jLM.LmInteract.LmReadMixin Class Reference

Public Member Functions
	setReplicate (self, replicate=1)

Public Attributes
list	replicates
	replicate = replicate
	trajData = self.h5['Simulations'][replicate]
	particleLattice
	speciesCountTimes = self.trajData['SpeciesCountTimes'][...]
	speciesCounts = dict()
	speciesList
	latticeTimes = self.trajData['LatticeTimes'][...]
	Nsps = len(speciesNames)
	Nsts = len(regionNames)
	timestep = float(self.h5['Parameters'].attrs['timestep'])
	latticeWriteInterval = float(self.h5['Parameters'].attrs['latticeWriteInterval'])
	speciesWriteInterval = float(self.h5['Parameters'].attrs['writeInterval'])
float	hookInterval = 0.0
	simulationTime = float(self.h5['Parameters'].attrs['maxTime'])
	bytesPerParticle = int(self.h5['Model/Diffusion'].attrs['bytes_per_particle'])
	pps = int(self.h5['Model/Diffusion'].attrs['particlesPerSite'])
	Nrxn = int(self.h5['Model/Diffusion'].attrs['numberReactions'])
	NdiffParams = len(self.diffRateList)
	regionList
int	NrxnParams = len(self.rxnRateList)

Protected Member Functions
	_loadFromH5 (self, replicate)
	_readReplicates (self)
	_initLattice (self)
	_loadReplicate (self)
	_initSpecies (self)
	_initRegions (self)
	_initParameters (self)
	_initDiffParams (self)
	_readDiffusionTable (self)
	_initRateParams (self)
	_readReactions (self)

Member Function Documentation

_initDiffParams()

jLM.LmInteract.LmReadMixin._initDiffParams ( self )

protected

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_initLattice()

jLM.LmInteract.LmReadMixin._initLattice ( self )

protected

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_initParameters()

jLM.LmInteract.LmReadMixin._initParameters ( self )

protected

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_initRateParams()

jLM.LmInteract.LmReadMixin._initRateParams ( self )

protected

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_initRegions()

jLM.LmInteract.LmReadMixin._initRegions ( self )

protected

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_initSpecies()

jLM.LmInteract.LmReadMixin._initSpecies ( self )

protected

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_loadFromH5()

jLM.LmInteract.LmReadMixin._loadFromH5 ( self, replicate )

protected

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_loadReplicate()

jLM.LmInteract.LmReadMixin._loadReplicate ( self )

protected

_readDiffusionTable()

jLM.LmInteract.LmReadMixin._readDiffusionTable ( self )

protected

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_readReactions()

jLM.LmInteract.LmReadMixin._readReactions ( self )

protected

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_readReplicates()

jLM.LmInteract.LmReadMixin._readReplicates ( self )

protected

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setReplicate()

jLM.LmInteract.LmReadMixin.setReplicate	(		self,
			replicate = 1 )

Select replicate from HDF5 file

Args:
    replicate (int):
        Replicate index (1-based)

Member Data Documentation

bytesPerParticle

jLM.LmInteract.LmReadMixin.bytesPerParticle = int(self.h5['Model/Diffusion'].attrs['bytes_per_particle'])

hookInterval

float jLM.LmInteract.LmReadMixin.hookInterval = 0.0

latticeTimes

jLM.LmInteract.LmReadMixin.latticeTimes = self.trajData['LatticeTimes'][...]

latticeWriteInterval

jLM.LmInteract.LmReadMixin.latticeWriteInterval = float(self.h5['Parameters'].attrs['latticeWriteInterval'])

NdiffParams

jLM.LmInteract.LmReadMixin.NdiffParams = len(self.diffRateList)

Nrxn

jLM.LmInteract.LmReadMixin.Nrxn = int(self.h5['Model/Diffusion'].attrs['numberReactions'])

NrxnParams

int jLM.LmInteract.LmReadMixin.NrxnParams = len(self.rxnRateList)

Nsps

jLM.LmInteract.LmReadMixin.Nsps = len(speciesNames)

Nsts

jLM.LmInteract.LmReadMixin.Nsts = len(regionNames)

particleLattice

jLM.LmInteract.LmReadMixin.particleLattice

pps

jLM.LmInteract.LmReadMixin.pps = int(self.h5['Model/Diffusion'].attrs['particlesPerSite'])

regionList

jLM.LmInteract.LmReadMixin.regionList

replicate

jLM.LmInteract.LmReadMixin.replicate = replicate

replicates

list jLM.LmInteract.LmReadMixin.replicates

simulationTime

jLM.LmInteract.LmReadMixin.simulationTime = float(self.h5['Parameters'].attrs['maxTime'])

speciesCounts

jLM.LmInteract.LmReadMixin.speciesCounts = dict()

speciesCountTimes

jLM.LmInteract.LmReadMixin.speciesCountTimes = self.trajData['SpeciesCountTimes'][...]

speciesList

jLM.LmInteract.LmReadMixin.speciesList

speciesWriteInterval

jLM.LmInteract.LmReadMixin.speciesWriteInterval = float(self.h5['Parameters'].attrs['writeInterval'])

timestep

jLM.LmInteract.LmReadMixin.timestep = float(self.h5['Parameters'].attrs['timestep'])

trajData

jLM.LmInteract.LmReadMixin.trajData = self.h5['Simulations'][replicate]

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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