sponge.control.SETTLE

class sponge.control.SETTLE(system: Molecule, index: Union[Tensor, ndarray, List[int]] = None, # (B, C, 3)                 distance: Union[Tensor, ndarray, List[float]] = None, # (B, C, 2))

SETTLE constraint controller.

Reference Shuichi Miyamoto and Peter A. Kollman. SETTLE An Analytical Version of the SHAKE and RATTLE Algorithm for Rigid Water Models.

Parameters

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

• index (Union[Tensor, ndarray, List[int]], optional) – Array of settle index of shape $(C,3)$ or $(B,C,3)$, and the data type is int. If None is given, the settle_index in system will be used. Default: None.

• distance (Union[Tensor, ndarray, List[float]], optional) – Array of settle distance of shape $(C,2)$ or $(B,C,2)$, and the type is float. If None is given, the settle_dis in system will be used. 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 SETTLE
>>> system = Molecule(template='water.tip3p.yaml')
>>> controller = SETTLE(system)

apply_transform(q: Tensor, vec: Tensor)

Apply the quaternion transform q to a given vector vec.

Parameters

• q (Tensor) – The transform quaternion.

• vec (Tensor) – The vector to be transformed.

Returns

Tensor, The transformed vector.

get_inverse(quater: Tensor)

Get the inverse operation of a given quaternion.

Parameters

quater (Tensor) – The given quaternion.

Returns

Tensor, $quate{r}^{-1}$.

get_mass_center(crd_)

Get the mass center of a given molecule.

Parameters

crd (Tensor) – The coordinates.

Returns

Tensor, The mass center of the molecule.

get_transform(crd_)

Get the transform between A0B0C0 and a0b0c0.

Parameters

crd (Tensor) – The given water molecular coordinates.

Returns

This function will return the transform and inverse transform from crd_ SETTLE axis.

get_vector_transform(vec1: Tensor, vec2: Tensor)

Get the transform quaternion from a vector to another.

Parameters

• vec1 (Tensor) – The initial vector.

• vec2 (Tensor) – The target vector.

Returns

Tensor, the transform quaternion.

get_vel_force_update(crd0_, vel0_)

Get the update of velocity and force.

Parameters

• crd0 (Tensor) – The coordinate after SETTLE in the origin axis.

• vel0 (Tensor) – The initial velocity.

Returns

Tensor, The constraint velocity. Tensor, The constraint force.

group_hamiltonian_product(q, vec)

Perform hamiltonian product in a 4-dimensional vector.

Parameters

• q (Tensor) – The transform quaternion.

• vec (Tensor) – The vector to be transformed.

Returns

Tensor, The Hamiltonian product of q and v, $qv{q}^{-1}$.

hamiltonian_product(q, v)

Perform Hamiltonian product.

Parameters

• q (Tensor) – The transform quaternion.

• v (Tensor) – The vector to be transformed.

Returns

Tensor, The Hamiltonian product of q and v, $qv{q}^{-1}$.

quaternion_multiply(tensor_1: Tensor, tensor_2: Tensor)

Calculate the quaternion multiplication.

Parameters

• tensor_1 (Tensor) – The first quaternion, if the size of last dimension is 3, it will be padded to 4 auto.

• tensor_2 (Tensor) – The second quaternion, if the size of last dimension is 3, it will be padded to 4 auto.

Returns

Tensor, the quaternion product of tensor_1 and tensor_2.