C++ API#

This section provides direct access to the C++ source code documentation using Doxygen and breathe.

Core Functions#

Lattice Classes#

class IntLattice : public lm::rdme::Lattice#

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

Subclassed by lm::rdme::CudaIntLattice

Public 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.

Parameters:

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

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.

Particle searching methods.

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 Static 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)#

class CudaByteLattice : public lm::rdme::ByteLattice#

Public 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()#

inline 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)#

class CudaIntLattice : public lm::rdme::IntLattice #

Public Functions

CudaIntLattice(lattice_coord_t size, si_dist_t spacing, uint particlesPerSite)#

CudaIntLattice(lattice_size_t xSize, lattice_size_t ySize, lattice_size_t zSize, si_dist_t spacing, uint particlesPerSite)#

virtual ~CudaIntLattice()#

virtual void copyToGPU()#

virtual void copyFromGPU()#

virtual void *getGPUMemorySrc()#

virtual void *getGPUMemoryDest()#

virtual void swapSrcDest()#

virtual void *getGPUMemorySiteTypes()#

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)#

Solver Classes#

class MESolver#

An abstract base class for all Master Equation solvers, this is essentially a representation of “the simulation instance”.

Subclassed by lm::cme::CMESolver

Public Functions

MESolver()#: Create the MESolver.

virtual ~MESolver()#

virtual void initialize(unsigned int replicate, map<string, string> *parameters, ResourceAllocator::ComputeResources *resources) = 0#

Initialize the simulation.

Parameters:

replicate – Replicate number out of total replicates
parameters – A map of all the parameters for the simulation
A – list of resources assigned to the simulation

virtual bool needsReactionModel() = 0#: Tells whether the solver needs a reaction model.

virtual bool needsDiffusionModel() = 0#: Tells whether the solver needs a reaction model.

virtual void generateTrajectory() = 0#: Actually run the simulation.

Warning

doxygenclass: Cannot find class “lm::me::CMESolver” in doxygen xml output for project “LatticeMicrobes” from directory: ./xml

Warning

doxygenclass: Cannot find class “lm::me::GillespieDSolver” in doxygen xml output for project “LatticeMicrobes” from directory: ./xml

Warning

doxygenclass: Cannot find class “lm::me::NextReactionSolver” in doxygen xml output for project “LatticeMicrobes” from directory: ./xml

RDME Solver Classes#

class RDMESolver : public lm::cme::CMESolver#

Subclassed by lm::rdme::IntMpdRdmeSolver, lm::rdme::MGPUIntMpdRdmeSolver, lm::rdme::MGPUMpdRdmeSolver, lm::rdme::MPIMpdRdmeSolver, lm::rdme::MpdRdmeSolver, lm::rdme::NextSubvolumeSolver

Public Functions

RDMESolver(RandomGenerator::Distributions neededDists)#

virtual ~RDMESolver()#

virtual void setDiffusionModel(DiffusionModel *dm, const uint8_t *lattice, size_t latticeSize, const uint8_t *latticeSites, size_t latticeSitesSize)#

virtual void buildDiffusionModel(const uint numberSiteTypesA, const double *DFA, const uint *RLA, lattice_size_t latticeXSize, lattice_size_t latticeYSize, lattice_size_t latticeZSize, site_size_t particlesPerSite, const unsigned int bytes_per_particle, si_dist_t latticeSpacing, const uint8_t *latticeData, const uint8_t *latticeSitesData, bool rowMajorData = true)#

class MpdRdmeSolver : public lm::rdme::RDMESolver #

Subclassed by lm::rdme::MpdTestHarness

Public Functions

MpdRdmeSolver()#

virtual ~MpdRdmeSolver()#

virtual void initialize(unsigned int replicate, map<string, string> *parameters, ResourceAllocator::ComputeResources *resources)#

Initialize the simulation.

Parameters:

replicate – Replicate number out of total replicates
parameters – A map of all the parameters for the simulation
A – list of resources assigned to the simulation

inline virtual bool needsReactionModel()#: Tells whether the solver needs a reaction model.

inline virtual bool needsDiffusionModel()#: Tells whether the solver needs a reaction model.

virtual void buildModel(const uint numberSpeciesA, const uint numberReactionsA, const uint *initialSpeciesCountsA, const uint *reactionTypeA, const double *kA, const int *SA, const uint *DA, const uint kCols = 1)#

virtual void buildDiffusionModel(const uint numberSiteTypesA, const double *DFA, const uint *RLA, lattice_size_t latticeXSize, lattice_size_t latticeYSize, lattice_size_t latticeZSize, site_size_t particlesPerSite, const unsigned int bytes_per_particle, si_dist_t latticeSpacing, const uint8_t *latticeData, const uint8_t *latticeSitesData, bool rowMajorData = true)#

virtual void generateTrajectory()#: Actually run the simulation.

virtual void setReactionRate(unsigned int rxid, float rate)#

class IntMpdRdmeSolver : public lm::rdme::RDMESolver #

Public Functions

IntMpdRdmeSolver()#

virtual ~IntMpdRdmeSolver()#

virtual void initialize(unsigned int replicate, map<string, string> *parameters, ResourceAllocator::ComputeResources *resources)#

Initialize the simulation.

