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_with_agents()`	Executes the simulation and returns a `CellContainer`.

class AgentSettings(**kwds)

Bases: object

Contains settings needed to specify properties of the RodAgent

to_rod_agent_dict(): Converts the class to a dictionary

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

growth_rate_distr: See RodAgent

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

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

neighbor_reduction: Reduces the growth rate with multiplier $((max - N)/max)^q $

spring_length_threshold: Threshold when the bacterium divides

class Configuration(**kwds)

Bases: object

Contains all settings needed to configure the simulation

static deserialize(data): TODO

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

static from_toml(filename): Parses the content of a given toml file and returns a Configuration object which contains the given values. See also from_toml_string().

static from_toml_string(toml_string): Parses the contents of a given string and returns a Configuration. See also from_toml_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

gel_pressure: See [cellular_raza-building_blocks::CartesianSubDomainRods]

n_saves: Interval in which results will be saved

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/.

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

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

storage_location: Store results in this given path. Only takes effect if more StorageOptions than memory are utilized.

storage_options: Define in which format to store results. Only uses memory by default

storage_suffix: Appends a suffix to the date which is generated automatically.

surface_friction: See [cellular_raza-building_blocks::CartesianCuboidRods]

surface_friction_distance: See [cellular_raza-building_blocks::CartesianCuboidRods]

t0: Starting time

t_max: Maximum solving time

class PhysicalInteraction(pyobject)

Bases: object

Describes all possible interaction variants

inner(): Extracts a copy of the inner value

radius: Obtains the radius of the interaction

strength: Getter for the strength of the interaction

class RodAgent(pos, vel, interaction, diffusion_constant=0.0, spring_tension=1.0, rigidity=2.0, spring_length=3.0, damping=1.0, growth_rate=0.1, growth_rate_distr=Ellipsis, spring_length_threshold=6.0, neighbor_reduction=None)

Bases: object

A basic cell-agent which makes use of RodMechanics

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

growth_rate_distr: Determines the mean and width of distribution for sampling new values of growth rate.

neighbor_reduction: Reduces the growth rate with multiplier $((max - N)/max)^q $

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

class StorageOption

Bases: object

Define how to store results of the simulation.

We currently support saving results in a [sled] database, or as a json file by using [serde_json].

Memory = StorageOption.Memory

Ron = StorageOption.Ron

SerdeJson = StorageOption.SerdeJson

Sled = StorageOption.Sled

SledTemp = StorageOption.SledTemp

generate_agents(n_agents, agent_settings, config, rng_seed=0, dx=Ellipsis, randomize_positions=0.0, n_vertices=8): Uses the generate_positions() function to generate positions and then sets parameters of the generated agents from the supplied AgentSettings.

generate_positions(n_agents, agent_settings, config, rng_seed=0, dx=Ellipsis, randomize_positions=0.0, n_vertices=8): Creates positions for multiple RodAgent which can be used for simulation purposes.

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.

class MiePotentialF32: See documentation at cellular_raza-building_blocks::MiePotentialF32.