kliff.neighbor#

class kliff.neighbor.NeighborList(conf, infl_dist, padding_need_neigh=False)[source]#

Neighbor list class.

This uses the same approach that LAMMPS and KIM adopt: The atoms in the configuration (assuming a total of N atoms) are named contributing atoms, and padding atoms are created to satisfy the boundary conditions. The contributing atoms are numbered as 1, 2, … N-1, and the padding atoms are numbered as N, N+1, N+2… Neighbors of atom can include both contributing atoms and padding atoms.

Parameters

conf (Configuration) – atomic configuration.
infl_dist (float) – Influence distance, within which atoms are interacting with each other. In literatures, this is usually referred as cutoff.
padding_need_neigh (bool) – Whether to generate neighbors for padding atoms.

coords#: 2D array Coordinates of contributing and padding atoms.

species#: list Species string of contributing and padding atoms.

image#: 1D array Atom index, of which an atom is an image. The image of a contributing atom is itself.

padding_coords#: 2D array Coordinates of padding atoms.

padding_species#: list Species string and padding atoms.

padding_image#: 1D array Atom index, of which a padding atom is an image.

Note

To get the total force on a contributing atom, the forces on all padding atoms that are images of the contributing atom should be added back to the contributing atom.

create_neigh()[source]#

get_neigh(index)[source]#

Get the indices, coordinates, and species string of a given atom.

Parameters

index (int) – Atom number whose neighbor info is requested.

Returns

Indices of neighbor atoms in self.coords and self.species. neigh_coords: 2D array of shape (N, 3), where N is the number of neighbors.

Coordinates of neighbor atoms.

neigh_species: Species symbol of neighbor atoms.

Return type

neigh_indices

get_numneigh_and_neighlist_1D(request_padding=False)[source]#

Get the number of neighbors and neighbor list for all atoms.

Parameters

request_padding (bool) – If True, the returned number of neighbors and neighbor list include those for padding atoms; If False, only return these for contributing atoms.

Returns

1D array; number of neighbors for all atoms. neighlist: 1D array; indices of the neighbors for all atoms stacked into a

1D array. Its total length is sum(numneigh), and the first numneigh[0] components are the neighbors of atom 0, the next numneigh[1] components are the neighbors of atom 1 ….

Return type

numneigh

get_coords()[source]#

Return coords of both contributing and padding atoms. Shape (N,3).

Return type: array

get_species()[source]#

Return species of both contributing and padding atoms.

Return type: List[str]

get_species_code(mapping)[source]#

Integer species code of both contributing and padding atoms.

Parameters: mapping (Dict[str, int]) – A mapping between species string and its code.
Return type: array
Returns: 1D array of integer species code.

get_image()[source]#

Return image of both contributing and padding atoms.

It is a 1D array of atom index, of which an atom is an image.

Note

The image of a contributing atom is itself.

Return type: array

get_padding_coords()[source]#

Return coords of padding atoms, 2D array of shape (N,3), where N is the number of padding atoms.

Return type: array

get_padding_speices()[source]#

Return species string of padding atoms.

Return type: List[str]

get_padding_species_code(mapping)[source]#

Integer species code of padding atoms.

Parameters: mapping (Dict[str, int]) – A mapping between species string and its code.
Return type: array
Returns: 1D array of integer species code for padding atoms.

get_padding_image()[source]#

Return image of padding atoms.

It is a 1D array of atom index, of which a padding atom is an image.

Return type: array

kliff.neighbor.assemble_forces(forces, n, padding_image)[source]#

Assemble forces on padding atoms back to contributing atoms.

Parameters

forces (array) – Partial forces on both contributing and padding atoms. 2D array of shape (Nc+Np, 3). where Nc is the number of contributing atoms, and Np is the number of padding atoms. The first Nc rows are the forces for contributing atoms.
n (int) – Number of contributing atoms, i.e. Nc.
padding_image (array) – atom index, of which the padding atom is an image. 1D int array of shape (Np,).

Return type

array

Returns

Total forces on contributing atoms. 2D array of shape (Nc, 3), where Nc is the number of contributing atoms.

kliff.neighbor.assemble_stress(coords, forces, volume)[source]#

Calculate the virial stress using the negative f dot r method.

Parameters

coords (array) – Coordinates of both contributing and padding atoms. 2D array of shape (Nc+Np, 3), where Nc is the number of contributing atoms, and Np is the number of padding atoms. The first Nc rows are the coords of contributing atoms.
forces (array) – Partial forces on both contributing and padding atoms. 2D array of shape (Nc+Np, 3), where Nc is the number of contributing atoms, and Np is the number of padding atoms. The first Nc rows are the forces on contributing atoms.
volume (float) – Volume of the configuration.

Return type

array

Returns

Virial stress in Voigt notation. 1D array of shape (6,).