1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
|
import pytest
import numpy as np
from ase.parallel import world
from ase.build import molecule, fcc111
from ase.build.attach import (attach, attach_randomly,
attach_randomly_and_broadcast)
def test_attach_molecules():
"""Attach two molecules and check that their minimal distance
is as required"""
m1 = molecule('C6H6')
m2 = molecule('NH3')
distance = 2.
m12 = attach(m1, m2, distance)
dmin = np.linalg.norm(m12[15].position - m12[8].position)
assert dmin == pytest.approx(distance, 1e-8)
def test_attach_to_surface():
"""Attach a molecule to a surafce at a given distance"""
slab = fcc111('Al', size=(3, 2, 2), vacuum=10.0)
mol = molecule('CH4')
distance = 3.
struct = attach(slab, mol, distance, (0, 0, 1))
dmin = np.linalg.norm(struct[10].position - struct[15].position)
assert dmin == pytest.approx(distance, 1e-8)
def test_attach_randomly():
"""Attach two molecules in random orientation."""
m1 = molecule('C6H6')
m2 = molecule('CF4')
distance = 2.5
if world.size > 1:
"Check that the coordinates are correctly distributed from master."
rng = np.random.RandomState(world.rank) # ensure different seed
atoms = attach_randomly_and_broadcast(m1, m2, distance, rng)
p0 = 1. * atoms[-1].position
world.broadcast(p0, 0)
for i in range(1, world.size):
pi = 1. * atoms[-1].position
world.broadcast(pi, i)
assert pi == pytest.approx(p0, 1e-8)
"Check that every core has its own structure"
rng = np.random.RandomState(world.rank) # ensure different seed
atoms = attach_randomly(m1, m2, distance, rng)
p0 = 1. * atoms[-1].position
world.broadcast(p0, 0)
for i in range(1, world.size):
pi = 1. * atoms[-1].position
world.broadcast(pi, i)
assert pi != pytest.approx(p0, 1e-8)
rng = np.random.RandomState(42) # ensure the same seed
pos2_ac = np.zeros((5, 3))
N = 25
for i in range(N):
atoms = attach_randomly(m1, m2, distance, rng=rng)
pos2_ac += atoms.get_positions()[12:, :]
# the average position should be "zero" approximately
assert (np.abs(pos2_ac / N) <= 1).all()
|
