sponge.partition.IndexDistances

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class sponge.partition.IndexDistances(use_pbc: bool = None, large_dis: float = 100, keepdims: bool = False)[source]

Calculate distance between atoms by neighbour index

Parameters

  • use_pbc (bool, optional) – Whether to use periodic boundary condition. Default: None.

  • large_dis (float, optional) – A large value that added to the distance equal to zero to prevent them from becoming zero values after Norm operation, which could lead to auto-differentiation errors. Default: 100.0.

  • keepdims (bool, optional) – If this is True, the last axis will be left in the result as dimensions with size one. Default: False.

Supported Platforms:

Ascend GPU

Examples

>>> import sponge
>>> from sponge.partition import IndexDistances
>>> import mindspore
>>> from mindspore import Tensor
>>> idx_distances = IndexDistances(use_pbc=False)
>>> coordinate = Tensor([[[0.0, 0.0, 0.0], [0.0, 0.0, 1.0]]])
>>> index = Tensor([[[1],[0]]])
>>> print(idx_distances(coordinate, index))
[[[1.] [1.]]]