def __init__(self, pattern, tile_x=1, tile_y=1, chain_length=10):
"""Create an alkylsilane monolayer on beta-cristobalite.
Parameters
----------
pattern : np.ndarray, shape=(n, 3), optional, default=None
An array of planar binding locations. If not provided, the entire
surface will be filled with `chain`.
tile_x : int, optional, default=1
Number of times to replicate substrate in x-direction.
tile_y : int, optional, default=1
Number of times to replicate substrate in y-direction.
chain_length : int, optional, default=10
Number of carbon atoms per chain.
"""
surface = Betacristobalite()
alkylsilane = AlkylSilane(chain_length)
hydrogen = H()
super(AlkaneMonolayer, self).__init__(surface,
alkylsilane,
backfill=hydrogen,
pattern=pattern,
tile_x=tile_x,
tile_y=tile_y)
# -- ==alkane_monolayer== --
def test_monolayer(self, ch2):
n = 8
m = 8
pattern = mb.Grid2DPattern(n, m)
chain = mb.Polymer(ch2, n=10)
monolayer = mb.Monolayer(surface=Betacristobalite(),
chains=chain,
backfill=H(),
pattern=pattern)
assert monolayer.n_particles == 1900 + n * m * (10 * 3) + (100 - n * m)
assert monolayer.n_bonds == 2400 + n * m * (10 * 2 + 9 + 1) + (100 -
n * m)
def __init__(self,
pattern,
tile_x=1,
tile_y=1,
chain_length=4,
alpha=pi / 4):
surface = Betacristobalite()
brush = Brush(chain_length=chain_length, alpha=alpha)
hydrogen = H()
super(PMPCLayer, self).__init__(surface,
brush,
backfill=hydrogen,
pattern=pattern,
tile_x=tile_x,
tile_y=tile_y)
def test_monolayer(self, ch2):
n = 8
m = 8
pattern = mb.Grid2DPattern(n, m)
chain = mb.recipes.Polymer(monomers=[ch2])
chain.build(n=10, add_hydrogens=False)
monolayer = mb.recipes.Monolayer(
surface=Betacristobalite(),
chains=chain,
backfill=H(),
pattern=pattern,
)
assert monolayer.n_particles == 2000 + n * m * 29
assert monolayer.n_bonds == 2500 + n * m * 29
def test_pattern_kwargs(self, ch2):
n = 8
m = 8
pattern = mb.Grid2DPattern(n, m)
chain = mb.Polymer(ch2, n=10)
monolayer = mb.Monolayer(surface=Betacristobalite(),
chains=H(),
guest_port_name='up',
backfill=chain,
backfill_port_name='down',
pattern=pattern)
chains = 100 - (n * m)
assert monolayer.n_particles == 1900 + chains * (10 * 3) + (100 -
chains)
assert monolayer.n_bonds == 2400 + chains * (10 * 2 + 9 + 1) + (100 -
chains)
def test_mixed_monolayer(self, ch2):
n = 8
m = 8
pattern = mb.Grid2DPattern(n, m)
fractions = [0.75, 0.25]
chain_a = mb.Polymer(ch2, n=5)
chain_b = mb.Polymer(ch2, n=15)
monolayer = mb.Monolayer(surface=Betacristobalite(),
chains=[chain_a, chain_b],
fractions=fractions,
backfill=H(),
pattern=pattern)
n_a = round(n * m * 0.75)
n_b = round(n * m * 0.25)
assert monolayer.n_particles == 1900 + n_a * 5 * 3 + n_b * 15 * 3 + (
100 - (n_a + n_b))
assert monolayer.n_bonds == 2400 + n_a * (5 * 2 + 4 + 1) + n_b * (
15 * 2 + 14 + 1) + (100 - (n_a + n_b))
def test_pattern_kwargs(self, ch2):
n = 8
m = 8
pattern = mb.Grid2DPattern(n, m)
chain = mb.recipes.Polymer(monomers=[ch2])
chain.build(n=10, add_hydrogens=False)
monolayer = mb.recipes.Monolayer(
surface=Betacristobalite(),
chains=H(),
guest_port_name="up",
backfill=chain,
backfill_port_name="down",
pattern=pattern,
)
chains = 100 - (n * m)
assert monolayer.n_particles == 2000 + chains * 29
assert monolayer.n_bonds == 2500 + chains * 29
def test_mixed_monolayer(self, ch2):
n = 8
m = 8
pattern = mb.Grid2DPattern(n, m)
fractions = [0.75, 0.25]
chain_a = mb.recipes.Polymer(monomers=[ch2])
chain_a.build(n=5, add_hydrogens=False)
chain_b = mb.recipes.Polymer(monomers=[ch2])
chain_b.build(n=15, add_hydrogens=False)
monolayer = mb.recipes.Monolayer(
surface=Betacristobalite(),
chains=[chain_a, chain_b],
fractions=fractions,
backfill=H(),
pattern=pattern,
)
n_a = round(n * m * 0.75)
n_b = round(n * m * 0.25)
assert monolayer.n_particles == 2000 + n_a * 14 + n_b * 44
assert monolayer.n_bonds == 2500 + n_a * 14 + n_b * 44
def betacristobalite(self):
from mbuild.lib.surfaces import Betacristobalite
return Betacristobalite()