jLM.RDME.Sim Class Reference

Inheritance diagram for jLM.RDME.Sim:

Collaboration diagram for jLM.RDME.Sim:

Public Member Functions
	particleStatistics (self, particleLattice=None, siteLattice=None)
	__init__ (self, name, filename, dimensions, latticeSpacing, regionName, latticeType=None, dt=None)
Public Member Functions inherited from jLM.RDME.SpatialModel
	simulationTime (self)
	simulationTime (self, val)
	speciesWriteInterval (self)
	speciesWriteInterval (self, val)
	latticeWriteInterval (self)
	latticeWriteInterval (self, val)
	perfPrintInterval (self)
	perfPrintInterval (self, val)
	hookInterval (self)
	hookInterval (self, val)
	__init__ (self, name, filename, dimensions, latticeSpacing, latticeType=None)
	resizeLattice (self, dimensions, latticeSpacing, latticeType=None)
	placeNumber (self, sp, x, y, z, n)
	distributeNumber (self, sp, reg, count)
	distributeConcentration (self, sp, reg, conc)
	transitionRate (self, sp, rFrom, rTo, rate, value=None)
	assignReaction (self, reaction, region)
	species (self, name, **kwargs)
	region (self, name, **kwargs)
	reaction (self, reactants, products, rate, value=None, regions=None, **kwargs)
	rateConst (self, rate, value, order, **kwargs)
	diffusionConst (self, rate, value, **kwargs)
	diffusionZero (self)
	maxDiffusionRate (self, latticeSpacing=None, dt=None)
	diffusionFast (self)
	setMaximumTimestep (self)
	run (self, solver=None, replicate=1, seed=None, cudaDevices=None, checkpointInterval=0, sample_frame=False, max_frames=100)

Public Attributes
	speciesList = BT.SimObjs(self, T.BuilderSpecies, idbase=1)
	regionList = BT.SimObjs(self, T.BuilderRegion)
	reactionList = BT.SimObjs(self, T.BuilderReaction)
	rxnRateList = BT.SimObjs(self, T.RateConst)
	sp = self.speciesList.getAutoNamespace()
	reg = self.regionList.getAutoNamespace()
	rc = self.rxnRateList.getAutoNamespace()
	dc = self.diffRateList.getAutoNamespace()
int	bytesPerParticle = 4
	timestep = dt
Public Attributes inherited from jLM.RDME.SpatialModel
	name = name
	filename = filename
	latticeType = latticeType
float	NA = 6.02214085774e23
int	siteV = 1000 * latticeSpacing**3
int	siteNAV = self.siteV * self.NA
	shape = nz,ny,nx
	latticeSpacing = latticeSpacing
	pps = lm.getCompiledLatticeMaxOccupancy()
	lattice = lm.IntLattice(nz,ny,nx, latticeSpacing, self.pps)
	siteLattice = self.lattice.getSiteLatticeView()
	particleLattice = self.lattice.getParticleLatticeView()
int	maxConcentration = self.pps/self.siteNAV
	diffRateList

Protected Attributes
bool	_particlesPlaced = False
Protected Attributes inherited from jLM.RDME.SpatialModel
int	_perfPrintInterval = 60
list	_particlePlacement = []
list	_particleDistCount = []
list	_particleDistConc = []
list	_transitionRates = []
list	_reactionLocations = []

Detailed Description

Define and run an RDME simulation

Constructor & Destructor Documentation

__init__()

jLM.RDME.Sim.__init__	(		self,
			name,
			filename,
			dimensions,
			latticeSpacing,
			regionName,
			latticeType = None,
			dt = None )

Create new RDME object

Args:
    name (str):
        Name of simulation
    filename (str):
        LM data filename
    dimensions ((nx,ny,nz)):
        Dimensions of lattice
    latticeSpacing (float):
        Lattice spacing in meters
    regionName (str):
        Name of the default region
    latticeType (str):
        "Byte" / "Int"
    dt (float):
        Timestep

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Member Function Documentation

particleStatistics()

jLM.RDME.Sim.particleStatistics	(		self,
			particleLattice = None,
			siteLattice = None )

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Member Data Documentation

_particlesPlaced

bool jLM.RDME.Sim._particlesPlaced = False

protected

bytesPerParticle

int jLM.RDME.Sim.bytesPerParticle = 4

dc

jLM.RDME.Sim.dc = self.diffRateList.getAutoNamespace()

rc

jLM.RDME.Sim.rc = self.rxnRateList.getAutoNamespace()

reactionList

jLM.RDME.Sim.reactionList = BT.SimObjs(self, T.BuilderReaction)

reg

jLM.RDME.Sim.reg = self.regionList.getAutoNamespace()

regionList

jLM.RDME.Sim.regionList = BT.SimObjs(self, T.BuilderRegion)

rxnRateList

jLM.RDME.Sim.rxnRateList = BT.SimObjs(self, T.RateConst)

sp

jLM.RDME.Sim.sp = self.speciesList.getAutoNamespace()

speciesList

jLM.RDME.Sim.speciesList = BT.SimObjs(self, T.BuilderSpecies, idbase=1)

timestep

jLM.RDME.Sim.timestep = dt

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

• /data2/LM_zls_github/Lattice-Microbes/src/jlm/jLM/RDME.py