jLM.RDME.File Class Reference

Inheritance diagram for jLM.RDME.File:

Collaboration diagram for jLM.RDME.File:

Public Member Functions
	__init__ (self, fname, replicate=1, latticeType=None, sample_frame=False, max_frames=100)
	vmd_precomp (self, file_name)
	close_hdf_file (self)
	init_worker (self, file_name)
	process_frame (self, frame_index, siteTypesLattice, numberSpecies, numberSiteTypes)
	write_to_h5 (self, file_name, maxParticleCounts, maxSiteCounts)
	reduce_trajectory_file (self, file_name, max_frames)
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
	h5 = h5py.File(fname, "r")
	speciesList = BT.SimObjs(self, T.TrajSpecies, idbase = 1)
	regionList = BT.SimObjs(self, T.TrajRegion)
	reactionList = BT.SimObjs(self, T.Reaction)
	rxnRateList = BT.SimObjs(self, T.RateConst)
	sp = self.speciesList.getAutoNamespace()
	reg = self.regionList.getAutoNamespace()
	rc = self.rxnRateList.getAutoNamespace()
	dc = self.diffRateList.getAutoNamespace()
	counts = dict()
	close_hdf_file
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

Additional Inherited Members
Protected Attributes inherited from jLM.RDME.SpatialModel
int	_perfPrintInterval = 60
list	_particlePlacement = []
list	_particleDistCount = []
list	_particleDistConc = []
list	_transitionRates = []
list	_reactionLocations = []

Detailed Description

Load a previously defined simulation

Constructor & Destructor Documentation

__init__()

jLM.RDME.File.__init__	(		self,
			fname,
			replicate = 1,
			latticeType = None,
			sample_frame = False,
			max_frames = 100 )

Load a RDME simulation file

Args:
    fname (str):
        LM data filename
    replicate (int):
        Replicate to load initially
    latticeType (str):
        "Byte" / "Int"
    sample_frame (bool):
        Sample frames or not
    max_frames (int):
        Number of frames after sampling

Note:
    jLM includes some metadata in the Lattice Microbes HDF5 file which 
    is necessary to reload the model.

Member Function Documentation

close_hdf_file()

jLM.RDME.File.close_hdf_file

(

self

)

init_worker()

jLM.RDME.File.init_worker	(		self,
			file_name )

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process_frame()

jLM.RDME.File.process_frame	(		self,
			frame_index,
			siteTypesLattice,
			numberSpecies,
			numberSiteTypes )

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reduce_trajectory_file()

jLM.RDME.File.reduce_trajectory_file	(		self,
			file_name,
			max_frames )

vmd_precomp()

jLM.RDME.File.vmd_precomp	(		self,
			file_name )

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write_to_h5()

jLM.RDME.File.write_to_h5	(		self,
			file_name,
			maxParticleCounts,
			maxSiteCounts )

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Member Data Documentation

close_hdf_file

jLM.RDME.File.close_hdf_file

counts

jLM.RDME.File.counts = dict()

dc

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

h5

jLM.RDME.File.h5 = h5py.File(fname, "r")

rc

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

reactionList

jLM.RDME.File.reactionList = BT.SimObjs(self, T.Reaction)

reg

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

regionList

jLM.RDME.File.regionList = BT.SimObjs(self, T.TrajRegion)

rxnRateList

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

sp

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

speciesList

jLM.RDME.File.speciesList = BT.SimObjs(self, T.TrajSpecies, idbase = 1)

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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