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sponge.control.BerendsenBarostat

class sponge.control.BerendsenBarostat(system: Molecule, pressure: float = 1, anisotropic: bool = False, control_step: int = 1, compressibility: float = 4.6e-05, time_constant: float = 1.0, **kwargs)

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

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 (sponge.system.Molecule) – Simulation system.

• pressure (float, optional) – Reference pressure $P_{ref}$ in unit $bar$ for pressure coupling. Default: 1.0.

• anisotropic (bool, optional) – Whether to perform anisotropic pressure control. Default: False.

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

• compressibility (float, optional) – Isothermal compressibility $\beta$ in unit $ba{r}^{-1}$. Default: 4.6e-5.

• time_constant (float, optional) – Time constant ${\tau }_p$ in unit picosecond for pressure coupling. Default: 1.

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 BerendsenBarostat
>>> system = Molecule(template='water.tip3p.yaml')
>>> controller = BerendsenBarostat(system)

set_time_step(dt: float)

Set simulation time step.

Parameters

dt (float) – Simulation time step.

Returns

sponge.control.BerendsenBarostat, current object of sponge.control.BerendsenBarostat.