def __init__(self, surface, chains, n_chains, seed, fractions=None,
backfill=None, **kwargs):
super(SurfaceMonolayer, self).__init__()
if surface.name == 'SilicaInterface' and n_chains > 0:
pattern = mb.Random2DPattern(n_chains, seed=seed)
elif surface.name == 'SilicaTip':
shift = 0.25
surface.translate_to([0, 0, 0])
surface.translate([0, 0, -1 * min(surface.xyz[:,2]) - shift])
radius = max(surface.xyz[:,2]) - min(surface.xyz[:,2])
pattern = RandomHemispherePattern(n=n_chains, seed=seed)
pattern.scale(radius)
elif surface.name == 'SilicaAsperity':
pass
else:
pattern = mb.Random2DPattern(n_chains, seed=seed)
if chains and n_chains > 0:
monolayer = Monolayer(surface=surface, chains=chains, pattern=pattern,
fractions=fractions, backfill=backfill, **kwargs)
else:
monolayer = Monolayer(surface=surface, chains=backfill, guest_port_name='up', **kwargs)
self.add(monolayer)
def test_apply_to_compound(self, betacristobalite, propyl, ch3):
pattern = mb.Random2DPattern(90)
chains, backfills = pattern.apply_to_compound(
guest=propyl, host=betacristobalite, backfill=ch3)
assert len(chains) == 90
assert len(backfills) == 10
with pytest.raises(AssertionError):
pattern = mb.Random2DPattern(101)
chains, backfills = pattern.apply_to_compound(
guest=propyl, host=betacristobalite, backfill=ch3)
def build_monolayer(chain_length, n_molecules, **kwargs):
from mbuild.examples import AlkaneMonolayer
pattern = mb.Random2DPattern(n_molecules)
monolayer = AlkaneMonolayer(pattern, tile_x=1, tile_y=1, chain_length=chain_length)
monolayer.name = 'alkane_n-{}_l-{}'.format(n_molecules, chain_length)
mb.translate(monolayer, [0, 0, 2])
return monolayer
def __init__(self, surface, chains, fractions=None, backfill=None, pattern=None,
tile_x=1, tile_y=1, rotate=True, seed=12345, **kwargs):
super(Monolayer, self).__init__()
# Replicate the surface.
tiled_compound = mb.recipes.TiledCompound(surface, n_tiles=(tile_x, tile_y, 1))
self.add(tiled_compound, label='tiled_surface')
if pattern is None: # Fill the surface.
pattern = mb.Random2DPattern(len(tiled_compound.referenced_ports()))
if isinstance(chains, mb.Compound):
chains = [chains]
if fractions:
fractions = list(fractions)
if len(chains) != len(fractions):
raise ValueError("Number of fractions does not match the number"
" of chain types provided")
n_chains = len(pattern.points)
# Attach chains of each type to binding sites based on
# respective fractions.
for chain, fraction in zip(chains[:-1], fractions[:-1]):
# Create sub-pattern for this chain type
subpattern = deepcopy(pattern)
n_points = int(round(fraction * n_chains))
pick = np.random.choice(subpattern.points.shape[0], n_points,
replace=False)
points = subpattern.points[pick]
subpattern.points = points
# Remove now-occupied points from overall pattern
pattern.points = np.array([point for point in pattern.points.tolist()
if point not in subpattern.points.tolist()])
# Attach chains to the surface
attached_chains, _ = subpattern.apply_to_compound(
guest=chain, host=self['tiled_surface'], backfill=None, **kwargs)
self.add(attached_chains)
else:
warn("\n No fractions provided. Assuming a single chain type.")
attached_chains, backfills = pattern.apply_to_compound(guest=chains[-1],
host=self['tiled_surface'], backfill=backfill, **kwargs)
self.add(attached_chains)
self.add(backfills)
if rotate:
np.random.seed(seed)
for chain in attached_chains:
rotation = np.random.random() * np.pi * 2.0
chain.spin(rotation, [0, 0, 1])
def build_monolayer(chain_length, n_molecules, **kwargs):
from mbuild.examples import AlkaneMonolayer
pattern = mb.Random2DPattern(n_molecules)
monolayer = AlkaneMonolayer(pattern,
tile_x=1,
tile_y=1,
chain_length=chain_length)
monolayer.name = 'alkane_n-{}_l-{}'.format(n_molecules, chain_length)
mb.translate(monolayer, [0, 0, 2])
box = monolayer.boundingbox
monolayer.periodicity += np.array([0, 0, 5 * box.lengths[2]])
return monolayer
def test_random_2d_seed(self):
pattern_a = mb.Random2DPattern(100, seed=12345)
pattern_b = mb.Random2DPattern(100, seed=12345)
assert np.array_equal(pattern_a, pattern_b)
def test_random_2d(self):
pattern = mb.Random2DPattern(100)
assert len(pattern) == 100
def alkane_monolayer(self):
from mbuild.examples import AlkaneMonolayer
pattern = mb.Random2DPattern(50, seed=1)
monolayer = AlkaneMonolayer(pattern=pattern)
return monolayer
