Abstract Base Classes

We make use of abstract base classes, protocols and type hints to improve the workflow design experience. Further, these can be used for cross-package interoperability with other ZnTrack based packages like IPSuite.

For most Node classes operating on lists of ASE objects, there are two scenarios: - The node operates on a single ASE object. - The node operates on a list of ASE objects. For both scenarios, the node is given a list of ASE objects via the data attribute. For the first scenario, the id of the ASE object is given via the data_id attribute which is omitted for the second scenario.

Abstract base classes and type hints.

class mlipx.abc.ASEKeys(value, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)

formation_energy = 'formation_energy'

isolated_energies = 'isolated_energies'

class mlipx.abc.ComparisonResults

figures: Dict[str, Figure]

frames: List[Atoms]

class mlipx.abc.DynamicsModifier

abstract modify(thermostat, step, total_steps) → None

property name: str

class mlipx.abc.DynamicsObserver

abstract check(atoms: Atoms) → bool

initialize(atoms: Atoms) → None

property name: str

class mlipx.abc.NodeWithCalculator(*args, **kwargs)

get_calculator(**kwargs) → Calculator

Load the ASE calculator for the desired MLIP.

get_spec() → dict | None

Get the meta data specification of the MLIP.

For details on the metadata specification, see: https://mlipx.readthedocs.io/en/latest/contributing.html#new-nodes

class mlipx.abc.NodeWithMolecularDynamics(*args, **kwargs)

get_molecular_dynamics(atoms: Atoms) → MolecularDynamics

class mlipx.abc.Optimizer(value, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)

BFGS = 'BFGS'

FIRE = 'FIRE'

LBFGS = 'LBFGS'

class mlipx.abc.ProcessAtoms(*, name: str | None = None, always_changed: bool = False, data: list[ase.atoms.Atoms], data_id: int = -1, frames_path: pathlib.Path = PosixPath('$nwd$/frames.h5'))

static compare(*nodes: ProcessAtoms) → ComparisonResults

data: list[Atoms]

data_id: int = -1

property figures: Dict[str, Figure]

property frames: List[Atoms]

frames_path: Path = PosixPath('$nwd$/frames.h5')

class mlipx.abc.ProcessFrames(*, name: str | None = None, always_changed: bool = False, data: list[ase.atoms.Atoms])

data: list[Atoms]