jLM.LmInteract.LmWriteMixin Class Reference

Public Member Functions
	h5 (self)
	finalize (self)
	copyParticleLattice (self, fname, diffusion_model=False, replicate=1, frame=-1)

Public Attributes
	filename
	Nrxn = len(self.reactionList)
	Nsps = len(self.speciesList)
	Nsts = len(self.regionList)
	lattice
	speciesWriteInterval
	latticeWriteInterval
	perfPrintInterval
	hookInterval
	simulationTime
	timestep
	bytesPerParticle
	regionList
	particleLattice
	siteLattice
	reactionList
	latticeSpacing
	pps
	diffRateList
	rxnRateList

Protected Member Functions
	_placeAllParticles (self)
	_buildReactionMatricies (self)
	_reactionModel (self)
	_buildReactionLocationMatrix (self)
	_buildDiffusionMatrix (self)
	_diffusionModel (self)
	_spatialModel (self)
	_storeParamData (self)

Protected Attributes
bool	_particlesPlaced = True
	_spCts = spCts
list	_particlePlacement = []
list	_particleDistCount = []
list	_particleDistConc = []
	_rxnParamMatrix = rxnParamMatrix
	_reactionLocations
	_transitionRates
	_diffParamMatrix = diffParamMatrix

Member Function Documentation

_buildDiffusionMatrix()

jLM.LmInteract.LmWriteMixin._buildDiffusionMatrix ( self )

protected

_buildReactionLocationMatrix()

jLM.LmInteract.LmWriteMixin._buildReactionLocationMatrix ( self )

protected

_buildReactionMatricies()

jLM.LmInteract.LmWriteMixin._buildReactionMatricies ( self )

protected

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_diffusionModel()

jLM.LmInteract.LmWriteMixin._diffusionModel ( self )

protected

_placeAllParticles()

jLM.LmInteract.LmWriteMixin._placeAllParticles ( self )

protected

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_reactionModel()

jLM.LmInteract.LmWriteMixin._reactionModel ( self )

protected

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_spatialModel()

jLM.LmInteract.LmWriteMixin._spatialModel ( self )

protected

_storeParamData()

jLM.LmInteract.LmWriteMixin._storeParamData ( self )

protected

copyParticleLattice()

jLM.LmInteract.LmWriteMixin.copyParticleLattice	(		self,
			fname,
			diffusion_model = False,
			replicate = 1,
			frame = -1 )

Copy particle lattice from existing simulation

Args:
    fname (str):
        LM simulation H5 file

Keyword Args:
    diffusion_model (bool):
        Use the initial condition particle lattice
    replicate (int):
        LM simulation replicate
    frame (int):
        LM simulation particle lattice frame. Negative values
        index from end.

finalize()

jLM.LmInteract.LmWriteMixin.finalize

(

self

)

h5()

jLM.LmInteract.LmWriteMixin.h5

(

self

)

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Member Data Documentation

_diffParamMatrix

jLM.LmInteract.LmWriteMixin._diffParamMatrix = diffParamMatrix

protected

_particleDistConc

list jLM.LmInteract.LmWriteMixin._particleDistConc = []

protected

_particleDistCount

list jLM.LmInteract.LmWriteMixin._particleDistCount = []

protected

_particlePlacement

list jLM.LmInteract.LmWriteMixin._particlePlacement = []

protected

_particlesPlaced

bool jLM.LmInteract.LmWriteMixin._particlesPlaced = True

protected

_reactionLocations

jLM.LmInteract.LmWriteMixin._reactionLocations

protected

_rxnParamMatrix

jLM.LmInteract.LmWriteMixin._rxnParamMatrix = rxnParamMatrix

protected

_spCts

jLM.LmInteract.LmWriteMixin._spCts = spCts

protected

_transitionRates

jLM.LmInteract.LmWriteMixin._transitionRates

protected

bytesPerParticle

jLM.LmInteract.LmWriteMixin.bytesPerParticle

diffRateList

jLM.LmInteract.LmWriteMixin.diffRateList

filename

jLM.LmInteract.LmWriteMixin.filename

hookInterval

jLM.LmInteract.LmWriteMixin.hookInterval

lattice

jLM.LmInteract.LmWriteMixin.lattice

latticeSpacing

jLM.LmInteract.LmWriteMixin.latticeSpacing

latticeWriteInterval

jLM.LmInteract.LmWriteMixin.latticeWriteInterval

Nrxn

jLM.LmInteract.LmWriteMixin.Nrxn = len(self.reactionList)

Nsps

jLM.LmInteract.LmWriteMixin.Nsps = len(self.speciesList)

Nsts

jLM.LmInteract.LmWriteMixin.Nsts = len(self.regionList)

particleLattice

jLM.LmInteract.LmWriteMixin.particleLattice

perfPrintInterval

jLM.LmInteract.LmWriteMixin.perfPrintInterval

pps

jLM.LmInteract.LmWriteMixin.pps

reactionList

jLM.LmInteract.LmWriteMixin.reactionList

regionList

jLM.LmInteract.LmWriteMixin.regionList

rxnRateList

jLM.LmInteract.LmWriteMixin.rxnRateList

simulationTime

jLM.LmInteract.LmWriteMixin.simulationTime

siteLattice

jLM.LmInteract.LmWriteMixin.siteLattice

speciesWriteInterval

jLM.LmInteract.LmWriteMixin.speciesWriteInterval

timestep

jLM.LmInteract.LmWriteMixin.timestep

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

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