sponge.control.Thermostat

class sponge.control.Thermostat(system: Molecule, temperature: Union[float, ndarray, Tensor, List[float]] = 300, control_step: int = 1, time_constant: float = 0.5, **kwargs)

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

The sponge.control.thermostat.Thermostat module is used for temperature coupling. It controls the atomic velocities and the kinetics of the system during the simulation process.

Parameters

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

• temperature (Union[float, ndarray, Tensor], optional) – Reference temperature $T_{ref}$ in unit Kelvin for temperature coupling. Default: 300.0.

• control_step (int, optional) – Step interval for controller execution. Default: 1.

• time_constant (float, optional) – Time constant ${\tau }_T$ in unit picosecond for temperature coupling. Default: 0.5.

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

get_ref_kinetics()

Get reference kinetics.

Returns

Tensor, reference kinetics.

reconstruct_temperature(temperature: Union[float, ndarray, Tensor, List[float]])

Reset the reference temperature.

Parameters

temperature (Union[float, ndarray, Tensor, List[float]]) – temperature.

property ref_kinetics: mindspore.common.tensor.Tensor

Reference kinetics.

Returns

Tensor, reference kinetics.

set_degrees_of_freedom(dofs: int)

Set degrees of freedom (DOFs).

Parameters

dofs (int) – degrees of freedom.

set_temperature(temperature: Union[float, ndarray, Tensor, List[float]])

Set the value of reference temperature. The size of the temperature array must be equal to current temperature.

Parameters

temperature (Union[float, ndarray, Tensor, List[float]]) – temperature.

property temperature: mindspore.common.tensor.Tensor

Reference temperature.

Returns

Tensor, reference temperature.

velocity_scale(sim_kinetics: Tensor, ref_kinetics: Tensor, ratio: float = 1)

Calculate the velocity scale factor for temperature coupling.

Parameters

• sim_kinetics (Tensor) – Simulation kinetics. Tensor of shape $(B,D)$. Data type is float.

• ref_kinetics (Tensor) – Reference kinetics. Tensor of shape $(B,D)$. Data type is float.

• ratio (float, optional) – Ratio of temperature coupling. Default: 1.

Returns

Tensor, velocity scale factor.