sim_branching

calculate_discretization(positions: ndarray, n_voxels: int, options: Options, raw: bool = False)

calculate_fractal_dim_for_pos(pos, options: Options, out_path: Path | None = None)

check_exists(options: Options) → Path | None

load_or_compute_full(options): Obtains a result for a given combination of options by either loading from existing files or performing a fully new numerical simulation.

See also

The load_or_compute_last_iter() function is cheaper when only loading the last iteration.

load_or_compute_last_iter(options)

plot_discretizations(last_pos, n_voxels_list, options, out_path: Path)

class BacteriaBranching

Bases: object

division_radius

growth_rate

interaction

mechanics

uptake_rate

class BacterialParameters(**kwargs)

Bases: object

cell_radius

damping_constant

division_threshold

growth_rate

n_bacteria_initial

potential_stiffness

potential_strength

uptake_rate

class DomainParameters(**kwargs)

Bases: object

diffusion_constant

domain_size: Overall size of the domain

domain_starting_size: Size of the square for initlal placement of bacteria

initial_concentration

reactions_dx: Discretization of the diffusion process

voxel_size

class Options(**kwargs)

Bases: object

static load_from_toml(path)

save_to_toml(path)

bacteria: Holds bacteria parameters. See BacterialParameters.

domain: Holds domain parameters. See DomainParameters.

n_threads: Specify how many threads to use for the simulation. Must be a positive integer value.

show_progressbar: Show or hide the progress bar during the simulation.

storage_location: If this variable is set to None, no output will be produced and results will only be returned in memory. If a path is given, results will be stored there with a timestamp of the beginning of the simulation.

time: Holds time parameters. See TimeParameters.

class SubDomainPlainIndex

Bases: object

Identifier or subdomains

class TimeParameters(**kwargs)

Bases: object

dt

save_interval

t_max

get_all_iterations(path)

Obtains all iterations for a given result.

The same comment from load_cells() applies.

load_cells(path): Loads all cells for all iterations from a given path.

Caution

Notice that this input expects a path containing the simulation results directly. This means for practical purposes that a date signature such as will have to be added (i.e. path=out/2025-04-26-T18-06-43).

load_cells_at_iteration(path, iteration)

Loads all cells from a given path for a specific iteration.

The same comment from load_cells() applies.

load_subdomains_at_iteration(path, iteration)

run_sim_branching(options): Performs a full numerical simulation with the given Options.

Warning

Although this function is fully working it is highly recommended to use the load_or_compute_full() function instead which will check first if a result with the given options has already been produced and thus reuse these existing results.

class MorsePotential: See the documentation at cellular_raza-building_blocks::MorsePotential.

class NewtonDamped2D: See the documentation at cellular_raza-building_blocks::NewtonDamped2D.