MLIP ASE Calculator

class mlip.simulation.ase.mlip_ase_calculator.MLIPForceFieldASECalculator(atoms: Atoms, edge_capacity_multiplier: float, force_field: ForceField, allow_nodes_to_change: bool = False, node_capacity_multiplier: float = 1.0)

Atomic Simulation Environment (ASE) Calculator for JAX models.

Implemented properties are energy and forces.

__init__(atoms: Atoms, edge_capacity_multiplier: float, force_field: ForceField, allow_nodes_to_change: bool = False, node_capacity_multiplier: float = 1.0) → None

Constructor.

Parameters:

  • atoms – Initial atomic structure.

  • edge_capacity_multiplier – Factor to multiply the number of edges by to obtain the edge capacity including padding.

  • force_field – Force field model used to compute the predictions.

  • allow_nodes_to_change – Whether the number or types of atoms/nodes may change for the same instance of this class. Defaults to False.

  • node_capacity_multiplier – Factor to multiply the number of nodes by to obtain the node capacity including padding. Defaults to 1.0.

calculate(atoms: Atoms | None = None, properties: list[str] | None = None, system_changes: list[str] = ['positions', 'numbers', 'cell', 'pbc', 'initial_charges', 'initial_magmoms']) → None

Compute properties (forces and/or energy) and save them in self.results dictionary for ASE simulation.

Parameters:

  • atoms – Atomic structure. Defaults to None.

  • properties – List of what needs to be calculated. Can be any combination of "energy", "forces". Defaults to None.

  • system_changes – List of what has changed since last calculation. Can be any combination of these six: "positions", "numbers", "cell", "pbc", initial_charges and "initial_magmoms". Defaults to ase.calculators.calculator.all_changes.

mlip.utils.no_pbc_cell.get_no_pbc_cell(positions: ndarray, graph_cutoff: float) → tuple[ndarray, ndarray]

Create a cell that contains all positions, with room to spare.

Parameters:

  • positions – A Nx3 array of the positions of the atoms in Angstrom.

  • graph_cutoff – The maximum distance for an edge to be computed between two atoms in Angstrom.

Returns:

A tuple of the cell, as an array of size 3, and a cell origin, as an array of size 3.