constraints

Pair-distance constraints for molecular dynamics.

import mlx_atomistic.constraints

Classes

`CompositeConstraints`

class CompositeConstraints
    def __init__(constraints: tuple[object, ...])

Apply multiple constraint objects through the standard constraint protocol.

Parameters

Name	Type	Default	Description
`constraints`	`tuple[object, ...]`

Methods

`apply_positions`

def apply_positions(positions, masses, cell: Cell | None = None) -> tuple[mx.array, mx.array]

Apply child position constraints in sequence.

Parameters

Name	Type	Default
`positions`
`masses`
`cell`	`Cell \| None`	`None`

Returns

tuple[mx.array, mx.array]

`apply_velocities`

def apply_velocities(positions, velocities, masses, cell: Cell | None = None) -> mx.array

Apply child velocity constraints in sequence.

Parameters

Name	Type	Default
`positions`
`velocities`
`masses`
`cell`	`Cell \| None`	`None`

Returns

mx.array

`max_error`

def max_error(positions, cell: Cell | None = None) -> mx.array

Return the maximum absolute error across child constraints.

Parameters

Name	Type	Default	Description
`positions`
`cell`	`Cell \| None`	`None`

Returns

mx.array

`DistanceConstraints`

class DistanceConstraints
    def __init__(pairs: object, distances: object, tolerance: float = 1e-05, max_iterations: int = 20)

Fixed pair-distance constraints.

Parameters

Name	Type	Default
`pairs`	`object`
`distances`	`object`
`tolerance`	`float`	`1e-05`
`max_iterations`	`int`	`20`

Methods

`apply_positions`

def apply_positions(positions, masses, cell: Cell | None = None) -> tuple[mx.array, mx.array]

Project positions onto the configured pair distances.

Parameters

Name	Type	Default
`positions`
`masses`
`cell`	`Cell \| None`	`None`

Returns

tuple[mx.array, mx.array]

`apply_velocities`

def apply_velocities(positions, velocities, masses, cell: Cell | None = None) -> mx.array

Remove constrained relative velocity components.

Parameters

Name	Type	Default
`positions`
`velocities`
`masses`
`cell`	`Cell \| None`	`None`

Returns

mx.array

`max_error`

def max_error(positions, cell: Cell | None = None) -> mx.array

Return the maximum absolute distance error.

Parameters

Name	Type	Default	Description
`positions`
`cell`	`Cell \| None`	`None`

Returns

mx.array

`SettleWaterConstraints`

class SettleWaterConstraints
    def __init__(waters: object, oh_distance: float = 1.0, hh_distance: float = 1.6329932, tolerance: float = 1e-05, max_velocity_iterations: int = 200)

Analytical rigid-water constraints for (oxygen, hydrogen, hydrogen) triplets.

Parameters

Name	Type	Default
`waters`	`object`
`oh_distance`	`float`	`1.0`
`hh_distance`	`float`	`1.6329932`
`tolerance`	`float`	`1e-05`
`max_velocity_iterations`	`int`	`200`

Methods

`apply_positions`

def apply_positions(positions, masses, cell: Cell | None = None) -> tuple[mx.array, mx.array]

Project water triplets onto the configured rigid geometry.

Parameters

Name	Type	Default
`positions`
`masses`
`cell`	`Cell \| None`	`None`

Returns

tuple[mx.array, mx.array]

`apply_velocities`

def apply_velocities(positions, velocities, masses, cell: Cell | None = None) -> mx.array

Remove constrained relative velocity components for SETTLE pairs.

Parameters

Name	Type	Default
`positions`
`velocities`
`masses`
`cell`	`Cell \| None`	`None`

Returns

mx.array

`max_error`

def max_error(positions, cell: Cell | None = None) -> mx.array

Return the maximum absolute SETTLE distance error.

Parameters

Name	Type	Default	Description
`positions`
`cell`	`Cell \| None`	`None`

Returns

mx.array