Parameters:

replicate – Replicate number out of total replicates
parameters – A map of all the parameters for the simulation
A – list of resources assigned to the simulation

inline virtual bool needsReactionModel()#: Tells whether the solver needs a reaction model.

inline virtual bool needsDiffusionModel()#: Tells whether the solver needs a reaction model.

virtual void buildModel(const uint numberSpeciesA, const uint numberReactionsA, const uint *initialSpeciesCountsA, const uint *reactionTypeA, const double *kA, const int *SA, const uint *DA, const uint kCols = 1)#

virtual void buildDiffusionModel(const uint numberSiteTypesA, const double *DFA, const uint *RLA, lattice_size_t latticeXSize, lattice_size_t latticeYSize, lattice_size_t latticeZSize, site_size_t particlesPerSite, const unsigned int bytes_per_particle, si_dist_t latticeSpacing, const uint8_t *latticeData, const uint8_t *latticeSitesData, bool rowMajorData = true)#

virtual void generateTrajectory()#: Actually run the simulation.

virtual void setReactionRate(unsigned int rxid, float rate)#

class MGPUMpdRdmeSolver : public lm::rdme::RDMESolver #

Public Functions

MGPUMpdRdmeSolver()#

virtual ~MGPUMpdRdmeSolver()#

virtual void initialize(unsigned int replicate, map<string, string> *parameters, ResourceAllocator::ComputeResources *resources)#

Initialize the simulation.

Parameters:

replicate – Replicate number out of total replicates
parameters – A map of all the parameters for the simulation
A – list of resources assigned to the simulation

inline virtual bool needsReactionModel()#: Tells whether the solver needs a reaction model.

inline virtual bool needsDiffusionModel()#: Tells whether the solver needs a reaction model.

virtual void buildModel(const uint numberSpeciesA, const uint numberReactionsA, const uint *initialSpeciesCountsA, const uint *reactionTypeA, const double *kA, const int *SA, const uint *DA, const uint kCols = 1)#

virtual void buildDiffusionModel(const uint numberSiteTypesA, const double *DFA, const uint *RLA, lattice_size_t latticeXSize, lattice_size_t latticeYSize, lattice_size_t latticeZSize, site_size_t particlesPerSite, const unsigned int bytes_per_particle, si_dist_t latticeSpacing, const uint8_t *latticeData, const uint8_t *latticeSitesData, bool rowMajorData = true)#

virtual void generateTrajectory()#: Actually run the simulation.

virtual void setReactionRate(unsigned int rxid, float rate)#

class MGPUIntMpdRdmeSolver : public lm::rdme::RDMESolver #

Public Functions

MGPUIntMpdRdmeSolver()#

virtual ~MGPUIntMpdRdmeSolver()#

virtual void initialize(unsigned int replicate, map<string, string> *parameters, ResourceAllocator::ComputeResources *resources)#

Initialize the simulation.

Parameters:

replicate – Replicate number out of total replicates
parameters – A map of all the parameters for the simulation
A – list of resources assigned to the simulation

inline virtual bool needsReactionModel()#: Tells whether the solver needs a reaction model.

inline virtual bool needsDiffusionModel()#: Tells whether the solver needs a reaction model.

virtual void buildModel(const uint numberSpeciesA, const uint numberReactionsA, const uint *initialSpeciesCountsA, const uint *reactionTypeA, const double *kA, const int *SA, const uint *DA, const uint kCols = 1)#

virtual void buildDiffusionModel(const uint numberSiteTypesA, const double *DFA, const uint *RLA, lattice_size_t latticeXSize, lattice_size_t latticeYSize, lattice_size_t latticeZSize, site_size_t particlesPerSite, const unsigned int bytes_per_particle, si_dist_t latticeSpacing, const uint8_t *latticeData, const uint8_t *latticeSitesData, bool rowMajorData = true)#

virtual void generateTrajectory()#: Actually run the simulation.

virtual void setReactionRate(unsigned int rxid, float rate)#

Shape Classes#

class Shape#

Abstract base class for all the shapes in Lattice Microbes simulation builder.

