tightbinder.topology.specify_partition_shape#

specify_partition_shape(system, shape, center, r)[source]#

Routine to determine which atoms are inside of a partition of the system.

Parameters:

system (System) – System object to extract the motif positions.
shape (str) – Either ‘square’ or ‘circle’. Shape of the partition we are considering.
center (ndarray) – Array with the coordinates of the center of the shape.
r (float) – Radius of the shape; for a square it corresponds to its side.

Return partition:

Indices of atoms referred to the motif ordering which are inside the specified partition.

Return type:

ndarray

Returns:

Array with indices of atoms on a side.