#include <CudaByteLattice.h>

Inheritance diagram for lm::rdme::CudaByteLattice:

Collaboration diagram for lm::rdme::CudaByteLattice:

Public Member Functions
	CudaByteLattice (lattice_coord_t size, si_dist_t spacing, uint particlesPerSite)
	CudaByteLattice (lattice_size_t xSize, lattice_size_t ySize, lattice_size_t zSize, si_dist_t spacing, uint particlesPerSite)
virtual	~CudaByteLattice ()
virtual void	copyToGPU ()
virtual void	copyFromGPU ()
virtual void *	getGPUMemorySrc ()
virtual void *	getGPUMemoryDest ()
virtual void	swapSrcDest ()
virtual void *	getGPUMemorySiteTypes ()
virtual size_t	getParticleMemorySize () const
virtual void	setSiteType (lattice_size_t x, lattice_size_t y, lattice_size_t z, site_t site)
	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	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 index, 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 index)
	Remove a particle to the specified site.
virtual void	removeAllParticles ()
	Empty all particles from the specified site.
virtual void	setFromRowMajorByteData (void *buffer, size_t bufferSize)
virtual void	getSiteLatticeView (uint8_t *siteLattice, int Nz, int Ny, int Nx)
virtual void	getParticleLatticeView (uint8_t *particleLattice, int Nw, int Nz, int Ny, int Nx, int Np)
Public Member Functions inherited from lm::rdme::ByteLattice
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.
	ByteLattice (lattice_coord_t size, si_dist_t spacing, uint particlesPerSite)
	ByteLattice (lattice_size_t xSize, lattice_size_t ySize, lattice_size_t zSize, si_dist_t spacing, uint particlesPerSite)
virtual	~ByteLattice ()
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 subvolume) const
	Get the site type at the specified location.
void	copySites (void *destBuffer, size_t latticeSize)
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 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	setSitesFromRowMajorByteData (void *buffer, size_t bufferSize)
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.

Protected Member Functions
virtual void	allocateCudaMemory ()
virtual void	deallocateCudaMemory ()
Protected Member Functions inherited from lm::rdme::ByteLattice
virtual void	allocateMemory ()
virtual void	deallocateMemory ()
virtual uint32_t *	getParticlesMemory ()
virtual uint8_t *	getSitesMemory ()

Protected Attributes
uint	cudaParticlesCurrent
size_t	cudaParticlesSize
void *	cudaParticles [2]
size_t	cudaSiteTypesSize
void *	cudaSiteTypes
bool	isGPUMemorySynched
Protected Attributes inherited from lm::rdme::ByteLattice
size_t	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

Additional Inherited Members
Static Public Member Functions inherited from lm::rdme::ByteLattice
static void	nativeSerialize (void destBuffer, void lattice, size_t latticeSize)
static void	nativeSerializeSites (void destBuffer, void lattice, size_t latticeSize)
static void	copyNativeToRowMajorByte (void destBuffer, void sourceBuffer, lattice_size_t xSize, lattice_size_t ySize, lattice_size_t zSize, uint particlesPerSite, size_t bufferSize)
static void	copyRowMajorByteToNative (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 void	copySitesNativeToRowMajorByte (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)

Constructor & Destructor Documentation

◆ CudaByteLattice() [1/2]

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

◆ CudaByteLattice() [2/2]

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

◆ ~CudaByteLattice()

virtual lm::rdme::CudaByteLattice::~CudaByteLattice ( )

virtual

Member Function Documentation

◆ addParticle() [1/2]

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

virtual

Add a particle to the specified site.

Reimplemented from lm::rdme::ByteLattice.

Reimplemented in CudaByteLatticeExtended, and lm::rdme::CudaByteLatticeExtended.

◆ addParticle() [2/2]

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

virtual

Add a particle to the specified site.

Reimplemented from lm::rdme::ByteLattice.

Reimplemented in CudaByteLatticeExtended, and lm::rdme::CudaByteLatticeExtended.

◆ allocateCudaMemory()

virtual void lm::rdme::CudaByteLattice::allocateCudaMemory ( )

protectedvirtual

Reimplemented in CudaByteLatticeExtended, and lm::rdme::CudaByteLatticeExtended.

◆ copyFromGPU()

virtual void lm::rdme::CudaByteLattice::copyFromGPU ( )

virtual

Reimplemented in CudaByteLatticeExtended, and lm::rdme::CudaByteLatticeExtended.

◆ copyToGPU()

virtual void lm::rdme::CudaByteLattice::copyToGPU ( )

virtual

Reimplemented in CudaByteLatticeExtended, and lm::rdme::CudaByteLatticeExtended.

