amd.utils module

Helpful utility functions.

amd.utils.neighbours_from_distance_matrix(n: int, dm: numpy.ndarray) → Tuple[numpy.ndarray, numpy.ndarray]

Given a distance matrix, find the n nearest neighbours of each item.

Parameters

n (int) – Number of nearest neighbours to find for each item.
dm (ndarray) – 2D distance matrix or 1D condensed distance matrix.

Returns

For item i, nn_dm[i][j] is the distance from item i to its j+1 st nearest neighbour, and inds[i][j] is the index of this neighbour (j+1 since index 0 is the first nearest neighbour).

Return type

tuple of ndarrays (nn_dm, inds)

amd.utils.diameter(cell): Diameter of a unit cell in 3 or fewer dimensions.

amd.utils.cellpar_to_cell(a, b, c, alpha, beta, gamma): Simplified version of function from ase.geometry. 3D unit cell parameters a,b,c,α,β,γ –> cell as 3x3 ndarray.

amd.utils.cellpar_to_cell_2D(a, b, alpha): UD unit cell parameters a,b,α –> cell as 2x2 ndarray.

amd.utils.lattice_cubic(scale=1, dims=3): Return a pair (motif, cell) representing a cubic lattice, passable to amd.AMD() or amd.PDD().

amd.utils.random_cell(length_bounds=(1, 2), angle_bounds=(60, 120), dims=3): Random unit cell.

class amd.utils.ETA(to_do, update_rate=100)

Bases: object

Pass total amount to do, then call .update() on every loop. This object will estimate an ETA and print it to the terminal.

update(): Call when one item is finished.