def _hexagonal(self):
"""Define hexagonal molecule.
Returns
-------
hex : Molecule
Hexagonal molecule object
"""
hex = Molecule()
hex.add("Si", [0, 0, 0])
hex.add("O", 0, r=self._b, theta=self._a, phi=60)
hex.add("Si", 1, r=self._b, bond=[0, 1])
hex.add("O", 2, r=self._b, theta=180, phi=0)
hex.add("Si", 3, r=self._b, bond=[2, 3])
hex.add("O", 4, r=self._b, theta=self._a, phi=300)
hex.add("Si", 5, r=self._b, bond=[4, 5])
hex.add("O", 6, r=-self._b, theta=self._a, phi=60)
hex.add("Si", 7, r=self._b, bond=[6, 7])
hex.add("O", 8, r=-self._b, theta=180, phi=0)
hex.add("Si", 9, r=self._b, bond=[8, 9])
hex.add("O", 10, r=-self._b, theta=self._a, phi=300)
hex.rotate("y", 90)
hex.rotate("z", 90)
hex.rotate("y", 180)
hex.rotate("x", geometry.angle(hex.bond(8, 6), [0, 1, 0]))
hex.rotate("x", -90)
return hex
def siloxane(self, sites, amount, normal, slx_dist=0.507, trials=1000, site_type="in"):
"""Attach siloxane bridges on the surface similar to Krishna et al.
(2009). Here silicon atoms of silanol groups wich are at least 0.31 nm
near each other can be converted to siloxan bridges, by removing one
oxygen atom of the silanol groups and moving the other at the center of
the two.
Parameters
----------
sites : list
List of silicon ids of which binding sites should be picked
amount : int
Number of molecules to attach
normal : function
Function that returns the normal vector of the surface for a given
position
slx_dist : float
Silicon atom distance to search for parters in proximity
trials : integer, optional
Number of trials picking a random site
site_type : string, optional
Site type - interior **in**, exterior **ex**
"""
# Check site type input
if not site_type in ["in", "ex"]:
print("Pore - Wrong attachement site-type...")
return
# Create siloxane molecule
mol = Molecule("siloxane", "SLX")
mol.add("O", [0, 0, 0], name="OM1")
mol.add("O", 0, r=0.09, name="OM1")
mount = 0
axis = [0, 1]
# Rotate molecule towards z-axis
mol_axis = mol.bond(*axis)
mol.rotate(geometry.cross_product(mol_axis, [0, 0, 1]), geometry.angle(mol_axis, [0, 0, 1]))
mol.zero()
# Search for silicon atoms near each other
si_atoms = [self._block.get_atom_list()[atom] for atom in sites]
si_dice = Dice(Molecule(inp=si_atoms), slx_dist+0.1, True)
si_proxi = si_dice.find_parallel(None, ["Si", "Si"], slx_dist, 1e-2)
si_matrix = {x[0]: x[1] for x in si_proxi}
# Run through number of siloxan bridges to add
mol_list = []
for i in range(amount):
# Randomly pick an available site pair
si = []
for j in range(trials):
si_rand = random.choice(sites)
if sites.index(si_rand) in si_matrix and si_matrix[sites.index(si_rand)]:
si_rand_proxi = sites[si_matrix[sites.index(si_rand)][0]]
if sites.index(si_rand_proxi) in si_matrix:
if self._sites[si_rand]["state"] and (self._sites[si_rand_proxi]["state"]):
si = [si_rand, si_rand_proxi]
break
# Place molecule on surface
if si and self._sites[si[0]]["state"] and self._sites[si[1]]["state"]:
# Create a copy of the molecule
mol_temp = copy.deepcopy(mol)
# Calculate center position
pos_vec_halve = [x/2 for x in geometry.vector(self._block.pos(si[0]), self._block.pos(si[1]))]
center_pos = [pos_vec_halve[x]+self._block.pos(si[0])[x] for x in range(self._dim)]
# Rotate molecule towards surface normal vector
surf_axis = normal(center_pos)
mol_temp.rotate(geometry.cross_product([0, 0, 1], surf_axis), -geometry.angle([0, 0, 1], surf_axis))
# Move molecule to mounting position and remove temporary atom
mol_temp.move(mount, center_pos)
mol_temp.delete(0)
# Add molecule to molecule list and global dictionary
mol_list.append(mol_temp)
if not mol_temp.get_short() in self._mol_dict[site_type]:
self._mol_dict[site_type][mol_temp.get_short()] = []
self._mol_dict[site_type][mol_temp.get_short()].append(mol_temp)
# Remove oxygen atom and if not geminal delete site
for si_id in si:
self._matrix.strip(self._sites[si_id]["o"][0])
if len(self._sites[si_id]["o"])==2:
self._sites[si_id]["o"].pop(0)
else:
del self._sites[si_id]
del si_matrix[sites.index(si_id)]
return mol_list