Base class for lattice type objects. More...

#include <Lattice.h>

Inheritance diagram for Lattice:

Collaboration diagram for Lattice:

Public Member Functions
virtual site_t	getMaxSiteType () const=0
	Get the maximum number of site types possible in the lattice.
virtual particle_t	getMaxParticle () const=0
	Get the maximum number of particle types possible in the lattice.
virtual site_size_t	getMaxOccupancy () const=0
	Get the maximum number of particles that can live in a site.
	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.
virtual void	getNeighboringSites (lattice_size_t index, lattice_size_t *neighboringIndices)=0
	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=0
	Get the site type at the specified location.
virtual site_t	getSiteType (lattice_size_t index) const=0
	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 site)=0
	Set the site type at the specified location.
virtual void	setSiteType (lattice_size_t index, site_t site)=0
	Set the site type at the specified location.
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 site_size_t	getOccupancy (lattice_size_t x, lattice_size_t y, lattice_size_t z) const=0
	Get the number of particles in the specified lattice site.
virtual site_size_t	getOccupancy (lattice_size_t index) const=0
	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=0
	Get the particle at the specified site with at the specified number in the particle list.
virtual particle_t	getParticle (lattice_size_t index, site_size_t particleIndex) const=0
	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)=0
	Add a particle to the specified site.
virtual void	addParticle (lattice_size_t index, particle_t particle)=0
	Add a particle to the specified site.
virtual void	removeParticles (lattice_size_t x, lattice_size_t y, lattice_size_t z)=0
	Remove a particle to the specified site.
virtual void	removeParticles (lattice_size_t index)=0
	Remove a particle to the specified site.
virtual void	removeAllParticles ()
	Empty all particles from the specified site.
virtual std::map< particle_t, uint >	getParticleCounts ()=0
	Get the number of each particle type in the lattice.
virtual std::vector< particle_loc_t >	findParticles (particle_t minParticleType, particle_t maxParticleType)=0
	Get the number of the specified particles types in the lattice.
virtual void	print () const
	Print the lattice to the console.
virtual void	setFromRowMajorByteData (void *buffer, size_t bufferSize)=0
virtual void	setSitesFromRowMajorByteData (void *buffer, size_t bufferSize)=0
virtual size_t	getLatticeMemorySize () const=0

Static Public Member Functions
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 Attributes
lattice_coord_t	size
lattice_size_t	numberSites
si_dist_t	spacing

Detailed Description

Base class for lattice type objects.

Constructor & Destructor Documentation

◆ Lattice() [1/2]

lm::rdme::Lattice::Lattice	(	lattice_coord_t	size,
		si_dist_t	spacing )

Create a Lattice object.

Parameters

size	Size of the lattice as (x,y,z)
spacing	Physical spacing between lattice sites

◆ Lattice() [2/2]

lm::rdme::Lattice::Lattice	(	lattice_size_t	xSize,
		lattice_size_t	ySize,
		lattice_size_t	zSize,
		si_dist_t	spacing )

Create a Lattice object.

Parameters

xSize	Number of sites in x
ySize	Number of sites in y
zSize	Number of sites in z
spacing	Physical spacing between lattice sites

◆ ~Lattice()

lm::rdme::Lattice::~Lattice ( )

virtual

Destroy the Lattice object.

Member Function Documentation

◆ addParticle() [1/2]

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

pure virtual

Add a particle to the specified site.

◆ addParticle() [2/2]

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

pure virtual

Add a particle to the specified site.

◆ findParticles()

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

pure virtual

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

◆ getLatticeMemorySize()

virtual size_t lm::rdme::Lattice::getLatticeMemorySize ( ) const

pure virtual

◆ getMaxOccupancy()

virtual site_size_t lm::rdme::Lattice::getMaxOccupancy ( ) const

pure virtual

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

◆ getMaxParticle()

virtual particle_t lm::rdme::Lattice::getMaxParticle ( ) const

pure virtual

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

◆ getMaxSiteType()

virtual site_t lm::rdme::Lattice::getMaxSiteType ( ) const

pure virtual

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

◆ getNearbySites()

std::vector< lattice_coord_t > lm::rdme::Lattice::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.

Parameters

xc	X location of the center site
yc	Y location of the center site
zc	Z location of the center site
minDistance	Minimum distance for halo of sites
maxDistance	Maximum distance for halo of sites

◆ getNeighboringSites()

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

pure 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

◆ getNumberSites()

lattice_size_t lm::rdme::Lattice::getNumberSites ( ) const

virtual

Get total number of sites in the Lattice.

