import numpy as np
from ase.geometry import get_distances
from ase.parallel import broadcast, world
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 _ 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')
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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