Records an organism's death and adds it to the graveyard. Only organisms that lived long enough (age >= 0.5) are added. Maintains graveyard sorted by

Resets the attack cooldown timer. # Arguments `cooldown_time` - Cooldown duration in seconds

Seeds empty pools with organisms from non-empty pools.

Selects a pool ID weighted by pool size (larger pools more likely).

Number of sexual deaths tracked

Returns the total number of brain inputs produced by all senses. # Arguments `params` - Simulation parameters # Returns The sum of input sizes fro

Applies periodic wrapping to a DNA value. # Arguments `value` - DNA value (may be outside [0, 1]) # Returns Wrapped value in [0, 1]

Increments the organism's age. # Arguments `dt` - Time delta in seconds

Performs asexual reproduction (cloning with mutation).

Performs asexual reproduction (indexed version for living organisms).

Average score improvement for asexual reproduction (last N deaths)

Average score improvement for inter-pool breeding (last N deaths)

Average score improvement for sexual reproduction (last N deaths)

Builds a spatial index from the current ecosystem state. # Arguments `ecosystem` - The ecosystem to build indices for # Returns A spatial index or

Clones a single parent organism.

Creates a new brain by averaging two parent brains. Both parents must be the same architecture type.

Creates a new head by averaging two parent heads.

Creates a new layer by averaging two parent layers.

Creates a new brain by weighted averaging two parent brains. Both parents must be the same architecture type. weight1 is the weight for parent1, weigh

Creates a new head by weighted averaging two parent heads.

Creates a new layer by weighted averaging two parent layers.

Executes asexual reproduction action. # Arguments `entity` - The organism reproducing `energy_contribution` - Amount of energy to give to offspring

Executes sexual reproduction action. # Arguments `entity` - The organism wanting to reproduce `energy_contribution` - Amount of energy this organism

Get direct reference to the food KD-tree.

Generates disjoint cluster centers for organisms and food. Creates two sets of cluster centers that are guaranteed not to overlap by ensuring minimum

Returns a reference to the graveyard.

Returns a reference to the graveyard.

Loads an ecosystem state from a JSON file. # Arguments `path` - Path to the JSON save file `params` - Simulation parameters (needed to reinitialize t

Mutates all weights by adding random noise.

Mutates weights and biases by adding random noise.

Creates an empty event queue.

Creates a new ecosystem with random organisms and food.

Creates a new projectile. # Arguments `pos` - Starting position `rotation` - Firing direction in radians `speed` - Projectile speed `damage` - Damag

Creates a new event log with specified capacity

Creates a new evolution engine.

Creates a new MLP brain with random weights.

Creates a new scent sense.

Creates a new perception system with the given senses. # Arguments `senses` - Vector of boxed sense implementations # Returns A new perception sys

Creates a new vision sense.

Creates a new proprioception sense.

Creates a new food item at a random position. # Arguments `screen_center` - The center point of the simulation area, used to calculate bounds. `ener

Creates a new attention head with random weights.

Creates a new layer with random weights and biases.

Creates a new transformer brain with random weights. Parameters: - `input_size`: Size of input vector - `output_size`: Size of output vector - `model

Get direct references to the trees (for backwards compatibility).

Calculates the periodic distance between two DNA vectors. DNA space is [0, 1] x [0, 1] with periodic boundary conditions (toroidal topology). For eac

Get direct reference to the projectiles KD-tree.

Query projectiles within a radius.

Generates a random position within a random cluster

Returns a random position within a random food cluster. Regenerates clusters if they're empty (e.g., after loading from file).

Generates a random position within a cluster belonging to a specific pool

Generates a random position using the same method as `Organism::new_random`.

Record a death and update statistics

Seeds a new organism from a different genetic pool.

Seeds a new organism from a different genetic pool (indexed version).

Returns a reference to the senses in this perception system.

Performs sexual reproduction (crossover between two parents).

Performs sexual reproduction (indexed version for living organisms).

Helper method to spawn from graveyard using the old cloning approach.

Spawns from a pool using the cloning approach (for small pools like graveyard).