pyLM.RDME.IntRDMESimulation Class Reference

Inheritance diagram for pyLM.RDME.IntRDMESimulation:

Collaboration diagram for pyLM.RDME.IntRDMESimulation:

Public Member Functions
	__init__ (self, dimensions, spacing, name="unnamed", defaultRegion="default")
	allocateLattice (self)
Public Member Functions inherited from pyLM.RDME.RDMESimulation
	__init__ (self, dimensions, spacing, name="unnamed", defaultRegion="default")
	addRegion (self, region)
	addCuboidRegion (self, name, a, b)
	addShape (self, shape)
	modifyRegion (self, region)
	defineSpecies (self, species)
	siteVolume (self)
	buildCapsidCell (self, length, diameter, membraneThickness, points=False)
	buildSphericalCell (self, diameter, membraneThickness, point=False)
	addParticles (self, species='unknown', region='default', count=1)
	packRegion (self, region, radius, percentage, obstacleID)
	setTransitionRate (self, species, via, to, rate)
	setTwoWayTransitionRate (self, species, one, two, rate)
	buildDiffusionModel (self)
	buildReactionModel (self)
	buildSpatialModel (self)
	setWriteInterval (self, time)
	setLatticeWriteInterval (self, time)
	setSimulationTime (self, time)
	setTimestep (self, time)
	setHookInterval (self, time)
	setRandomSeed (self, seed)
	setOverflowHandler (self, mode)
	getLattice (self, force=False)
	setLatticeSite (self, index, siteType)
	getLatticeSite (self, index)
	addParticleAt (self, index, particleType)
	addParticleAtIdx (self, index, particleType)
	Create an HDF5 version of the simulation amenable for later running or stand-alone running.
	save (self, filename)
	run (self, filename, method, replicates=1, seed=None, cudaDevices=None, checkpointInterval=0)
	runMPI (self, filename, method, replicates=1, driver="mpirun", ppe=1, seed=None)
	runSolver (self, filename, solver, replicates=1, cudaDevices=None, checkpointInterval=0)
	buildVector (self, arg1, arg2, arg3)
	buildPoint (self, arg1, arg2, arg3)
	buildSphere (self, arg1, arg2, arg3)
	buildEllipse (self, arg1, arg2, arg3, arg4, arg5, arg6, arg7)
	buildDifference (self, arg1, arg2, arg3)

Additional Inherited Members
Public Attributes inherited from pyLM.RDME.RDMESimulation
dict	siteTypes = {}
dict	particleMap = {}
list	customAddedParticleList = []
list	species_id = []
dict	regions = {}
list	transitionRates = []
dict	initial_counts = {}
dict	parameters = {}
	continousDimensions = dimensions
	latticeSpacing = spacing
int	bytesPerParticle = 1
	lm_builder = lm.LatticeBuilder(dimensions[0], dimensions[1], dimensions[2], spacing, 1, 0)
bool	hasBeenDiscretized = False
	name = name
list	replicates = []
str	filename = ""
	lattice = self.allocateLattice()
Protected Member Functions inherited from pyLM.RDME.RDMESimulation
	_repr_html_ (self)

Constructor & Destructor Documentation

__init__()

pyLM.RDME.IntRDMESimulation.__init__	(		self,
			dimensions,
			spacing,
			name = "unnamed",
			defaultRegion = "default" )

Member Function Documentation

allocateLattice()

pyLM.RDME.IntRDMESimulation.allocateLattice

(

self

)

Reimplemented from pyLM.RDME.RDMESimulation.

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

• /data2/LM_zls_github/Lattice-Microbes/src/pylm/pyLM/RDME.py