jLM.RDMEExtended.FileExtended Class Reference

Inheritance diagram for jLM.RDMEExtended.FileExtended:

Collaboration diagram for jLM.RDMEExtended.FileExtended:

Public Member Functions
	__init__ (self, fname, replicate=1, latticeType=None, sample_frame=False, max_frames=100, enable_size_checking=False)
	load_particle_sizes_from_metadata (self)
	analyze_trajectory_occupancy (self, frame_indices=None)
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.File
	__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
	replicate = replicate
Public Attributes inherited from jLM.ParticleSizeSupport.ParticleSizeMixin
	lattice
	siteLattice = self.lattice.getSiteLatticeView()
	particleLattice = self.lattice.getParticleLatticeView()
	speciesList
Public Attributes inherited from jLM.RDME.File
	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 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 File class with particle size analysis support.

Constructor & Destructor Documentation

__init__()

jLM.RDMEExtended.FileExtended.__init__	(		self,
			fname,
			replicate = 1,
			latticeType = None,
			sample_frame = False,
			max_frames = 100,
			enable_size_checking = False )

Load RDME simulation file with particle size support.

Args:
    fname (str): LM data filename
    replicate (int): Replicate to load
    latticeType (str): "Byte" / "Int"
    sample_frame (bool): Sample frames
    max_frames (int): Number of frames after sampling
    enable_size_checking (bool): Enable size checking for analysis

Note:
    Size checking is typically disabled for analysis since the
    file may contain data from simulations with different constraints.

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Member Function Documentation

analyze_trajectory_occupancy()

jLM.RDMEExtended.FileExtended.analyze_trajectory_occupancy	(		self,
			frame_indices = None )

Analyze occupancy distribution across trajectory frames.

Args:
    frame_indices: List of frame indices to analyze (None for all)

Returns:
    Dictionary with time-resolved occupancy statistics

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load_particle_sizes_from_metadata()

jLM.RDMEExtended.FileExtended.load_particle_sizes_from_metadata

(

self

)

Load particle sizes from HDF5 metadata if available.

Returns:
    Dictionary of particle sizes or empty dict if not found

Member Data Documentation

replicate

jLM.RDMEExtended.FileExtended.replicate = 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/RDMEExtended.py