Simulation

This module contains functionality to configure and run simulations.

Define Agent Properties
`AgentSettings`	A template for defining an agent.
`RodMechanicsSettings`	Defines properties of to the RodMechanics struct.
`MorsePotentialF32`	Define interaction properties of the agent.

Running a Simulation
`Configuration`	Bundles all information required for a simulation.
`run_simulation()`	Executes the simulation and returns a `CellContainer`.

class AgentSettings(**kwds)

Bases: object

Contains settings needed to specify properties of the RodAgent

growth_rate: Rate with which the length of the bacterium grows

interaction: Settings for the interaction part of RodAgent. See also MorsePotentialF32.

mechanics: Settings for the mechanics part of RodAgent. See also RodMechanicsSettings.

n_vertices: Number of vertices to use for this agent

spring_length_threshold: Threshold when the bacterium divides

class Configuration(**kwds)

Bases: object

Contains all settings needed to configure the simulation

static from_json(json_string): Deserializes this struct from a json string

to_hash(): Attempts to create a hash from the contents of this Configuration. Warning: This feature is experimental.

to_json(): Serializes this struct to the json format

domain_height: We assume that the domain is a thin 3D slice. This specifies the height of the domain.

domain_size: Overall domain size of the simulation. This may determine an upper bound on the number of agents which can be put into the simulation.

dt: Time increment

n_agents: Number of agents to put into the simulation. Depending on the size specified, this number may be lowered artificially to account for the required space.

n_threads: Number of threads used for solving the system.

n_voxels: Number of voxels used to solve the system. This may yield performance improvements but specifying a too high number will yield incorrect results. See also https://cellular-raza.com/internals/concepts/domain/decomposition/.

randomize_position: Determines the amount with which positions should be randomized. Should be a value between 0.0 and 1.0.

rng_seed: Initial seed for randomizations. This can be useful to run multiple simulations with identical parameters but slightly varying initial conditions.

save_interval: Interval in which results will be saved

show_progressbar: Specifies if a progress bar should be shown during the solving process.

t0: Starting time

t_max: Maximum solving time

class RodAgent(pos, vel, diffusion_constant=0.0, spring_tension=1.0, rigidity=2.0, spring_length=3.0, damping=1.0, radius=3.0, strength=0.1, potential_stiffness=0.5, cutoff=10.0, growth_rate=0.1, spring_length_threshold=6.0)

Bases: object

A basic cell-agent which makes use of RodMechanics

growth_rate: Rate with which the cell grows in units 1/MIN.

pos: Position of the agent given by a matrix containing all vertices in order.

radius: The interaction radius as given by the [MorsePotentialF32] interaction struct.

spring_length_threshold: Threshold at which the cell will divide in units MICROMETRE.

vel: Velocity of the agent given by a matrix containing all velocities at vertices in order.

class RodMechanicsSettings

Bases: object

Contains all settings required to construct RodMechanics

damping: Damping constant

diffusion_constant: Controls magnitude of32 stochastic motion

pos

rigidity: Stif32fness at each joint connecting two edges

spring_length: Target spring length

spring_tension: Spring tension between individual vertices

vel

run_simulation(config, agent_settings)

Use the run_simulation_with_agents()

Executes the simulation with the given Configuration

Deprecated since version 0.4: Use the run_simulation_with_agents() function instead.

run_simulation_with_agents(config, agents): Executes a simulation given a Configuration and a list of RodAgent.

sort_cellular_identifiers(identifiers)

Sorts an iterator of CellIdentifier deterministically.

This function is usefull for generating identical masks every simulation run. This function is implemented as standalone since sorting of a CellIdentifier is typically not supported.

Parameters:: identifiers (list) – A list of CellIdentifier
Returns:: The sorted list.
Return type:: list

class MorsePotentialF32: Famous Morse potential for diatomic molecules. See the documentation at cellular_raza-building_blocks::MorsePotentialF32.