A class that defines regions of a lattice based on a set of geometries defined by shapes. It also allows packing different types of particles into different regions. More...

#include <LatticeBuilder.h>

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Classes
struct	ParticlePlacement
	A representation of a placement operation that needs to occur (i.e. where to place (siteType), what to place (particleType) and how many (count)) More...

Public Member Functions
	LatticeBuilder (si_dist_t xLen, si_dist_t yLen, si_dist_t zLen, si_dist_t collisionGridSpacing, uint32_t seedTop, uint32_t seedBottom=0)
	Create a Lattice Builder.
virtual	~LatticeBuilder ()
virtual void	addRegion (Shape *shape)
	Add a region to the lattice.
virtual bool	placeObject (Shape *shape)
	Add an shape to the lattice.
virtual void	removeObject (Shape *s)
	Remove the shape from the lattice.
virtual bool	placeSphere (point center, si_dist_t radius, site_t type)
	Place a sphere in the lattice (for obstacles)
virtual void	removeSphere (point center, si_dist_t radius, site_t type)
	Remove a sphere in the lattice (for obstacles)
virtual uint	placeRandomSphere (si_dist_t radius, site_t type, site_t region)
	Place a sphere randomly in the lattice (for obstacles)
virtual void	placeRandomSpheres (uint count, si_dist_t radius, site_t type, site_t region)
	Place many spheres randomly in the lattice (for obstacles)
virtual void	fillWithRandomSpheres (double volumeFraction, si_dist_t radius, site_t type, site_t region)
	Fill a region with random spheres to a specified volume fraction.
virtual void	getSpatialModel (lm::io::SpatialModel *spatialModel)
	Gets a spatial model of the lattice for interface with python. NOTE: this operation clears the object passed in from python.
virtual void	addParticles (particle_t particleType, site_t siteType, uint count)
	Add particles of a given type.
virtual void	discretizeTo (lm::rdme::Lattice *lattice, site_t obstacleSiteType, double fractionObstacleSitesOccupied)
	Discretizes the regions to a square lattice.

Protected Member Functions
virtual void	discretizeObstaclesTo (lm::rdme::Lattice *lattice, site_t obstacleSiteType, double fractionObstacleSitesOccupied)
	Discretizes the obstacles to a square lattice.

Protected Attributes
si_dist_t	xLen
si_dist_t	yLen
si_dist_t	zLen
std::vector< site_t >	definedRegions
std::map< site_t, std::vector< Shape * > >	regionShapes
std::map< site_t, bounding_box >	regionBounds
std::vector< Shape * >	objects
std::vector< ParticlePlacement >	particles
Shape ***	collisionGrid
uint *	collisionGridSize
uint *	collisionGridOccupancy
si_dist_t	collisionGridSpacing
double	recipCollisionGridSpacing
uint	collisionGridXSize
uint	collisionGridYSize
uint	collisionGridZSize
RandomGenerator *	rng

Detailed Description

A class that defines regions of a lattice based on a set of geometries defined by shapes. It also allows packing different types of particles into different regions.

Constructor & Destructor Documentation

◆ LatticeBuilder()

lm::builder::LatticeBuilder::LatticeBuilder	(	si_dist_t	xLen,
		si_dist_t	yLen,
		si_dist_t	zLen,
		si_dist_t	collisionGridSpacing,
		uint32_t	seedTop,
		uint32_t	seedBottom = 0 )

Create a Lattice Builder.

Parameters

xLen	Length of the domain along x-axis
yLen	Length of the domain along y-axis
zLen	Length of the domain along z-axis
collisionGridSpacing	The spacing for collision objects
seedTop	High 32 bits of the seed (allows a constant seed for debugging)
seedBottom	Low 32 bits of the seed

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◆ ~LatticeBuilder()

lm::builder::LatticeBuilder::~LatticeBuilder ( )

virtual

Member Function Documentation

◆ addParticles()

void lm::builder::LatticeBuilder::addParticles	(	particle_t	particleType,
		site_t	siteType,
		uint	count )

virtual

Add particles of a given type.

Parameters

particleType	The type of particles to randomly place in the lattice
siteType	Type of lattice site into which to place
count	Number of particles to place

◆ addRegion()

void lm::builder::LatticeBuilder::addRegion ( Shape * shape )

virtual

Add a region to the lattice.

Parameters

shape A Shape object to add as a region

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◆ discretizeObstaclesTo()

void lm::builder::LatticeBuilder::discretizeObstaclesTo	(	lm::rdme::Lattice *	lattice,
		site_t	obstacleSiteType,
		double	fractionObstacleSitesOccupied )

protectedvirtual

Discretizes the obstacles to a square lattice.

Parameters

lattice	Lattice object into which to place
obstacleSiteType	An identifier for obstacle sites in the lattice
fractionObstacleSitesOccupied	Percentage of obstacle sites to be filled

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◆ discretizeTo()

void lm::builder::LatticeBuilder::discretizeTo	(	lm::rdme::Lattice *	lattice,
		site_t	obstacleSiteType,
		double	fractionObstacleSitesOccupied )

virtual

Discretizes the regions to a square lattice.

Parameters

lattice	Lattice object into which to place
obstacleSiteType	An identifier for obstacle sites in the lattice
fractionObstacleSitesOccupied	Percentage of obstacle sites to be filled

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◆ fillWithRandomSpheres()

void lm::builder::LatticeBuilder::fillWithRandomSpheres	(	double	volumeFraction,
		si_dist_t	radius,
		site_t	type,
		site_t	region )

virtual

Fill a region with random spheres to a specified volume fraction.

