pyLM.CME#

Functions

getReactionString(rct, prd, rate)

setLMLogConsole([level])

Set the logger to write to the console as the code is working

setLMLogFile(filename[, level])

Set up file handler to print log to file

setLMLoggerLevel(level)

Set the level of the logger for the application

visualizeRDMEInitialConditions(sim)

Visualize the RDME simulation volume inside Jupyter.

writeTable(columnNames, rows)

Classes

CMESimulation([volume, name])

A constructor for the CMESimulation

tqdm(*_, **__)

Decorate an iterable object, returning an iterator which acts exactly like the original iterable, but prints a dynamically updating progressbar every time a value is requested.
class pyLM.CME.CMESimulation(volume=None, name='unnamed')[source]#

Bases: object

A constructor for 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:

CMESimulation

addConcentration(species='unknown', conc=0.0)[source]#

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

Parameters:

  • species – The name of the specie to add

  • concentration – The concentration of the species (Molar). Particle count is rounded to nearest integer.

addParticles(species='unknown', count=1)[source]#

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

Parameters:

  • species – The name of the specie to add particles to

  • count – The number of that particle to start with (default 1)

addReaction(reactant, product, rate)[source]#

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

Reaction rates are specified as stochastic rates: i.e. in units of \(1/\mathrm{s}\).

Parameters:

  • reactant – The list or reactants

  • product – The list of products

  • rate – The stochastic rate of reaction

buildReactionModel()[source]#

Return the Lattice Microbes ReactionModel object for fine-tuning

Returns:

The reaction model for the simulation

defineSpecies(species)[source]#

Define a species of particles that exist in the simulation

Parameters:

species – A list of species to add to the simulation

run(filename, method, replicates=1, seed=None, cudaDevices=None, checkpointInterval=0)[source]#

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

Parameters:

  • 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

runMPI(filename, method, replicates=1, driver='mpirun', ppe=1, seed=None)[source]#

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

Parameters:

  • 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 (e.g. number of nodes)

  • seed – A seed for the random number generator to use when running the simulation; None indicates default

runSolver(filename, solver, replicates=1, cudaDevices=None, checkpointInterval=0)[source]#

Run a simulation with a given solver

Parameters:

  • filename – The HDF file to write to

  • solver – An MESolver object

  • replicates – The number of replicates to serially run

save(filename)[source]#

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

Parameters:

filename – The filename to save the simulation setup in

setHookInterval(time)[source]#

Set the simulation hook interval

Parameters:

time – Time length between hook calls

setRandomSeed(seed)[source]#

Set a known random seed

Parameters:

seed – Random seed

setSimulationTime(time)[source]#

Set the total simulation time

Parameters:

time – Time length of the simulation

setTimestep(time)[source]#

set the simulation time step :param time: The length of simulation timestep for CME

setWriteInterval(time)[source]#

Set the simulation state write-to-disk interval :param time: Time length between writes