◆ getOccupancy() [1/2]

virtual site_size_t lm::rdme::Lattice::getOccupancy ( lattice_size_t index ) const

pure virtual

Get the number of particles in the specified lattice site.

◆ getOccupancy() [2/2]

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

pure virtual

Get the number of particles in the specified lattice site.

◆ getParticle() [1/2]

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

pure virtual

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

◆ getParticle() [2/2]

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

pure virtual

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

◆ getParticleCounts()

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

pure virtual

Get the number of each particle type in the lattice.

Particle searching methods.

◆ getSiteType() [1/2]

virtual site_t lm::rdme::Lattice::getSiteType ( lattice_size_t index ) const

pure virtual

Get the site type at the specified location.

◆ getSiteType() [2/2]

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

pure virtual

Get the site type at the specified location.

◆ getSize()

lattice_coord_t lm::rdme::Lattice::getSize ( ) const

virtual

Get size of the Lattice.

◆ getSpacing()

si_dist_t lm::rdme::Lattice::getSpacing ( ) const

virtual

Get spacing between lattice sites.

◆ getXSize()

lattice_size_t lm::rdme::Lattice::getXSize ( ) const

virtual

Get x dimension of the Lattice.

◆ getYSize()

lattice_size_t lm::rdme::Lattice::getYSize ( ) const

virtual

Get y dimension of the Lattice.

◆ getZSize()

lattice_size_t lm::rdme::Lattice::getZSize ( ) const

virtual

Get z dimension of the Lattice.

◆ print()

void lm::rdme::Lattice::print ( ) const

virtual

Print the lattice to the console.

◆ removeAllParticles()

void lm::rdme::Lattice::removeAllParticles ( )

virtual

Empty all particles from the specified site.

◆ removeParticles() [1/2]

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

pure virtual

Remove a particle to the specified site.

◆ removeParticles() [2/2]

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

pure virtual

Remove a particle to the specified site.

◆ rowMajorByteSerialize()

void lm::rdme::Lattice::rowMajorByteSerialize	(	void *	destBuffer,
		void *	lattice,
		size_t	bufferSize )

static

◆ rowMajorByteSerializeSites()

void lm::rdme::Lattice::rowMajorByteSerializeSites	(	void *	destBuffer,
		void *	lattice,
		size_t	bufferSize )

static

◆ rowMajorIntSerialize()

void lm::rdme::Lattice::rowMajorIntSerialize	(	void *	destBuffer,
		void *	lattice,
		size_t	bufferSize )

static

◆ setFromRowMajorByteData()

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

pure virtual

◆ setSitesFromRowMajorByteData()

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

pure virtual

◆ setSiteType() [1/2]

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

pure virtual

Set the site type at the specified location.

◆ setSiteType() [2/2]

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

pure virtual

Set the site type at the specified location.

Member Data Documentation

◆ numberSites

lattice_size_t lm::rdme::Lattice::numberSites

protected

◆ size

lattice_coord_t lm::rdme::Lattice::size

protected

◆ spacing

si_dist_t lm::rdme::Lattice::spacing

protected

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

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

Public Member Functions

Static Public Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

◆ Lattice() [1/2]

◆ Lattice() [2/2]

◆ ~Lattice()

Member Function Documentation

◆ addParticle() [1/2]

◆ addParticle() [2/2]

◆ findParticles()

◆ getLatticeMemorySize()

◆ getMaxOccupancy()

◆ getMaxParticle()

◆ getMaxSiteType()

◆ getNearbySites()

◆ getNeighboringSites()

◆ getNumberSites()

◆ getOccupancy() [1/2]

◆ getOccupancy() [2/2]

◆ getParticle() [1/2]

◆ getParticle() [2/2]

◆ getParticleCounts()

◆ getSiteType() [1/2]

◆ getSiteType() [2/2]

◆ getSize()

◆ getSpacing()

◆ getXSize()

◆ getYSize()

◆ getZSize()

◆ print()

◆ removeAllParticles()

◆ removeParticles() [1/2]

◆ removeParticles() [2/2]

◆ rowMajorByteSerialize()

◆ rowMajorByteSerializeSites()

◆ rowMajorIntSerialize()

◆ setFromRowMajorByteData()

◆ setSitesFromRowMajorByteData()

◆ setSiteType() [1/2]

◆ setSiteType() [2/2]

Member Data Documentation

◆ numberSites

◆ size

◆ spacing