sponge.partition.IndexColvar

class sponge.partition.IndexColvar(use_pbc: bool = None)

Collective variables based on index

Parameters

use_pbc (bool, optional) – Whether to calculate the CV at periodic boundary condition (PBC). If None is given, it will be determined at runtime based on whether the pbc_box is given or not. Default: None.

Supported Platforms:

Ascend GPU

set_pbc(use_pbc: bool)

Set periodic boundary condition

Parameters

use_pbc (bool) – Whether to calculate the CV at periodic boundary condition (PBC). If None is given, it will be determined at runtime based on whether the pbc_box is given or not.

vector_in_pbc(vector: Tensor, pbc_box: Tensor)

Make the difference of vecters at the range from -0.5 box to 0.5 box.

Parameters

• vector (Tensor) – Tensor of shape \((B, A, D)\). Data type is float. Coordinate of system

• pbc_box (Tensor) – Tensor of shape \((B, D)\). Data type is float. Periodic boundary condition Box.