Extended ByteLattice with particle size awareness. More...

#include <ByteLatticeExtended.h>

Inheritance diagram for lm::rdme::ByteLatticeExtended:

Collaboration diagram for lm::rdme::ByteLatticeExtended:

Public Member Functions
	ByteLatticeExtended (lattice_coord_t size, si_dist_t spacing, uint particlesPerSite, bool enableSizeChecking=true)
	Constructor with particle size support.
	ByteLatticeExtended (lattice_size_t xSize, lattice_size_t ySize, lattice_size_t zSize, si_dist_t spacing, uint particlesPerSite, bool enableSizeChecking=true)
	Constructor with particle size support.
virtual	~ByteLatticeExtended ()=default
	Destructor.
void	setParticleSize (particle_t particleType, uint32_t size)
	Set the size for a particle type.
uint32_t	getParticleSize (particle_t particleType) const
	Get the size for a particle type.
uint32_t	getSizeBasedOccupancy (lattice_size_t x, lattice_size_t y, lattice_size_t z) const
	Get current occupancy considering particle sizes.
uint32_t	getSizeBasedOccupancy (lattice_size_t subvolume) const
	Get current occupancy considering particle sizes.
bool	canAddParticle (lattice_size_t x, lattice_size_t y, lattice_size_t z, particle_t particle) const
	Check if particle can be added without exceeding capacity.
bool	canAddParticle (lattice_size_t subvolume, particle_t particle) const
	Check if particle can be added without exceeding capacity.
virtual void	addParticleWithSizeCheck (lattice_size_t x, lattice_size_t y, lattice_size_t z, particle_t particle)
	Add particle with size validation.
virtual void	addParticleWithSizeCheck (lattice_size_t subvolume, particle_t particle)
	Add particle with size validation.
uint32_t	getMaxParticleCount (lattice_size_t x, lattice_size_t y, lattice_size_t z, particle_t particleType) const
	Get maximum number of particles of a type that can fit.
uint32_t	getMaxParticleCount (lattice_size_t subvolume, particle_t particleType) const
	Get maximum number of particles of a type that can fit.
void	setSizeCheckingEnabled (bool enable)
	Enable or disable size checking.
bool	isSizeCheckingEnabled () const
	Check if size checking is enabled.
const ParticleSizeManager &	getParticleSizeManager () const
	Get the particle size manager.
void	validateSizeConstraints () const
	Validate entire lattice for size constraints.
std::map< uint32_t, uint32_t >	getSizeBasedOccupancyStats () const
	Get occupancy statistics considering particle sizes.
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.
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 subvolume, site_t site)
	Set 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 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	setSitesFromRowMajorByteData (void *buffer, size_t bufferSize)
virtual void	getParticleLatticeView (uint8_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.

Protected Member Functions
site_size_t	getParticlesAtSite (lattice_size_t subvolume, particle_t *particles, site_size_t maxCount) const
	Get particles at a site for size calculation.
Protected Member Functions inherited from lm::rdme::ByteLattice
virtual void	allocateMemory ()
virtual void	deallocateMemory ()
virtual uint32_t *	getParticlesMemory ()
virtual uint8_t *	getSitesMemory ()

Protected Attributes
std::unique_ptr< ParticleSizeManager >	sizeManager_
	Particle size manager.
bool	sizeCheckingEnabled_
	Enable size validation.
uint32_t	maxSiteCapacity_
	Maximum site capacity.
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)

Detailed Description

Extended ByteLattice with particle size awareness.

This class extends the standard ByteLattice to support particles with different sizes, providing capacity validation and overflow prevention.

Constructor & Destructor Documentation

◆ ByteLatticeExtended() [1/2]

lm::rdme::ByteLatticeExtended::ByteLatticeExtended	(	lattice_coord_t	size,
		si_dist_t	spacing,
		uint	particlesPerSite,
		bool	enableSizeChecking = true )

Constructor with particle size support.

Parameters

size	Lattice dimensions
spacing	Lattice spacing
particlesPerSite	Maximum particles per site
enableSizeChecking	Enable particle size validation (default: true)

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◆ ByteLatticeExtended() [2/2]

lm::rdme::ByteLatticeExtended::ByteLatticeExtended	(	lattice_size_t	xSize,
		lattice_size_t	ySize,
		lattice_size_t	zSize,
		si_dist_t	spacing,
		uint	particlesPerSite,
		bool	enableSizeChecking = true )

Constructor with particle size support.

Parameters

xSize	X dimension
ySize	Y dimension
zSize	Z dimension
spacing	Lattice spacing
particlesPerSite	Maximum particles per site
enableSizeChecking	Enable particle size validation (default: true)

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◆ ~ByteLatticeExtended()

virtual lm::rdme::ByteLatticeExtended::~ByteLatticeExtended ( )

virtualdefault

Destructor.

Member Function Documentation

◆ addParticleWithSizeCheck() [1/2]

void lm::rdme::ByteLatticeExtended::addParticleWithSizeCheck	(	lattice_size_t	subvolume,
		particle_t	particle )

virtual

Add particle with size validation.

Parameters

subvolume	Subvolume index
particle	Particle type to add

Exceptions

ParticleSizeException if adding would exceed capacity

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◆ addParticleWithSizeCheck() [2/2]

void lm::rdme::ByteLatticeExtended::addParticleWithSizeCheck	(	lattice_size_t	x,
		lattice_size_t	y,
		lattice_size_t	z,
		particle_t	particle )

virtual

Add particle with size validation.

Parameters

x	X coordinate
y	Y coordinate
z	Z coordinate
particle	Particle type to add

Exceptions

ParticleSizeException if adding would exceed capacity

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◆ canAddParticle() [1/2]

bool lm::rdme::ByteLatticeExtended::canAddParticle	(	lattice_size_t	subvolume,
		particle_t	particle ) const

Check if particle can be added without exceeding capacity.

