class matlantis_features.features.md.ase_md_system.ASEMDSystem(atoms: Union[Atoms, MatlantisAtoms], step: int = 0, time: float = 0.0)#

Bases: MDSystemBase

MD System using ASE backend.

Methods

__init__(atoms[, step, time])

Create MD System using ASE backend.

init_temperature(temperature[, stationary, …])

Initialize the velocities by the Maxwell-Boltzmann distribution of the specified temperature.
__init__(atoms: Union[Atoms, MatlantisAtoms], step: int = 0, time: float = 0.0)#

Create MD System using ASE backend.

Parameters

  • atoms (ASEAtoms or MatlantisAtoms) – ASE’s Atoms object representing the simulation system.

  • step (int, optional) – How many MD steps have been run before the task. Defaults to 0.

  • time (float, optional) – How long time (in fs) has it been simulated before the task. Defaults to 0.0.

init_temperature(temperature: float, stationary: bool = False, zero_rotation: bool = False, rng: Optional[RandomState] = None) → None#

Initialize the velocities by the Maxwell-Boltzmann distribution of the specified temperature.

Parameters

  • temperature (float) – Target temperature in K unit.

  • stationary (bool, optional) – If True, set the center-of-mass momentum to zero.
    Defaults to False.

  • zero_rotation (bool, optional) – If True, set the total angular momentum to zero by counteracting rigid rotations.
    Defaults to False.

  • rng (RandomState or None, optional) – Random number generator to generate the distribution.
    If None, the default generator of ASE implementation is used.
    Defaults to None.