sponge.control.AndersenBarostat

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

An Andersen barostat module, which is a subclass of Barostat.

Reference Andersen, Hans Christian. Molecular dynamics simulations at constant pressure and/or temperature [J]. Journal of Chemical Physics, 1980, 72.

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