sponge.control.Lincs

View Source On Gitee
class sponge.control.Lincs(system: Molecule, bonds: Union[Tensor, str] = 'h-bonds', potential: PotentialCell = None, **kwargs)[source]

A LINCS (LINear Constraint Solver) constraint module, which is a subclass of sponge.control.Constraint.

Parameters

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

  • bonds (Union[Tensor, str], optional) – Bonds to be constrained. This arguments accept a Tensor of shape \((K, 2)\) with data type int, or a string with value "h-bonds" or "all-bonds". Default: "h-bonds".

  • potential (sponge.potential.PotentialCell, optional) – Potential Cell. Default: None.

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