pyLM.CME.CMESimulation Class Reference

A CME simulation that contains reactions and species. More...

Public Member Functions
def	__init__
	A constructor fo the CMESimulation. More...
def	defineSpecies
	Define a specie/s of particles that exist in the simulation. More...
def	addParticles
	Add a specified number of particles of the specified type to the specified region. More...
def	addConcentration
	Add a concentration of particles of the specified type to the simulation. More...
def	addReaction
	Adds a 0th, 1st or 2nd order reaction. More...
def	buildReactionModel
	Return the Lattice Microbes ReactionModel object for fine-tuning. More...
def	setRandomSeed
def	setWriteInterval
	Set the simulation state write-to-disk interval. More...
def	setSimulationTime
	Set the total simulation time. More...
def	setTimestep
def	save
	Create an HDF5 version of the simulation amenable for later running or stand-alone running. More...
def	run
	Run the simulation using the specified solver the specified amount of time. More...
def	runMPI
	Run the simulation using a call to mpirun with the given options. More...
def	runSolver

Public Attributes
	particleMap
	species_id
	initial_counts
	reactions
	parameters
	volume
	name
	replicates
	filename

Detailed Description

A CME simulation that contains reactions and species.

Constructor & Destructor Documentation

def pyLM.CME.CMESimulation.__init__	(		self,
			volume = None,
			name = "unnamed"
	)

A constructor fo the CMESimulation.

Parameters

volume	The reaction vessel volume (in Litres). Specifying 'None' signifies that the user has already accounted for volume in rate constants.
name	The name of the CME simulation; Default: "unnamed"

Returns

self

Member Function Documentation

def pyLM.CME.CMESimulation.addConcentration	(		self,
			species = 'unknown',
			conc = 0.0
	)

Add a concentration of particles of the specified type to the simulation.

Parameters

self
species	The name of the specie to add
concentration	The concentration of the species (Molar). Particle count is rounded to nearest integer.

Exceptions

An	error if the volume is not specified

def pyLM.CME.CMESimulation.addParticles	(		self,
			species = 'unknown',
			count = 1
	)

Add a specified number of particles of the specified type to the specified region.

Parameters

self
species	The name of the specie to add particles to
count	The number of that particle to start with (default 1)

def pyLM.CME.CMESimulation.addReaction	(		self,
			reactant,
			product,
			rate
	)

Adds a 0th, 1st or 2nd order reaction.

Parameters

self
reactant	The list or reactants
product	The list of products
rate	The rate of reaction

def pyLM.CME.CMESimulation.buildReactionModel

(

self

)

Return the Lattice Microbes ReactionModel object for fine-tuning.

Parameters

self

Returns

The reaction model for the simulation

def pyLM.CME.CMESimulation.defineSpecies	(		self,
			species
	)

Define a specie/s of particles that exist in the simulation.

Parameters

self
species	A list of species to add to the simulation

def pyLM.CME.CMESimulation.run	(		self,
			filename,
			method,
			replicates = 1,
			seed = None
	)

Run the simulation using the specified solver the specified amount of time.

Parameters

self
filename	The HDF file to write to
method	The class name for the solver to use (e.g., lm::cme::GillespieDSolver")
replicates	The number of replicates to serially run
seed	A seed for the random number generator to use when running the simulation; None indicates default

def pyLM.CME.CMESimulation.runMPI	(		self,
			filename,
			method,
			replicates = 1,
			driver = "mpirun",
			ppe = 1,
			seed = None
	)

Run the simulation using a call to mpirun with the given options.

Parameters

self
filename	The HDF file to write to
method	The class name for the solver to use (e.g., lm::cme::GillespieDSolver")
replicates	The number of replicates to serially run
driver	The program to execute the parallel run, e.g. "mpirun", "aprun", "ibrun", etc.
ppe	The number of processing elements to use
seed	A seed for the random number generator to use when running the simulation; None indicates default

def pyLM.CME.CMESimulation.runSolver	(		self,
			filename,
			solver,
			replicates = 1
	)

def pyLM.CME.CMESimulation.save	(		self,
			filename
	)

Create an HDF5 version of the simulation amenable for later running or stand-alone running.

Parameters

self
filename	The filename to save the simulation setup in

def pyLM.CME.CMESimulation.setRandomSeed	(		self,
			seed
	)

def pyLM.CME.CMESimulation.setSimulationTime	(		self,
			time
	)

Set the total simulation time.

Parameters

self
time	Time length of the simulation

def pyLM.CME.CMESimulation.setTimestep	(		self,
			time
	)

def pyLM.CME.CMESimulation.setWriteInterval	(		self,
			time
	)

Set the simulation state write-to-disk interval.

Parameters

self
time	Time length between writes

Member Data Documentation

pyLM.CME.CMESimulation.filename

pyLM.CME.CMESimulation.initial_counts

pyLM.CME.CMESimulation.name

pyLM.CME.CMESimulation.parameters

pyLM.CME.CMESimulation.particleMap

pyLM.CME.CMESimulation.reactions

pyLM.CME.CMESimulation.replicates

pyLM.CME.CMESimulation.species_id

pyLM.CME.CMESimulation.volume

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The documentation for this class was generated from the following file:

• CME.py