pestifer.util.linkcell module

Custom link-cell algorithm for pair-wise searches in 3D space The Linkcell object is used by the RingCheck algorithm to detect pierced rings

class pestifer.util.linkcell.Linkcell(corners: ndarray = array([[0., 0., 0.], [100., 100., 100.]]), cutoff: float = 10.0, atidxlabel: str = 'serial', atposlabel: list[str] = ['x', 'y', 'z'])

Bases: object

A class for implementing the link-cell algorithm for pairwise distance calculations in 3D space.

Parameters:

• corners (np.ndarray, optional) – A 2x3 array defining the lower left and upper right corners of the simulation box in Angstroms. Default is a box from (0,0,0) to (100,100,100).

• cutoff (float, optional) – The cutoff distance for the link-cell algorithm in Angstroms. Default is 10.0.

• atidxlabel (str, optional) – The label for the atom index in the link-cell structure. Default is ‘serial’.

• atposlabel (list, optional) – A list of labels for the atom positions in the link-cell structure. Default is [‘x’, ‘y’, ‘z’].

cellndx_of_ldx(i: int)

Returns (i,j,k)-index of cell with scalar index i

Parameters:

i (int) – The scalar index of the cell.

Returns:

A 3-element array representing the (i,j,k) index of the cell with scalar index i.

Return type:

np.ndarray

cellndx_of_point(R: ndarray)

Returns the (i,j,k) cell index of point R

Parameters:

R (np.ndarray) – A 3-element array representing the coordinates of the point.

Returns:

A 3-element array representing the (i,j,k) index of the cell containing the point R.

Return type:

np.ndarray

ldx_of_cellndx(C: ndarray)

Returns scalar index of cell with (i,j,k)-index C

Parameters:

C (np.ndarray) – A 3-element array representing the (i,j,k) index of the cell

Returns:

The scalar index of the cell with (i,j,k)-index C.

Return type:

int

ldx_searchlist_of_ldx(i: int)

Returns the list of cells to search around and including central cell i.

Parameters:

i (int) – The scalar index of the central cell.

wrap_point(ri: ndarray)

Wraps point ri into the base periodic image

Parameters:

ri (np.ndarray) – A 3-element array representing the coordinates of the point to be wrapped.

Returns:

A tuple containing:

• R: The wrapped coordinates of the point.

• box_lengths: An array indicating how many times the point was wrapped in each dimension.

Return type:

tuple