jLM.RDMEExtended Namespace Reference

Classes
class	FileExtended
class	SimExtended
class	SpatialModelExtended

Functions
	create_simulation_with_sizes (name, filename, dimensions, latticeSpacing, regionName, particle_sizes=None, **kwargs)

Detailed Description

Extended RDME classes with particle size support

This module provides extended versions of the main RDME classes that include
particle size awareness and capacity validation.

Author: Lattice-Microbes Development Team
Copyright 2024 Luthey-Schulten Group, University of Illinois

Function Documentation

create_simulation_with_sizes()

jLM.RDMEExtended.create_simulation_with_sizes	(		name,
			filename,
			dimensions,
			latticeSpacing,
			regionName,
			particle_sizes = None,
		**	kwargs )

Convenience function to create a simulation with predefined particle sizes.

Args:
    name (str): Simulation name
    filename (str): Filename
    dimensions (tuple): Lattice dimensions
    latticeSpacing (float): Lattice spacing
    regionName (str): Default region name
    particle_sizes (dict): Dictionary mapping species name to size
    **kwargs: Additional arguments for SimExtended

Returns:
    SimExtended instance with particle sizes configured

Example:
    >>> sim = create_simulation_with_sizes(
    ...     "test", "test.lm", (50, 50, 50), 1e-6, "cytoplasm",
    ...     particle_sizes={"Protein": 1, "Complex": 3, "Ribosome": 8}
    ... )