class matlantis_features.features.md.ase_integrators.AndersenIntegrator(timestep: float, temperature: float, andersen_prob: float = 0.01, fixcm: bool = True, random_seed: int = 0)#

Bases: ASEIntegrator

Andersen thermostat integrator generating NVT ensemble, using the ASE backend.

Methods

__init__(timestep, temperature[, …])

Create the Andersen integrator.

create_ase_dynamics(atoms)

Create the ASE’s Dynamics object.

set_temperature(value)

Set the target temperature of integrator.
__init__(timestep: float, temperature: float, andersen_prob: float = 0.01, fixcm: bool = True, random_seed: int = 0)#

Create the Andersen integrator.

Parameters

  • timestep (float) – Integration time step in fs unit.

  • temperature (float) – Target temperature of the integrator in K unit.

  • andersen_prob (float, optional) – A random collision probability (0-1).
    with this probability, atoms get assigned random velocity components.
    Defaults to 0.01.

  • fixcm (bool, optional) – If True, the position and momentum of the center of mass is kept unperturbed.
    Defaults to True.

  • random_seed (int, optional) – Random number generator’s seed used for the simulation.
    Defaults to 0.

create_ase_dynamics(atoms: Atoms) → Dynamics#

Create the ASE’s Dynamics object.

Parameters

atoms (Atoms) – ASE’s Atoms object containing the system to simulate.

Returns

ASE’s Dynamics object.

Return type

Dynamics

set_temperature(value: float) → None#

Set the target temperature of integrator.

If this integrator does not support temperature control,
this method raises the NotImplementedError exception.

Parameters

value (float) – Temperature in K unit.