sponge.control.Barostat

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

Base class for barostat module in MindSPONGE, which is a subclass of sponge.control.Controller.

The sponge.control.Barostat module is used for pressure coupling. It controls the atomic coordinates and the size of the PBC box of the system during the simulation process.

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: 1.0.

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

• time_constant (float, optional) – Time constant \(\tau_p\) in unit picosecond for pressure coupling. Default: 1.0.

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

property compressibility: mindspore.common.tensor.Tensor

Isothermal compressibility.

Returns

Tensor, isothermal compressibility.

property pressure: mindspore.common.tensor.Tensor

Reference pressure.

Returns

Tensor, reference pressure.

pressure_scale(sim_press: Tensor, ref_press: Tensor, ratio: float = 1)

Calculate the coordinate scale factor for pressure coupling.

Parameters

• sim_press (Tensor) – Current pressure.

• ref_press (Tensor) – Reference pressure.

• ratio (float, optional) – Ratio of pressure coupling. Default: 1.0

Returns

Tensor, scale factor for pressure coupling.

reconstruct_pressure(pressure: Union[float, ndarray, Tensor, List[float]])

Reset the reference pressure.

Parameters

pressure (Union[float, ndarray, Tensor, List[float]]) – pressure.

Returns

sponge.control.Barostat, current object of barostat.

set_pressure(pressure: Union[float, ndarray, Tensor, List[float]])

Set the value of reference pressure. The size of the pressure array must be equal to current pressure.

Parameters

pressure (Union[float, ndarray, Tensor, List[float]]) – pressure.

Returns

Tensor, reference pressure.