sponge.control.Integrator

class sponge.control.Integrator(system: Molecule, thermostat: Thermostat = None, barostat: Barostat = None, constraint: Union[Constraint, List[Constraint]] = None, **kwargs)

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

The sponge.control.Integrator module is used to control the atomic coordinates and velocities during the simulation process.

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 (Union[sponge.control.Constraint, List[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 Integrator
>>> system = Molecule(template='water.tip3p.yaml')
>>> controller = Integrator(system)

add_constraint(constraint: Constraint)

Add constraint algorithm for integrator.

Parameters

constraint (sponge.control.Constraint) – Constraint algorithm.

classmethod get_name(controller: Controller)

Get name of controller.

Parameters

controller (sponge.control.Controller) – Controller object.

set_barostat(barostat: Barostat)

Set barostat algorithm for integrator.

Parameters

barostat (sponge.control.Barostat) – Barostat algorithm.

set_constraint(constraint: Union[Constraint, List[Constraint]], num_constraints: int = 0)

Set constraint algorithm for integrator.

Parameters

• constraint (Union[sponge.control.Constraint, List[sponge.control.Constraint]]) – Constraint algorithm.

• num_constraints (int, optional) – Number of constraints. Default: 0.

set_degrees_of_freedom(dofs: int)

Set degrees of freedom (DOFs).

Parameters

dofs (int) – Degrees of freedom.

set_thermostat(thermostat: Thermostat)

Set thermostat algorithm for integrator.

Parameters

thermostat (sponge.control.Thermostat) – Thermostat algorithm.

set_time_step(dt: float)

Set simulation time step.

Parameters

dt (float) – Simulation time step.