sponge.control.Constraint

class sponge.control.Constraint(system: Molecule, **kwargs)

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

The sponge.control.Constraint module is used for bond constraint. It controls the atomic coordinates, the atomic velocities, the atomic forces and the virial of the system during the simulation process.

Parameters

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

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