Subclassed by lm::builder::Capsule, lm::builder::CapsuleShell, lm::builder::Cone, lm::builder::Cuboid, lm::builder::Cylinder, lm::builder::Difference, lm::builder::Ellipse, lm::builder::Hemisphere, lm::builder::Intersection, lm::builder::Mesh, lm::builder::Sphere, lm::builder::Torus, lm::builder::Union, lm::builder::UnionSet

Public Types

enum ShapeType#

Possible shape types that can be used in Lattice Microbes.

Values:

enumerator SPHERE = 1#

enumerator HEMISPHERE = 2#

enumerator CYLINDER = 3#

enumerator CAPSULE = 4#

enumerator CUBOID = 5#

enumerator CAPSULE_SHELL = 6#

enumerator UNION = 7#

enumerator DIFFERENCE = 8#

enumerator INTERSECTION = 9#

enumerator MESH = 10#

enumerator TORUS = 11#

enumerator ELLIPSE = 12#

enumerator CONE = 13#

enumerator UNIONSET = 14#

Public Functions

Shape(ShapeType shapeType, bounding_box boundingBox, site_t type, vector at = vector(0.0, 0.0, 1.0), vector up = vector(0.0, 1.0, 0.0))#

Create a Shape.

Parameters:

shapeType – The type of shape should be of type ShapeType
boundingBox – The extents of the object used for fast collision/contains checking
type – The type of site that the object represents
at – A vector describing what direction the object is pointing “at”; default: (0,0,1)
up – A vector describing what direction is “up” relative to “at”; default: (0,1,0)

virtual ~Shape()#: Destroy the Shape.

virtual bool boundingBoxesIntersect(Shape *query)#

Checks if another shape’s bounding box interstects with this shape’s bounding box.

Parameters:: query – The other shape to test
Returns:: true/false

virtual bool intersects(Shape *query) = 0#

Check if two shapes intersect.

Parameters:: query – The other shape to check
Returns:: true/false

virtual bool contains(point query) = 0#

Determine if the shape contains the specified point.

Parameters:: query – Point to test
Returns:: true/false

virtual bool contains(Shape *query) = 0#

Determine if the shape contains the specified shape.

Parameters:: query – Shape to test
Returns:: true/false

inline virtual bounding_box getBoundingBox()#: Get the bounding box.

inline virtual site_t getType()#: Get the site type associated with the shape.

inline virtual ShapeType getShapeType()#: Get the shape type.

virtual double getVolume() = 0#: Get the total internal volume of the shape.

virtual void discretizeTo(lm::rdme::Lattice *lattice)#

Discretize the object to the specified lattice.

Parameters:: lattice – Lattice in which to discretize the shape

class Sphere : public lm::builder::Shape #

A Shape that represents a Sphere.

Public Functions

Sphere(point center, si_dist_t radius, site_t type)#

Create a Sphere.

Parameters:

center – Point center of the circle of the slice plane through the sphere
radius – Radius of the sphere
type – The type of the sites within the sphere

virtual ~Sphere()#: Destroy the Sphere.

virtual bool intersects(Shape *query)#

Check if two shapes intersect.

Parameters:: query – The other shape to check
Returns:: true/false

virtual bool contains(point query)#

Determine if the shape contains the specified point.

Parameters:: query – Point to test
Returns:: true/false

virtual bool contains(Shape *query)#

Determine if the shape contains the specified shape.

Parameters:: query – Shape to test
Returns:: true/false

virtual void setCenter(point center)#

Set the center of the sphere.

Parameters:: center – Point of the center

inline virtual point getCenter()#: Get the center of the sphere.

inline virtual si_dist_t getRadius()#: Get the radius of the sphere.

virtual double getVolume()#: Get the volume bounded by the sphere.

class Cylinder : public lm::builder::Shape #

A Shape representing a cylinder.

Public Functions

Cylinder(point p1, point p2, si_dist_t radius, site_t type)#

Create a Cylinder.

Parameters:

p1 – Point of first end of cylinder
p2 – Point of second end of cylinder
radius – Radius of the capsule cylinder/hemispheres ends
type – Site type of the capsule

virtual ~Cylinder()#: Destroy the Capsule.

virtual bool intersects(Shape *query)#

Check if two shapes intersect.

Parameters:: query – The other shape to check
Returns:: true/false

virtual bool contains(point query)#

Determine if the shape contains the specified point.

