jLM.RDMEExtended.SpatialModelExtended Class Reference

Inheritance diagram for jLM.RDMEExtended.SpatialModelExtended:

Collaboration diagram for jLM.RDMEExtended.SpatialModelExtended:

Public Member Functions
	__init__ (self, name, filename, dimensions, latticeSpacing, latticeType=None, enable_size_checking=True)
Public Member Functions inherited from jLM.ParticleSizeSupport.ParticleSizeMixin
	__init__ (self, *args, **kwargs)
ParticleSizeValidator	size_validator (self)
	enable_particle_sizes (self, bool enable=True)
	set_particle_size (self, species, int size)
int	get_particle_size (self, species)
dict	get_all_particle_sizes (self)
	distribute_concentration_safe (self, species, region, float concentration)
	distribute_number_safe (self, species, region, int count)
Dict	get_capacity_summary (self)
	validate_all_species (self)
	print_capacity_summary (self)
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)

Additional Inherited Members
Public Attributes inherited from jLM.ParticleSizeSupport.ParticleSizeMixin
	lattice
	siteLattice = self.lattice.getSiteLatticeView()
	particleLattice = self.lattice.getParticleLatticeView()
	speciesList
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 Member Functions inherited from jLM.ParticleSizeSupport.ParticleSizeMixin
	_upgrade_to_extended_lattice (self)
	_copy_lattice_data (self, source, dest)
Protected Attributes inherited from jLM.ParticleSizeSupport.ParticleSizeMixin
	_size_validator = None
dict	_particle_sizes = {}
Protected Attributes inherited from jLM.RDME.SpatialModel
int	_perfPrintInterval = 60
list	_particlePlacement = []
list	_particleDistCount = []
list	_particleDistConc = []
list	_transitionRates = []
list	_reactionLocations = []

Detailed Description

Extended SpatialModel with particle size support.

Constructor & Destructor Documentation

__init__()

jLM.RDMEExtended.SpatialModelExtended.__init__	(		self,
			name,
			filename,
			dimensions,
			latticeSpacing,
			latticeType = None,
			enable_size_checking = True )

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

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