API Reference

Main Entry Point

Main program for the Simples lattice model.

This script initializes a 3D lattice of Simples and runs the simulation using either deterministic, stochastic, or hybrid updates.

main.run_simulation()[source]

Entities

Simples Factory

Module entities.simples defines the Simple class, representing a closed geometric surface in the lattice network.

Each Simple interacts with neighbors via energy-driven rules: - surface tension - bending rigidity - neighbor coupling - area redistribution (local conservation)

class entities.simples_factory.Simple(idx, neighbors=None, A0=1.0)[source]

Bases: object

Represents a closed geometric surface (Simple) in the SimplesModel network.

idx

Unique identifier for the Simple.

Type:: int

neighbors

Indices of neighboring Simples in the lattice.

Type:: list of int

A0

Total area of the Simple.

Type:: float

H0

Reference mean curvature.

Type:: float

H

Current mean curvature (patch-averaged if needed).

Type:: float

K

Current Gaussian curvature.

Type:: float

area

Dictionary of area per patch: ‘xp’, ‘xm’, ‘yp’, ‘ym’, ‘zp’, ‘zm’, ‘free’.

Type:: dict

curvature

Curvature deviations per patch (for local energy and interactions).

Type:: dict

PATCHES = ['xp', 'xm', 'yp', 'ym', 'zp', 'zm', 'free']

apply_update(delta)[source]

Apply an external delta stimulus and redistribute it internally.

Parameters:: delta (dict) – External energy / curvature stimulus per patch.