Parameters

volumeFraction	Total fraction of volume that should be filled with spheres
radius	Radius of spheres
type	The type of site to fill (i.e. the type of site to exclude other objects from)
region	The region of the lattice to place spheres into

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◆ getSpatialModel()

void lm::builder::LatticeBuilder::getSpatialModel ( lm::io::SpatialModel * spatialModel )

virtual

Gets a spatial model of the lattice for interface with python. NOTE: this operation clears the object passed in from python.

Parameters

spatialModel An object of a spatial model for interaction in python or HDF5. The model will be filled with the current lattice

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◆ placeObject()

bool lm::builder::LatticeBuilder::placeObject ( Shape * shape )

virtual

Add an shape to the lattice.

Parameters

shape A Shape object to add as a region

Returns: true if the object to place does not intersect another object

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◆ placeRandomSphere()

uint lm::builder::LatticeBuilder::placeRandomSphere	(	si_dist_t	radius,
		site_t	type,
		site_t	region )

virtual

Place a sphere randomly in the lattice (for obstacles)

Parameters

radius	Radius of the sphere obstacle
type	The type of site in which to place sphere
region	The region in which to place obstacle randomly

Returns: number of times a placement operation occured

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◆ placeRandomSpheres()

void lm::builder::LatticeBuilder::placeRandomSpheres	(	uint	count,
		si_dist_t	radius,
		site_t	type,
		site_t	region )

virtual

Place many spheres randomly in the lattice (for obstacles)

Parameters

radius	Radius of the sphere obstacle
type	The type of site in which to place sphere
region	The region in which to place obstacle randomly

Returns: number of times a placement operation occured

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◆ placeSphere()

bool lm::builder::LatticeBuilder::placeSphere	(	point	center,
		si_dist_t	radius,
		site_t	type )

virtual

Place a sphere in the lattice (for obstacles)

Parameters

center	The center point of sphere obstacle
radius	Radius of the sphere obstacle
type	The type of site in which to place sphere

Returns: true if the sphere did not intersect

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◆ removeObject()

void lm::builder::LatticeBuilder::removeObject ( Shape * s )

virtual

Remove the shape from the lattice.

s Shape to remove

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◆ removeSphere()

void lm::builder::LatticeBuilder::removeSphere	(	point	center,
		si_dist_t	radius,
		site_t	type )

virtual

Remove a sphere in the lattice (for obstacles)

Parameters

center	The center point of sphere obstacle
radius	Radius of the sphere obstacle
type	The type of site in which to place sphere

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Member Data Documentation

◆ collisionGrid

Shape*** lm::builder::LatticeBuilder::collisionGrid

protected

◆ collisionGridOccupancy

uint* lm::builder::LatticeBuilder::collisionGridOccupancy

protected

◆ collisionGridSize

uint* lm::builder::LatticeBuilder::collisionGridSize

protected

◆ collisionGridSpacing

si_dist_t lm::builder::LatticeBuilder::collisionGridSpacing

protected

◆ collisionGridXSize

uint lm::builder::LatticeBuilder::collisionGridXSize

protected

◆ collisionGridYSize

uint lm::builder::LatticeBuilder::collisionGridYSize

protected

◆ collisionGridZSize

uint lm::builder::LatticeBuilder::collisionGridZSize

protected

◆ definedRegions

std::vector<site_t> lm::builder::LatticeBuilder::definedRegions

protected

◆ objects

std::vector<Shape *> lm::builder::LatticeBuilder::objects

protected

◆ particles

std::vector<ParticlePlacement> lm::builder::LatticeBuilder::particles

protected

◆ recipCollisionGridSpacing

double lm::builder::LatticeBuilder::recipCollisionGridSpacing

protected

◆ regionBounds

std::map<site_t,bounding_box> lm::builder::LatticeBuilder::regionBounds

protected

◆ regionShapes

std::map<site_t,std::vector<Shape *> > lm::builder::LatticeBuilder::regionShapes

protected

◆ rng

RandomGenerator* lm::builder::LatticeBuilder::rng

protected

◆ xLen

si_dist_t lm::builder::LatticeBuilder::xLen

protected

◆ yLen

si_dist_t lm::builder::LatticeBuilder::yLen

protected

◆ zLen

si_dist_t lm::builder::LatticeBuilder::zLen

protected

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

/data2/LM_zls_github/Lattice-Microbes/src/builder/LatticeBuilder.h
/data2/LM_zls_github/Lattice-Microbes/src/builder/LatticeBuilder.cpp

Classes

Public Member Functions

Protected Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

◆ LatticeBuilder()

◆ ~LatticeBuilder()

Member Function Documentation

◆ addParticles()

◆ addRegion()

◆ discretizeObstaclesTo()

◆ discretizeTo()

◆ fillWithRandomSpheres()

◆ getSpatialModel()

◆ placeObject()

◆ placeRandomSphere()

◆ placeRandomSpheres()

◆ placeSphere()

◆ removeObject()

◆ removeSphere()

Member Data Documentation

◆ collisionGrid

◆ collisionGridOccupancy

◆ collisionGridSize

◆ collisionGridSpacing

◆ collisionGridXSize

◆ collisionGridYSize

◆ collisionGridZSize

◆ definedRegions

◆ objects

◆ particles

◆ recipCollisionGridSpacing

◆ regionBounds

◆ regionShapes

◆ rng

◆ xLen

◆ yLen

◆ zLen