sponge.control.SETTLE

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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))[source]

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)[source]

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)[source]

Get the inverse operation of a given quaternion.

Parameters

quater (Tensor) – The given quaternion.

Returns

Tensor, \(quater^{-1}\).

get_mass_center(crd_)[source]

Get the mass center of a given molecule.

Parameters

crd (Tensor) – The coordinates.

Returns

Tensor, The mass center of the molecule.

get_transform(crd_)[source]

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)[source]

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_)[source]

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)[source]

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, \(q v q^{-1}\).

hamiltonian_product(q, v)[source]

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, \(q v q^{-1}\).

quaternion_multiply(tensor_1: Tensor, tensor_2: Tensor)[source]

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.