amd.utils module

Helpful utility functions, e.g. unit cell diameter, converting cell parameters to Cartesian form, and an ETA class.

amd.utils.diameter(cell)

Diameter of a unit cell (as a square matrix in Cartesian form) in 3 or fewer dimensions.

amd.utils.cellpar_to_cell(a, b, c, alpha, beta, gamma)

Simplified version of function from ase.geometry of the same name. 3D unit cell parameters a,b,c,α,β,γ –> cell as 3x3 NumPy array.

amd.utils.cellpar_to_cell_2D(a, b, alpha)

2D unit cell parameters a,b,α –> cell as 2x2 ndarray.

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 (numpy.ndarray) – 2D distance matrix or 1D condensed distance matrix.

Returns

nn_dm, inds – 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[numpy.ndarray, numpy.ndarray]

amd.utils.lattice_cubic(scale=1, dims=3)

Return a pair (motif, cell) representing a hexagonal lattice, passable to amd.AMD() or amd.PDD().

amd.utils.lattice_hexagonal(scale=1)

Dimension 3 only. 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)

Dimensions 2 and 3 only. Random unit cell with uniformally chosen length and angle parameters between bounds.