◆ deallocateCudaMemory()

virtual void lm::rdme::CudaByteLattice::deallocateCudaMemory ( )

protectedvirtual

Reimplemented in CudaByteLatticeExtended, and lm::rdme::CudaByteLatticeExtended.

◆ getGPUMemoryDest()

virtual void * lm::rdme::CudaByteLattice::getGPUMemoryDest ( )

virtual

◆ getGPUMemorySiteTypes()

virtual void * lm::rdme::CudaByteLattice::getGPUMemorySiteTypes ( )

virtual

◆ getGPUMemorySrc()

virtual void * lm::rdme::CudaByteLattice::getGPUMemorySrc ( )

virtual

◆ getParticleLatticeView()

virtual void lm::rdme::CudaByteLattice::getParticleLatticeView	(	uint8_t **	particleLattice,
		int *	Nw,
		int *	Nz,
		int *	Ny,
		int *	Nx,
		int *	Np )

virtual

Reimplemented from lm::rdme::ByteLattice.

◆ getParticleMemorySize()

virtual size_t lm::rdme::CudaByteLattice::getParticleMemorySize ( ) const

inlinevirtual

◆ getSiteLatticeView()

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

virtual

Reimplemented from lm::rdme::ByteLattice.

◆ removeAllParticles()

virtual void lm::rdme::CudaByteLattice::removeAllParticles ( )

virtual

Empty all particles from the specified site.

Reimplemented from lm::rdme::ByteLattice.

Reimplemented in CudaByteLatticeExtended, and lm::rdme::CudaByteLatticeExtended.

◆ removeParticles() [1/2]

virtual void lm::rdme::CudaByteLattice::removeParticles ( lattice_size_t index )

virtual

Remove a particle to the specified site.

Reimplemented from lm::rdme::ByteLattice.

Reimplemented in CudaByteLatticeExtended, and lm::rdme::CudaByteLatticeExtended.

◆ removeParticles() [2/2]

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

virtual

Remove a particle to the specified site.

Reimplemented from lm::rdme::ByteLattice.

Reimplemented in CudaByteLatticeExtended, and lm::rdme::CudaByteLatticeExtended.

◆ setFromRowMajorByteData()

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

virtual

Reimplemented from lm::rdme::ByteLattice.

◆ setSiteType() [1/2]

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

virtual

Set the site type at the specified location.

Reimplemented from lm::rdme::ByteLattice.

◆ setSiteType() [2/2]

virtual void lm::rdme::CudaByteLattice::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.

Reimplemented from lm::rdme::ByteLattice.

◆ swapSrcDest()

virtual void lm::rdme::CudaByteLattice::swapSrcDest ( )

virtual

Member Data Documentation

◆ cudaParticles

void* lm::rdme::CudaByteLattice::cudaParticles[2]

protected

◆ cudaParticlesCurrent

uint lm::rdme::CudaByteLattice::cudaParticlesCurrent

protected

◆ cudaParticlesSize

size_t lm::rdme::CudaByteLattice::cudaParticlesSize

protected

◆ cudaSiteTypes

void* lm::rdme::CudaByteLattice::cudaSiteTypes

protected

◆ cudaSiteTypesSize

size_t lm::rdme::CudaByteLattice::cudaSiteTypesSize

protected

◆ isGPUMemorySynched

bool lm::rdme::CudaByteLattice::isGPUMemorySynched

protected

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

/data2/LM_zls_github/Lattice-Microbes/src/rdme/CudaByteLattice.h

Public Member Functions

Protected Member Functions

Protected Attributes

Additional Inherited Members

Constructor & Destructor Documentation

◆ CudaByteLattice() [1/2]

◆ CudaByteLattice() [2/2]

◆ ~CudaByteLattice()

Member Function Documentation

◆ addParticle() [1/2]

◆ addParticle() [2/2]

◆ allocateCudaMemory()

◆ copyFromGPU()

◆ copyToGPU()

◆ deallocateCudaMemory()

◆ getGPUMemoryDest()

◆ getGPUMemorySiteTypes()

◆ getGPUMemorySrc()

◆ getParticleLatticeView()

◆ getParticleMemorySize()

◆ getSiteLatticeView()

◆ removeAllParticles()

◆ removeParticles() [1/2]

◆ removeParticles() [2/2]

◆ setFromRowMajorByteData()

◆ setSiteType() [1/2]

◆ setSiteType() [2/2]

◆ swapSrcDest()

Member Data Documentation

◆ cudaParticles

◆ cudaParticlesCurrent

◆ cudaParticlesSize

◆ cudaSiteTypes

◆ cudaSiteTypesSize

◆ isGPUMemorySynched