Source code for ase.build.attach

import numpy as np

from ase.parallel import world, broadcast
from ase.geometry import get_distances


def random_unit_vector(rng):
    """Random unit vector equally distributed on the sphere

    Parameter
    ---------
    rng: random number generator object
    """
    ct = -1 + 2 * rng.random()
    phi = 2 * np.pi * rng.random()
    st = np.sqrt(1 - ct**2)
    return np.array([st * np.cos(phi), st * np.sin(phi), ct])


def nearest(atoms1, atoms2, cell=None, pbc=None):
    """Return indices of nearest atoms"""
    p1 = atoms1.get_positions()
    p2 = atoms2.get_positions()
    vd_aac, d2_aa = get_distances(p1, p2, cell, pbc)
    i1, i2 = np.argwhere(d2_aa == d2_aa.min())[0]
    return i1, i2, vd_aac[i1, i2]


[docs]def attach(atoms1, atoms2, distance, direction=(1, 0, 0), maxiter=50, accuracy=1e-5): """Attach two structures Parameters ---------- atoms1: Atoms cell and pbc of this object are used atoms2: Atoms distance: float minimal distance (Angstrom) direction: unit vector (3 floats) relative direction between center of masses maxiter: int maximal number of iterations to get required distance, default 100 accuracy: float required accuracy for minimal distance (Angstrom), default 1e-5 Returns ------- Joined structure as an atoms object. """ atoms = atoms1.copy() atoms2 = atoms2.copy() direction = np.array(direction, dtype=float) direction /= np.linalg.norm(direction) assert len(direction) == 3 dist2 = distance**2 i1, i2, dv_c = nearest(atoms, atoms2, atoms.cell, atoms.pbc) for i in range(maxiter): dv2 = (dv_c**2).sum() vcost = np.dot(dv_c, direction) a = np.sqrt(max(0, dist2 - dv2 + vcost**2)) move = a - vcost if abs(move) < accuracy: atoms += atoms2 return atoms # we need to move atoms2.translate(direction * move) i1, i2, dv_c = nearest(atoms, atoms2, atoms.cell, atoms.pbc) raise RuntimeError('attach did not converge')
[docs]def attach_randomly(atoms1, atoms2, distance, rng=np.random): """Randomly attach two structures with a given minimal distance Parameters ---------- atoms1: Atoms object atoms2: Atoms object distance: float Required distance rng: random number generator object defaults to np.random.RandomState() Returns ------- Joined structure as an atoms object. """ atoms2 = atoms2.copy() atoms2.rotate('x', random_unit_vector(rng), center=atoms2.get_center_of_mass()) return attach(atoms1, atoms2, distance, direction=random_unit_vector(rng))
[docs]def attach_randomly_and_broadcast(atoms1, atoms2, distance, rng=np.random, comm=world): """Randomly attach two structures with a given minimal distance and ensure that these are distributed. Parameters ---------- atoms1: Atoms object atoms2: Atoms object distance: float Required distance rng: random number generator object defaults to np.random.RandomState() comm: communicator to distribute Communicator to distribute the structure, default: world Returns ------- Joined structure as an atoms object. """ if comm.rank == 0: joined = attach_randomly(atoms1, atoms2, distance, rng) broadcast(joined, 0, comm=comm) else: joined = broadcast(None, 0, comm) return joined