sponge.control.LeapFrog

class sponge.control.LeapFrog(system: Molecule, thermostat: Thermostat = None, barostat: Barostat = None, constraint: Constraint = None, **kwargs)

A leap-frog integrator based on "middle scheme" developed by Jian Liu, et al. It is a subclass of sponge.control.Integrator.

Reference Zhang, Z.; Yan, K; Liu, X.; Liu, J. A Leap-Frog Algorithm-based Efficient Unified Thermostat Scheme for Molecular Dynamics [J]. Chinese Science Bulletin, 2018, 63(33).

Parameters

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

• thermostat (sponge.control.Thermostat, optional) – Thermostat for temperature coupling. Default: None.

• barostat (sponge.control.Barostat, optional) – Barostat for pressure coupling. Default: None.

• constraint (sponge.control.Constraint, optional) – Constraint algorithm. 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 LeapFrog
>>> system = Molecule(template='water.tip3p.yaml')
>>> controller = LeapFrog(system)