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Specifications and Common Mistakes

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sponge.control.VelocityVerlet

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

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

Reference Zhang, Z.; Liu, X.; Chen, Z.; Zheng, H.; Yan, K.; Liu, J. A Unified Thermostat Scheme for Efficient Configurational Sampling for Classical/Quantum Canonical Ensembles via Molecular Dynamics [J]. The Journal of Chemical Physics, 2017, 147(3).

Parameters

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

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

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

• constraint (sponge.control.Constraint) – 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 VelocityVerlet
>>> system = Molecule(template='water.tip3p.yaml')
>>> controller = VelocityVerlet(system)

set_velocity_half(velocity_half: Tensor)

set the veloctiy before half step