class matlantis_features.features.md.ase_integrators.NPTBerendsenIntegrator(timestep: float, temperature: float, pressure: float, taut: float = 500, taup: float = 1000, compressibility: float = 67.2, fixcm: bool = True)#

Bases: ASEIntegrator

Berendsen thermo/barostat integrator generating NPT ensemble, using the ASE backend.

Methods

__init__(timestep, temperature, pressure[, …])

Create Berendsen thermo/barostat 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, pressure: float, taut: float = 500, taup: float = 1000, compressibility: float = 67.2, fixcm: bool = True)#

Create Berendsen thermo/barostat integrator.

Parameters

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

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

  • pressure (float) – Target pressure of the integrator in atomic units (eV/Angstrom^3).

  • taut (float, optional) – Time constant for Berendsen temperature coupling in fs. Defaults to 500 fs.

  • taup (float, optional) – Time constant for Berendsen pressure coupling. Defaults to 1 ps.

  • compressibility (float, optional) – The compressibility of the material, in atomic units (Angstrom^3/eV).
    Defaults to 67.2.

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

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.