cr_trichome_rust#

A Python module implemented in Rust.

class SimulationSettings(cell_mechanics_area=500.0, cell_mechanics_spring_tension=2.0, cell_mechanics_central_pressure=0.5, cell_mechanics_interaction_range=5.0, cell_mechanics_potential_strength=6.0, cell_mechanics_damping_constant=0.2, cell_mechanics_diffusion_constant=0.0, domain_size=800.0, n_times=20001, dt=0.005, t_start=0.0, save_interval=50, n_threads=1, seed=2)#

Bases: object

This class contains all settings needed to run a full simulation with the run_sim function.

cell_mechanics_area(float)#: Defines the total size of each cell. Currently all cells are assigned identical sizes.

cell_mechanics_spring_tension(float)#: Spring constant of the edges of the cell.

cell_mechanics_central_pressure(float)#: Internal pressure which pushes vertices outwards from the middle.

cell_mechanics_interaction_range(float)#: Maximal interaction range until which other cells will be attracted via an outside potential. This value is also used to calculate the discretization of the total simulation domain.

cell_mechanics_potential_strength(float)#: Interaction strength for repelling and attracting strength between the cells.

cell_mechanics_damping_constant(float)#: Damping constant $lambda$ for the physical mechanics of the cell.

cell_mechanics_diffusion_constant(float)#: Amplitude of the Wiener process in the phyical mechanics of the cell.

domain_size(float)#: Total size of the simulation quadratically-sized domain.

n_times(int)#: Number of integration steps to take.

dt(float)#: Temporal discretization used for solving all equations.

t_start(float)#: Initial time point at which the simulation is started.

save_interval(int)#: Every nth step will be saved to the output folder.

n_threads(int)#: Number of threads to use for parallelization.

seed(int)#: Initial seed of random number generator for the simulation.

static default()#

run_sim(settings)#

Parameters:

settings (SimulationSettings) – All settings which need to be specified to run a full simulation.
Raises – ValueError : When the simulation aborts due to an unexpected error.