sponge.control.Brownian

class sponge.control.Brownian(system: Molecule, temperature: float = 300, friction_coefficient: float = 1000.0, **kwargs)

A Brownian integrator module, which is a subclass of sponge.control.Integrator.

Parameters

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

• temperature (float, optional) – Simulation temperature T (K). Default: 300.0.

• friction_coefficient (float, optional) – Friction coefficient g (amu/ps). Default: 1e3.

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

set_barostat(barostat: None = None)

Set barostat algorithm for integrator.

Parameters

barostat (None) – Barostat algorithm, which needs to be None for Brownian integrator. Default: None.

set_constraint(constraint: None = None, num_constraints: int = 0)

Set constraint algorithm for integrator.

Parameters

• constraint (None) – Constraint algorithm, which needs to be None for Brownian integrator. Default: None.

• num_constraints (int, optional) – Number of constraints. Default: 0.0.

set_thermostat(thermostat: None = None)

Set thermostat algorithm for integrator.

Parameters

thermostat (None) – Thermostat algorithm, which needs to be None for Brownian integrator. Default: None.

set_time_step(dt: float)

Set simulation time step.

Parameters

dt (float) – Simulation time step.