jLM.RDME.SpatialModel Class Reference

Inheritance diagram for jLM.RDME.SpatialModel:

Collaboration diagram for jLM.RDME.SpatialModel:

Public Member Functions
	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
	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 Attributes
int	_perfPrintInterval = 60
list	_particlePlacement = []
list	_particleDistCount = []
list	_particleDistConc = []
list	_transitionRates = []
list	_reactionLocations = []

Detailed Description

Base RDME model 

Constructor & Destructor Documentation

__init__()

jLM.RDME.SpatialModel.__init__	(		self,
			name,
			filename,
			dimensions,
			latticeSpacing,
			latticeType = None )

Member Function Documentation

assignReaction()

jLM.RDME.SpatialModel.assignReaction	(		self,
			reaction,
			region )

Assign a reaction to a region

Args:
    reaction (:py:class:`~jLM.Types.Reaction`):
        Reaction
    region (:py:class:`~jLM.Types.Region`):
        Target region

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diffusionConst()

jLM.RDME.SpatialModel.diffusionConst	(		self,
			rate,
			value,
		**	kwargs )

Lookup/create diffusion constant instance

Args:
    rate (str):
        Name of diffusion constant
    value (float):
        Value of diffusion constant
    texRepr (str):
        TeX math mode representation of the rate constant
    annotation (str):
        Description text

Returns:
    :py:class:`~jLM.Types.DiffusionConst`:
        DiffusionConst instance

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diffusionFast()

jLM.RDME.SpatialModel.diffusionFast

(

self

)

Lookup/create a maximum-valued diffusion constant instance

Returns:
    :py:class:`~jLM.Types.DiffusionConst`: 
        DiffusionConst instance

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diffusionZero()

jLM.RDME.SpatialModel.diffusionZero

(

self

)

Lookup/create a zero-valued diffusion constant instance

Returns:
    :py:class:`~jLM.Types.DiffusionConst`:
        DiffusionConst instance

distributeConcentration()

jLM.RDME.SpatialModel.distributeConcentration	(		self,
			sp,
			reg,
			conc )

Distribute a concentration of particles uniformly through a region

Args:
    sp (:py:class:`~jLM.Types.Species`]):
        Species type
    reg (:py:class:`~jLM.Types.Region`]):
        Region type
    conc (float):
        Concentration of particles

Reimplemented in jLM.RDMEExtended.SimExtended.

distributeNumber()

jLM.RDME.SpatialModel.distributeNumber	(		self,
			sp,
			reg,
			count )

Distribute a number of particles uniformly through a region

Args:
    sp (:py:class:`~jLM.Types.Species`]):
        Species type
    reg (:py:class:`~jLM.Types.Region`]):
        Region type
    count (int):
        Number of particles

Reimplemented in jLM.RDMEExtended.SimExtended.

hookInterval() [1/2]

jLM.RDME.SpatialModel.hookInterval

(

self

)

Simulation time between calls to hookSimulation

hookInterval() [2/2]

jLM.RDME.SpatialModel.hookInterval	(		self,
			val )

latticeWriteInterval() [1/2]

jLM.RDME.SpatialModel.latticeWriteInterval

(

self

)

Simulation time between writing the lattice to the HDF5 file

latticeWriteInterval() [2/2]

jLM.RDME.SpatialModel.latticeWriteInterval	(		self,
			val )

maxDiffusionRate()

jLM.RDME.SpatialModel.maxDiffusionRate	(		self,
			latticeSpacing = None,
			dt = None )

Compute max allowed diffusion constant for the simulation 

Args:
    latticeSpacing (float):
        Lattice spacing in meters
    dt (float):
        Timestep in seconds

Returns:
    float:
        Maximum diffusion constant in m^/s

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perfPrintInterval() [1/2]

jLM.RDME.SpatialModel.perfPrintInterval

(

self

)

Real elapsed time between writing simulation progress to stdout

perfPrintInterval() [2/2]

jLM.RDME.SpatialModel.perfPrintInterval	(		self,
			val )

placeNumber()

jLM.RDME.SpatialModel.placeNumber	(		self,
			sp,
			x,
			y,
			z,
			n )

Place a number of particles at a specific subvolume

Args:
    sp (:py:class:`~jLM.Types.Species`):
        Species type
    x (int):
        x-coordinate
    y (int):
        y-coordinate
    z (int):
        z-coordinate
    n (int):
        Number of particles

rateConst()

jLM.RDME.SpatialModel.rateConst	(		self,
			rate,
			value,
			order,
		**	kwargs )

Lookup/create reaction rate constant instance

Args:
    rate (str):  
        Name of rate constant
    value (float): 
        Value of rate constant
    order (int): 
        Order of reaction
    texRepr (str): 
        TeX math mode representation of the rate constant
    annotation (str): 
        Description text

Returns:
    :py:class:`~jLM.Types.RateConst`:
        RateConst instance

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reaction()

jLM.RDME.SpatialModel.reaction	(		self,
			reactants,
			products,
			rate,
			value = None,
			regions = None,
		**	kwargs )

Lookup/create reaction instance

The product/reactants can be specified as a string, Species 
instance, list of strings, list of Species instances, or the 
empty list, denoting no species. The reaction rate can be 
created in place if a string is given for `rate` and the value
of the rate constant is specified by `value`.  Rates must be 
provided in standard chemical kinetic units, e.g. for a reaction

