice::getParticle	(	lattice_size_t	index,
		site_size_t	particleIndex ) const

virtual

Get the particle at the specified site with at the specified number in the particle list.

Implements lm::rdme::Lattice.

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◆ getParticle() [2/2]

particle_t lm::rdme::IntLattice::getParticle	(	lattice_size_t	x,
		lattice_size_t	y,
		lattice_size_t	z,
		site_size_t	particleIndex ) const

virtual

Get the particle at the specified site with at the specified number in the particle list.

Implements lm::rdme::Lattice.

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◆ getParticleCounts()

std::map< particle_t, uint > lm::rdme::IntLattice::getParticleCounts ( )

virtual

Get the number of each particle type in the lattice.

Particle searching methods.

Implements lm::rdme::Lattice.

◆ getParticleLatticeView()

void lm::rdme::IntLattice::getParticleLatticeView	(	uint32_t **	particleLattice,
		int *	Nw,
		int *	Nz,
		int *	Ny,
		int *	Nx,
		int *	Np )

virtual

◆ getParticlesMemory()

uint32_t * lm::rdme::IntLattice::getParticlesMemory ( )

protectedvirtual

◆ getSiteLatticeView()

void lm::rdme::IntLattice::getSiteLatticeView	(	uint8_t **	siteLattice,
		int *	Nz,
		int *	Ny,
		int *	Nx )

virtual

◆ getSitesMemory()

uint8_t * lm::rdme::IntLattice::getSitesMemory ( )

protectedvirtual

◆ getSiteType() [1/2]

site_t lm::rdme::IntLattice::getSiteType ( lattice_size_t index ) const

virtual

Get the site type at the specified location.

Implements lm::rdme::Lattice.

◆ getSiteType() [2/2]

site_t lm::rdme::IntLattice::getSiteType	(	lattice_size_t	x,
		lattice_size_t	y,
		lattice_size_t	z ) const

virtual

Get the site type at the specified location.

Implements lm::rdme::Lattice.

◆ getSiteTypes()

void * lm::rdme::IntLattice::getSiteTypes ( )

virtual

◆ nativeSerialize()

void lm::rdme::IntLattice::nativeSerialize	(	void *	destBuffer,
		void *	lattice,
		size_t	latticeSize )

static

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◆ removeAllParticles()

void lm::rdme::IntLattice::removeAllParticles ( )

virtual

Empty all particles from the specified site.

Reimplemented from lm::rdme::Lattice.

Reimplemented in lm::rdme::CudaIntLattice.

◆ removeParticles() [1/2]

void lm::rdme::IntLattice::removeParticles ( lattice_size_t index )

virtual

Remove a particle to the specified site.

Implements lm::rdme::Lattice.

Reimplemented in lm::rdme::CudaIntLattice.

◆ removeParticles() [2/2]

void lm::rdme::IntLattice::removeParticles	(	lattice_size_t	x,
		lattice_size_t	y,
		lattice_size_t	z )

virtual

Remove a particle to the specified site.

Implements lm::rdme::Lattice.

Reimplemented in lm::rdme::CudaIntLattice.

◆ setFromRowMajorByteData()

void lm::rdme::IntLattice::setFromRowMajorByteData	(	void *	buffer,
		size_t	bufferSize )

virtual

Implements lm::rdme::Lattice.

Reimplemented in lm::rdme::CudaIntLattice.

◆ setFromRowMajorData()

void lm::rdme::IntLattice::setFromRowMajorData	(	void *	buffer,
		size_t	bufferSize )

virtual

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◆ setSitesFromRowMajorByteData()

void lm::rdme::IntLattice::setSitesFromRowMajorByteData	(	void *	buffer,
		size_t	bufferSize )

virtual

Implements lm::rdme::Lattice.

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◆ setSiteType() [1/2]

void lm::rdme::IntLattice::setSiteType	(	lattice_size_t	index,
		site_t	site )

virtual

Set the site type at the specified location.

Implements lm::rdme::Lattice.

Reimplemented in lm::rdme::CudaIntLattice.

◆ setSiteType() [2/2]

void lm::rdme::IntLattice::setSiteType	(	lattice_size_t	x,
		lattice_size_t	y,
		lattice_size_t	z,
		site_t	site )

virtual

Set the site type at the specified location.

Implements lm::rdme::Lattice.

Reimplemented in lm::rdme::CudaIntLattice.

◆ MGPUIntMpdRdmeSolver

friend class MGPUIntMpdRdmeSolver

friend

◆ MGPUMpdRdmeSolver

friend class MGPUMpdRdmeSolver

friend

◆ MPIMpdRdmeSolver

friend class MPIMpdRdmeSolver

friend

Member Data Documentation

◆ particles

uint32_t* lm::rdme::IntLattice::particles

protected

◆ siteTypes

uint8_t* lm::rdme::IntLattice::siteTypes

protected

◆ wordsPerSite

uint lm::rdme::IntLattice::wordsPerSite

protected

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

/data2/LM_zls_github/Lattice-Microbes/src/rdme/IntLattice.h
/data2/LM_zls_github/Lattice-Microbes/src/rdme/IntLattice.cpp

Public Member Functions

Static Public Member Functions

Protected Member Functions

Protected Attributes

Friends

Detailed Description

Constructor & Destructor Documentation

◆ IntLattice() [1/2]

◆ IntLattice() [2/2]

◆ ~IntLattice()

Member Function Documentation

◆ addParticle() [1/2]

◆ addParticle() [2/2]

◆ allocateMemory()

◆ copyNativeToRowMajor()

◆ copyRowMajorToNative()

◆ copySitesRowMajorByteToNative()

◆ deallocateMemory()

◆ findParticles()

◆ getLatticeMemorySize()

◆ getMaxOccupancy()

◆ getMaxParticle()

◆ getMaxSiteType()

◆ getNeighboringSites()

◆ getOccupancy() [1/2]

◆ getOccupancy() [2/2]

◆ getParticle() [1/2]

◆ getParticle() [2/2]

◆ getParticleCounts()

◆ getParticleLatticeView()

◆ getParticlesMemory()

◆ getSiteLatticeView()

◆ getSitesMemory()

◆ getSiteType() [1/2]

◆ getSiteType() [2/2]

◆ getSiteTypes()

◆ nativeSerialize()

◆ removeAllParticles()

◆ removeParticles() [1/2]

◆ removeParticles() [2/2]

◆ setFromRowMajorByteData()

◆ setFromRowMajorData()

◆ setSitesFromRowMajorByteData()

◆ setSiteType() [1/2]

◆ setSiteType() [2/2]

Friends And Related Symbol Documentation

◆ MGPUIntMpdRdmeSolver

◆ MGPUMpdRdmeSolver

◆ MPIMpdRdmeSolver

Member Data Documentation

◆ particles

◆ siteTypes

◆ wordsPerSite