protocols

Reusable molecular dynamics protocol runners.

import mlx_atomistic.protocols

Classes

`MinimizeThenNVTProtocol`

class MinimizeThenNVTProtocol
    def __init__(minimize_steps: int = 200, minimize_step_size: float = 0.0001, force_tolerance: float = 0.001, equilibration_steps: int = 1000, production_steps: int = 5000, dt: float = 0.001, sample_interval: int = 100, temperature: float = 300.0, friction: float = 1.0, seed: int | None = 7, diagnostic_interval: int = 1, compile_force_evaluator: bool = True, ensemble: str = 'NVT', proof_mode: str = NVT_PROOF_MODE, barostat: str | bool | None = None, npt_barostat: bool = False, membrane_barostat: str | bool | None = None)

Minimal production-style protocol: minimize, equilibrate, then sample NVT.

Parameters

Name	Type	Default
`minimize_steps`	`int`	`200`
`minimize_step_size`	`float`	`0.0001`
`force_tolerance`	`float`	`0.001`
`equilibration_steps`	`int`	`1000`
`production_steps`	`int`	`5000`
`dt`	`float`	`0.001`
`sample_interval`	`int`	`100`
`temperature`	`float`	`300.0`
`friction`	`float`	`1.0`
`seed`	`int \| None`	`7`
`diagnostic_interval`	`int`	`1`
`compile_force_evaluator`	`bool`	`True`
`ensemble`	`str`	`'NVT'`
`proof_mode`	`str`	`NVT_PROOF_MODE`
`barostat`	`str \| bool \| None`	`None`
`npt_barostat`	`bool`	`False`
`membrane_barostat`	`str \| bool \| None`	`None`

Methods

`compatibility_report`

def compatibility_report(*, raise_on_blockers: bool = False) -> ProtocolCompatibilityReport

Return the fail-closed GPCRmd proof compatibility decision.

Parameters

Name	Type	Default	Description
`raise_on_blockers`	`bool`	`False`

Returns

ProtocolCompatibilityReport

`protocol_metadata`

def protocol_metadata() -> dict[str, Any]

Return normalized metadata for accepted NVT proof runs.

Returns

dict[str, Any]

`ProtocolCompatibilityError`

class ProtocolCompatibilityError(ValueError)
    def __init__(report: ProtocolCompatibilityReport)

Raised when a requested protocol is outside the GPCRmd MLX proof gate.

Parameters

Name	Type	Default	Description
`report`	`ProtocolCompatibilityReport`

`ProtocolCompatibilityReport`

class ProtocolCompatibilityReport
    def __init__(accepted: bool, ensemble: str, proof_mode: str, barostat: str, blockers: tuple[str, ...], metadata: dict[str, Any])

Compatibility decision for the GPCRmd MLX proof protocol.

Parameters

Name	Type	Default	Description
`accepted`	`bool`
`ensemble`	`str`
`proof_mode`	`str`
`barostat`	`str`
`blockers`	`tuple[str, ...]`
`metadata`	`dict[str, Any]`

`ProtocolResult`

class ProtocolResult
    def __init__(minimization: MinimizationResult, equilibration: NVTResult | None, production: NVTResult, protocol_metadata: dict[str, Any] = dict())

Outputs from a minimize/equilibrate/production workflow.

Parameters

Name	Type	Default
`minimization`	`MinimizationResult`
`equilibration`	`NVTResult \| None`
`production`	`NVTResult`
`protocol_metadata`	`dict[str, Any]`	`dict()`

Functions

`protocol_readiness_report`

def protocol_readiness_report(protocol_metadata: Mapping[str, Any] | None = None, *, ensemble: str | None = None, proof_mode: str | None = None, barostat: str | bool | None = None, npt_barostat: bool | None = None, membrane_barostat: str | bool | None = None) -> ReadinessReport

Return the protocol gate as a shared readiness report.

Parameters

Name	Type	Default
`protocol_metadata`	`Mapping[str, Any] \| None`	`None`
`ensemble`	`str \| None`	`None`
`proof_mode`	`str \| None`	`None`
`barostat`	`str \| bool \| None`	`None`
`npt_barostat`	`bool \| None`	`None`
`membrane_barostat`	`str \| bool \| None`	`None`

Returns

ReadinessReport

`run_minimize_then_nvt`

def run_minimize_then_nvt(positions, velocities, masses, force_terms: ForceTerm | list[ForceTerm] | tuple[ForceTerm, ...], *, protocol: MinimizeThenNVTProtocol | None = None, cell: Cell | None = None, constraints: DistanceConstraints | None = None, unit_system: MDUnitSystem | None = None, neighbor_manager: NeighborListManager | None = None, reporters: RuntimeReporter | list[RuntimeReporter] | tuple[RuntimeReporter, ...] | None = None) -> ProtocolResult

Run minimization, optional NVT equilibration, and NVT production in MLX.

Parameters

Name	Type	Default
`positions`
`velocities`
`masses`
`force_terms`	`ForceTerm \| list[ForceTerm] \| tuple[ForceTerm, ...]`
`protocol`	`MinimizeThenNVTProtocol \| None`	`None`
`cell`	`Cell \| None`	`None`
`constraints`	`DistanceConstraints \| None`	`None`
`unit_system`	`MDUnitSystem \| None`	`None`
`neighbor_manager`	`NeighborListManager \| None`	`None`
`reporters`	`RuntimeReporter \| list[RuntimeReporter] \| tuple[RuntimeReporter, ...] \| None`	`None`

Returns

ProtocolResult

`validate_gpcrmd_protocol_request`

def validate_gpcrmd_protocol_request(protocol_metadata: Mapping[str, Any] | None = None, *, ensemble: str | None = None, proof_mode: str | None = None, barostat: str | bool | None = None, npt_barostat: bool | None = None, membrane_barostat: str | bool | None = None, raise_on_blockers: bool = False) -> ProtocolCompatibilityReport

Validate the current GPCRmd proof protocol gate.

The proof gate accepts NVT and the first orthorhombic Monte Carlo NPT path.

Parameters

Name	Type	Default
`protocol_metadata`	`Mapping[str, Any] \| None`	`None`
`ensemble`	`str \| None`	`None`
`proof_mode`	`str \| None`	`None`
`barostat`	`str \| bool \| None`	`None`
`npt_barostat`	`bool \| None`	`None`
`membrane_barostat`	`str \| bool \| None`	`None`
`raise_on_blockers`	`bool`	`False`

Returns

ProtocolCompatibilityReport