Parameters:: query – Point to test
Returns:: true/false

virtual bool contains(Shape *query)#

Determine if the shape contains the specified shape.

Parameters:: query – Shape to test
Returns:: true/false

inline virtual point getP1()#: Get point of first end of cylinder.

inline virtual point getP2()#: Get point of second end of cylinder.

inline virtual si_dist_t getRadius()#: Get the radius of the cylinder/hemisphere ends.

virtual double getVolume()#: Get the total internal volume of the Capsule.

class Capsule : public lm::builder::Shape #

A Shape representing a cylinder with hemispherical ends.

Public Functions

Capsule(point p1, point p2, si_dist_t radius, site_t type)#

Create a Capsule.

Parameters:

p1 – Point of first end of cylinder
p2 – Point of second end of cylinder
radius – Radius of the capsule cylinder/hemispheres ends
type – Site type of the capsule

virtual ~Capsule()#: Destroy the Capsule.

virtual bool intersects(Shape *query)#

Check if two shapes intersect.

Parameters:: query – The other shape to check
Returns:: true/false

virtual bool contains(point query)#

Determine if the shape contains the specified point.

Parameters:: query – Point to test
Returns:: true/false

virtual bool contains(Shape *query)#

Determine if the shape contains the specified shape.

Parameters:: query – Shape to test
Returns:: true/false

inline virtual point getP1()#: Get point of first end of cylinder.

inline virtual point getP2()#: Get point of second end of cylinder.

inline virtual si_dist_t getRadius()#: Get the radius of the cylinder/hemisphere ends.

virtual double getVolume()#: Get the total internal volume of the Capsule.

class Cuboid : public lm::builder::Shape #

A cube-like Shape.

Public Functions

Cuboid(point p1, point p2, site_t type)#

Create a Cuboid that is axis aligned.

Parameters:

p1 – Point of the lower corner
p2 – Point of the upper corner
type – The type of the sites within the cuboid

Cuboid(point center, si_dist_t w, si_dist_t h, si_dist_t d, site_t type, vector at = vector(1.0, 0.0, 0.0), vector up = vector(0.0, 1.0, 0.0))#

Create a Cuboid based on two orientations, and a width, height, depth.

center The definition of the center of the cuboid

Parameters:

w – Width (along x axis when unrotated)
h – Height (along y axis when unrotated)
d – Depth (along z axis when unrotated)
at – A vector representing where the cuboid is pointing (default along x axis)
at – A vector representing where the cuboid up is (default along y axis)

virtual ~Cuboid()#: Destroy the Cuboid.

virtual bool intersects(Shape *query)#

Check if two shapes intersect.

Parameters:: query – The other shape to check
Returns:: true/false

virtual bool contains(point query)#

Determine if the shape contains the specified point.

Parameters:: query – Point to test
Returns:: true/false

virtual bool contains(Shape *query)#

Determine if the shape contains the specified shape.

Parameters:: query – Shape to test
Returns:: true/false

inline virtual point getP1()#: Get the lower point.

inline virtual point getP2()#: Get the upper point.

virtual double getVolume()#: Get the volume bounded by the cuboid shape.

class Cone : public lm::builder::Shape #

A Shape that represents a Cone.

Public Functions

Cone(point center, si_dist_t radius, si_dist_t height, site_t type, vector normal = vector(1.0, 0.0, 0.0))#

Create a Cone.

Parameters:

center – Point center of the circle of the base
radius – Radius of the base
height – Height of the cone
type – The type of the sites within the cone
normal – Normal to the center of the cone base

virtual ~Cone()#: Destroy the Sphere.

virtual bool intersects(Shape *query)#

Check if two shapes intersect.

Parameters:: query – The other shape to check
Returns:: true/false

virtual bool contains(point query)#

Determine if the shape contains the specified point.

Parameters:: query – Point to test
Returns:: true/false

virtual bool contains(Shape *query)#

Determine if the shape contains the specified shape.

Parameters:: query – Shape to test
Returns:: true/false

inline virtual point getCenter()#: Get the center of the cone.

inline virtual si_dist_t getRadius()#: Get the radius of the cone.

inline virtual si_dist_t getHeight()#: Get the height of the cone.

virtual double getVolume()#: Get the volume bounded by the cone.

class Hemisphere : public lm::builder::Shape #

A hemisphere Shape.

Public Functions

Hemisphere(point center, si_dist_t radius, vector orientation, site_t type)#

Create a Hemisphere.

