rgrow.Simulation

class rgrow.Simulation(tileset: TileSet, system: System | None = None, states: List[State] | None = None)

__init__(tileset: TileSet, system: System | None = None, states: List[State] | None = None)

Methods

__init__(tileset[, system, states])
add_n_states(n)	Add n states to the simulation.
add_state()	Add a state to the simulation.
canvas_copy([state_index])	Returns a copy of the current canvas for state_index (default 0).
canvas_view([state_index])	Returns the current canvas for state_index (default 0), as a direct view of the state array.
check_state([n])	Check that the simulation has at least n states.
ensure_state([n])	Ensure that the simulation has at least n states.
evolve([state_index, for_events, ...])	Evolve a particular state, with index state_index, subject to some bounds.
evolve_all([for_events, total_events, ...])	Evolve all states, stopping each as they reach the boundary conditions.
evolve_some(state_indices[, for_events, ...])	Evolve some states, stopping each as they reach the boundary conditions.
get_system_param(name)	Gets a system parameter.
mismatch_array([state_index])	Returns an array of mismatches in the state.
n_mismatches([state_index])	Returns the number of mismatches in the state.
name_canvas([state_index])	Returns the current canvas for state_index (default 0), as an array of tile names.
plot_state([state_index, ax])	Plot a state as a pcolormesh.
set_system_param(name, value)	Sets a system parameter to a value.
state_events([state_index])	Returns the number of events simulated for a state.
state_ntiles([state_index])	Returns the number of tiles in the state.
state_time([state_index])	Returns the amount of time simulated (in seconds) for the state.
tile_cmap()	Returns a matplotlib colormap for tile numbers.

Attributes

states_events	Returns the number of events simulated for each state.
states_ntiles	Returns the number of tiles in each state.
states_time	Returns the amount of time simulated (in seconds) for each state.
tile_colors	Returns the colors of each tile in the system.
tile_concs	Returns the concentration of each tile in the system.
tile_names	Returns the names of each tile in the system.
tile_stoics	Returns the stoichiometry of each tile in the system.
tileset
system
states