sponge.control.LeapFrog

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

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)