def test_2d_replication(self, betacristobalite):
nx = 2
ny = 2
nz = 1
tiled = TiledCompound(betacristobalite, [nx, ny, nz])
assert tiled.n_particles == 1900 * nx * ny
assert tiled.n_bonds == 2400 * nx * ny
for at in tiled.particles():
if at.name.startswith("Si"):
assert len(tiled.bond_graph.neighbors(at)) <= 4
elif at.name.startswith("O"):
assert len(tiled.bond_graph.neighbors(at)) <= 2
def test_no_replication(self, betacristobalite):
nx = 1
ny = 1
nz = 1
tiled = TiledCompound(betacristobalite, [nx, ny, nz])
assert tiled.n_particles == 1900 * nx * ny
assert tiled.n_bonds == 2400 * nx * ny
def test_negative_periodicity(self, betacristobalite):
nx = -2
ny = 3
nz = 2
with pytest.raises(ValueError):
TiledCompound(betacristobalite, [nx, ny, nz])
def test_incorrect_periodicity(self, betacristobalite):
nx = 2
ny = 2
nz = 2
with pytest.raises(ValueError):
TiledCompound(betacristobalite, [nx, ny, nz])
if surface_roughness == 1.0:
mb.load(
"amorphous_silica_sr1.0.pdb",
compound=self,
relative_to_module=self.__module__,
)
self.periodicity = (True, True, False)
self.box = mb.Box([5.4366, 4.7082, 1.0])
else:
raise ValueError(
"Amorphous silica input file with surface "
"roughness of {0:.1f} does not exist. If you have "
"this structure, please submit a pull request to "
"add it! ".format(surface_roughness))
count = 0
for particle in list(self.particles()):
if particle.name == "OB":
count += 1
port = mb.Port(anchor=particle,
orientation=[0, 0, 1],
separation=0.1)
self.add(port, "port_{}".format(count))
if __name__ == "__main__":
from mbuild.lib.recipes import TiledCompound
single = AmorphousSilicaSurface()
multiple = TiledCompound(single, n_tiles=(2, 1, 1), name="tiled")
multiple.save("amorphous_silica_surface.mol2")
def __init__(
self,
surface,
chains,
fractions=None,
backfill=None,
pattern=None,
tile_x=1,
tile_y=1,
**kwargs
):
from mbuild.lib.recipes import TiledCompound
super(Monolayer, self).__init__()
# Replicate the surface.
tiled_compound = 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))
warn("\n Adding {} of chain {}".format(n_points, chain))
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.")
# Attach final chain type. Remaining sites get a backfill.
warn("\n Adding {} of chain {}".format(len(pattern), chains[-1]))
attached_chains, backfills = pattern.apply_to_compound(
guest=chains[-1],
host=self["tiled_surface"],
backfill=backfill,
**kwargs
)
self.add(attached_chains)
self.add(backfills)