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sponge.partition.NeighbourList

class sponge.partition.NeighbourList(system: Molecule, cutoff: float = None, pace: int = 20, exclude_index: Tensor = None, num_neighbours: int = None, num_cell_cut: int = 1, cutoff_scale: float = 1.2, cell_cap_scale: float = 1.25, grid_num_scale: float = 2, use_grids: bool = False, cast_fp16: bool = False)

Neighbour list

Parameters

• system (Molecule) – Simulation system.

• cutoff (float, optional) – Cut-off distance. If None is given under periodic boundary condition (PBC), the cutoff will be assigned with the default value of 1 nm. Default: None.

• pace (int, optional) – Update frequency for neighbour list. Default: 20

• exclude_index (Tensor, optional) – Tensor of the indices of the neighbouring atoms which could be excluded from the neighbour list. The shape of Tensor is $(B,A,Ex)$, and the data type is int. Default: None.

• num_neighbours (int, optional) – Maximum number of neighbours. If None is given, this value will be calculated by the ratio of the number of neighbouring grids to the total number of grids. Default: None.

• num_cell_cut (int, optional) – Number of subdivision of grid cells according to cutoff. Default: 1

• cutoff_scale (float, optional) – Factor to scale cutoff distance. Default: 1.2

• cell_cap_scale (float, optional) – Scale factor for cell_capacity. Default: 1.25

• grid_num_scale (float, optional) – Scale factor to calculate num_neighbours by ratio of grids. If num_neighbours is not None, it will not be used. Default: 2

• use_grids (bool, optional) – Whether to use grids to calculate the neighbour list. Default: None.

• cast_fp16 (bool, optional) – If this is set to True, the data will be cast to float16 before sort. For use with some devices that only support sorting of float16 data. Default: False.

Note

• B: Batchsize, i.e. number of walkers of the simulation.

• A: Number of the atoms in the simulation system.

• N: Number of the maximum neighbouring atoms.

• D: Dimension of position coordinates.

• Ex: Maximum number of excluded neighbour atoms.

Supported Platforms:

Ascend GPU

Examples

>>> import sponge
>>> from sponge.partition import NeighbourList
>>> from sponge.system import Molecule
>>> system = Molecule(template='water.spce.yaml')
>>> neighbourlist = NeighbourList(system, 0.5)
>>> neighbourlist(system.coordinate, system.pbc_box)
(Tensor(shape=[1, 3, 2], dtype=Int64, value=
 [[[1, 2],
 [0, 2],
 [0, 1]]]),
 Tensor(shape=[1, 3, 2, 3], dtype=Float32, value=
 [[[[ 8.16490427e-02,  5.77358976e-02,  0.00000000e+00],
     [-8.16490427e-02,  5.77358976e-02,  0.00000000e+00]],
 [[-8.16490427e-02, -5.77358976e-02,  0.00000000e+00],
     [-1.63298085e-01,  0.00000000e+00,  0.00000000e+00]],
 [[ 8.16490427e-02, -5.77358976e-02,  0.00000000e+00],
     [ 1.63298085e-01,  0.00000000e+00,  0.00000000e+00]]]]),
 Tensor(shape=[1, 3, 2], dtype=Float32, value=
 [[[ 1.00000001e-01,  1.00000001e-01],
 [ 1.00000001e-01,  1.63298085e-01],
 [ 1.00000001e-01,  1.63298085e-01]]]),
 Tensor(shape=[1, 3, 2], dtype=Bool, value=
 [[[ True,  True],
 [ True,  True],
 [ True,  True]]]))
>>> neighbourlist.calculate(system.coordinate, system.pbc_box)
(Tensor(shape=[1, 3, 2], dtype=Int64, value=
 [[[1, 2],
 [0, 2],
 [0, 1]]]),
 Tensor(shape=[1, 3, 2], dtype=Bool, value=
 [[[ True,  True],
 [ True,  True],
 [ True,  True]]]))
>>> neighbourlist.pace
20

calculate(coordinate: Tensor, pbc_box: Tensor = None)

calculate neighbour list.

Parameters

• coordinate (Tensor) – Tensor of shape $(B,A,D)$. Data type is float. Position coordinate.

• pbc_box (Tensor, optional) – Tensor of shape $(B,D)$. Data type is float. Size of PBC box.

Returns

neigh_idx (Tensor), Tensor of shape $(B,A,N)$. Data type is int. Index of neighbouring atoms of each atoms in system.

neigh_mask (Tensor), Tensor of shape $(B,A,N)$. Data type is bool. Mask for neighbour list neigh_idx.

Note

• B: Batchsize, i.e. number of walkers of the simulation.

• A: Number of the atoms in the simulation system.

• N: Number of the maximum neighbouring atoms.

• D: Dimension of position coordinates.

get_neighbour_list()

get neighbour list.

Returns

neigh_idx (Tensor), Tensor of shape $(B,A,N)$. Data type is int. Index of neighbouring atoms of each atoms in system.

neigh_mask (Tensor):, Tensor of shape $(B,A,N)$. Data type is bool. Mask for neighbour list neigh_idx.

Note

• B: Batchsize, i.e. number of walkers of the simulation.

• A: Number of the atoms in the simulation system.

• N: Number of the maximum neighbouring atoms.

property pace: int

Update frequency for neighbour list

Returns

int, update pace

print_info()

print information of neighbour list

set_exclude_index(exclude_index: Tensor)

set exclude index

Parameters

exclude_index (Tensor) – Tensor of shape $(B,A,Ex)$. Data type is int.

update(coordinate: Tensor, pbc_box: Tensor = None)

update neighbour list.

Parameters

• coordinate (Tensor) – Tensor of shape $(B,A,D)$. Data type is float. Position coordinate.

• pbc_box (Tensor, optional) – Tensor of shape $(B,D)$. Data type is float. Size of PBC box.

Returns

neigh_idx (Tensor), Tensor of shape $(B,A,N)$. Data type is int. Index of neighbouring atoms of each atoms in system.

neigh_mask (Tensor), Tensor of shape $(B,A,N)$. Data type is bool. Mask for neighbour list neigh_idx.

Note

• B: Batchsize, i.e. number of walkers of the simulation.

• A: Number of the atoms in the simulation system.

• N: Number of the maximum neighbouring atoms.

• D: Dimension of position coordinates.