Parameters:

center – Point center of the circle of the slice plane through the Hemisphere
radius – Radius of the Hemisphere
orientation – Orientation normal to the center point of the center point in the direction of the curved part of the hemisphere
type – The type of the sites within the hemisphere

virtual ~Hemisphere()#: Destroy the Hemisphere.

virtual bool intersects(Shape *query)#

Check if two shapes intersect.

Parameters:: query – The other shape to check
Returns:: true/false

virtual bool contains(point query)#

Determine if the shape contains the specified point.

Parameters:: query – Point to test
Returns:: true/false

virtual bool contains(Shape *query)#

Determine if the shape contains the specified shape.

Parameters:: query – Shape to test
Returns:: true/false

inline virtual point getCenter()#: Get the center of the Hemisphere.

inline virtual si_dist_t getRadius()#: Get the radius of the Hemisphere.

inline virtual vector getOrientation()#: Get the orientation vector of the Hemisphere.

virtual double getVolume()#: Get the volume contained by the Hemisphere.

Builder Classes#

class LatticeBuilder#

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.

Public 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.

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

virtual ~LatticeBuilder()#

virtual void addRegion(Shape *shape)#

Add a region to the lattice.

Parameters:: shape – A Shape object to add as a region

virtual bool placeObject(Shape *shape)#

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

virtual void removeObject(Shape *s)#

Remove the shape from the lattice.

s Shape to remove

virtual bool placeSphere(point center, si_dist_t radius, site_t type)#

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

virtual void removeSphere(point center, si_dist_t radius, site_t type)#

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

virtual uint placeRandomSphere(si_dist_t radius, site_t type, site_t region)#

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

virtual void placeRandomSpheres(uint count, si_dist_t radius, site_t type, site_t region)#

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

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.

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

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.

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

virtual void addParticles(particle_t particleType, site_t siteType, uint count)#

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

virtual void discretizeTo(lm::rdme::Lattice *lattice, site_t obstacleSiteType, double fractionObstacleSitesOccupied)#

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

Warning

doxygenclass: Cannot find class “lm::builder::bounding_box” in doxygen xml output for project “LatticeMicrobes” from directory: ./xml

Warning

doxygenclass: Cannot find class “lm::builder::point” in doxygen xml output for project “LatticeMicrobes” from directory: ./xml

Threading Classes#

class WorkerManager#

A singleton manager that creates and manages workers that run on a processing node.

Public Functions

WorkerManager()#: Create the WorkerManager.

~WorkerManager()#: Destroy the WorkerManager.

void addWorker(Worker *worker)#

Adds a worker to the manager.

Parameters:: worker – Worker to add

void removeWorker(Worker *worker)#

Removes a worker from the manager.

Parameters:: worker – Worker handle for which to remove

void abortWorkers()#: Aborts all the worker threads.

void checkpointWorkers()#: Causes all the worker threads to checkpoint (checkpointing is currently unimplemented)

void stopWorkers()#: Stops all the worker threads (e.g. merges them with the master)

Public Static Functions

static WorkerManager *getInstance()#

Get the global worker manager.

Returns:: globalWorkerManager Global thread manager instance handle

class Worker : public lm::thread::Thread #

An actual worker Thread that runs a simulation replicate.

Subclassed by lm::main::CheckpointSignaler, lm::main::LocalDataOutputWorker, lm::main::ReplicateRunner, lm::main::SignalHandler

Public Functions

Worker()#: Creates thread and attaches it to the manager.

virtual ~Worker()#: Removes thread from manager and deletes thread.

virtual void abort()#: Set the aborted status for a thread and wakes thread.

virtual void checkpoint()#: Checkpoint (currently unimplemented)

class Thread#

A base class wrapping pthreads.

Subclassed by lm::thread::Worker

Public Functions

Thread()#: Creates a pthread locking mechanism and initializes “Thread”.

virtual ~Thread()#: Destory the Thread.

virtual void start()#: If no thread exists, creates a new thread and begins execution.

virtual void stop()#: Joins the thread with the parent waiting if necessary.

virtual void wake() = 0#: Wakes a sleeping thead.

inline virtual pthread_t getId()#

Returns the pthread based id for the Thread.

Returns:: pthread assigned id

virtual void setAffinity(int cpuNumber)#

Binds the thread to a CPU core.

Parameters:: The – cpu core for which to bind the thread

Utility Classes#

Warning

doxygenclass: Cannot find class “Timer” in doxygen xml output for project “LatticeMicrobes” from directory: ./xml

C++ API#

Core Functions#

Lattice Classes#

Solver Classes#

RDME Solver Classes#

Shape Classes#

Builder Classes#

Threading Classes#

Utility Classes#

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