.. math:: \mathrm{A} + \mathrm{B} \overset{k}{\to} \mathrm{C},

the rate coefficent, :math:`k` has units of 
:math:`\mathrm{M}^{-1}\mathrm{s}^{-1}`


Args:
    reactants ([:py:class:`~jLM.Types.Species`]):
        Species, or list of species acting as reactants
    products ([:py:class:`~jLM.Types.Species`]):
        Species, or list of species acting as products
    rate ([:py:class:`~jLM.Types.RateConst`]):
        Rate constant
    value (float):
        Optional value of rate constant
    regions (py:class:`~jLM.Types.Region`]):
        List of applicable regions

Returns:
    :py:class:`~jLM.Types.Reaction`:
       Reaction instance

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region()

jLM.RDME.SpatialModel.region	(		self,
			name,
		**	kwargs )

Lookup/create region instance

Args:
    name (str):
        Name of the region
    texRepr (str):
        TeX math mode representation of the region
    annotation (str):
        Description text

Returns:
    :py:class:`~jLM.Types.Region`:
       Region instance

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resizeLattice()

jLM.RDME.SpatialModel.resizeLattice	(		self,
			dimensions,
			latticeSpacing,
			latticeType = None )

run()

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

Run the RDME simulation

Args:
    solver (:py:class:`lm.RDMESolver`):
        Rdme solver
    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

Returns:
    :py:class:`jLM.File`:
        Simulation result

Reimplemented in jLM.RDMEExtended.SimExtended.

setMaximumTimestep()

jLM.RDME.SpatialModel.setMaximumTimestep

(

self

)

Set the simulation timestep using the fastest diffusion rate

simulationTime() [1/2]

jLM.RDME.SpatialModel.simulationTime

(

self

)

Total simulated time

simulationTime() [2/2]

jLM.RDME.SpatialModel.simulationTime	(		self,
			val )

species()

jLM.RDME.SpatialModel.species	(		self,
			name,
		**	kwargs )

Lookup/create species instance

Args:
    name (str):
        Name of the species
    texRepr (str):
        TeX math mode representation of the species
    annotation (str):
        Description text

Returns:
    :py:class:`~jLM.Types.Species`: 
        Species instance

Reimplemented in jLM.RDMEExtended.SimExtended.

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speciesWriteInterval() [1/2]

jLM.RDME.SpatialModel.speciesWriteInterval

(

self

)

Simulation time between writing the species counts to the HDF5 file

speciesWriteInterval() [2/2]

jLM.RDME.SpatialModel.speciesWriteInterval	(		self,
			val )

transitionRate()

jLM.RDME.SpatialModel.transitionRate	(		self,
			sp,
			rFrom,
			rTo,
			rate,
			value = None )

Define the diffusive transition rate between regions

This allows for fine grained detail over the diffusion matrix.
The transition is defined for the species `sp` from region
`rFrom` to `rTo`. If `None` is given for any of these
parameters, then the entire axis of the matrix is affected,
i.e. `None` is a wildcard. The rate is specified with the
`rate` parameter, either as a DiffusionConst instance, or as
a string to lookup the previously created DiffusionConst. If a
string is provided and a DiffusionConst instance has not been
created, providing the parameter `value` will create the new
constant.

Args:
    sp (:py:class:`~jLM.Types.Species`]): 
        Species type or None
    rFrom (:py:class:`~jLM.Types.Region`]):
        Region type or None
    rTo (:py:class:`~jLM.Types.Region`]):
        Region type or None
    rate (:py:class:`~jLM.Types.DiffusionConst`]):
        Diffusion rate
    value (float):
        Value of diffusion constant if new

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Member Data Documentation

_particleDistConc

list jLM.RDME.SpatialModel._particleDistConc = []

protected

_particleDistCount

list jLM.RDME.SpatialModel._particleDistCount = []

protected

_particlePlacement

list jLM.RDME.SpatialModel._particlePlacement = []

protected

_perfPrintInterval

int jLM.RDME.SpatialModel._perfPrintInterval = 60

protected

_reactionLocations

list jLM.RDME.SpatialModel._reactionLocations = []

protected

_transitionRates

list jLM.RDME.SpatialModel._transitionRates = []

protected

diffRateList

jLM.RDME.SpatialModel.diffRateList

filename

jLM.RDME.SpatialModel.filename = filename

lattice

jLM.RDME.SpatialModel.lattice = lm.IntLattice(nz,ny,nx, latticeSpacing, self.pps)

latticeSpacing

jLM.RDME.SpatialModel.latticeSpacing = latticeSpacing

latticeType

jLM.RDME.SpatialModel.latticeType = latticeType

maxConcentration

int jLM.RDME.SpatialModel.maxConcentration = self.pps/self.siteNAV

NA

float jLM.RDME.SpatialModel.NA = 6.02214085774e23

name

jLM.RDME.SpatialModel.name = name

particleLattice

jLM.RDME.SpatialModel.particleLattice = self.lattice.getParticleLatticeView()

pps

jLM.RDME.SpatialModel.pps = lm.getCompiledLatticeMaxOccupancy()

shape

jLM.RDME.SpatialModel.shape = nz,ny,nx

siteLattice

jLM.RDME.SpatialModel.siteLattice = self.lattice.getSiteLatticeView()

siteNAV

int jLM.RDME.SpatialModel.siteNAV = self.siteV * self.NA

siteV

int jLM.RDME.SpatialModel.siteV = 1000 * latticeSpacing**3

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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