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sponge.control.BerendsenThermostat

class sponge.control.BerendsenThermostat(system: Molecule, temperature: float = 300, control_step: int = 1, time_constant: float = 0.5, scale_min: float = 0.8, scale_max: float = 1.25, **kwargs)

A Berendsen (weak coupling) thermostat module, which is a subclass of sponge.control.Thermostat.

Reference Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F.; DiNola, A.; Haak, J. R.. Molecular Dynamics with Coupling to an External Bath [J]. The Journal of Chemical Physics, 1984, 81(8).

Parameters

• ( (system) – class: sponge.system.Molecule): Simulation system.

• temperature (float, optional) – Reference temperature $T_{ref}$ in unit Kelvin for temperature coupling. Default: 300.0.

• control_step (int, optional) – Step interval for controller execution. Default: 1.

• time_constant (float, optional) – Time constant ${\tau }_T$ in unit picosecond for temperature coupling. Default: 0.5.

• scale_min (float, optional) – The minimum value to clip the velocity scale factor. Default: 0.8.

• scale_max (float, optional) – The maximum value to clip the velocity scale factor. Default: 1.25.

Inputs:

• coordinate (Tensor) - Coordinate. Tensor of shape $(B,A,D)$. Data type is float. Here $B$ is the number of walkers in simulation, $A$ is the number of atoms and $D$ is the spatial dimension of the simulation system, which is usually 3.

• velocity (Tensor) - Velocity. Tensor of shape $(B,A,D)$. Data type is float.

• force (Tensor) - Force. Tensor of shape $(B,A,D)$. Data type is float.

• energy (Tensor) - Energy. Tensor of shape $(B,1)$. Data type is float.

• kinetics (Tensor) - Kinetics. Tensor of shape $(B,D)$. Data type is float.

• virial (Tensor) - Virial. Tensor of shape $(B,D)$. Data type is float.

• pbc_box (Tensor) - Pressure boundary condition box. Tensor of shape $(B,D)$. Data type is float.

• step (int) - Simulation step. Default: 0.

Outputs:

• coordinate, Tensor of shape $(B,A,D)$. Coordinate. Data type is float.

• velocity, Tensor of shape $(B,A,D)$. Velocity. Data type is float.

• force, Tensor of shape $(B,A,D)$. Force. Data type is float.

• energy, Tensor of shape $(B,1)$. Energy. Data type is float.

• kinetics, Tensor of shape $(B,D)$. Kinetics. Data type is float.

• virial, Tensor of shape $(B,D)$. Virial. Data type is float.

• pbc_box, Tensor of shape $(B,D)$. Periodic boundary condition box. Data type is float.

Supported Platforms:

Ascend GPU

Examples

>>> from sponge import Molecule
>>> from sponge.control import BerendsenThermostat
>>> system = Molecule(template='water.tip3p.yaml')
>>> controller = BerendsenThermostat(system)

set_time_step(dt)

Set simulation time step

Parameters

dt (float) – Simulation time step