def test_apply_to_compound_noscale(self, betacristobalite, propyl):
pattern = mb.Grid2DPattern(3,3)
chains, _ = pattern.apply_to_compound(guest=propyl, host=betacristobalite,
scale=False)
chain_positions = [chain.pos for chain in chains]
for i, pos in enumerate(chain_positions):
for pos2 in chain_positions[i+1:]:
assert betacristobalite.min_periodic_distance(pos, pos2) < 1.5
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 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 test_grid_2d(self):
pattern = mb.Grid2DPattern(10, 5)
assert len(pattern) == 50
def __init__(self,
lipids,
ref_atoms,
n_lipids_x=10,
n_lipids_y=10,
area_per_lipid=1.0,
solvent=None,
lipid_box=None,
spacing_z=0.5,
solvent_per_lipid=None,
n_solvent=None,
random_seed=12345,
mirror=True):
super(Bilayer, self).__init__()
# Santitize inputs.
if sum([lipid[1] for lipid in lipids]) != 1.0:
raise ValueError('Lipid fractions do not add up to 1.')
assert len(ref_atoms) == len(lipids)
self.lipids = lipids
self.ref_atoms = ref_atoms
self._lipid_box = lipid_box
# 2D Lipid locations.
self.n_lipids_x = n_lipids_x
self.n_lipids_y = n_lipids_y
self.apl = area_per_lipid
self.n_lipids_per_layer = self.n_lipids_x * self.n_lipids_y
self.pattern = mb.Grid2DPattern(n_lipids_x, n_lipids_y)
self.pattern.scale(np.sqrt(self.apl * self.n_lipids_per_layer))
# Solvent info.
self.solvent = solvent
self.n_solvent = n_solvent
self.solvent_per_lipid = solvent_per_lipid
# Other inputs.
self.spacing = np.array([0, 0, spacing_z])
self.random_seed = random_seed
self.mirror = mirror
self._number_of_each_lipid_per_layer = []
self._solvent_per_layer = None
# Containers for lipids and solvent.
self.lipid_components = mb.Compound()
self.solvent_components = mb.Compound()
# Assemble the lipid layers
seed(self.random_seed)
top_layer, top_lipid_labels = self.create_layer()
self.lipid_components.add(top_layer)
if self.mirror == True:
bottom_layer, bottom_lipid_labels = self.create_layer(
lipid_indices=top_lipid_labels, flip_orientation=True)
else:
bottom_layer, bottom_lipid_labels = self.create_layer(
flip_orientation=True)
self.lipid_components.add(bottom_layer)
# solvate the lipids
#self.solvate_bilayer() # TODO: needs fixing
# add everything to the big list
self.add(self.lipid_components)
self.add(self.solvent_components)
print(self.number_of_each_lipid_per_layer)
def __init__(self, lipids, ref_atoms, n_lipids_x=10, n_lipids_y=10,
area_per_lipid=1.0, lipid_box=None, spacing_z=None,
solvent=None, solvent_per_lipid=None, n_solvent=None,
solvent_density=None, solvent_mass=None, tilt=0,
random_seed=12345, mirror=True):
super(Bilayer, self).__init__()
# Santitize inputs
i = 0
while i < len(lipids):
if lipids[i][1] == 0:
lipids.remove(i)
else:
i += 1
if sum([lipid[1] for lipid in lipids]) != 1.0:
raise ValueError('Lipid fractions do not add up to 1.')
assert len(ref_atoms) == len(lipids)
self.lipids = lipids
self.ref_atoms = ref_atoms
self._lipid_box = lipid_box
# 2D Lipid locations
self.n_lipids_x = n_lipids_x
self.n_lipids_y = n_lipids_y
self.apl = area_per_lipid
self.n_lipids_per_layer = self.n_lipids_x * self.n_lipids_y
self.pattern = mb.Grid2DPattern(n_lipids_x, n_lipids_y)
self.pattern.scale(np.sqrt(self.apl * self.n_lipids_per_layer))
# Z-orientation parameters
self.tilt = tilt
if spacing_z:
self.spacing = spacing_z
else:
self.spacing = max([lipid[0].boundingbox.lengths[2]
for lipid in self.lipids]) * np.cos(self.tilt)
# Solvent parameters
if solvent:
self.solvent = solvent
if solvent_per_lipid != None:
self.n_solvent = (self.n_lipids_x *
self.n_lipids_y *
2 * solvent_per_lipid)
elif n_solvent != None:
self.n_solvent = n_solvent
else:
raise ValueError("Requires either n_solvent_per_lipid ",
"or n_solvent arguments")
# Other parameters
self.random_seed = random_seed
self.mirror = mirror
# Initialize variables and containers for lipids and solvent
self.lipid_components = mb.Compound()
self.solvent_components = mb.Compound()
self._number_of_each_lipid_per_layer = []
# Assemble the lipid layers
seed(self.random_seed)
self.tilt_about = [random(), random(), 0]
top_layer, top_lipid_labels = self.create_layer()
self.lipid_components.add(top_layer)
if self.mirror == True:
bottom_layer, bottom_lipid_labels = self.create_layer(
lipid_indices=top_lipid_labels,
flip_orientation=True)
else:
bottom_layer, bottom_lipid_labels = self.create_layer(
flip_orientation=True)
bottom_layer.translate([0, 0, 0])
self.lipid_components.add(bottom_layer)
self.lipid_components.translate_to([0, 0, 0])
# Assemble solvent components
solvent_top = self.solvate(solvent_mass, solvent_density)
solvent_bot = mb.clone(solvent_top)
solvent_top.translate_to(
[0, 0, self.spacing + 0.5 * solvent_top.boundingbox.lengths[2]]
)
solvent_bot.translate_to(
[0, 0, -self.spacing - 0.5 * solvent_top.boundingbox.lengths[2]]
)
self.solvent_components.add(solvent_top)
self.solvent_components.add(solvent_bot)
# Add all compounds
self.add(self.lipid_components)
self.add(self.solvent_components)
