Simulation State¶

Holds all the information of the current state of a simulation.

This object is populated during a simulation and is processed by the loggers of a simulation.

When running batched simulations, some of the fields may be of type list[numpy.ndarray] instead of just numpy.ndarray.

atomic_numbers¶

The atomic numbers of the system.

Type:: numpy.ndarray | list[numpy.ndarray] | None

positions¶

The positions along the trajectory. Has shape M x N x 3, with M being the number of steps divided by the logging interval, and N being the number of atoms of the system. The unit is Angstrom.

Type:: numpy.ndarray | list[numpy.ndarray] | None

forces¶

The forces along the trajectory with the same shape as the positions. The unit is eV / Angstrom.

Type:: numpy.ndarray | list[numpy.ndarray] | None

velocities¶

The velocities along the trajectory with the same shape as the positions, in units of \(\sqrt{eV/u}\).

Type:: numpy.ndarray | list[numpy.ndarray] | None

temperature¶

The temperatures along the trajectory in Kelvin.

Type:: numpy.ndarray | list[numpy.ndarray] | None

kinetic_energy¶

The total kinetic energy along the trajectory in eV.

Type:: numpy.ndarray | list[numpy.ndarray] | None

cell¶

The cell vectors along the trajectory, with shape M x 3 x 3. The unit is Angstrom.

Type:: numpy.ndarray | list[numpy.ndarray] | None

potential_energy¶

The total potential energy along the trajectory in eV.

Type:: numpy.ndarray | list[numpy.ndarray] | None

partial_charges¶

The partial charges of each system along the trajectory.

Type:: numpy.ndarray | list[numpy.ndarray] | None

step¶

The current number of steps performed.

Type:: int

compute_time_seconds¶

The compute time in seconds used so far for the run (not including logging times).

Type:: float

__init__(atomic_numbers: ndarray | list[ndarray] | None = None, positions: ndarray | list[ndarray] | None = None, forces: ndarray | list[ndarray] | None = None, velocities: ndarray | list[ndarray] | None = None, temperature: ndarray | list[ndarray] | None = None, kinetic_energy: ndarray | list[ndarray] | None = None, cell: ndarray | list[ndarray] | None = None, potential_energy: ndarray | list[ndarray] | None = None, partial_charges: ndarray | list[ndarray] | None = None, step: int = 0, compute_time_seconds: float = 0.0) → None¶

Simulation state for Nudged Elastic Band (NEB) transition state searches.

Inherits all the fields from SimulationState and adds one new one.

forces_real¶

Per-image physical forces from the force-field calculator, evaluated at each image’s current geometry before any NEB modification, meaning without the band-tangent projection or spring forces between images that are applied to the inherited forces field. Endpoints are included. Shape: (num_images, num_atoms, 3) per snapshot, unit eV/Å.

Type:: numpy.ndarray | list[numpy.ndarray] | None

__init__(atomic_numbers: ndarray | list[ndarray] | None = None, positions: ndarray | list[ndarray] | None = None, forces: ndarray | list[ndarray] | None = None, velocities: ndarray | list[ndarray] | None = None, temperature: ndarray | list[ndarray] | None = None, kinetic_energy: ndarray | list[ndarray] | None = None, cell: ndarray | list[ndarray] | None = None, potential_energy: ndarray | list[ndarray] | None = None, partial_charges: ndarray | list[ndarray] | None = None, step: int = 0, compute_time_seconds: float = 0.0, forces_real: ndarray | list[ndarray] | None = None) → None¶

Public simulation state returned to the user after a metadynamics run.

Extends SimulationState with per-step collective variable (CV) trajectories, bias potential values, and the full history of deposited Gaussian hills.

bias_cv_values¶

Values of the collective variables used by the bias potential along the trajectory. Has shape (num_snapshots, num_cvs).

Type:: numpy.ndarray | None

bias_potential¶

Bias potential values along the trajectory in eV. Has shape (num_snapshots,).

Type:: numpy.ndarray | None

gaussian_centers¶

Center of each deposited hill in CV space. Has shape (num_hills, num_cvs).

Type:: numpy.ndarray | None

gaussian_heights¶

Height of each deposited hill in eV. Has shape (n_hills,).

Type:: numpy.ndarray | None

__init__(atomic_numbers: ndarray | list[ndarray] | None = None, positions: ndarray | list[ndarray] | None = None, forces: ndarray | list[ndarray] | None = None, velocities: ndarray | list[ndarray] | None = None, temperature: ndarray | list[ndarray] | None = None, kinetic_energy: ndarray | list[ndarray] | None = None, cell: ndarray | list[ndarray] | None = None, potential_energy: ndarray | list[ndarray] | None = None, partial_charges: ndarray | list[ndarray] | None = None, step: int = 0, compute_time_seconds: float = 0.0, bias_cv_values: ndarray | None = None, bias_potential: ndarray | None = None, gaussian_centers: ndarray | None = None, gaussian_heights: ndarray | None = None) → None¶