sponge.partition.GridNeighbours

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class sponge.partition.GridNeighbours(cutoff: float, coordinate: Tensor, pbc_box: Tensor = None, atom_mask: Tensor = None, exclude_index: Tensor = None, num_neighbours: int = None, cell_capacity: int = None, num_cell_cut: int = 1, cutoff_scale: float = 1.2, cell_cap_scale: float = 1.25, grid_num_scale: float = 1.5)[source]

Neighbour list calculated by grids

Parameters

  • cutoff (float) – Cutoff distance.

  • coordinate (Tensor) – Tensor of shape \((B, A, D)\). Data type is float32. position coordinates of atoms in the simulation system.

  • pbc_box (Tensor, optional) – Tensor of shape \((B, A, D)\). Data type is float32. Box size of periodic boundary condition. Default: None.

  • atom_mask (Tensor, optional) – Tensor of shape \((B, A)\). Data type is bool_. Mask of atoms in the system. Default: None.

  • exclude_index (Tensor, optional) – Tensor of shape \((B, A, Ex)\). Data type is int32. Index of neighbour atoms which could be excluded from the neighbour list. Default: None.

  • num_neighbours (int, optional) – 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.

  • cell_capacity (int, optional) – Capacity number of atoms in grid cell. If None is given, this value will be multiplied by a factor of the maximum number of atoms in the grid cell at the initial coordinate. Default: None.

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

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

  • cell_cap_scale (float, optional) – Factor to scale cell_capacity. Default: 1.25

  • grid_num_scale (float, optional) – Scale factor to calculate num_neighbours by the ratio of grids. If num_neighbours is not None, it will not be used. Default: 1.5

Note

  • B: Number of simulation walker.

  • A: Number of atoms in system.

  • N: Number of neighbour atoms.

  • D: Dimension of position coordinates.

  • Ex: Maximum number of excluded neighbour atoms.

Supported Platforms:

Ascend GPU

Examples

>>> import sponge
>>> from sponge.partition import GridNeighbours
>>> import mindspore
>>> from mindspore import Tensor
>>> coordinate = Tensor([[[0.0, 0.0, 0.0], [0.0, 0.0, 1.0]]])
>>> grid_neighbours = GridNeighbours(0.5, coordinate)
>>> grid_neighbours(coordinate)
(Tensor(shape=[1, 2, 2], dtype=Int32, value=
 [[[0, 1],
 [0, 1]]]),
 Tensor(shape=[1, 2, 2], dtype=Bool, value=
 [[[False,  True],
 [ True, False]]]))
check_neighbour_list()[source]

check the number of neighbouring atoms in neighbour list

get_neighbours_from_grids(atom_grid_idx: Tensor, num_neighbours: int)[source]

Get neighbour list from grids.

Parameters

  • atom_grid_idx (Tensor) – Tensor of shape \((B, A, D)\). Data type is int. Grid index for each atom.

  • num_neighbours (int) – Number of neighbour atoms.

print_info()[source]

Print information of neighbour list.

set_exclude_index(exclude_index: Tensor)[source]

Set excluded neighbour index.

Parameters

exclude_index (Tensor) – Tensor of shape \((B, A, Ex)\). Data type is int. Index of atoms that should be exclude from neighbour list.