Parameters

subvolume	Subvolume index
particle	Particle type to add

Returns: True if particle can be added

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◆ canAddParticle() [2/2]

bool lm::rdme::ByteLatticeExtended::canAddParticle	(	lattice_size_t	x,
		lattice_size_t	y,
		lattice_size_t	z,
		particle_t	particle ) const

Check if particle can be added without exceeding capacity.

Parameters

x	X coordinate
y	Y coordinate
z	Z coordinate
particle	Particle type to add

Returns: True if particle can be added

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◆ getMaxParticleCount() [1/2]

uint32_t lm::rdme::ByteLatticeExtended::getMaxParticleCount	(	lattice_size_t	subvolume,
		particle_t	particleType ) const

Get maximum number of particles of a type that can fit.

Parameters

subvolume	Subvolume index
particleType	Particle type

Returns: Maximum number of particles that can fit

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◆ getMaxParticleCount() [2/2]

uint32_t lm::rdme::ByteLatticeExtended::getMaxParticleCount	(	lattice_size_t	x,
		lattice_size_t	y,
		lattice_size_t	z,
		particle_t	particleType ) const

Get maximum number of particles of a type that can fit.

Parameters

x	X coordinate
y	Y coordinate
z	Z coordinate
particleType	Particle type

Returns: Maximum number of particles that can fit

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◆ getParticlesAtSite()

site_size_t lm::rdme::ByteLatticeExtended::getParticlesAtSite	(	lattice_size_t	subvolume,
		particle_t *	particles,
		site_size_t	maxCount ) const

protected

Get particles at a site for size calculation.

Parameters

subvolume	Subvolume index
particles	Output array for particles
maxCount	Maximum particles to retrieve

Returns: Number of particles retrieved

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◆ getParticleSize()

uint32_t lm::rdme::ByteLatticeExtended::getParticleSize ( particle_t particleType ) const

Get the size for a particle type.

Parameters

particleType Particle type ID

Returns: Size of the particle (default: 1)

◆ getParticleSizeManager()

const ParticleSizeManager & lm::rdme::ByteLatticeExtended::getParticleSizeManager ( ) const

Get the particle size manager.

Returns: Reference to the particle size manager

◆ getSizeBasedOccupancy() [1/2]

uint32_t lm::rdme::ByteLatticeExtended::getSizeBasedOccupancy ( lattice_size_t subvolume ) const

Get current occupancy considering particle sizes.

Parameters

subvolume Subvolume index

Returns: Total size of particles at the site

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◆ getSizeBasedOccupancy() [2/2]

uint32_t lm::rdme::ByteLatticeExtended::getSizeBasedOccupancy	(	lattice_size_t	x,
		lattice_size_t	y,
		lattice_size_t	z ) const

Get current occupancy considering particle sizes.

Parameters

x	X coordinate
y	Y coordinate
z	Z coordinate

Returns: Total size of particles at the site

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◆ getSizeBasedOccupancyStats()

std::map< uint32_t, uint32_t > lm::rdme::ByteLatticeExtended::getSizeBasedOccupancyStats ( ) const

Get occupancy statistics considering particle sizes.

Returns: Map of site occupancy -> count of sites

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◆ isSizeCheckingEnabled()

bool lm::rdme::ByteLatticeExtended::isSizeCheckingEnabled ( ) const

Check if size checking is enabled.

Returns: True if size checking is enabled

◆ setParticleSize()

void lm::rdme::ByteLatticeExtended::setParticleSize	(	particle_t	particleType,
		uint32_t	size )

Set the size for a particle type.

Parameters

particleType	Particle type ID
size	Size of the particle (must be > 0)

◆ setSizeCheckingEnabled()

void lm::rdme::ByteLatticeExtended::setSizeCheckingEnabled ( bool enable )

Enable or disable size checking.

Parameters

enable True to enable size checking

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◆ validateSizeConstraints()

void lm::rdme::ByteLatticeExtended::validateSizeConstraints ( ) const

Validate entire lattice for size constraints.

Exceptions

ParticleSizeException if any site violates size constraints

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Member Data Documentation

◆ maxSiteCapacity_

uint32_t lm::rdme::ByteLatticeExtended::maxSiteCapacity_

protected

Maximum site capacity.

◆ sizeCheckingEnabled_

bool lm::rdme::ByteLatticeExtended::sizeCheckingEnabled_

protected

Enable size validation.

◆ sizeManager_

std::unique_ptr<ParticleSizeManager> lm::rdme::ByteLatticeExtended::sizeManager_

protected

Particle size manager.

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

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

Public Member Functions

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ ByteLatticeExtended() [1/2]

◆ ByteLatticeExtended() [2/2]

◆ ~ByteLatticeExtended()

Member Function Documentation

◆ addParticleWithSizeCheck() [1/2]

◆ addParticleWithSizeCheck() [2/2]

◆ canAddParticle() [1/2]

◆ canAddParticle() [2/2]

◆ getMaxParticleCount() [1/2]

◆ getMaxParticleCount() [2/2]

◆ getParticlesAtSite()

◆ getParticleSize()

◆ getParticleSizeManager()

◆ getSizeBasedOccupancy() [1/2]

◆ getSizeBasedOccupancy() [2/2]

◆ getSizeBasedOccupancyStats()

◆ isSizeCheckingEnabled()

◆ setParticleSize()

◆ setSizeCheckingEnabled()

◆ validateSizeConstraints()

Member Data Documentation

◆ maxSiteCapacity_

◆ sizeCheckingEnabled_

◆ sizeManager_