jLM.RDMEExtended.SimExtended Class Reference

Inheritance diagram for jLM.RDMEExtended.SimExtended:

Collaboration diagram for jLM.RDMEExtended.SimExtended:

Public Member Functions
	__init__ (self, *, name, filename, dimensions, latticeSpacing, regionName, latticeType=None, dt=None, enable_size_checking=True)
	species (self, name, particle_size=1, **kwargs)
	set_verbosity (self, verbosity)
	distributeConcentration (self, sp, reg, conc)
	distributeNumber (self, sp, reg, count)
	construct (self)
	run (self, solver=None, replicate=1, seed=None, cudaDevices=None, checkpointInterval=0, sample_frame=False, max_frames=100)
	get_site_analysis (self, x, y, z)
	analyze_occupancy_distribution (self)
	print_occupancy_stats (self)
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.Sim
	particleStatistics (self, particleLattice=None, siteLattice=None)
	__init__ (self, name, filename, dimensions, latticeSpacing, regionName, latticeType=None, dt=None)
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)
	transitionRate (self, sp, rFrom, rTo, rate, value=None)
	assignReaction (self, reaction, region)
	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)

Public Attributes
bool	particle_sizes_passed = False
	verbosity = verbosity
Public Attributes inherited from jLM.ParticleSizeSupport.ParticleSizeMixin
	lattice
	siteLattice = self.lattice.getSiteLatticeView()
	particleLattice = self.lattice.getParticleLatticeView()
	speciesList
Public Attributes inherited from jLM.RDME.Sim
	speciesList = BT.SimObjs(self, T.BuilderSpecies, idbase=1)
	regionList = BT.SimObjs(self, T.BuilderRegion)
	reactionList = BT.SimObjs(self, T.BuilderReaction)
	rxnRateList = BT.SimObjs(self, T.RateConst)
	sp = self.speciesList.getAutoNamespace()
	reg = self.regionList.getAutoNamespace()
	rc = self.rxnRateList.getAutoNamespace()
	dc = self.diffRateList.getAutoNamespace()
int	bytesPerParticle = 4
	timestep = dt
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
	_configure_solver_particle_sizes (self, solver)
Protected Member Functions inherited from jLM.ParticleSizeSupport.ParticleSizeMixin
	_upgrade_to_extended_lattice (self)
	_copy_lattice_data (self, source, dest)

Additional Inherited Members
Protected Attributes inherited from jLM.ParticleSizeSupport.ParticleSizeMixin
	_size_validator = None
dict	_particle_sizes = {}
Protected Attributes inherited from jLM.RDME.Sim
bool	_particlesPlaced = False
Protected Attributes inherited from jLM.RDME.SpatialModel
int	_perfPrintInterval = 60
list	_particlePlacement = []
list	_particleDistCount = []
list	_particleDistConc = []
list	_transitionRates = []
list	_reactionLocations = []

Detailed Description

Extended Sim class with particle size support.

Constructor & Destructor Documentation

__init__()

jLM.RDMEExtended.SimExtended.__init__	(		self,
		*	,
			name,
			filename,
			dimensions,
			latticeSpacing,
			regionName,
			latticeType = None,
			dt = None,
			enable_size_checking = True )

Create new RDME simulation with particle size support.

Args:
    name (str): Simulation name
    filename (str): LM data filename
    dimensions (tuple): Lattice dimensions (nx, ny, nz)
    latticeSpacing (float): Lattice spacing in meters
    regionName (str): Name of the default region
    latticeType (str): "Byte" / "Int" (default: "Byte")
    dt (float): Timestep
    enable_size_checking (bool): Enable particle size validation

Example:
    >>> sim = jLM.RDMEExtended.SimExtended(
    ...     "test", "test.lm", (50, 50, 50), 1e-6, "cytoplasm",
    ...     enable_size_checking=True
    ... )
    >>> # Set particle sizes
    >>> sim.set_particle_size("SmallProtein", 1)
    >>> sim.set_particle_size("LargeComplex", 4)
    >>> # Distribute with validation
    >>> sim.distribute_concentration_safe("SmallProtein", "cytoplasm", 1e-6)

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Member Function Documentation

_configure_solver_particle_sizes()

jLM.RDMEExtended.SimExtended._configure_solver_particle_sizes ( self, solver )

protected

Helper method to configure solver with particle sizes.

Args:
    solver: The solver instance to configure

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analyze_occupancy_distribution()

jLM.RDMEExtended.SimExtended.analyze_occupancy_distribution

(

self

)

Analyze the distribution of site occupancies.

Returns:
    Dictionary with occupancy statistics

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construct()

jLM.RDMEExtended.SimExtended.construct

(

self

)

Construct the simulation with particle size validation.

Raises:
    ParticleSizeError: If any species violates size constraints

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distributeConcentration()

jLM.RDMEExtended.SimExtended.distributeConcentration	(		self,
			sp,
			reg,
			conc )

Override to add size validation by default.

For unsafe distribution (bypassing validation), use:
super().distributeConcentration(sp, reg, conc)

Reimplemented from jLM.RDME.SpatialModel.

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distributeNumber()

jLM.RDMEExtended.SimExtended.distributeNumber	(		self,
			sp,
			reg,
			count )

Override to add size validation by default.

For unsafe distribution (bypassing validation), use:
super().distributeNumber(sp, reg, count)

Reimplemented from jLM.RDME.SpatialModel.

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get_site_analysis()

jLM.RDMEExtended.SimExtended.get_site_analysis	(		self,
			x,
			y,
			z )

Get detailed analysis of a specific site.

Args:
    x, y, z: Site coordinates

Returns:
    Dictionary with site information including size data

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print_occupancy_stats()

jLM.RDMEExtended.SimExtended.print_occupancy_stats

(

self

)

Print occupancy distribution statistics.

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run()

jLM.RDMEExtended.SimExtended.run	(		self,
			solver = None,
			replicate = 1,
			seed = None,
			cudaDevices = None,
			checkpointInterval = 0,
			sample_frame = False,
			max_frames = 100 )

Run the RDME simulation with particle size support.

This override configures the solver with particle sizes before running.

Args:
    solver: RDME solver (auto-configures if IntMpdRdmeSolverExtended)
    replicate (int): Index of replicate
    seed (int): RNG seed
    cudaDevices ([int]): List of CUDA device indexes
    checkpointInterval (int): Number of seconds between checkpoints
    sample_frame (bool): Sample frames or not
    max_frames (int): Number of frames after sampling

Reimplemented from jLM.RDME.SpatialModel.

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set_verbosity()

jLM.RDMEExtended.SimExtended.set_verbosity	(		self,
			verbosity )

Set the verbosity level.

species()

jLM.RDMEExtended.SimExtended.species	(		self,
			name,
			particle_size = 1,
		**	kwargs )

Create/lookup species with optional particle size.

Args:
    name (str): Species name
    particle_size (int): Size of particles (default: 1)
    **kwargs: Additional arguments

Returns:
    Species object with size configured

Reimplemented from jLM.RDME.SpatialModel.

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Member Data Documentation

particle_sizes_passed

bool jLM.RDMEExtended.SimExtended.particle_sizes_passed = False

verbosity

jLM.RDMEExtended.SimExtended.verbosity = verbosity

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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