initialize

Initial configurations and velocities for reduced-unit MD.

import mlx_atomistic.initialize

Functions

fcc_lattice

def fcc_lattice(n_particles: int, *, density: float = 0.8) -> tuple[mx.array, Cell]

Return positions on an FCC lattice and a cubic cell.

Parameters

Name	Type	Default	Description
n_particles	int
density	float	0.8

Returns

• tuple[mx.array, Cell]

random_velocities

def random_velocities(n_particles: int, *, temperature: float = 1.0, masses = None, seed: int | None = None) -> mx.array

Return Maxwell-like random velocities in reduced units.

Parameters

Name	Type	Default	Description
n_particles	int
temperature	float	1.0
masses		None
seed	int | None	None

Returns

• mx.array

remove_center_of_mass_velocity

def remove_center_of_mass_velocity(velocities, masses = None) -> mx.array

Remove center-of-mass velocity.

Parameters

Name	Type	Default	Description
velocities
masses		None

Returns

• mx.array

rescale_temperature

def rescale_temperature(velocities, masses = None, *, temperature: float = 1.0) -> mx.array

Rescale velocities to a target reduced temperature.

Parameters

Name	Type	Default	Description
velocities
masses		None
temperature	float	1.0

Returns

• mx.array

simple_cubic_lattice

def simple_cubic_lattice(n_particles: int, *, density: float = 0.8) -> tuple[mx.array, Cell]

Return positions on a simple cubic lattice and a cubic cell.

Parameters

Name	Type	Default	Description
n_particles	int
density	float	0.8

Returns

• tuple[mx.array, Cell]

thermal_velocities

def thermal_velocities(n_particles: int, *, temperature: float = 1.0, masses = None, seed: int | None = None) -> mx.array

Return random velocities with zero COM velocity and target temperature.

Parameters

Name	Type	Default	Description
n_particles	int
temperature	float	1.0
masses		None
seed	int | None	None

Returns

• mx.array