units

Internal unit systems for atomistic simulations.

import mlx_atomistic.units

Classes

LennardJonesReducedUnits

class LennardJonesReducedUnits
    def __init__(sigma: float = 1.0, epsilon: float = 1.0, mass: float = 1.0, boltzmann: float = 1.0)

Lennard-Jones reduced-unit system for v1 molecular dynamics.

The numerical MD kernels operate on dimensionless values by default: sigma = 1, epsilon = 1, particle mass = 1, and k_B = 1.

Parameters

Name	Type	Default	Description
sigma	float	1.0
epsilon	float	1.0
mass	float	1.0
boltzmann	float	1.0

Properties

• energy float — Energy unit.
• force float — Force unit.
• length float — Length unit.
• temperature float — Temperature unit.
• time float — Time unit tau = sigma * sqrt(mass / epsilon).
• velocity float — Velocity unit.

Methods

from_reduced_energy

def from_reduced_energy(value: float) -> float

Convert a reduced energy into the represented unit system.

Parameters

Name	Type	Default	Description
value	float

Returns

• float

from_reduced_length

def from_reduced_length(value: float) -> float

Convert a reduced length into the represented unit system.

Parameters

Name	Type	Default	Description
value	float

Returns

• float

from_reduced_temperature

def from_reduced_temperature(value: float) -> float

Convert a reduced temperature into the represented unit system.

Parameters

Name	Type	Default	Description
value	float

Returns

• float

to_reduced_energy

def to_reduced_energy(value: float) -> float

Convert an energy into reduced units.

Parameters

Name	Type	Default	Description
value	float

Returns

• float

to_reduced_length

def to_reduced_length(value: float) -> float

Convert a length into reduced units.

Parameters

Name	Type	Default	Description
value	float

Returns

• float

to_reduced_temperature

def to_reduced_temperature(value: float) -> float

Convert a temperature into reduced units.

Parameters

Name	Type	Default	Description
value	float

Returns

• float

MDUnitSystem

class MDUnitSystem
    def __init__(coordinates: str = 'angstrom', mass: str = 'dalton', charge: str = 'elementary_charge', energy: str = 'kilojoule_per_mole', time: str = 'picosecond', temperature: str = 'kelvin', coulomb_constant: float = COULOMB_CONSTANT_KJ_MOL_ANGSTROM, boltzmann_constant: float = BOLTZMANN_CONSTANT_KJ_MOL_K)

Explicit physical units used by production molecular mechanics kernels.

The recommended MLX production convention is Angstrom, ps, dalton, elementary charge, kJ/mol, and K. The Coulomb constant below matches those units when distances are stored in Angstrom.

Parameters

Name	Type	Default	Description
coordinates	str	'angstrom'
mass	str	'dalton'
charge	str	'elementary_charge'
energy	str	'kilojoule_per_mole'
time	str	'picosecond'
temperature	str	'kelvin'
coulomb_constant	float	COULOMB_CONSTANT_KJ_MOL_ANGSTROM
boltzmann_constant	float	BOLTZMANN_CONSTANT_KJ_MOL_K

Properties

• coordinate_scale_to_angstrom float — Scale stored coordinates into Angstrom.
• force_to_acceleration_scale float — Scale (kJ/mol/length) / dalton into stored-length/ps**2.
• kinetic_energy_scale float — Scale 0.5 * dalton * velocity**2 into kJ/mol.

Methods

from_metadata

def from_metadata(units: Mapping[str, str]) -> MDUnitSystem

Create and validate a physical MD unit system from artifact metadata.

Parameters

Name	Type	Default	Description
units	Mapping[str, str]

Returns

• MDUnitSystem

validate

def validate() -> None

Reject reduced or ambiguous units for production artifacts.

Returns

• None